Impact of a novel protein meal on the gastrointesinal microbiota and host transciptome of larval zebrafish Danio rerio
Rurangwa, E. ; Sipkema, D. ; Kals, J. ; Veld, M. ter; Forlenza, M. ; Bacanu, G.M. ; Smidt, H. ; Palstra, A.P. - \ 2015
Frontiers in Physiology 6 (2015). - ISSN 1664-042X - 27 p.
large gene lists - intestinal microbiota - gut microbiota - digestive physiology - solea-senegalensis - metal uptake - sp-nov - fish - expression - iron
Larval zebrafish was subjected to a methodological exploration of the gastrointestinal microbiota and transcriptome. Assessed was the impact of two dietary inclusion levels of a novel protein meal (NPM) of animal origin (ragworm Nereis virens) on the gastrointestinal tract (GIT). Microbial development was assessed over the first 21 days post egg fertilisation (dpf) through 16S rRNA gene-based microbial composition profiling by pyrosequencing. Differentially expressed genes in the GIT were demonstrated at 21 dpf by whole transcriptome sequencing (mRNAseq). Larval zebrafish showed rapid temporal changes in microbial colonization but domination occurred by one to three bacterial species generally belonging to Proteobacteria and Firmicutes. The high iron content of NPM may have led to an increased relative abundance of bacteria that were related to potential pathogens and bacteria with an increased iron metabolism. Functional classification of the 328 differentially expressed genes indicated that the GIT of larvae fed at higher NPM level was more active in transmembrane ion transport and protein synthesis. mRNAseq analysis did not reveal a major activation of genes involved in the immune response or indicating differences in iron uptake and homeostasis in zebrafish fed at the high inclusion level of NPM
The Colletotrichum gigasporum species complex
Liu, F. ; Cai, L. ; Crous, P.W. ; Damm, U. - \ 2014
Persoonia 33 (2014). - ISSN 0031-5850 - p. 83 - 97.
sp-nov - primer sets - endophytes - pathogens - china - gloeosporioides - anthracnose - diversity - sequences - acutatum
In a preliminary analysis, 21 Colletotrichum strains with large conidia preserved in the CBS culture collection clustered with a recently described species, C. gigasporum, forming a clade distinct from other currently known Colletotrichum species complexes. Multi-locus phylogenetic analyses (ITS, ACT, TUB2, CHS-1, GAPDH) as well as each of the single-locus analyses resolved seven distinct species, one of them being C. gigasporum. Colletotrichum gigasporum and its close allies thus constitute a previously unknown species complex with shared morphological features. Five of the seven species accepted in the C. gigasporum species complex are described here as novel species, namely C. arxii, C. magnisporum, C. pseudomajus, C. radicis and C. vietnamense. A species represented by a single sterile strain, namely CBS 159.50, was not described as novel species, and is treated as Colletotrichum sp. CBS 159.50. Furthermore, C. thailandicum is reduced to synonymy with C. gigasporum.
Maharachchikumbura, S.S.N. ; Hyde, K.D. ; Groenewald, J.Z. ; Xu, J. ; Crous, P.W. - \ 2014
Studies in Mycology 79 (2014). - ISSN 0166-0616 - p. 121 - 186.
ribosomal dna-sequences - sp-nov - morphological characters - conidial structure - camellia-sinensis - natural-products - twig blight - primer sets - leaf-spot - disease
Species of Pestalotiopsis occur commonly as plant pathogens, and represent a fungal group known to produce a wide range of chemically novel, diverse metabolites. In the present study, we investigated 91 Pestalotiopsis isolates from the CBS-KNAW Fungal Biodiversity Centre (CBS) culture collection. The phylogeny of the Amphisphaeriaceae was constructed based on analysis of 28S nrRNA gene (LSU) sequence data, and taxonomic changes are proposed to reflect more natural groupings. We combined morphological and DNA data, and segregated two novel genera from Pestalotiopsis, namely Neopestalotiopsis and Pseudopestalotiopsis. The three genera are easily distinguishable on the basis of their conidiogenous cells and colour of their median conidial cells. We coupled morphological and combined sequence data of internal transcribed spacer (ITS), partial ß-tubulin (TUB) and partial translation elongation factor 1-alpha (TEF) gene regions, which revealed 30 clades in Neopestalotiopsis and 43 clades in Pestalotiopsis. Based on these data, 11 new species are introduced in Neopestalotiopsis, 24 in Pestalotiopsis, and two in Pseudopestalotiopsis. Several new combinations are proposed to emend monophyly of Neopestalotiopsis, Pestalotiopsis and Pseudopestalotiopsis.
Introducing the Consolidated Species Concept to resolve species in the Teratosphaeriaceae
Quaedvlieg, W. ; Binder, M. ; Groenewald, J.Z. ; Summerell, B.A. ; Carnegie, A.J. ; Burgess, T.I. ; Crous, P.W. - \ 2014
Persoonia 33 (2014). - ISSN 0031-5850 - p. 1 - 40.
internal transcribed spacer - mycosphaerella-spp. - sp-nov - eucalyptus leaves - gene genealogies - south-africa - leaf spots - phylogenetic reassessment - reproductive isolation - multigene phylogeny
The Teratosphaeriaceae represents a recently established family that includes numerous saprobic, extremophilic, human opportunistic, and plant pathogenic fungi. Partial DNA sequence data of the 28S rRNA and RPB2 genes strongly support a separation of the Mycosphaerellaceae from the Teratosphaeriaceae, and also provide support for the Extremaceae and Neodevriesiaceae, two novel families including many extremophilic fungi that occur on a diversity of substrates. In addition, a multi-locus DNA sequence dataset was generated (ITS, LSU, Btub, Act, RPB2, EF-1a and Cal) to distinguish taxa in Mycosphaerella and Teratosphaeria associated with leaf disease of Eucalyptus, leading to the introduction of 23 novel genera, five species and 48 new combinations. Species are distinguished based on a polyphasic approach, combining morphological, ecological and phylogenetic species concepts, named here as the Consolidated Species Concept (CSC). From the DNA sequence data generated, we show that each one of the five coding genes tested, reliably identify most of the species present in this dataset (except species of Pseudocercospora). The ITS gene serves as a primary barcode locus as it is easily generated and has the most extensive dataset available, while either Btub, EF-1a or RPB2 provide a useful secondary barcode locus.
Fungal Planet description sheets: 214–280
Crous, P.W. ; Shivas, R.G. ; Quaedvlieg, W. ; Bank, M. van der; Zhang, Y. ; Summerell, B.A. ; Guarro, J. ; Wingfield, M.J. ; Wood, A.R. ; Alfenas, A.C. ; Braun, U. ; Cano-Lira, J.F. ; Garcia, D. ; Marin-Felix, Y. ; Alvarado, P. ; Andrade, J.P. ; Armengol, J. ; Assefa, A. ; Breeÿen, A. den; Camele, I. ; Cheewangkoon, R. ; Souza, J.T. De; Duong, T.A. ; Esteve-Raventós, F. ; Fournier, J. ; Frisullo, S. ; García-Jiménez, J. ; Gardiennet, A. ; Gené, J. ; Hernández-Restrepo, M. ; Hirooka, Y. ; Hospenthal, D.R. ; King, A. ; Lechat, C. ; Lombard, L. ; Mang, S.M. ; Marbach, P.A.S. ; Marincowitz, S. ; Montaño-Mata, N.J. ; Moreno, G. ; Perez, C.A. ; Pérez Sierra, A.M. ; Robertson, J.L. ; Roux, J. ; Rubio, E. ; Schumacher, R.K. ; Stchigel, A.M. ; Sutton, D.A. ; Tan, Y.P. ; Thompson, E.H. ; Vanderlinde, E. ; Walker, A.K. ; Walker, D.M. ; Wickes, B.L. ; Wong, P.T.W. ; Groenewald, J.Z. - \ 2014
Persoonia 32 (2014). - ISSN 0031-5850 - p. 184 - 306.
sp-nov - phylogeny reveals - eucalyptus-microfungi - host-associations - gene phylogeny - sequence data - diaporthales - morphology - gnomoniaceae - conioscypha
Novel species of microfungi described in the present study include the following from South Africa: Cercosporella dolichandrae from Dolichandra unguiscati, Seiridium podocarpi from Podocarpus latifolius, Pseudocercospora parapseudarthriae from Pseudarthria hookeri, Neodevriesia coryneliae from Corynelia uberata on leaves of Afrocarpus falcatus, Ramichloridium eucleae from Euclea undulata and Stachybotrys aloeticola from Aloe sp. (South Africa), as novel member of the Stachybotriaceae fam. nov. Several species were also described from Zambia, and these include Chaetomella zambiensis on unknown Fabaceae, Schizoparme pseudogranati from Terminalia stuhlmannii, Diaporthe isoberliniae from Isoberlinia angolensis, Peyronellaea combreti from Combretum mossambiciensis, Zasmidium rothmanniae and Phaeococcomyces rothmanniae from Rothmannia engleriana, Diaporthe vangueriae from Vangueria infausta and Diaporthe parapterocarpi from Pterocarpus brenanii. Novel species from the Netherlands include: Stagonospora trichophoricola, Keissleriella trichophoricola and Dinemasporium trichophoricola from Trichophorum cespitosum, Phaeosphaeria poae, Keissleriella poagena, Phaeosphaeria poagena, Parastagonospora poagena and Pyrenochaetopsis poae from Poa sp., Septoriella oudemansii from Phragmites australis and Dendryphion europaeum from Hedera helix (Germany) and Heracleum sphondylium (the Netherlands). Novel species from Australia include: Anungitea eucalyptorum from Eucalyptus leaf litter, Beltraniopsis neolitseae and Acrodontium neolitseae from Neolitsea australiensis, Beltraniella endiandrae from Endiandra introrsa, Phaeophleospora parsoniae from Parsonia straminea, Penicillifer martinii from Cynodon dactylon, Ochroconis macrozamiae from Macrozamia leaf litter, Triposporium cycadicola, Circinotrichum cycadis, Cladosporium cycadicola and Acrocalymma cycadis from Cycas spp. Furthermore, Vermiculariopsiella dichapetali is described from Dichapetalum rhodesicum (Botswana), Marasmius vladimirii from leaf litter (India), Ophiognomonia acadiensis from Picea rubens (Canada), Setophoma vernoniae from Vernonia polyanthes and Penicillium restingae from soil (Brazil), Pseudolachnella guaviyunis from Myrcianthes pungens (Uruguay) and Pseudocercospora neriicola from Nerium oleander (Italy). Novelties from Spain include: Dendryphiella eucalyptorum from Eucalyptus globulus, Conioscypha minutispora from dead wood, Diplogelasinospora moalensis and Pseudoneurospora canariensis from soil and Inocybe lanatopurpurea from reforested woodland of Pinus spp. Novelties from France include: Kellermania triseptata from Agave angustifolia, Zetiasplozna acaciae from Acacia melanoxylon, Pyrenochaeta pinicola from Pinus sp. and Pseudonectria rusci from Ruscus aculeatus. New species from China include: Dematiocladium celtidicola from Celtis bungeana, Beltrania pseudorhombica, Chaetopsina beijingensis and Toxicocladosporium pini from Pinus spp. and Setophaeosphaeria badalingensis from Hemerocallis fulva. Novel genera of Ascomycetes include Alfaria from Cyperus esculentus (Spain), Rinaldiella from a contaminated human lesion (Georgia), Hyalocladosporiella from Tectona grandis (Brazil), Pseudoacremonium from Saccharum spontaneum and Melnikomyces from leaf litter (Vietnam), Annellosympodiella from Juniperus procera (Ethiopia), Neoceratosperma from Eucalyptus leaves (Thailand), Ramopenidiella from Cycas calcicola (Australia), Cephalotrichiella from air in the Netherlands, Neocamarosporium from Mesembryanthemum sp. and Acervuloseptoria from Ziziphus mucronata (South Africa) and Setophaeosphaeria from Hemerocallis fulva (China). Several novel combinations are also introduced, namely for Phaeosphaeria setosa as Setophaeosphaeria setosa, Phoma heteroderae as Peyronellaea heteroderae and Phyllosticta maydis as Peyronellaea maydis. Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.
Phylogenetic circumscription of Arthrographis (Eremomycetaceae, Dothideomycetes)
Giraldo, A. ; Gené, J. ; Sutton, D.A. ; Madrid, H. ; Cano, J. ; Crous, P.W. ; Guarro, J. - \ 2014
Persoonia 32 (2014). - ISSN 0031-5850 - p. 102 - 114.
keratinophilic fungi - molecular-data - ribosomal dna - sp-nov - ascomycota - tubeufiaceae - systematics - arthropsis - evolution - revision
Numerous members of Ascomycota and Basidiomycota produce only poorly differentiated arthroconidial asexual morphs in culture. These arthroconidial fungi are grouped in genera where the asexual-sexual connections and their taxonomic circumscription are poorly known. In the present study we explored the phylogenetic relationships of two of these ascomycetous genera, Arthrographis and Arthropsis. Analysis of D1/D2 sequences of all species of both genera revealed that both are polyphyletic, with species being accommodated in different orders and classes. Because genetic variability was detected among reference strains and fresh isolates resembling the genus Arthrographis, we carried out a detailed phenotypic and phylogenetic analysis based on sequence data of the ITS region, actin and chitin synthase genes. Based on these results, four new species are recognised, namely Arthrographis chlamydospora, A. curvata, A. globosa and A. longispora. Arthrographis chlamydospora is distinguished by its cerebriform colonies, branched conidiophores, cuboid arthroconidia and terminal or intercalary globose to subglobose chlamydospores. Arthrographis curvata produced both sexual and asexual morphs, and is characterised by navicular ascospores and dimorphic conidia, namely cylindrical arthroconidia and curved, cashew-nut-shaped conidia formed laterally on vegetative hyphae. Arthrographis globosa produced membranous colonies, but is mainly characterised by doliiform to globose arthroconidia. Arthrographis longispora also produces membranous colonies, but has poorly differentiated conidiophores and long arthroconidia. Morphological variants are described for A. kalrae and our results also revealed that Eremomyces langeronii and A. kalrae, traditionally considered the sexual and asexual morphs of the same species, are not conspecific.
Sulfate Reduction at Low Ph To Remediate Acid Mine Drainage
Sánchez-Andrea, I. ; Sanz, J.L. ; Bijmans, M.F.M. ; Stams, A.J.M. - \ 2014
Journal of Hazardous Materials 269 (2014). - ISSN 0304-3894 - p. 98 - 109.
fluidized-bed reactor - metal-contaminated water - rate-determining step - reducing bacteria - waste-water - microbial community - sp-nov - biological treatment - constructed wetland - passive treatment
Industrial activities and the natural oxidation of metallic sulfide-ores produce sulfate-rich waters with low pH and high heavy metals content, generally termed acid mine drainage (AMD). This is of great environmental concern as some heavy metals are highly toxic. Within a number of possibilities, biological treatment applying sulfate-reducing bacteria (SRB) is an attractive option to treat AMD and to recover metals. The process produces alkalinity, neutralizing the AMD. Simultaneously. The sulfide that is produced react with the metal in solution and precipitates them as metal sulfides. Here, important factors for biotechnological application of SRB such as the inocula, the pH of the process, the substrates and the reactor design are discussed. Microbial communities of sulfidogenic reactors treating AMD which comprise fermentative-, acetogenic- and SRB as well as methanogenic archaea are reviewed
Species of the Colletotrichum gloeosporioides complex associated with anthracnose diseases of Proteaceae
Liu, F. ; Damm, U. ; Cai, L. ; Crous, P.W. - \ 2013
Fungal Diversity 61 (2013)1. - ISSN 1560-2745 - p. 89 - 105.
yunnan provinces - fungal pathogens - primer sets - sp-nov - china - guizhou - hosts
Anthracnose disease of Proteaceae has in the past chiefly been attributed to infections by C. acutatum, C. boninense and C. gloeosporioides. In the present study, a multi-locus phylogenetic analysis (ACT, CAL, CHS-1, GAPDH, GS, ITS, TUB2) revealed that strains of the C. gloeosporioides complex associated with Proteaceae belong to at least six species. These include C. alienum, C. aotearoa, C. kahawae (subsp. ciggaro), C. siamense, and two new taxa, C. proteae and C. grevilleae. The most economically important pathogen of Proteaceae seems to be C. alienum, and not C. gloeosporioides as previously reported. All taxa associated with Proteaceae are morphologically described on different media in culture, except strains of C. siamense, which proved to be sterile. Furthermore, C. populi is synonymised with C. aenigma.
Families of Dothideomycetes
Hyde, K.D. ; Gareth Jones, E.B. ; Liu, J.K. ; Ariyawansa, H. ; Boehm, E. ; Boonmee, S. ; Braun, U. ; Chomnunti, P. ; Crous, P.W. ; Dai, D.Q. ; Diederich, P. ; Dissanayake, A. ; Doilom, M. ; Doveri, F. ; Hongsanan, S. ; Jayawardena, R. ; Lawrey, J.D. ; Li, Y.M. ; Liu, Y.X. ; Lücking, R. ; Monkai, J. ; Muggia, L. ; Nelsen, M.P. ; Pang, K.L. ; Phookamsak, R. ; Senanayake, I.C. ; Shearer, C.A. ; Suetrong, S. ; Tanaka, K. ; Thambugala, K.M. ; Wijayawardene, N.N. ; Wikee, S. ; Wu, H.X. ; Zhang, Y. ; Aguirre-Hudson, B. ; Alias, S.A. ; Aptroot, A. ; Bahkali, A.H. ; Berezza, J.L. ; Bhat, D.J. ; Camporesi, E. ; Chukeatirote, E. ; Gueidan, C. ; Hawksworth, D.L. ; Hirayama, K. ; Hoog, S. de; Kang, J.C. ; Knudsen, K. ; Li, W.J. ; Li, X.H. ; Liu, Z.Y. ; Mapook, A. ; McKenzie, E.H.C. ; Miller, A.N. ; Mortimer, P.E. ; Phillips, A.J.L. ; Raja, H.A. ; Scheuer, C. ; Schumm, F. ; Taylor, J.E. ; Tian, Q. ; Tibpromma, S. ; Wanasinghe, D.N. ; Wang, Y. ; Xu, J.C. ; Yacharoen, S. ; Yan, J.Y. ; Zhang, M. - \ 2013
Fungal Diversity 63 (2013)1. - ISSN 1560-2745 - p. 1 - 313.
ribosomal dna-sequences - morphologically similar genera - foliicolous lichenized fungi - intertidal mangrove wood - leaf-inhabiting fungi - fresh-water habitats - new-zealand fungi - russian far-east - papua-new-guinea - sp-nov
Dothideomycetes comprise a highly diverse range of fungi characterized mainly by asci with two wall layers (bitunicate asci) and often with fissitunicate dehiscence. Many species are saprobes, with many asexual states comprising important plant pathogens. They are also endophytes, epiphytes, fungicolous, lichenized, or lichenicolous fungi. They occur in terrestrial, freshwater and marine habitats in almost every part of the world. We accept 105 families in Dothideomycetes with the new families Anteagloniaceae, Bambusicolaceae, Biatriosporaceae, Lichenoconiaceae, Muyocopronaceae, Paranectriellaceae, Roussoellaceae, Salsugineaceae, Seynesiopeltidaceae and Thyridariaceae introduced in this paper. Each family is provided with a description and notes, including asexual and asexual states, and if more than one genus is included, the type genus is also characterized. Each family is provided with at least one figure-plate, usually illustrating the type genus, a list of accepted genera, including asexual genera, and a key to these genera. A phylogenetic tree based on four gene combined analysis add support for 64 of the families and 22 orders, including the novel orders, Dyfrolomycetales, Lichenoconiales, Lichenotheliales, Monoblastiales, Natipusillales, Phaeotrichales and Strigulales. The paper is expected to provide a working document on Dothideomycetes which can be modified as new data comes to light. It is hoped that by illustrating types we provide stimulation and interest so that more work is carried out in this remarkable group of fungi.
The Botryosphaeriaceae: genera and species known from culture
Phillips, A.J.L. ; Alves, A. ; Abdollahzadeh, J. ; Slippers, B. ; Wingfield, M.J. ; Groenewald, J.Z. ; Crous, P.W. - \ 2013
Studies in Mycology 76 (2013)1. - ISSN 0166-0616 - p. 51 - 167.
native syzygium-cordatum - grapevine trunk diseases - dna-sequence data - castilla-y-leon - new-south-wales - 1st report - sp-nov - neofusicoccum-parvum - sphaeropsis-sapinea - western-australia
In this paper we give an account of the genera and species in the Botryosphaeriaceae. We consider morphological characters alone as inadequate to define genera or identify species, given the confusion it has repeatedly introduced in the past, their variation during development, and inevitable overlap as representation grows. Thus it seems likely that all of the older taxa linked to the Botryosphaeriaceae, and for which cultures or DNA sequence data are not available, cannot be linked to the species in this family that are known from culture. Such older taxa will have to be disregarded for future use unless they are epitypified. We therefore focus this paper on the 17 genera that can now be recognised phylogenetically, which concentrates on the species that are presently known from culture. Included is a historical overview of the family, the morphological features that define the genera and species and detailed descriptions of the 17 genera and 110 species. Keys to the genera and species are also provided. Phylogenetic relationships of the genera are given in a multi-locus tree based on combined SSU, ITS, LSU, EF1-a and ß-tubulin sequences. The morphological descriptions are supplemented by phylogenetic trees (ITS alone or ITS + EF1-a) for the species in each genus.
Characterisation of Neofusicoccum species causing mango dieback in Italy
Ismail, A.M. ; Cirvilleri, G. ; Lombard, L. ; Crous, P.W. ; Groenewald, J.Z. ; Polizzi, G. - \ 2013
Journal of Plant Pathology: rivista di patologia vegetale 95 (2013)3. - ISSN 1125-4653 - p. 549 - 557.
mangifera-indica - phylogenetic analysis - south-africa - 1st report - sp-nov - botryosphaeria - pathogenicity - lasiodiplodia - morphology - grapevine
Species of Botryosphaeriaceae are important fungal pathogens of mango worldwide. A survey of 11 mango orchards located in the provinces of Catania, Messina, Palermo and Ragusa (Sicily, southern Italy), resulted in the isolation of a large number (76) of Neofusicoccum isolates associated with decline and dieback symptoms. Isolates were identified based on morphology and DNA sequence data analyses of the internal transcribed spacer region of the nrDNA and partial translation of the elongation factor 1-alpha gene regions. Two species of Neofusicoccum were identified, which included N. parvum and N. australe, the former of which was the dominant species. The high incidence in local orchards and the pathogenicity results indicate that N. parvum and N. australe are important pathogens of mango in Sicily where they may significantly limit mango production.
Fungal Planet description sheets: 154–213
Crous, P.W. ; Wingfield, M.J. ; Guarro, J. ; Cheewangkoon, R. ; Bank, M. van der; Swart, W.J. ; Stchigel, A.M. ; Cano-Lira, J.F. ; Roux, J. ; Madrid, H. ; Damm, U. ; Wood, A.R. ; Shuttleworth, L.A. ; Hodges, C.S. ; Munster, M. ; Jesús Yáñez-Morales, M. de; Zúñiga-Estrada, L. ; Cruywagen, E.M. ; Hoog, G.S. de; Silvera, C. ; Najafzadeh, J. ; Davison, E.M. ; Davison, P.J.N. ; Barrett, M.D. ; Barrett, R.L. ; Manamgoda, D.S. ; Minnis, A.M. ; Kleczewski, N.M. ; Flory, S.L. ; Castlebury, L.A. ; Clay, K. ; Hyde, K.D. ; Maússe-Sitoe, S.N.D. ; Chen, S. ; Lechat, C. ; Hairaud, M. ; Lesage-Meessen, L. ; Pawlowska, J. ; Wilk, M. ; Sliwinska-Wyrzychowska, A. ; Metrak, M. ; Wrzosek, M. ; Pavlic-Zupanc, D. ; Maleme, H.M. ; Slippers, B. ; Mac Cormack, W.P. ; Archuby, D.I. ; Grünwald, N.J. ; Tellería, M.T. ; Dueñas, M. ; Martín, M.P. ; Marincowitz, S. ; Beer, Z.W. de; Perez, C.A. ; Gené, J. ; Marin-Felix, Y. ; Groenewald, J.Z. - \ 2013
Persoonia 31 (2013). - ISSN 0031-5850 - p. 188 - 296.
sp-nov - colletotrichum-sansevieriae - anamorph genus - south-africa - 1st report - phytophthora-ipomoeae - leaf-blight - genera - phylogeny - botryosphaeriaceae
Novel species of microfungi described in the present study include the following from South Africa: Camarosporium aloes, Phaeococcomyces aloes and Phoma aloes from Aloe, C. psoraleae, Diaporthe psoraleae and D. psoraleae-pinnatae from Psoralea, Colletotrichum euphorbiae from Euphorbia, Coniothyrium prosopidis and Peyronellaea prosopidis from Prosopis, Diaporthe cassines from Cassine, D. diospyricola from Diospyros, Diaporthe maytenicola from Maytenus, Harknessia proteae from Protea, Neofusicoccum ursorum and N. cryptoaustrale from Eucalyptus, Ochrocladosporium adansoniae from Adansonia, Pilidium pseudoconcavum from Greyia radlkoferi, Stagonospora pseudopaludosa from Phragmites and Toxicocladosporium ficiniae from Ficinia. Several species were also described from Thailand, namely: Chaetopsina pini and C. pinicola from Pinus spp., Myrmecridium thailandicum from reed litter, Passalora pseudotithoniae from Tithonia, Pallidocercospora ventilago from Ventilago, Pyricularia bothriochloae from Bothriochloa and Sphaerulina rhododendricola from Rhododendron. Novelties from Spain include Cladophialophora multiseptata, Knufia tsunedae and Pleuroascus rectipilus from soil and Cyphellophora catalaunica from river sediments. Species from the USA include Bipolaris drechsleri from Microstegium, Calonectria blephiliae from Blephilia, Kellermania macrospora (epitype) and K. pseudoyuccigena from Yucca. Three new species are described from Mexico, namely Neophaeosphaeria agaves and K. agaves from Agave and Phytophthora ipomoeae from Ipomoea. Other African species include Calonectria mossambicensis from Eucalyptus (Mozambique), Harzia cameroonensis from an unknown creeper (Cameroon), Mastigosporella anisophylleae from Anisophyllea (Zambia) and Teratosphaeria terminaliae from Terminalia (Zimbabwe). Species from Europe include Auxarthron longisporum from forest soil (Portugal), Discosia pseudoartocreas from Tilia (Austria), Paraconiothyrium polonense and P. lycopodinum from Lycopodium (Poland) and Stachybotrys oleronensis from Iris (France). Two species of Chrysosporium are described from Antarctica, namely C. magnasporum and C. oceanitesii. Finally, Licea xanthospora is described from Australia, Hypochnicium huinayensis from Chile and Custingophora blanchettei from Uruguay. Novel genera of Ascomycetes include Neomycosphaerella from Pseudopentameris macrantha (South Africa), and Paramycosphaerella from Brachystegia sp. (Zimbabwe). Novel hyphomycete genera include Pseudocatenomycopsis from Rothmannia (Zambia), Neopseudocercospora from Terminalia (Zambia) and Neodeightoniella from Phragmites (South Africa), while Dimorphiopsis from Brachystegia (Zambia) represents a novel coelomycetous genus. Furthermore, Alanphillipsia is introduced as a new genus in the Botryosphaeriaceae with four species, A. aloes, A. aloeigena and A. aloetica from Aloe spp. and A. euphorbiae from Euphorbia sp. (South Africa). A new combination is also proposed for Brachysporium torulosum (Deightoniella black tip of banana) as Corynespora torulosa. Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.
Circumscription of the anthracnose pathogens Colletotrichum lindemuthianum and C. nigrum
Liu, F. ; Cai, L. ; Crous, P.W. ; Damm, U. - \ 2013
Mycologia 105 (2013)4. - ISSN 0027-5514 - p. 844 - 860.
molecular diversity - differential cultivars - genetic-variability - sequence-analysis - host-specificity - primer sets - sp-nov - glomerella - resistance - identification
The anthracnose pathogen of common bean (Phaseolus vulgaris) is usually identified as Colletotrichum lindemuthianum, while anthracnose of potato (Solanum tuberosum), peppers (Capsicum annuum), tomato (S. lycopersicum) and several other crop plants is often attributed to C. coccodes. In order to study the phylogenetic relationships of these important pathogens, we conducted a multigene analysis (ITS, ACT, TUB2, CHS-1, GAPDH) of strains previously identified as C. lindemuthianum, C. coccodes and other related species, as well as representative species of the major Colletotrichum species complexes. Strains of C. lindemuthianum belonged to a single clade; we selected an authentic specimen as lectotype, and an appropriate specimen and culture from the CBS collection to serve as epitype. Two clades were resolved within C. coccodes s. lat. One clade included the ex-neotype strain of C. coccodes on Solanum, while an epitype was selected for C. nigrum, which represents the oldest name of the second clade, which occurs on Capsicum, Solanum, as well as several other host plants. Furthermore, we recognized C. lycopersici as a synonym of C. nigrum, and C. biologicum as a synonym of C. coccodes.
Diaporthe: a genus of endophytic, saprobic and plant pathogenic fungi
Gomes, R.R. ; Glienke, C. ; Videira, S.I.R. ; Lombard, L. ; Groenewald, J.Z. ; Crous, P.W. - \ 2013
Persoonia 31 (2013). - ISSN 0031-5850 - p. 1 - 41.
internal transcribed spacer - south-africa - species concepts - sp-nov - coelomycete phomopsis - foeniculum-vulgare - multigene analysis - north-america - ribosomal dna - twig dieback
Diaporthe (Phomopsis) species have often been reported as plant pathogens, non-pathogenic endophytes or saprobes, commonly isolated from a wide range of hosts. The primary aim of the present study was to resolve the taxonomy and phylogeny of a large collection of Diaporthe species occurring on diverse hosts, either as pathogens, saprobes, or as harmless endophytes. In the present study we investigated 243 isolates using multilocus DNA sequence data. Analyses of the rDNA internal transcribed spacer (ITS1, 5.8S, ITS2) region, and partial translation elongation factor 1-alpha (TEF1), beta-tubulin (TUB), histone H3 (HIS) and calmodulin (CAL) genes resolved 95 clades. Fifteen new species are described, namely Diaporthe arengae, D. brasiliensis, D. endophytica, D. hongkongensis, D. inconspicua, D. infecunda, D. mayteni, D. neoarctii, D. oxe, D. paranensis, D. pseudomangiferae, D. pseudophoenicicola, D. raonikayaporum, D. schini and D. terebinthifolii. A further 14 new combinations are introduced in Diaporthe, and D. anacardii is epitypified. Although species of Diaporthe have in the past chiefly been distinguished based on host association, results of this study confirm several taxa to have wide host ranges, suggesting that they move freely among hosts, frequently co-colonising diseased or dead tissue. In contrast, some plant pathogenic and endophytic taxa appear to be strictly host specific. Given this diverse ecological behaviour among members of Diaporthe, future species descriptions lacking molecular data (at least ITS and HIS or TUB) should be strongly discouraged.
Glycerol fermentation to hydrogen by Thermotoga maritima: Proposed pathway and bioenergetic considerations
Maru, B.T. ; Bielen, A.A.M. ; Constanti, M. ; Medina, F. ; Kengen, S.W.M. - \ 2013
International Journal of Hydrogen Energy 38 (2013)14. - ISSN 0360-3199 - p. 5563 - 5572.
biohydrogen production - escherichia-coli - caldicellulosiruptor-saccharolyticus - 3-phosphate dehydrogenase - anaerobic fermentation - nucleotide-sequence - dark fermentation - embden-meyerhof - sp-nov - bacteria
The production of biohydrogen from glycerol, by the hyperthermophilic bacterium Thermotoga maritima DSM 3109, was investigated in batch and chemostat systems. T. maritima converted glycerol to mainly acetate, CO2 and H2. Maximal hydrogen yields of 2.84 and 2.41 hydrogen per glycerol were observed for batch and chemostat cultivations, respectively. For batch cultivations: i) hydrogen production rates decreased with increasing initial glycerol concentration, ii) growth and hydrogen production was optimal in the pH range of 7–7.5, and iii) a yeast extract concentration of 2 g/l led to optimal hydrogen production. Stable growth could be maintained in a chemostat, however, when dilution rates exceeded 0.025 h-1 glycerol conversion was incomplete. A detailed overview of the catabolic pathway involved in glycerol fermentation to hydrogen by T. maritima is given. Based on comparative genomics the ability to grow on glycerol can be considered as a general trait of Thermotoga species. The exceptional bioenergetics of hydrogen formation from glycerol is discussed
Molecular typing of Dutch isolates of Xanthomonas arboricola pathovar pruni isolated from ornamental cherry laurel
Bergsma-Vlami, M. ; Martin, W. ; Koenraadt, H. ; Teunissen, H. ; Pothier, J.F. ; Duffy, B. ; Doorn, J. van - \ 2012
Journal of Plant Pathology: rivista di patologia vegetale 94 (2012)Supp.1. - ISSN 1125-4653 - p. S29 - S35.
pectate lyase secretion - acutatum-sensu-lato - colletotrichum-acutatum - c-gloeosporioides - sp-nov - fruit - diversity - infection - susceptibility - pathogenicity
Xanthomonas arboricola pv. pruni (Xap) has been found in several cherry laurel (Prunus laurocerasus) nurseries in the Netherlands, causing leaf spot. As no information is available yet about the epidemiology of this quarantine bacterium in cherry laurel, molecular typing of Xap isolates can considerably improve our understanding of pathogen spread between various cherry laurel production systems in different regions of the Netherlands and pathogen relatedness among different disease outbreaks. In this study, the genotypic diversity within a population of 25 Xap isolates isolated from different cherry laurel cultivars grown in different locations in the Netherlands between 2008-2010, was assessed using Multiple-locus variable-number analysis (MLVA). The identity of these Xap isolates was initially determined based on the EPPO standard PM 7/64. Confirmation of the identity of these Xap isolates was additionally achieved with diverse methodologies, including gyrase subunit B (gyrB) sequence typing, BOXand ERIC-PCR, AFLP, and Xap-specific PCR’s: one based on the previously described Pagani primers (2004) (conventional-PCR and its TaqMan-PCR variant) and one based on the recently described Pothier primers (2011c). Based on the results of the MLVA analysis, the Dutch population of Xap isolates could be divided into two groups; however no correlation with the geographical origin or any other character of these isolates could be established. Additionally, based on colony morphology, a panel of 5 look-a-likes were isolated from symptomatic leaves of P. laurocerasus which reacted in the Xap-specific PCR described by Pagani (2004) but that did not react in the Xap-specific PCR described by Pothier et al. (2011c). Further characterisation of these look-a-like isolates with AFLP, BOXand ERIC-PCR, and gyrB sequencing showed that the Xap-specific PCR described by Pagani does not discriminate between Xap and the look-a-like isolates. Similarly to Pagani PCR, the performance of a pathogenicity test with a pure culture of the isolate was not always discriminative between Xap and the look-a-like isolates, unraveling a complexity in Xanthomonas pathogenicity. Therefore, in routine screening based on the EPPO standard PM 7/64, complementary techniques such as BOX- ERIC-PCR, gyrB sequencing, Xap-specific PCR described by Pothier (2011c), MLVA and AFLP should be used to obtain a reliable diagnosis of Xap and avoid false positive results.
A multi-locus backbone tree for Pestalotiopsis, with a polyphasic characterization of 14 new species
Maharachchikumbura, S.S.N. ; Guo, L.D. ; Cai, L. ; Chukeatirote, E. ; Wu, W.P. ; Sun, X. ; Crous, P.W. ; Bhat, D.J. ; McKenzie, E.H.C. ; Bahkali, A.H. ; Hyde, K.D. - \ 2012
Fungal Diversity 56 (2012)1. - ISSN 1560-2745 - p. 95 - 129.
dna-sequence database - rna-polymerase-ii - endophytic fungus - beta-tubulin - antifungal metabolites - primer sets - sp-nov - phylogeny - diversity - plant
Pestalotiopsis is a taxonomically confused, pathogenic and chemically creative genus requiring a critical re-examination using a multi-gene phylogeny based on ex-type and ex-epitype cultures. In this study 40 isolates of Pestalotiopsis, comprised of 28 strains collected from living and dead plant material of various host plants from China were studied by means of morphology and analysis of ITS, ß–tubulin and tef1 gene sequence data. Based on molecular and morphological data we describe 14 new species (Pestalotiopsis asiatica, P. chinensis, P. chrysea, P. clavata, P. diversiseta, P. ellipsospora, P. inflexa, P. intermedia, P. linearis, P. rosea, P. saprophyta, P. umberspora, P. unicolor and P. verruculosa) and three species are epitypified (P. adusta, P. clavispora and P. foedans). Of the 10 gene regions (ACT, ß-tubulin, CAL, GPDH, GS, ITS, LSU, RPB 1, SSU and tef1) utilized to resolve cryptic Pestalotiopsis species, ITS, ß–tubulin and tef1 proved to be the better markers. The other gene regions were less useful due to poor success in PCR amplification and/or in their ability to resolve species boundaries. As a single gene tef1 met the requirements for an ideal candidate and functions well for species delimitation due to its better species resolution and PCR success. Although ß-tubulin showed fairly good differences among species, a combination of ITS, ß-tubulin and tef1 gene data gave the best resolution as compared to single gene analysis. This work provides a backbone tree for 22 ex-type/epitypified species of Pestalotiopsis and can be used in future studies of the genus.
The Colletotrichum acutatum complex
Damm, U. ; Cannon, P.F. ; Woudenberg, J.H.C. ; Crous, P.W. - \ 2012
Studies in Mycology 73 (2012)1. - ISSN 0166-0616 - p. 37 - 113.
key lime anthracnose - glomerella leaf-spot - f-sp aeschynomene - bitter rot - sp-nov - molecular characterization - olive anthracnose - c-gloeosporioides - endophytic fungi - causal agent
Colletotrichum acutatum is known as an important anthracnose pathogen of a wide range of host plants worldwide. Numerous studies have reported subgroups within the C. acutatum species complex. Multilocus molecular phylogenetic analysis (ITS, ACT, TUB2, CHS-1, GAPDH, HIS3) of 331 strains previously identified as C. acutatum and other related taxa, including strains from numerous hosts with wide geographic distributions, confirmed the molecular groups previously recognised and identified a series of novel taxa. Thirty-one species are accepted, of which 21 have not previously been recognised. Colletotrichum orchidophilum clusters basal to the C. acutatum species complex. There is a high phenotypic diversity within this complex, and some of the species appear to have preferences to specific hosts or geographical regions. Others appear to be plurivorous and are present in multiple regions. In this study, only C. salicis and C. rhombiforme formed sexual morphs in culture, although sexual morphs have been described from other taxa (especially as laboratory crosses), and there is evidence of hybridisation between different species. One species with similar morphology to C. acutatum but not belonging to this species complex was also described here as new, namely C. pseudoacutatum.
The Colletotrichum boninense species complex
Damm, U. ; Cannon, P.F. ; Woudenberg, J.H.C. ; Johnston, P.R. ; Weir, B.S. ; Tan, Y.P. ; Shivas, R.G. ; Crous, P.W. - \ 2012
Studies in Mycology 73 (2012). - ISSN 0166-0616 - p. 1 - 36.
1st report - glomerella-acutata - primer sets - sp-nov - anthracnose - identification - diversity - teleomorph - gloeosporioides - compatibility
Although only recently described, Colletotrichum boninense is well established in literature as an anthracnose pathogen or endophyte of a diverse range of host plants worldwide. It is especially prominent on members of Amaryllidaceae, Orchidaceae, Proteaceae and Solanaceae. Reports from literature and preliminary studies using ITS sequence data indicated that C. boninense represents a species complex. A multilocus molecular phylogenetic analysis (ITS, ACT, TUB2, CHS-1, GAPDH, HIS3, CAL) of 86 strains previously identified as C. boninense and other related strains revealed 18 clades. These clades are recognised here as separate species, including C. boninense s. str., C. hippeastri, C. karstii and 12 previously undescribed species, C. annellatum, C. beeveri, C. brassicicola, C. brasiliense, C. colombiense, C. constrictum, C. cymbidiicola, C. dacrycarpi, C. novae-zelandiae, C. oncidii, C. parsonsiae and C. torulosum. Seven of the new species are only known from New Zealand, perhaps reflecting a sampling bias. The new combination C. phyllanthi was made, and C. dracaenae Petch was epitypified and the name replaced with C. petchii. Typical for species of the C. boninense species complex are the conidiogenous cells with rather prominent periclinal thickening that also sometimes extend to form a new conidiogenous locus or annellations as well as conidia that have a prominent basal scar. Many species in the C. boninense complex form teleomorphs in culture.
Fungal Planet description sheets: 107-127
Crous, P.W. ; Summerell, B.A. ; Shivas, R.G. ; Burgess, T.I. ; Decock, C.A. ; Dreyer, L.L. ; Granke, L.L. ; Guest, D.I. ; Hardy, G.E.St.J. ; Hausbeck, M.K. ; Hüberli, D. ; Jung, T. ; Koukol, O. ; Lennox, C.L. ; Liew, E.C.Y. ; Lombard, L. ; McTaggart, A.R. ; Pryke, J.S. ; Roets, F. ; Saude, C. ; Shuttleworth, L.A. ; Stukely, M.J.C. ; Vánky, K. ; Webster, B.J. ; Windstam, S.T. ; Groenewald, J.Z. - \ 2012
Persoonia 28 (2012). - ISSN 0031-5850 - p. 138 - 182.
sp-nov - allied genera - south-africa - diaporthales - eucalyptus - genus - cryphonectriaceae - gnomoniaceae - reevaluation - evolutionary
Novel species of microfungi described in the present study include the following from Australia: Phytophthora amnicola from still water, Gnomoniopsis smithogilvyi from Castanea sp., Pseudoplagiostoma corymbiae from Corymbia sp., Diaporthe eucalyptorum from Eucalyptus sp., Sporisorium andrewmitchellii from Enneapogon aff. lindleyanus, Myrmecridium banksiae from Banksia, and Pilidiella wangiensis from Eucalyptus sp. Several species are also described from South Africa, namely: Gondwanamyces wingfieldii from Protea caffra, Montagnula aloes from Aloe sp., Diaporthe canthii from Canthium inerne, Phyllosticta ericarum from Erica gracilis, Coleophoma proteae from Protea caffra, Toxicocladosporium strelitziae from Strelitzia reginae, and Devriesia agapanthi from Agapanthus africanus. Other species include Phytophthora asparagi from Asparagus officinalis (USA), and Diaporthe passiflorae from Passiflora edulis (South America). Furthermore, novel genera of coelomycetes include Chrysocrypta corymbiae from Corymbia sp. (Australia), Trinosporium guianense, isolated as a contaminant (French Guiana), and Xenosonderhenia syzygii, from Syzygium cordatum (South Africa). Pseudopenidiella piceae from Picea abies (Czech Republic), and Phaeocercospora colophospermi from Colophospermum mopane (South Africa) represent novel genera of hyphomycetes. Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.
The genus Cladosporium
Bench, K. ; Braun, U. ; Groenewald, J.Z. ; Crous, P.W. - \ 2012
Studies in Mycology 72 (2012)1. - ISSN 0166-0616 - p. 1 - 401.
leaf blotch pathogens - allii-cepae - sensu-lato - taxonomic revision - causal organism - lichenicolous fungi - sp-nov - sporotrichum-gougerotii - aromatic-hydrocarbons - molecular diagnostics
A monographic revision of the hyphomycete genus Cladosporium s. lat. (Cladosporiaceae, Capnodiales) is presented. It includes a detailed historic overview of Cladosporium and allied genera, with notes on their phylogeny, systematics and ecology. True species of Cladosporium s. str. (anamorphs of Davidiella), are characterised by having coronate conidiogenous loci and conidial hila, i.e., with a convex central dome surrounded by a raised periclinal rim. Recognised species are treated and illustrated with line drawings and photomicrographs (light as well as scanning electron microscopy). Species known from culture are described in vivo as well as in vitro on standardised media and under controlled conditions. Details on host range/substrates and the geographic distribution are given based on published accounts, and a re-examination of numerous herbarium specimens. Various keys are provided to support the identification of Cladosporium species in vivo and in vitro. Morphological datasets are supplemented by DNA barcodes (nuclear ribosomal RNA gene operon, including the internal transcribed spacer regions ITS1 and ITS2, the 5.8S nrDNA, as well as partial actin and translation elongation factor 1-a gene sequences) diagnostic for individual species. In total 993 names assigned to Cladosporium s. lat., including Heterosporium (854 in Cladosporium and 139 in Heterosporium), are treated, of which 169 are recognized in Cladosporium s. str. The other taxa are doubtful, insufficiently known or have been excluded from Cladosporium in its current circumscription and re-allocated to other genera by the authors of this monograph or previous authors.
Polyclonal Antibody-based ELISA in combination with specific PCR amplification of ITS 1 regions for the detection and quantitation of Lasiodiplodia theobromae, causal agent of 2 gummosis in cashew nut plants
Muniz, C.R. ; Freire, F.C.O. ; Viana, F.M.P. ; Cardoso, J.E. ; Correia, D. ; Jalink, H. ; Kema, G.H.J. ; Silva, G.F. ; Guedes, M.I.F. - \ 2012
Annals of Applied Biology 160 (2012)3. - ISSN 0003-4746 - p. 217 - 224.
south-africa - sp-nov - botryosphaeriaceae - pathogens - endophytes - pinus - stem
Members of Botryosphaeriaceae family are associated with serious diseases in different plants 18 across the world. In cashew nut plants (Anacardium occidentale L.), the fungus Lasiodiplodia 19 theobromae causes a severe group of symptoms related to gummosis that results in decreased nut 20 production. The aim of this work was to develop an indirect enzyme-linked immunosorbent 21 assay (ELISA) with sufficient sensitivity and specificity to detect the fungus both in vitro and in 22 planta (artificially and naturally infected) and to increase the detection specificity within the 23 fungi group using primers specific for the internal transcribed spacer (ITS) sequences. A 24 collection of L. theobromae isolates was obtained, and antisera against the fungus were raised in 25 rabbits. Cross-reactivity against Neofusicoccum sp., Colletotrichum gloeosporioides, Phomopsis 26 anacardii and Pestalotiopsis guepinii was examined. Naturally and artificially infected vegetal 27 material was employed in the ELISAs. The fungi ITS sequences were determined, and single 28 nucleotide polymorphisms were identified and used for primer design. For the naturally infected 29 2 plants, there was an approximately 4-fold variation in the absorbance values. Some positive 1 readings for asymptomatic samples were detected. For the artificially infected samples, an 2 ELISA-based weekly time-course analysis was conducted, and the values for samples from 0 and 3 7 days were lower than the threshold value. Beginning on day 14, the infection could be 4 detected, with rates varying from 40% on day 14 to 80% on day 21 and 100% by the end of the 5 experiment. The ITS sequencing revealed few polymorphisms among the L. theobromae isolates, 6 but for Colletotrichum gloeosporioides, Phomopsis anacardii, Pestalotiopsis guepinii and 7 Neofusicoccum sp., the sequences were sufficient to permit reliable discrimination. The 8 feasibility of ELISA as an early detection technique to assist in gummosis management was 9 demonstrated. PCR amplification based on ITS regions increases and complements serological 10 specificity
Zhang, Y. ; Crous, P.W. ; Schoch, C.L. ; Hyde, K.D. - \ 2012
Fungal Diversity 53 (2012)1. - ISSN 1560-2745 - p. 1 - 221.
ribosomal dna-sequences - australian fresh-water - intertidal mangrove wood - sp-nov - north-america - marine fungi - molecular phylogeny - trematosphaeria-circinans - shiraia-bambusicola - multigene phylogeny
One hundred and five generic types of Pleosporales are described and illustrated. A brief introduction and detailed history with short notes on morphology, molecular phylogeny as well as a general conclusion of each genus are provided. For those genera where the type or a representative specimen is unavailable, a brief note is given. Altogether 174 genera of Pleosporales are treated. Phaeotrichaceae as well as Kriegeriella, Zeuctomorpha and Muroia are excluded from Pleosporales. Based on the multigene phylogenetic analysis, the suborder Massarineae is emended to accommodate five families, viz. Lentitheciaceae, Massarinaceae, Montagnulaceae, Morosphaeriaceae and Trematosphaeriaceae.
Degradation of 4-n-nonylphenol under nitrate reducing conditions
Weert, J.P.A. de; Vinas, M. ; Grotenhuis, J.T.C. ; Rijnaarts, H.H.M. ; Langenhoff, A.A.M. - \ 2011
Biodegradation 22 (2011)1. - ISSN 0923-9820 - p. 175 - 187.
anaerobic degradation - desulfobacterium-phenolicum - polychlorinated-biphenyls - nonionic surfactants - sewage-sludge - n-hexadecane - sp-nov - nonylphenol - biodegradation - 4-nonylphenol
Nonylphenol (NP) is an endocrine disruptor present as a pollutant in river sediment. Biodegradation of NP can reduce its toxicological risk. As sediments are mainly anaerobic, degradation of linear (4-n-NP) and branched nonylphenol (tNP) was studied under methanogenic, sulphate reducing and denitrifying conditions in NP polluted river sediment. Anaerobic bioconversion was observed only for linear NP under denitrifying conditions. The microbial population involved herein was further studied by enrichment and molecular characterization. The largest change in diversity was observed between the enrichments of the third and fourth generation, and further enrichment did not affect the diversity. This implies that different microorganisms are involved in the degradation of 4-n-NP in the sediment. The major degrading bacteria were most closely related to denitrifying hexadecane degraders and linear alkyl benzene sulphonate (LAS) degraders. The molecular structures of alkanes and LAS are similar to the linear chain of 4-n-NP, this might indicate that the biodegradation of linear NP under denitrifying conditions starts at the nonyl chain. Initiation of anaerobic NP degradation was further tested using phenol as a structure analogue. Phenol was chosen instead of an aliphatic analogue, because phenol is the common structure present in all NP isomers while the structure of the aliphatic chain differs per isomer. Phenol was degraded in all cases, but did not affect the linear NP degradation under denitrifying conditions and did not initiate the degradation of tNP and linear NP under the other tested conditions.
A molecular, morphological and ecological re-appraisal of Venturiales¿a new order of Dothideomycetes
Zhang, Y. ; Crous, P.W. ; Schoch, C.L. ; Bahkali, A.H. ; Guo, L.D. ; Hyde, K.D. - \ 2011
Fungal Diversity 51 (2011)1. - ISSN 1560-2745 - p. 249 - 277.
phylogenetic trees - bayesian-inference - sequence-data - apple scab - sp-nov - venturiaceae - genera - fungi - herpotrichiellaceae - classification
The Venturiaceae was traditionally assigned to Pleosporales although its diagnostic characters readily distinguish it from other pleosporalean families. These include a parasitic or saprobic lifestyle, occurring on leaves or stems of dicotyledons; small to medium-sized ascomata, often with setae; deliquescing pseudoparaphyses; 8-spored, broadly cylindrical to obclavate asci; 1-septate, yellowish, greenish or pale brown to brown ascospores; and hyphomycetous anamorphs. Phylogenetically, core genera of Venturiaceae form a monophyletic clade within Dothideomycetes, and represent a separate sister lineage from current orders, thus a new order—Venturiales is introduced. A new family, Sympoventuriaceae, is introduced to accommodate taxa of a well-supported subclade within Venturiales, which contains Sympoventuria, Veronaeopsis simplex and Fusicladium-like species. Based on morphology and DNA sequence analysis, eight genera are included in Venturiaceae, viz. Acantharia, Apiosporina (including Dibotryon), Caproventuria, Coleroa, Pseudoparodiella, Metacoleroa, Tyrannosorus and Venturia. Molecular phylogenetic information is lacking for seven genera previously included in Venturiales, namely Arkoola, Atopospora, Botryostroma, Lasiobotrys, Trichodothella, Trichodothis and Rhizogenee and these are discussed, but their inclusion in Venturiaceae is doubtful. Crotone, Gibbera, Lineostroma, Phaeocryptopus, Phragmogibbera, Platychora, Polyrhizon, Rosenscheldiella, Uleodothis and Xenomeris are excluded from Venturiales, and their ordinal placement needs further investigation. Zeuctomorpha is treated as a synonym of Acantharia.
Impact of subacute ruminal acidosis (SARA) adaptation and recovery on the density and diversity of bacteria in the rumen of dairy cows
Hook, S.E. ; Steele, M.A. ; Northwood, K.S. ; Dijkstra, J. ; France, J. ; Wright, A.G. ; McBride, B.W. - \ 2011
FEMS microbiology ecology 78 (2011)2. - ISSN 0168-6496 - p. 275 - 284.
high-grain diet - real-time pcr - sp-nov - gen-nov - sequence - ph - dynamics - communities - population - cattle
Subacute ruminal acidosis (SARA) is characterized by ruminal pH depression and microbial perturbation. The impact of SARA adaptation and recovery on rumen bacterial density and diversity was investigated following high-grain feeding. Four ruminally cannulated dairy cows were fed a hay diet, transitioned to a 65% grain diet for 3 weeks, and returned to the hay diet for 3 weeks. Rumen fluid, rumen solids, and feces were sampled during weeks 0 (hay), 1 and 3 (high grain), and 4 and 6 (hay). SARA was diagnosed during week 1, with a pH below 5.6 for 4.6±1.4 h. Bacterial density was significantly lower in the rumen solids with high grain (P=0.047). Rumen fluid clone libraries from weeks 0, 3, and 6 were assessed at the 98% level and 154 operational taxonomic units were resolved. Week 3 diversity significantly differed from week 0, and community structure differed from weeks 0 and 6 (P
Biological treatment of refinery spent caustics under halo-alkaline conditions
Graaff, M. de; Bijmans, M.F.M. ; Abbas, B. ; Euverink, G.J.W. ; Muyzer, G. ; Janssen, A.J.H. - \ 2011
Bioresource Technology 102 (2011)15. - ISSN 0960-8524 - p. 7257 - 7264.
sulfur-oxidizing bacteria - soda lake - sp-nov - oxidation processes - mono lake - gen. nov. - diversity - sulfide - water - bacteriochlorophyll
The present research demonstrates the biological treatment of refinery sulfidic spent caustics in a continuously fed system under halo-alkaline conditions (i.e. pH 9.5; Na(+)= 0.8M). Experiments were performed in identical gas-lift bioreactors operated under aerobic conditions (80-90% saturation) at 35°C. Sulfide loading rates up to 27 mmol L(-1)day(-1) were successfully applied at a HRT of 3.5 days. Sulfide was completely converted into sulfate by the haloalkaliphilic sulfide-oxidizing bacteria belonging to the genus Thioalkalivibrio. Influent benzene concentrations ranged from 100 to 600 µM. At steady state, benzene was removed by 93% due to high stripping efficiencies and biodegradation. Microbial community analysis revealed the presence of haloalkaliphilic heterotrophic bacteria belonging to the genera Marinobacter, Halomonas and Idiomarina which might have been involved in the observed benzene removal. The work shows the potential of halo-alkaliphilic bacteria in mitigating environmental problems caused by alkaline waste.
Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction
Fang, K. ; Zhao, H. ; Changyue Sun, ; Lam, M.C. ; Chang, S. ; Zhang, K. ; Panda, G. ; Godinho, M. ; Martins Dos Santos, V.A.P. ; Wang, J. - \ 2011
BMC Systems Biology 5 (2011). - ISSN 1752-0509 - 16 p.
cystic-fibrosis sputum - coenzyme-a carboxylase - survival in-vivo - cepacia complex - pseudomonas-aeruginosa - escherichia-coli - drug targets - sp-nov - antimicrobial peptides - core-oligosaccharide
BACKGROUND: Burkholderia cenocepacia is a threatening nosocomial epidemic pathogen in patients with cystic fibrosis (CF) or a compromised immune system. Its high level of antibiotic resistance is an increasing concern in treatments against its infection. Strain B. cenocepacia J2315 is the most infectious isolate from CF patients. There is a strong demand to reconstruct a genome-scale metabolic network of B. cenocepacia J2315 to systematically analyze its metabolic capabilities and its virulence traits, and to search for potential clinical therapy targets. RESULTS: We reconstructed the genome-scale metabolic network of B. cenocepacia J2315. An iterative reconstruction process led to the establishment of a robust model, iKF1028, which accounts for 1,028 genes, 859 internal reactions, and 834 metabolites. The model iKF1028 captures important metabolic capabilities of B. cenocepacia J2315 with a particular focus on the biosyntheses of key metabolic virulence factors to assist in understanding the mechanism of disease infection and identifying potential drug targets. The model was tested through BIOLOG assays. Based on the model, the genome annotation of B. cenocepacia J2315 was refined and 24 genes were properly re-annotated. Gene and enzyme essentiality were analyzed to provide further insights into the genome function and architecture. A total of 45 essential enzymes were identified as potential therapeutic targets. CONCLUSIONS: As the first genome-scale metabolic network of B. cenocepacia J2315, iKF1028 allows a systematic study of the metabolic properties of B. cenocepacia and its key metabolic virulence factors affecting the CF community. The model can be used as a discovery tool to design novel drugs against diseases caused by this notorious pathogen
Microbiota of cocoa powder with particular reference to aerobic thermoresistant spore-formers
Líma, L.J.R. ; Kamphuis, H.J. ; Nout, M.J.R. ; Zwietering, M.H. - \ 2011
Food Microbiology 28 (2011)3. - ISSN 0740-0020 - p. 573 - 582.
bacillus-subtilis - heat-resistance - sp-nov - aflp - heterogeneity - bacteria - sequence - strains - milk - rna
The microbiological criteria of commercial cocoa powder are defined in guidelines instituted by the cocoa industry. Twenty-five commercial samples were collected with the aim of assessing the compliance with the microbiological quality guidelines and investigating the occurrence and properties of aerobic Thermoresistant Spores (ThrS). Seventeen samples complied with the guidelines, but one was positive for Salmonella, five for Enterobacteriaceae and two had mould levels just exceeding the maximum admissible level. The treatment of the cocoa powder suspensions from 100 °C to 170 °C for 10 min, revealed the presence of ThrS in 36% of the samples. In total 61 ThrS strains were isolated, of which the majority belonged to the Bacillus subtilis complex (65.6%). Strains resporulation and spore crops inactivation at 110 °C for 5 min showed a wide diversity of heat-resistance capacities. Amplified fragment length polymorphism analysis revealed not only a large intraspecies diversity, but also different clusters of heat-resistant spore-forming strains. The heat-resistance of spores of six B. subtilis complex strains was further examined by determination of their D and z-values. We concluded that B. subtilis complex spores, in particular those from strain M112, were the most heat-resistant and these may survive subsequent preservation treatments, being potentially problematic in food products, such as chocolate milk
Hydrogenotrophic Sulfate Reduction in a Gas-Lift Bioreactor Operated at 9 degrees C
Nevatalo, L.M. ; Bijmans, M.F.M. ; Lens, P.N.L. ; Kaksonen, A.H. ; Puhakka, J.A. - \ 2010
Journal of Microbiology and Biotechnology 20 (2010)3. - ISSN 1017-7825 - p. 615 - 621.
reducing bacteria - retention time - carbon-dioxide - growth-rate - sp-nov - reactor - temperature - methanogenesis - oxidation - sulfide
The viability of low-temperature sulfate reduction with hydrogen as electron donor was studied with a bench-scale gas-lift bioreactor (GLB) operated at 9 degrees C. Prior to the GLB experiment, the temperature range of sulfate reduction of the inoculum was assayed. The results of the temperature gradient assay indicated that the inoculum was a psychrotolerant mesophilic enrichment culture that had an optimal temperature for sulfate reduction of 31 degrees C, and minimum and maximum temperatures of 7 degrees C and 41 degrees C, respectively. In the GLB experiment at 9 degrees C, a sulfate reduction rate of 500-600 mg l(-1) d(-1), corresponding to a specific activity of 173 mg SO42- g VSS-1 d(-1), was obtained. The electron flow from the consumed H-2-gas to sulfate reduction varied between 27% and 52%, whereas the electron flow to acetate production decreased steadily from 15% to 5%. No methane was produced. Acetate was produced from CO2 and H-2 by homoacetogenic bacteria. Acetate supported the growth of some heterotrophic sulfate-reducing bacteria. The sulfate reduction rate in the GLB was limited by the slow biomass growth rate at 9 degrees C and low biomass retention in the reactor. Nevertheless, this study demonstrated the potential sulfate reduction rate of psychrotolerant sulfate-reducing mesophiles at suboptimal temperature.
Isolation and Partial Characterization of Bacterial Strains on Low Organic Carbon Medium from Soils Fertilized with Different Organic Amendments
Senechkin, I.V. ; Speksnijder, A.G.C.L. ; Semenov, A.M. ; Bruggen, A.H.C. van; Overbeek, L.S. van - \ 2010
Microbial Ecology 60 (2010)4. - ISSN 0095-3628 - p. 829 - 839.
16s ribosomal-rna - oligotrophic bacteria - bradyrhizobium-japonicum - microbial-populations - sp-nov - diversity - community - nitrogen - dynamics - roots
A total of 720 bacterial strains were isolated from soils with four different organic amendment regimes on a low organic carbon (low-C) agar medium (10 mu g C ml(-1)) traditionally used for isolation of oligotrophs. Organic amendments in combination with field history resulted in differences in dissolved organic carbon contents in these soils. There were negative correlations between total and dissolved organic carbon content and the number of isolates on low-C agar medium, whereas these correlations were absent for bacterial strains isolated from the same soil on high-C agar medium (1,000 mu g C ml(-1)). Repeated transfers (up to ten times) of the isolates from low-C agar medium to fresh low- and high-C agar media were done to test for exclusive growth under oligotrophic conditions. The number of isolates exclusively growing under oligotrophic conditions dropped after each subsequent transfer from 241 after the first to 98 after the third transfer step. Identification on the basis of partial 16S rRNA gene sequences revealed that most of the 241 isolates (as well as the subset of 98 isolates) belong to widespread genera such as Streptomyces, Rhizobium, Bradyrhizobium, and Mesorhizobium, and the taxonomic composition of dominant genera changed from the first transfer step to the third. A selected subset of 17 isolates were further identified and characterized for exclusive growth on low-C agar medium. Two isolates continued to grow only on low-C agar medium up to the tenth transfer step and matched most closely with Rhizobium sullae and an uncultured bacterium on the basis of the almost full-length 16S rRNA gene. It was concluded that the vast majority of strains which are isolated on low-C agar media belong to the trophic group of microorganisms adapted to a "broad range" of carbon concentrations, including well-known and widespread bacterial genera. Oligotrophy is a physiological, not a taxonomic property, and can only be identified by cultural means so far. We showed that true oligotrophs that are unable to grow on high carbon media are rare and belong to genera that also contain broad-range and copiotrophic strains.
Sequence data reveals phylogenetic affinities of fungal anamorphs Bahusutrabeeja, Diplococcium, Natarajania, Paliphora, Polyschema, Rattania and Spadicoides
Shenoy, B.D. ; Jeewon, R. ; Wang, H. ; Amandeep, K. ; Ho, W.H. ; Bhat, D.J. ; Crous, P.W. ; Hyde, K.D. - \ 2010
Fungal Diversity 44 (2010)1. - ISSN 1560-2745 - p. 161 - 169.
sp-nov - sensu-lato - molecular systematics - polyphasic approach - submerged wood - western-ghats - allied genera - hong-kong - gen. nov - chaetosphaeria
Partial 28S rRNA gene sequence-data of the strains of the anamorphic genera Bahusutrabeeja, Diplococcium, Natarajania, Paliphora, Polyschema, Rattania and Spadicoides were analysed to predict their phylogenetic relationships and taxonomic placement within the Ascomycota. Results indicate that Diplococcium and morphologically similar genera, i.e. Spadicoides, Paliphora and Polyschema do not share a recent common ancestor. The type species of Diplococcium, D. spicatum is referred to Helotiales (Leotiomycetes). The placement of Spadicoides bina, the type of the genus, is unresolved but it is shown to be closely associated with Porosphaerella species, which are sister taxa to Coniochaetales (Sordariomycetes). Three Polyschema species analysed in this study represent a monophyletic lineage and are related to Lentithecium fluviatile and Leptosphaeria calvescens in Pleosporales (Dothideomycetes). DNA sequence analysis also suggests that Paliphora intermedia is a member of Chaetosphaeriaceae (Sordariomycetes). The type species of Bahusutrabeeja, B. dwaya, is phylogenetically related to Neodeightonia (=Botryosphaeria) subglobosa in Botryosphaeriales (Dothideomycetes). Monotypic genera Natarajania and Rattania are phylogenetically related to members of Diaporthales and Chaetosphaeriales, respectively. Future studies with extended gene datasets and type strains are required to resolve many novel but morphologically unexplainable phylogenetic scenarios revealed from this study. It is increasingly becoming evident that a fungal
A case for re-inventory of Australia’s plant pathogens
Hyde, K.D. ; Chomnunti, P. ; Crous, P.W. ; Groenewald, J.Z. ; Damm, U. ; Ko Ko, T.W. ; Shivas, R.G. ; Summerell, B.A. ; Tan, Y.P. - \ 2010
Persoonia 25 (2010). - ISSN 0031-5850 - p. 50 - 60.
phenotypic characters differentiate - multiple gene genealogies - sp-nov - western-australia - south-africa - colletotrichum-gloeosporioides - mycosphaerella-spp. - molecular phylogeny - polyphasic approach - cryptic speciation
Australia has efficient and visible plant quarantine measures, which through various border controls and survey activities attempt to prevent the entry of unwanted pests and diseases. The ability to successfully perform this task relies heavily on determining what pathogens are present and established in Australia as well as those pathogens that are exotic and threatening. There are detailed checklists and databases of fungal plant pathogens in Australia, compiled, in part, from surveys over many years sponsored by Federal and State programmes. These checklists and databases are mostly specimen-based, which enables validation of records with reference herbarium specimens and sometimes associated cultures. Most of the identifications have been based on morphological examination. The use of molecular methods, particularly the analysis of DNA sequence data, has recently shown that several well-known and important plant pathogenic species are actually complexes of cryptic species. We provide examples of this in the important plant pathogenic genera Botryosphaeria and its anamorphs, Colletotrichum, Fusarium, Phomopsis / Diaporthe and Mycosphaerella and its anamorphs. The discovery of these cryptic species indicates that many of the fungal names in checklists need scrutiny. It is difficult, and often impossible, to extract DNA for sequence analysis from herbarium specimens in order to validate identifications that may now be considered suspect. This validation can only be done if specimens are recollected, re-isolated and subjected to DNA analysis. Where possible, herbarium specimens as well as living cultures are needed to support records. Accurate knowledge of the plant pathogens within Australia's borders is an essential prerequisite for the effective discharge of plant quarantine activities that will prevent or delay the arrival of unwanted plant pathogens.
(Per)chlorate reduction by an acetogenic bacterium, Sporomusa sp., isolated from an underground gas storage
Balk, M. ; Mehboob, F. ; Gelder, A.H. van; Rijpstra, I. ; Sinninghe-Damsté, J.S. ; Stams, A.J.M. - \ 2010
Applied Microbiology and Biotechnology 88 (2010)2. - ISSN 0175-7598 - p. 595 - 603.
sp-nov - homoacetogenic bacterium - strain gr-1 - perchlorate - chlorate - metabolism - water - milk - soil - identification
A mesophilic bacterium, strain An4, was isolated from an underground gas storage reservoir with methanol as substrate and perchlorate as electron acceptor. Cells were Gram-negative, spore-forming, straight to curved rods, 0.5-0.8 microm in diameter, and 2-8 microm in length, growing as single cells or in pairs. The cells grew optimally at 37 degrees C, and the pH optimum was around 7. Strain An4 converted various alcohols, organic acids, fructose, acetoin, and H(2)/CO(2) to acetate, usually as the only product. Succinate was decarboxylated to propionate. The isolate was able to respire with (per)chlorate, nitrate, and CO(2). The G+C content of the DNA was 42.6 mol%. Based on the 16S rRNA gene sequence analysis, strain An4 was most closely related to Sporomusa ovata (98% similarity). The bacterium reduced perchlorate and chlorate completely to chloride. Key enzymes, perchlorate reductase and chlorite dismutase, were detected in cell-free extracts
Novel fungal genera and species associated with the sooty blotch and flyspeck complex on apple in China and the USA
Yang, H.L. ; Sun, G.Y. ; Batzer, J.C. ; Crous, P.W. ; Groenewald, J.Z. ; Gleason, M.L. - \ 2010
Persoonia (2010)24. - ISSN 0031-5850 - p. 29 - 37.
ribosomal dna - sp-nov - sporidesmium - sequences - disease
Fungi in the sooty blotch and flyspeck (SBFS) complex cause blemishes on apple and pear fruit that result in economic losses for growers. The SBFS fungi colonise the epicuticular wax layer of pomaceous fruit but do not invade the cuticle. Fungi causing fuliginous and punctate mycelial types on apple are particularly difficult to identify based on morphological criteria because many species in the SBFS complex share the same mycelial phenotypes. We compared the morphology and nuclear ribosomal DNA phylogeny (ITS, LSU) of 11 fungal strains isolated from SBFS blemishes on apple obtained from two provinces in China and five states in the USA. Parsimony analysis, supported by cultural characteristics and morphology in vitro, provided support to delimit the isolates into three novel genera, representing five new species. Phaeothecoidiella, with two species, P. missouriensis and P. illinoisensis, is introduced as a new genus with pigmented endoconidia in the Dothideomycetes. Houjia (Capnodiales) is introduced for H. pomigena and H. yanglingensis. Although morphologically similar to Stanjehughesia (Chaetosphaeriaceae), Houjia is distinct in having solitary conidiogenous cells. Sporidesmajora (Capnodiales), based on S. pennsylvaniensis, is distinguished from Sporidesmium (Sordariomycetes) in having long, multiseptate conidiophores that frequently have a subconical, darkly pigmented apical cell, and very long, multi-euseptate conidia
Phylogeny and systematics of the genus Calonectria
Lombard, L. ; Crous, P.W. ; Wingfield, B.D. ; Wingfield, M.J. - \ 2010
Studies in Mycology 66 (2010)1. - ISSN 0166-0616 - p. 31 - 69.
internal transcribed spacers - sp-nov - cylindrocladium-floridanum - species concepts - dna-sequences - ribosomal dna - beta-tubulin - morphology - polymorphism - spathiphylli
Species of Calonectria are important plant pathogens, several of which have a worldwide distribution. Contemporary taxonomic studies on these fungi have chiefly relied on DNA sequence comparisons of the ß-tubulin gene region. Despite many new species being described, there has been no phylogenetic synthesis for the group since the last monographic study almost a decade ago. In the present study, the identity of a large collection of Calonectria isolates from various geographic regions was determined using morphological and DNA sequence comparisons. This resulted in the discovery of seven new species; Ca. densa, Ca. eucalypti, Ca. humicola, Ca. orientalis, Ca. pini, Ca. pseudoscoparia and Ca. sulawesiensis, bringing the total number of currently accepted Calonectria species to 68. A multigene phylogeny was subsequently constructed for all available Calonectria spp., employing seven gene regions, namely actin, ß-tubulin, calmodulin, histone H3, the internal transcribed spacer regions 1 and 2 and the 5.8S gene of the ribosomal RNA, 28S large subunit RNA gene and translation elongation 1-alpha. Based on these data 13 phylogenetic groups could be distinguished within the genus Calonectria that correlated with morphological features. Dichotomous and synoptic keys to all Calonectria spp. currently recognised are also provided.
Highlights of the Didymellaceae: A polyphasic approach to characterise Phoma and related pleosporalean genera
Aveskamp, M.M. ; Gruyter, J. de; Woudenberg, J.H.C. ; Verkley, G.J.M. ; Crous, P.W. - \ 2010
Studies in Mycology 65 (2010)1. - ISSN 0166-0616 - p. 1 - 60.
ribosomal dna-sequences - powdery mildew fungi - transcribed spacer sequences - medicaginis var pinodella - maculans species complex - 7 mu-m - leptosphaeria-maculans - sp-nov - genetic diversity - ascochyta-rabiei
Fungal taxonomists routinely encounter problems when dealing with asexual fungal species due to poly- and paraphyletic generic phylogenies, and unclear species boundaries. These problems are aptly illustrated in the genus Phoma. This phytopathologically significant fungal genus is currently subdivided into nine sections which are mainly based on a single or just a few morphological characters. However, this subdivision is ambiguous as several of the section-specific characters can occur within a single species. In addition, many teleomorph genera have been linked to Phoma, three of which are recognised here. In this study it is attempted to delineate generic boundaries, and to come to a generic circumscription which is more correct from an evolutionary point of view by means of multilocus sequence typing. Therefore, multiple analyses were conducted utilising sequences obtained from 28S nrDNA (Large Subunit - LSU), 18S nrDNA (Small Subunit - SSU), the Internal Transcribed Spacer regions 1 & 2 and 5.8S nrDNA (ITS), and part of the ß-tubulin (TUB) gene region. A total of 324 strains were included in the analyses of which most belonged to Phoma taxa, whilst 54 to related pleosporalean fungi. In total, 206 taxa were investigated, of which 159 are known to have affinities to Phoma. The phylogenetic analysis revealed that the current Boeremaean subdivision is incorrect from an evolutionary point of view, revealing the genus to be highly polyphyletic. Phoma species are retrieved in six distinct clades within the Pleosporales, and appear to reside in different families. The majority of the species, however, including the generic type, clustered in a recently established family, Didymellaceae. In the second part of this study, the phylogenetic variation of the species and varieties in this clade was further assessed. Next to the genus Didymella, which is considered to be the sole teleomorph of Phoma s. str., we also retrieved taxa belonging to the teleomorph genera Leptosphaerulina and Macroventuria in this clade. Based on the sequence data obtained, the Didymellaceae segregate into at least 18 distinct clusters, of which many can be associated with several specific taxonomic characters. Four of these clusters were defined well enough by means of phylogeny and morphology, so that the associated taxa could be transferred to separate genera. Aditionally, this study addresses the taxonomic description of eight species and two varieties that are novel to science, and the recombination of 61 additional taxa.
Biohydrogen production from untreated and hydrolyzed potato steam peels by the extreme thermophiles Caldicellulosiruptor saccharolyticus and Thermotoga neapolitana
Mars, A.E. ; Veuskens, T. ; Budde, M.A.W. ; Doeveren, P.F.N.M. van; Lips, S.J.J. ; Bakker, R.R. ; Vrije, G.J. de; Claassen, P.A.M. - \ 2010
International Journal of Hydrogen Energy 35 (2010)15. - ISSN 0360-3199 - p. 7730 - 7737.
fermentative hydrogen-production - sp-nov - starch - bacterium - waste - microflora - substrate
Production of hydrogen by the extreme thermophiles Caldicellulosiruptor saccharolyticus and Thermotoga neapolitana was studied in serum flasks and in pH-controlled bioreactors with glucose, and hydrolyzed and untreated potato steam peels (PSP) as carbon sources. Two types of PSP hydrolysates were used: one in which the starch in the PSP was liquefied with alpha-amylase, and one in which the liquefied starch was further hydrolyzed to glucose by amyloglucosidase. When the PSP hydrolysates or untreated PSP were added at circa 10–14 g/L of glucose units, both strains grew well and produced hydrogen with reasonable to high molar yields (2.4–3.8 moles H2/mole glucose units), and no significant production of lactate. The hydrogen production rates and yields were similar with untreated PSP, hydrolyzed PSP, and pure glucose, showing that C. saccharolyticus and T. neapolitana are well equipped for the utilization of starch. When the concentrations of the substrates were increased, growth and hydrogen production of both strains were hampered. At substrate concentrations of circa 30–40 g/L of glucose units, the molar hydrogen yield of C. saccharolyticus was severely reduced due to the formation of high amounts of lactate, while T. neapolitana was unable to grow at all. The results showed that PSP and PSP hydrolysates are very suitable substrates for efficient fermentative hydrogen production at moderate substrate loadings.
Population Dynamics of a Single-Stage Sulfidogenic Bioreactor Treating Synthetic Zinc-Containing Waste Streams
Dar, S.A. ; Bijmans, M.F.M. ; Dinkla, I.J.T. ; Geurkink, B. ; Lens, P.N.L. ; Dopson, M. - \ 2009
Microbial Ecology 58 (2009)3. - ISSN 0095-3628 - p. 529 - 537.
sulfate-reducing bacteria - gradient gel-electrophoresis - polymerase-chain-reaction - scatologenes strain sl1 - acid-mine drainage - environmental-samples - microbial diversity - sulfide toxicity - ribosomal-rna - sp-nov
Waste streams from industrial processes such as metal smelting or mining contain high concentrations of sulfate and metals with low pH. Dissimilatory sulfate reduction carried out by sulfate-reducing bacteria (SRB) at low pH can combine sulfate reduction with metal-sulfide precipitation and thus open possibilities for selective metal recovery. This study investigates the microbial diversity and population changes of a single-stage sulfidogenic gas-lift bioreactor treating synthetic zinc-rich waste water at pH 5.5 by denaturing gradient gel electrophoresis of 16S rRNA gene fragments and quantitative polymerase chain reaction. The results indicate the presence of a diverse range of phylogenetic groups with the predominant microbial populations belonging to the Desulfovibrionaceae from delta-Proteobacteria. Desulfovibrio desulfuricans-like populations were the most abundant among the SRB during the three stable phases of varying sulfide and zinc concentrations and increased from 13% to 54% of the total bacterial populations over time. The second largest group was Desulfovibrio marrakechensis-like SRB that increased from 1% to about 10% with decreasing sulfide concentrations. Desulfovibrio aminophilus-like populations were the only SRB to decrease in numbers with decreasing sulfide concentrations. However, their population was <1% of the total bacterial population in the reactor at all analyzed time points. The number of dissimilatory sulfate reductase (DsrA) gene copies per number of SRB cells decreased from 3.5 to 2 DsrA copies when the sulfide concentration was reduced, suggesting that the cells' sulfate-reducing capacity was also lowered. This study has identified the species present in a single-stage sulfidogenic bioreactor treating zinc-rich wastewater at low pH and provides insights into the microbial ecology of this biotechnological process.
Multi-locus phylogeny of Pleosporales: a taxonomic, ecological and evolutionary re-evaluation
Zhang, Y. ; Schoch, C.L. ; Fournier, J. ; Crous, P.W. ; Gruyter, J. de; Woudenberg, J.H.C. ; Hirayama, K. ; Tanaka, K. ; Pointing, S.B. ; Spatafora, J.W. ; Hyde, K.D. - \ 2009
Studies in Mycology 64 (2009)1. - ISSN 0166-0616 - p. 85 - 102.
ribosomal dna-sequences - stagonospora-nodorum - molecular phylogeny - leptosphaeria-maculans - phaeosphaeria-nodorum - multigene phylogeny - multiple alignment - endophytic fungi - sp-nov - ascomycota
Five loci, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, are used for analysing 129 pleosporalean taxa representing 59 genera and 15 families in the current classification of Pleosporales. The suborder Pleosporineae is emended to include four families, viz. Didymellaceae, Leptosphaeriaceae, Phaeosphaeriaceae and Pleosporaceae. In addition, two new families are introduced, i.e. Amniculicolaceae and Lentitheciaceae. Pleomassariaceae is treated as a synonym of Melanommataceae, and new circumscriptions of Lophiostomataceae s. str, Massarinaceae and Lophiotrema are proposed. Familial positions of Entodesmium and Setomelanomma in Phaeosphaeriaceae, Neophaeosphaeria in Leptosphaeriaceae, Leptosphaerulina, Macroventuria and Platychora in Didymellaceae, Pleomassaria in Melanommataceae and Bimuria, Didymocrea, Karstenula and Paraphaeosphaeria in Montagnulaceae are clarified. Both ecological and morphological characters show varying degrees of phylogenetic significance. Pleosporales is most likely derived from a saprobic ancestor with fissitunicate asci containing conspicuous ocular chambers and apical rings. Nutritional shifts in Pleosporales likely occured from saprotrophic to hemibiotrophic or biotrophic.
Colletotrichum - names in current use
Hyde, K.D. ; Cai, L. ; Cannon, P.F. ; Crouch, J.A. ; Crous, P.W. ; Damm, U. ; Goodwin, P.H. ; Chen, H. ; Johnston, P.R. ; Jones, E.B.G. ; Liu, Z.Y. ; McKenzie, E.H.C. ; Moriwaki, J. ; Noireung, P. ; Pennycook, S.R. ; Pfenning, L.H. ; Prihastuti, H. ; Sato, T. ; Shivas, R.G. ; Tan, Y.P. ; Taylor, P.W.J. ; Weir, B.S. ; Yang, Y.L. ; Zhang, J.Z. - \ 2009
Fungal Diversity 39 (2009). - ISSN 1560-2745 - p. 147 - 182.
vegetative compatibility groups - iwokrama-forest-reserve - coffea-arabica l. - potato black dot - infection process - molecular characterization - leaf-spot - sp-nov - anthracnose resistance - biological-control
Filamentous fungi in the genus Colletotrichum are destructive pathogens that cause disease and crop losses in plants worldwide. Taxonomy and nomenclature in the group is confusing, even to scientists working in the field, and inaccurate diagnosis of species is not uncommon. In this review, we provide a overview of the 66 Colletotrichum names that are in common use, and the 19 recently used names which are regarded as doubtful. This paper represents the first comprehensive overview of the genus in 17 years, and is the first summary treatment of Colletotrichum to incorporate data generated through DNA analysis and phylogenetic systematics. Species are listed alphabetically and annotated with their taxonomic entry, teleomorph, hosts and disease, brief summaries of taxonomic and phylogenetic research, and outstanding issues for the genus that are neccesary to stabilize species names. Sequence data and type culture collection resources are also summarized. The paper serves to provide a new starting point for usage of current names in Colletotrichum and indicates future work needed
Colletotrichum species with curved conidia from herbaceous hosts
Damm, U. ; Woudenberg, J.H.C. ; Cannon, P.F. ; Crous, P.W. - \ 2009
Fungal Diversity 39 (2009). - ISSN 1560-2745 - p. 45 - 87.
spored graminicolous colletotrichum - sequence-analysis - infection process - mulberry leaves - primer sets - lily bulbs - leaf-spot - sp-nov - anthracnose - dematium
Colletotrichum (Glomerellaceae, Sordariomycetes) species with dark setae and curved conidia are known as anthracnose pathogens of a number of economically important hosts and are often identified as C. dematium. Colletotrichum dematium has been synonymised with many species, including the type of the genus, C. lineola. Since there is no living strain of the original material of either species available, we re-collected C. lineola from the original location to serve as an epitype of that name, and chose an appropriate epitype specimen and associated strain of C. dematium from the CBS collection. A multilocus molecular phylogenetic analysis (ITS, ACT, Tub2, CHS-1, GAPDH, HIS3) of 97 isolates of C. lineola, C. dematium and other Colletotrichum species with curved conidia from herbaceous hosts resulted in 20 clades, with 12 clades containing strains that had previously been identified as C. dematium. The epitype strains of C. lineola and C. dematium reside in two closely related clades. Other clades represent four previously undescribed species, C. anthrisci, C. liriopes, C. rusci and C. verruculosum, isolated respectively from Anthriscus in the Netherlands, Liriope in Mexico, Ruscus in Italy and Crotalaria in Zimbabwe. The new combinations C. spaethianum and C. tofieldiae are made. Colletotrichum truncatum is epitypified, as well as C. circinans, C. curcumae and C. fructi. Three further unidentified Colletotrichum taxa were detected in the phylogenetic analysis, which may require description after further research. Each species is comprehensively described and illustrated
Myrtaceae, a cache of fungal biodiversity
Cheewangkoon, R. ; Groenewald, J.Z. ; Summerell, B.A. ; Hyde, K.D. ; To-anun, C. ; Crous, P.W. - \ 2009
Persoonia 23 (2009). - ISSN 0031-5850 - p. 55 - 85.
south-africa - eucalyptus leaves - sp-nov - interspecific hybridization - cylindrocladium-floridanum - syzygium-cordatum - host-specificity - ribosomal dna - sequence-data - genera nova
Twenty-six species of microfungi are treated, the majority of which are associated with leaf spots of Corymbia, Eucalyptus and Syzygium spp. (Myrtaceae). The treated species include three new genera, Bagadiella, Foliocryphia and Pseudoramichloridium, 20 new species and one new combination. Novelties on Eucalyptus include: Antennariella placitae, Bagadiella lunata, Cladoriella rubrigena, C. paleospora, Cyphellophora eucalypti, Elsinoë eucalypticola, Foliocryphia eucalypti, Leptoxyphium madagascariense, Neofabraea eucalypti, Polyscytalum algarvense, Quambalaria simpsonii, Selenophoma australiensis, Sphaceloma tectificae, Strelitziana australiensis and Zeloasperisporium eucalyptorum. Stylaspergillus synanamorphs are reported for two species of Parasympodiella, P. eucalypti sp. nov. and P. elongata, while Blastacervulus eucalypti, Minimedusa obcoronata and Sydowia eucalypti are described from culture. Furthermore, Penidiella corymbia and Pseudoramichloridium henryi are newly described on Corymbia, Pseudocercospora palleobrunnea on Syzygium and Rachicladosporium americanum on leaf litter. To facilitate species identification, as well as determine phylogenetic relationships, DNA sequence data were generated from the internal transcribed spacers (ITS1, 5.8S nrDNA, ITS2) and the 28S nrDNA (LSU) regions of all taxa studied
Microbial enrichment of a novel growing substrate and its effect on plant growth.
Trifonova, R.D. ; Postma, J. ; Schilder, M.T. ; Elsas, J.D. van - \ 2009
Microbial Ecology 58 (2009)3. - ISSN 0095-3628 - p. 632 - 641.
torrefied grass fibers - beneficial microorganisms - sp-nov - bacteria - cultures - rhizosphere - amendments - removal
Abstract The quality of torrefied grass fibers (TGF) as a new potting soil ingredient was tested in a greenhouse experiment. TGF was colonized with previously selected microorganisms. Four colonization treatments were compared: (1) no inoculants, (2) the fungus Coniochaeta ligniaria F/TGF15 alone, (3) the fungus followed by inoculation with two selected bacteria, and (4) the fungus with seven selected bacteria. Cultivation-based and DNA-based methods, i.e., PCR-DGGE and BOX-PCR, were applied to assess the bacterial and fungal communities established in the TGF. Although colonization was not performed under sterile conditions, all inoculated strains were recovered from TGF up to 26 days incubation. Stable fungal and bacterial populations of 108 and 109¿CFU/g TGF, respectively, were reached. As a side effect of the torrefaction process that aimed at the chemical stabilization of grass fibers, potentially phytotoxic compounds were generated. These phytotoxic compounds were cold-extracted from the fibers and analyzed by gas chromatography mass spectrometry. Four of 15 target compounds that had previously been found in the extract of TGF were encountered, namely phenol, 2-methoxyphenol, benzopyran-2-one, and tetrahydro-5,6,7,7a-benzofuranone. The concentration of these compounds decreased significantly during incubation. The colonized TGF was mixed with peat (P) in a range of 100%:0%, 50%:50%, 20%:80%, and 0%:100% TGF/P (w/w), respectively, to assess suitability for plant growth. Germination of tomato seeds was assessed three times, i.e., with inoculated TGF that had been incubated for 12, 21, and 26 days. In these tests, 90–100% of the seeds germinated in 50%:50% and 20%:80% TGF/P, whereas on average only 50% of the seeds germinated in pure TGF. Germination was not improved by the microbial inoculants. However, plant fresh weight as well as leaf area of 28-day-old tomato plants were significantly increased in all treatments where C. ligniaria F/TGF15 was inoculated compared to the control treatment without microbial inoculants. Colonization with C. ligniaria also protected the substrate from uncontrolled colonization by other fungi. The excellent colonization of TGF by the selected plant-health promoting bacteria in combination with the fungus C. ligniaria offers the possibility to create disease suppressive substrate, meanwhile replacing 20% to 50% of peat in potting soil by TGF.
DNA phylogeny reveals polyphyly of Phoma section Peyronellaea and multiple taxonomic novelties
Aveskamp, M.M. ; Verkley, G.J.M. ; Gruyter, J. de; Murace, M.A. ; Perelló, A. ; Woudenberg, J.H.C. ; Groenewald, J.Z. ; Crous, P.W. - \ 2009
Mycologia 101 (2009)3. - ISSN 0027-5514 - p. 363 - 382.
genus phoma - sp-nov - monograph - plenodomus - inference - trees - taxa
Species of the anamorph genus Phoma are commonly isolated from a wide range of ecological niches. They are notoriously difficult to identify due to the paucity of morphological features and the plasticity of these when cultivated on agar media. Species linked to Phoma section Peyronellaea are typified by the production of dictyochlamydospores and thus have additional characters to use in taxon delineation. However, the taxonomy of this section is still not fully understood. Furthermore the production of such chlamydospores also is known in some other sections of Phoma. DNA sequences were generated from three loci, namely ITS, actin, and ß-tubulin, to clarify the phylogeny of Phoma taxa that produce dictyochlamydospores. Results were unable to support section Peyronellaea as a taxonomic entity. Dictyochlamydospore formation appears to be a feature that developed, or was lost, many times during the evolution of Phoma. Furthermore, based on the multigene analyses, five new Phoma species could be delineated while a further five required taxonomic revision to be consistent with the genetic variation observed
Efficient hydrogen production from the lignocellulosic energy crop Miscanthus by the extreme thermophilic bacteria Caldicellulosiruptor saccharolyticus and Thermotoga neapolitana
Vrije, G.J. de; Bakker, R.R. ; Budde, M.A.W. ; Lai, M.H. ; Mars, A.E. ; Claassen, P.A.M. - \ 2009
Biotechnology for Biofuels 2 (2009). - ISSN 1754-6834 - 15 p.
biohydrogen production - dark fermentation - corn stover - sp-nov - biomass - pretreatment - degradation - wastes - xylose - microorganisms
The production of hydrogen from biomass by fermentation is one of the routes that can contribute to a future sustainable hydrogen economy. Lignocellulosic biomass is an attractive feedstock because of its abundance, low production costs and high polysaccharide content. Batch cultures of Caldicellulosiruptor saccharolyticus and Thermotoga neapolitana produced hydrogen, carbon dioxide and acetic acid as the main products from soluble saccharides in Miscanthus hydrolysate. The presence of fermentation inhibitors, such as furfural and 5-hydroxylmethyl furfural, in this lignocellulosic hydrolysate was avoided by the mild alkaline-pretreatment conditions at a low temperature of 75°C. Both microorganisms simultaneously and completely utilized all pentoses, hexoses and oligomeric saccharides up to a total concentration of 17 g l-1 in pH-controlled batch cultures. T. neapolitana showed a preference for glucose over xylose, which are the main sugars in the hydrolysate. Hydrogen yields of 2.9 to 3.4 mol H2 per mol of hexose, corresponding to 74 to 85% of the theoretical yield, were obtained in these batch fermentations. The yields were higher with cultures of C. saccharolyticus compared to T. neapolitana. In contrast, the rate of substrate consumption and hydrogen production was higher with T. neapolitana. At substrate concentrations exceeding 30 g l-1, sugar consumption was incomplete, and lower hydrogen yields of 2.0 to 2.4 mol per mol of consumed hexose were obtained. Efficient hydrogen production in combination with simultaneous and complete utilization of all saccharides has been obtained during the growth of thermophilic bacteria on hydrolysate of the lignocellulosic feedstock Miscanthus. The use of thermophilic bacteria will therefore significantly contribute to the energy efficiency of a bioprocess for hydrogen production from biomass
Fungal Radiation in the Cape Floristic Region: an analysis based on Gondwanamyces and Ophiostoma
Roets, F. ; Wingfield, M.J. ; Crous, P.W. ; Dreyer, L.L. - \ 2009
Molecular Phylogenetics and Evolution 51 (2009)1. - ISSN 1055-7903 - p. 111 - 119.
protea-infructescences - south-africa - sp-nov - phylogenetic inference - pollination systems - evolution - flora - ceratocystiopsis - beetles - genus
The Cape Floristic Region (CFR) displays high levels of plant diversity and endemism, and has received focused botanical systematic attention. In contrast, fungal diversity patterns and co-evolutionary processes in this region have barely been investigated. Here we reconstruct molecular phylogenies using the ITS and ß-tubulin gene regions of the ophiostomatoid fungi Gondwanamyces and Ophiostoma associated with southern African Protea species. Results indicate that they evolved in close association with Protea. In contrast to Protea, Ophiostoma species migrated to the CFR from tropical and subtropical Africa, where they underwent subsequent radiation. In both Gondwanamyces and Ophiostoma vector arthropods probably facilitated long-distance migration and shorter-distance dispersal. Although ecological parameters shaped most associations between ophiostomatoid fungi and Protea, there is congruence between fungal¿host-associations and the systematic classification of Protea. These results confirm that the entire biotic environment must be considered in order to understand diversity and evolution in the CFR as a whole.
Effect of tungsten and molybdenum on growth of a syntrophic coculture of Syntrophobacter fumaroxidans and Methanospirillum hungatei
Plugge, C.M. ; Jiang, B. ; Bok, F.A.M. de; Tsai, C. ; Stams, A.J.M. - \ 2009
Archives of Microbiology 191 (2009)1. - ISSN 0302-8933 - p. 55 - 61.
interspecies electron-transfer - formate dehydrogenases - anaerobic-digestion - methanobacterium-thermoautotrophicum - formylmethanofuran dehydrogenase - methanococcus-vannielii - methanogenic bacteria - microbial communities - hydrogen-transfer - sp-nov
The effect of tungsten (W) and molybdenum (Mo) on the growth of Syntrophobacter fumaroxidans and Methanospirillum hungatei was studied in syntrophic cultures and the pure cultures of both the organisms. Cells that were grown syntropically were separated by Percoll density centrifugation. Measurement of hydrogenase and formate dehydrogenase levels in cell extracts of syntrophically grown cells correlated with the methane formation rates in the co-cultures. The effect of W and Mo on the activity of formate dehydrogenase was considerable in both the organisms, whereas hydrogenase activity remained relatively constant. Depletion of tungsten and/or molybdenum, however, did not affect the growth of the pure culture of S. fumaroxidans on propionate plus fumarate significantly, although the specific activities of hydrogenase and especially formate dehydrogenase were influenced by the absence of Mo and W. This indicates that the organism has a low W or Mo requirement under these conditions. Growth of M. hungatei on either formate or H(2)/CO(2) required tungsten, and molybdenum could replace tungsten to some extent. Our results suggest a more prominent role for H(2) as electron carrier in the syntrophic conversion of propionate, when the essential trace metals W and Mo for the functioning of formate dehydrogenase are depleted
Sulfate Reduction at pH 4 During the Thermophilic (55 degrees C) Acidification of Sucrose in UASB Reactors
Lopes, S.I.C. ; Capela, M.I. ; Dar, S.A. ; Muyzer, G. ; Lens, P.N.L. - \ 2008
Biotechnology Progress 24 (2008)6. - ISSN 8756-7938 - p. 1278 - 1289.
acid-mine drainage - gradient gel-electrophoresis - anaerobic granular sludge - in-situ hybridization - mill waste-water - sp-nov - reducing bacterium - metal fractionation - bioreactor - sulfur
Continuous sulfate reduction at pH 4.0 was demonstrated in a pH controlled thermophilic (55 degrees C) upflow anaerobic sludge bed reactor fed with sucrose at a COD/SO42- ratio of 0.9 and an organic loading rate of 0.8 and 1.9 gCOD (l(reactor) d)(-1) for a period of 78 days. A near v complete sulfate reduction efficiency was achieved throughout the reactor run, corresponding to sulfate removal rates of 0.91 and 1.92 g (l(reactor) d)(-1) at sulfate loading rates of 0.94 and 2 g (l(reactor) d)(-1), respectively, by keeping the sulfide concentration below 20 mg l(-1) due to stripping with nitrogen gas. Acidification was always complete and acetate was the only, degradation intermediate left in the effluent, which did not exceed 180 mgCOD l(-1) in pseudo-stationary states. The sludge was well retained ill the reactor and kept its granular form. A, Cu, Se, and Mo accumulated in the sludge, whereas Co, Ni, Fe, and Mn leached from the sludge, despite their continuous supply to the reactor via the influent. The bacterial diversity in the reactor sludge at the end of the reactor run was low and the culture was dominated by one acidifying species, resembling Thermoanaerobacterium sp., and one sulfate reducing species, resembling Desulfotomaculum sp.
Species of Botryosphaeriaceae occurring on Proteaceae
Marincowitz, S. ; Groenewald, J.Z. ; Wingfield, M.J. ; Crous, P.W. - \ 2008
Persoonia 21 (2008). - ISSN 0031-5850 - p. 111 - 118.
south-africa - western-cape - sp-nov - pathogens - fungi - endophytes - morphology - speciation - australia - canker
The Botryosphaeriaceae includes several species that are serious canker and leaf pathogens of Proteaceae. In the present study, sequence data for the ITS nrDNA region were used in conjunction with morphological observations to resolve the taxonomy of species of Botryosphaeriaceae associated with Proteaceae. Neofusicoccum luteum was confirmed from Buckinghamia and Banksia in Australia, and on Protea cynaroides in South Africa. A major pathogen of Banksia coccinea in Australia was shown to be N. australe and not N. luteum as previously reported. Neofusicoccum protearum was previously reported on Proteaceae from Australia, Madeira, Portugal and South Africa, and is shown here to also occur in Hawaii and Tenerife (Canary Islands). Furthermore, several previous records of N. ribis on Proteaceae were shown to be N. parvum. Saccharata capensis is described as a new species that is morphologically similar to S. proteae. There is no information currently available regarding its potential importance as plant pathogen and pathogenicity tests should be conducted with it in the future.
Ophiostoma gemellus and Sporothrix variecibatus from mites infesting Protea infructescences in South Africa
Roets, F. ; Beer, Z.W. de; Wingfield, M.J. ; Crous, P.W. ; Dreyer, L.L. - \ 2008
Mycologia 100 (2008)3. - ISSN 0027-5514 - p. 496 - 510.
phoretic mites - bark beetles - sp-nov - phylogenetic inference - ceratocystis-minor - ips-typographus - fungi - scolytidae - coleoptera - complex
Ophiostoma (Ophiostomatales) represents a large genus of fungi mainly known from associations with bark beetles (Curculionidae: Scolytinae) infesting conifers in the northern hemisphere. Few southern hemisphere native species are known, and the five species that consistently occur in the infructescences of Protea spp. in South Africa are ecologically unusual. Little is known about the vectors of Ophiostoma spp. from Protea infructescences, however recent studies have considered the possible role of insects and mites in the distribution of these exceptional fungi. In this study we describe a new species of Ophiostoma and a new Sporothrix spp. with affinities to Ophiostoma, both initially isolated from mites associated with Protea spp. They are described as Ophiostoma gemellus sp. nov. and Sporothrix variecibatus sp. nov. based on their morphology and comparisons of DNA sequence data of the 28S ribosomal, ß-tubulin and internal transcribed spacer (ITS1, 5.8S, ITS2) regions. DNA sequences of S. variecibatus were identical to those of a Sporothrix isolate obtained from Eucalyptus leaf litter in the same area in which S. variecibatus occurs in Protea infructescences. Results of this study add evidence to the view that mites are the vectors of Ophiostoma spp. that colonize Protea infructescences. They also show that DNA sequence comparisons are likely to reveal additional cryptic species of Ophiostoma in this unusual niche.
Resolving the phylogenetic and taxonomic status of dark-spored teleomorph genera in the Botryosphaeriaceae
Phillips, A.J.L. ; Alves, A. ; Pennycook, S.R. ; Johnston, P.R. ; Ramaley, A. ; Akulov, A. ; Crous, P.W. - \ 2008
Persoonia 21 (2008). - ISSN 0031-5850 - p. 29 - 55.
sp-nov - primer sets - anamorph - characters - confidence - speciation - inference - prunus - trees - spp.
Species in the Botryosphaeriaceae are common plant pathogens and saprobes found on a variety of mainly woody hosts. Teleomorphs typically have hyaline, aseptate ascospores. However, some have been reported with brown ascospores and their taxonomic status is uncertain. A multi-gene approach (SSU, ITS, LSU, EF1-a and ß-tubulin) was used to resolve the correct phylogenetic position of the dark-spored 'Botryosphaeria' teleomorphs and related asexual species. Neodeightonia and Phaeobotryon are reinstated for species with brown ascospores that are either 1-septate (Neodeightonia) or 2-septate (Phaeobotryon). Phaeobotryosphaeria is reinstated for species with brown, aseptate ascospores that bear an apiculus at either end. The status of Sphaeropsis is clarified and shown to be the anamorph of Phaeobotryosphaeria. Two new genera, namely Barriopsis for species having brown, aseptate ascospores without apiculi and Spencermartinsia for species having brown, 1-septate ascospores with an apiculus at either end are introduced. Species of Dothiorella have brown, 1-septate ascospores and differ from Spencermartinsia in the absence of apiculi. These six genera can also be distinguished from one another based on morphological characters of their anamorphs. Although previously placed in the Botryosphaeriaceae, Dothidotthia, was shown to belong in the Pleosporales, and the new family Dothidotthiaceae is introduced to accommodate it
Anaerobic methanethiol degradation and methanogenic community analysis in an alkaline (pH 10) biological process for liquefied petroleum gas desulfurization
Leerdam, R.C. van; Bonilla-Salinas, M. ; Bok, F.A.M. de; Bruning, H. ; Lens, P.N.L. ; Stams, A.J.M. ; Janssen, A.J.H. - \ 2008
Biotechnology and Bioengineering 101 (2008)4. - ISSN 0006-3592 - p. 691 - 701.
organic sulfur-compounds - sludge-blanket reactor - methylotrophic methanogen - oxidizing bacteria - sulfide oxidation - soda lakes - sp-nov - sediments - dimethylsulfide - bioreactor
Anaerobic methanethiol (MT) degradation by mesophilic (30 degrees C) alkaliphilic (pH 10) communities was studied in a lab-scale Upflow Anaerobic Sludge Bed (UASB) reactor inoculated with a mixture of sediments from the Wadden Sea (The Netherlands), Soap Lake (Central Washington), and Russian soda lakes. MT degradation started after 32 days of incubation. During the first 252 days, complete degradation was achieved till a volumetric loading rate of 7.5 mmol MT/L/day, and sulfide, methane, and carbon dioxide were the main reaction products. Temporary inhibition of MT degradation occurred after MT peak loads and in the presence of dimethyl disulfide (DMDS), which is the autooxidation product of MT. From day 252 onwards, methanol was dosed to the reactor as co-substrate at a loading rate of 3-6 mmol/L/day to stimulate growth of methylotrophic methanogens. Methanol was completely degraded and also a complete MT degradation was achieved till a volumetric loading rate of 13 mmol MT/L/day (0.77 mmol MT/gVSS/day). However, from day 354 till the end of the experimental run (day 365), acetate was formed and MT was not completely degraded anymore, indicating that methanol-degrading homoacetogenic bacteria had partially outcompeted the methanogenic MT-degrading archea. The archeal community in the reactor sludge was analyzed by DGGE and sequencing of 16S rRNA genes. The methanogenic archea responsible for the degradation of MT in the reactor were related to Methanolobus oregonensis. A pure culture, named strain SODA, was obtained by serial dilutions in medium containing both trimethyl amine and dimethyl sulfide (DMS). Strain SODA degraded MT, DMS, trimethyl amine, and methanol. Flow sheet simulations revealed that for sufficient MT removal from liquefied petroleum gas, the extraction and biological degradation process should be operated above pH 9.
Methanethiol degradation in anaerobic bioreactors at elevated pH (>8): Reactor performance and microbial community analysis
Leerdam, R.C. van; Bok, F.A.M. de; Bonilla-Salinas, M. ; Doesburg, W. van; Lomans, B.P. ; Lens, P.N.L. ; Stams, A.J.M. ; Janssen, A.J.H. - \ 2008
Bioresource Technology 99 (2008)18. - ISSN 0960-8524 - p. 8967 - 8973.
organic sulfur-compounds - sludge-blanket reactor - methylotrophic methanogen - sp-nov - methanosarcina-mazei - dimethyl sulfide - estuarine methanogen - hydrogen transfer - sediments - bacteria
The degradation of methanethiol (MT) at 30 °C under saline¿alkaline (pH 8¿10, 0.5 M Na+) conditions was studied in a lab-scale Upflow Anaerobic Sludge Blanket (UASB) reactor inoculated with estuarine sediment from the Wadden Sea (The Netherlands). At a sodium concentration of 0.5 M and a pH between 8 and 9 complete MT degradation to sulfide, methane and carbon dioxide was possible at a maximum loading rate of 22 mmol MT L¿1 day¿1 and a hydraulic retention time of 6 h. The presence of yeast extract (100 mg/L) in the medium was essential for complete MT degradation. 16S rRNA based DGGE and sequence analysis revealed that species related to the genera Methanolobus and Methanosarcina dominated the archaeal community in the reactor sludge. Their relative abundance fluctuated in time, possibly as a result of the changing operational conditions in the reactor. The most dominant MT-degrading archaeon was enriched from the reactor and obtained in pure culture. This strain WR1, which was most closely related to Methanolobus taylorii, degraded MT, dimethyl sulfide (DMS), methanol and trimethylamine. Its optimal growth conditions were 0.2 M NaCl, 30 °C and pH 8.4. In batch and reactor experiments operated at pH 10, MT was not degraded
Pathways for the anaerobic microbial debromination ofpolybrominated diphenyl ethers
Robrock, K.R. ; Korytar, P. ; Alvarex-Cohen, L. - \ 2008
Environmental Science and Technology 42 (2008)8. - ISSN 0013-936X - p. 2845 - 2852.
sp-nov - reductive dechlorination - desulfitobacterium-dehalogenans - polychlorinated-biphenyls - dehalococcoides strains - enrichment cultures - gas-chromatography - flame-retardant - gen-nov - bacterium
The debromination pathways of seven polybrominated diphenyl ethers (PBDEs) by three different cultures of anaerobic dehalogenating bacteria were investigated using comprehensive two-dimensional gas chromatography (GC × GC). The congeners analyzed were the five major components of the industrially used octa-BDE mixture (octa-BDEs 196, 203, and 197, hepta-BDE 183, and hexa-BDE 153) as well as the two most commonly detected PBDEs in the environment, penta-BDE 99 and tetra-BDE 47. Among the dehalogenating cultures evaluated in this study were a trichloroethene-enriched consortium containing multiple Dehalococcoides species, and two pure cultures, Dehalobacter restrictus PER-K23 and Desulfitobacterium hafniense PCP-1. PBDE samples were analyzed by GC × GC coupled to an electron capture detector to maximize separation and identification of the product congeners. All studied congeners were debrominated to some extent by the three cultures and all exhibited similar debromination pathways with preferential removal of para and meta bromines. Debromination of the highly brominated congeners was extremely slow, with usually less than 10% of nM concentrations of PBDEs transformed after three months. In contrast, debromination of the lesser brominated congeners, such as penta 99 and tetra 47, was faster, with some cultures completely debrominating nM levels of tetra 47 within weeks.
Discovery of fungus-mite mutualism in a unique niche
Roets, F. ; Wingfield, M.J. ; Crous, P.W. ; Dreyer, L.L. - \ 2007
Environmental Entomology 36 (2007)5. - ISSN 0046-225X - p. 1226 - 1237.
protea infructescences - sp-nov - bark beetles - ophiostoma - gondwanamyces - symbiosis
The floral heads (infructescences) of South African Protea L. represent a most unusual niche for fungi of the economically important genus Ophiostoma Syd. and P. Syd. emend. Z.W. de Beer et al. Current consensus holds that most members of Ophiostoma are vectored by tree-infesting bark beetles. However, it has recently been suggested that mites, phoretic on these bark beetles, may play a central role in the dispersal of Ophiostoma. No bark beetles are known from Protea. Therefore, identifying the vectors of Ophiostoma in Protea infructescences would independently evaluate the role of various arthropods in the dispersal of Ophiostoma. Infructescence-colonizing arthropods were tested for the presence of Ophiostoma DNA using polymerase chain reaction (PCR) and for reproductive propagules by isolation on agar plates. PCR tests revealed that few insects carried Ophiostoma DNA. In contrast, various mites (Proctolaelaps vandenbergi Ryke, two species of Tarsonemus Canestrini and Fonzago, and one Trichouropoda Berlese species) frequently carried Ophiostoma propagules. DNA sequence comparisons for 28S ribosomal DNA confirmed the presence of O. splendens G. J. Marais and M. J. Wingf., O. palmiculminatum Roets et al., and O. phasma Roets et al. on these mites. Two apparently undescribed species of Ophiostoma were also identified. Light and scanning electron microscopy revealed specialized structures in Trichouropoda and one Tarsonemus sp. that frequently contained Ophiostoma spores. The Trichouropoda sp. was able to complete its life cycle on a diet consisting solely of its identified phoretic Ophiostoma spp. This study provides compelling evidence that mites are the primary vectors of infructescence-associated Ophiostoma spp. in South Africa.
Phylogenetic and morphotaxonomic revision of Ramichloridium and allied genera
Arzanlou, M. ; Groenewald, J.Z. ; Gams, W. ; Braun, U. ; Crous, P.W. - \ 2007
Studies in Mycology 58 (2007)1. - ISSN 0166-0616 - p. 57 - 93.
ribosomal dna - sp-nov - anamorphs - veronaea - taxonomy - fungi - herpotrichiellaceae - pheohyphomycosis - identification - phialophora
The phylogeny of the genera Periconiella, Ramichloridium, Rhinocladiella and Veronaea was explored by means of partial sequences of the 28S (LSU) rRNA gene and the ITS region (ITS1, 5.8S rDNA and ITS2). Based on the LSU sequence data, ramichloridium-like species segregate into eight distinct clusters. These include the Capnodiales (Mycosphaerellaceae and Teratosphaeriaceae), the Chaetothyriales (Herpotrichiellaceae), the Pleosporales, and five ascomycete clades with uncertain affinities. The type species of Ramichloridium, R. apiculatum, together with R. musae, R. biverticillatum, R. cerophilum, R. verrucosum, R. pini, and three new species isolated from Strelitzia, Musa and forest soil, respectively, reside in the Capnodiales clade. The human-pathogenic species R. mackenziei and R. basitonum, together with R. fasciculatum and R. anceps, cluster with Rhinocladiella (type species: Rh. atrovirens, Herpotrichiellaceae, Chaetothyriales), and are allocated to this genus. Veronaea botryosa, the type species of the genus Veronaea, also resides in the Chaetothyriales clade, whereas Veronaea simplex clusters as a sister taxon to the Venturiaceae (Pleosporales), and is placed in a new genus, Veronaeopsis. Ramichloridium obovoideum clusters with Carpoligna pleurothecii (anamorph: Pleurothecium sp., Chaetosphaeriales), and a new combination is proposed in Pleurothecium. Other ramichloridium-like clades include R. subulatum and R. epichloes (incertae sedis, Sordariomycetes), for which a new genus, Radulidium is erected. Ramichloridium schulzeri and its varieties are placed in a new genus, Myrmecridium (incertae sedis, Sordariomycetes). The genus Pseudovirgaria (incertae sedis) is introduced to accommodate ramichloridium-like isolates occurring on various species of rust fungi. A veronaea-like isolate from Bertia moriformis with phylogenetic affinity to the Annulatascaceae (Sordariomycetidae) is placed in a new genus, Rhodoveronaea. Besides Ramichloridium, Periconiella is also polyphyletic. Thysanorea is introduced to accommodate Peticoniella papuana (Herpotrichiellaceae), which is unrelated to the type species, P velutina (Mycosphaerellaceae).
Transcriptional activation by CprK1 is regulated by protein structural changes induced by effector binding and redox state
Mazon, H. ; Gabor, K. ; Leys, D. ; Heck, A.J.R. ; Oost, J. van der; Heuvel, R.H.H. van den - \ 2007
Journal of Biological Chemistry 282 (2007)15. - ISSN 0021-9258 - p. 11281 - 11290.
ionization mass-spectrometry - camp-receptor-protein - desulfitobacterium-dehalogenans - macromolecular complexes - reductive dehalogenase - conformational-changes - limited proteolysis - dna-binding - sp-nov - hafniense
The transcriptional activator CprK1 from Desulfitobacterium-hafniense, a member of the ubiquitous cAMP receptor protein/fumarate nitrate reduction regulatory protein family, activates transcription of genes encoding proteins involved in reductive dehalogenation of chlorinated aromatic compounds. 3-Chloro-4-hydroxyphenylacetate is a known effector for CprK1, which interacts tightly with the protein, and induces binding to a specific DNA sequence ("dehalobox," TTAAT¿-ATTAA) located in the promoter region of chlorophenol reductive dehalogenase genes. Despite the availability of recent x-ray structures of two CprK proteins in distinct states, the mechanism by which CprK1 activates transcription is poorly understood. In the present study, we have investigated the mechanism of CprK1 activation and its effector specificity. By using macromolecular native mass spectrometry and DNA binding assays, analogues of 3-chloro-4-hydroxyphenylacetate that have a halogenated group at the ortho position and a chloride or acetic acid group at the para position were found to be potent effectors for CprK1. By using limited proteolysis it was demonstrated that CprK1 requires a cascade of structural events to interact with dehalobox dsDNA. Upon reduction of the intermolecular disulfide bridge in oxidized CprK1, the protein becomes more dynamic, but this alone is not sufficient for DNA binding. Activation of CprK1 is a typical example of allosteric regulation; the binding of a potent effector molecule to reduced CprK1 induces local changes in the N-terminal effector binding domain, which subsequently may lead to changes in the hinge region and as such to structural changes in the DNA binding domain that are required for specific DNA binding.
Microbial communities involved in anaerobic degradation of unsaturated or saturated long chain fatty acids
Sousa, D.Z. ; Pereira, M.A. ; Stams, A.J.M. ; Alves, M.M. ; Smidt, H. - \ 2007
Applied and Environmental Microbiology 73 (2007)4. - ISSN 0099-2240 - p. 1054 - 1064.
sp-nov - methanogenic bacteria - oleic-acid - syntrophobacter-wolinii - syntrophic bacterium - enrichment culture - granular sludge - sp. nov. - gen-nov - coculture
Anaerobic long-chain fatty acid (LCFA)-degrading bacteria were identified by combining selective enrichment studies with molecular approaches. Two distinct enrichment cultures growing on unsaturated and saturated LCFAs were obtained by successive transfers in medium containing oleate and palmitate, respectively, as the sole carbon and energy sources. Changes in the microbial composition during enrichment were analyzed by denaturing gradient gel electrophoresis (DGGE) profiling of PCR-amplified 16S rRNA gene fragments. Prominent DGGE bands of the enrichment cultures were identified by 16S rRNA gene sequencing. A significant part of the retrieved 16S rRNA gene sequences was most similar to those of uncultured bacteria. Bacteria corresponding to predominant DGGE bands in oleate and palmitate enrichment cultures clustered with fatty acid-oxidizing bacteria within Syntrophomonadaceae and Syntrophobacteraceae families. A low methane yield, corresponding to 9 to 18% of the theoretical value, was observed in the oleate enrichment, and acetate, produced according to the expected stoichiometry, was not further converted to methane. In the palmitate enrichment culture, the acetate produced was completely mineralized and a methane yield of 48 to 70% was achieved from palmitate degradation. Furthermore, the oleate enrichment culture was able to use palmitate without detectable changes in the DGGE profile. However, the palmitate-specialized consortia degraded oleate only after a lag phase of 3 months, after which the DGGE profile had changed. Two predominant bands appeared, and sequence analysis showed affiliation with the Syntrophomonas genus. These bands were also present in the oleate enrichment culture, suggesting that these bacteria are directly involved in oleate degradation, emphasizing possible differences between the degradation of unsaturated and saturated LCFAs.
Diversity of the human gastrointestinal tract microbiota revisited
Rajilic-Stojanovic, M. ; Smidt, H. ; Vos, W.M. de - \ 2007
Environmental Microbiology 9 (2007)9. - ISSN 1462-2912 - p. 2125 - 2136.
16s ribosomal-rna - human fecal flora - gradient gel-electrophoresis - human clinical specimens - rdna sequence-analysis - human intestinal-tract - human oral-cavity - sp-nov - gen. nov. - human feces
Since the early days of microbiology, more than a century ago, representatives of over 400 different microbial species have been isolated and fully characterized from human gastrointestinal samples. However, during the past decade molecular ecological studies based on ribosomal RNA (rRNA) sequences have revealed that cultivation has been able only to access a small fraction of the microbial diversity within the gastrointestinal tract. The increasing number of deposited rRNA sequences calls for the setting up a curated database that allows handling of the excessive degree of redundancy that threatens the usability of public databases. The integration of data from cultivation-based studies and molecular inventories of small subunit (SSU) rRNA diversity, presented here for the first time, provides a systematic framework of the microbial diversity in the human gastrointestinal tract of more than 1000 different species-level phylogenetic types (phylotypes). Such knowledge is essential for the design of high-throughput approaches such as phylogenetic DNA microarrays for the comprehensive analysis of gastrointestinal tract microbiota at multiple levels of taxonomic resolution. Development of such approaches is likely to be pivotal to generating novel insights in microbiota functionality in health and disease.
Anaerobic methanethiol degradation in upflow anaerobic sludge bed reactors at high salinity (> 0.5 M Na+)
Leerdam, R.C. van; Bok, F.A.M. de; Lens, P.N.L. ; Stams, A.J.M. ; Janssen, A.J.H. - \ 2007
Biotechnology and Bioengineering 98 (2007)1. - ISSN 0006-3592 - p. 91 - 100.
mill waste-water - sulfur-compounds - methylotrophic methanogen - estuarine methanogen - blanket reactor - sp-nov - sediments - sulfide - sulfate - adaptation
The feasibility of anaerobic methanethiol (MT) degradation at elevated sodium concentrations was investigated in a mesophilic (30°C) lab-scale upflow anaerobic sludge bed (UASB) reactor, inoculated with estuarine sediment originating from the Wadden Sea (The Netherlands). MT was almost completely degraded (>95%) to sulfide, methane and carbon dioxide at volumetric loading rates up to 37 mmol MT·L-1·day-1, 0.5 M sodium (NaCl or NaHCO3) and between pH 7.3 and 8.4. Batch experiments revealed that inhibition of MT degradation started at sodium (both NaCl and NaHCO3) concentrations exceeding 0.8 M. Sulfide inhibited MT degradation already around 3 mM (pH 8.3).
Methanol utilizing Desulfotomaculum species utilizes hydrogen in a methanol-fed sulfate-reducing bioreactor
Balk, M. ; Weijma, J. ; Goorissen, H.P. ; Ronteltap, M. ; Hansen, T.A. ; Stams, A.J.M. - \ 2007
Applied Microbiology and Biotechnology 73 (2007)5. - ISSN 0175-7598 - p. 1203 - 1211.
sp-nov - anaerobic reactor - bacterium - acetate - propionate - degradation - metabolism - growth
A sulfate-reducing bacterium, strain WW1, was isolated from a thermophilic bioreactor operated at 65 degrees C with methanol as sole energy source in the presence of sulfate. Growth of strain WW1 on methanol or acetate was inhibited at a sulfide concentration of 200 mg l(-1), while on H-2/CO2, no apparent inhibition occurred up to a concentration of 500 mg l(-1). When strain WW1 was co-cultured under the same conditions with the methanol-utilizing, non-sulfate-reducing bacteria, Thermotoga lettingae and Moorella mulderi, both originating from the same bioreactor, growth and sulfide formation were observed up to 430 mg l(-1). These results indicated that in the co-cultures, a major part of the electron flow was directed from methanol via H-2/CO2 to the reduction of sulfate to sulfide. Besides methanol, acetate, and hydrogen, strain WW1 was also able to use formate, malate, fumarate, propionate, succinate, butyrate, ethanol, propanol, butanol, isobutanol, with concomitant reduction of sulfate to sulfide. In the absence of sulfate, strain WW1 grew only on pyruvate and lactate. On the basis of 16S rRNA analysis, strain WW1 was most closely related to Desulfotomaculum thermocisternum and Desulfotomaculum australicum. However, physiological properties of strain WW1 differed in some aspects from those of the two related bacteria.
Taxonomy, phylogeny and identification of Botryosphaeriaceae associated with pome and stone fruit trees in South Africa and other regions of the world
Slippers, B. ; Smit, W.A. ; Crous, P.W. ; Coutinho, T.A. ; Wingfield, B.D. ; Wingfield, M.J. - \ 2007
Plant Pathology 56 (2007)1. - ISSN 0032-0862 - p. 128 - 139.
sp-nov - apple fruit - western-australia - wetness duration - peach-trees - dothidea - obtusa - infection - fungi - rot
Species of Botryosphaeria are well-recognized pathogens of pome and stone fruit trees. The taxonomy of these fungi, however, has been confused in the past. Recent taxonomic changes to the Botryosphaeriaceae further influence the literature pertaining to these fungi. This study reviews the taxonomic status of Botryosphaeriaceae associated with fruit tree diseases, identifies them in South Africa and elsewhere, and develops a reliable identification technique for them. Comparisons were made using DNA sequence data from the nuclear ITS rRNA operon and anamorph morphology. These analyses distinguished six clades amongst isolates associated with fruit tree diseases, corresponding to Neofusicoccum ribis (= B. ribis), N. parvum (= B. parva), N. australe (= B. australis), B. dothidea, Diplodia mutila (= B. stevensii) and 'Botryosphaeria' obtusa (the genus Botryosphaeria is no longer available for the fungus known as B. obtusa, but a new name has not been proposed yet). Isolates from fruit trees in South Africa were grouped in the N. australe and 'Botryosphaeria' obtusa clades. This is the first report of N. australe from fruit trees. PCR-RFLP analysis using the restriction endonucleases CfoI and HaeIII distinguished the major clades. However, two groups of closely related species, N. ribis and N. parvum, and N. australe and N. luteum (= B. lutea), had identical RFLP profiles. Using RFLP, it was shown that 'Botryosphaeria' obtusa is the dominant species on fruit trees in the Western Cape Province of South Africa. These results and methods will be useful in future epidemiological studies and disease management of Botryosphaeriaceae from fruit trees
Identification of Bilophila wadsworthia by specific PCR which targets the taurine:pyruvate aminotransferase
Laue, H. ; Smits, T.H.M. ; Schumacher, U.K. ; Claros, M.C. ; Hartemink, R. ; Cook, A.M. - \ 2006
FEMS Microbiology Letters 261 (2006)1. - ISSN 0378-1097 - p. 74 - 79.
sp-nov - transcription - bacteria - quantification - dissimilation - purification - appendicitis - respiration - reduction - specimens
The bile-resistant, strictly anaerobic bacterium Bilophila wadsworthia is found in human faecal flora, in human infections and in environmental samples. A specific PCR primer set for the gene encoding the first metabolic enzyme in the degradative pathway for taurine in B. wadsworthia, taurine:pyruvate aminotransferase (tpa), was developed and tested. In addition, enrichment cultures were started from faecal samples of primates and felines and shown to contain B. wadsworthia. These were subcultured on agar media and then identified by PCR fingerprinting. PCR for tpa was successful in all positive enrichment cultures and showed no amplification signal in a variety of other bacterial species. Therefore, this PCR method could be a promising tool for rapid detection of B. wadsworthia in biological samples
Microbial CO conversions with applications in synthesis gas purification and bio-desulfurization.
Sipma, J. ; Henstra, A.M. ; Parshina, S.N. ; Lens, P.N.L. ; Lettinga, G. ; Stams, A.J.M. - \ 2006
Critical Reviews in Biotechnology 26 (2006)1. - ISSN 0738-8551 - p. 41 - 65.
carbon-monoxide dehydrogenase - acid-mine drainage - h-2-forming methylenetetrahydromethanopterin dehydrogenase - biological sulfate reduction - metal-free hydrogenase - sp-nov - carboxydothermus-hydrogenoformans - gen.-nov. - clostridium-thermoaceticum - rhodospi
Recent advances in the field of microbial physiology demonstrate that carbon monoxide is a readily used substrate by a wide variety of anaerobic micro-organisms, and may be employed in novel biotechnological. processes for production of bulk and fine chemicals or in biological treatment of waste streams. Synthesis gas produced from fossil fuels or biomass is rich in hydrogen and carbon monoxide. Conversion of carbon monoxide to hydrogen allows use of synthesis gas in existing hydrogen utilizing processes and is interesting in view of a transition from hydrogen production from fossil fuels to sustainable (CO2-neutral) biomass. The conversion of CO with H2O to CO2 and H-2 is catalyzed by a rapidly increasing group of micro-organisms. Hydrogen is a preferred electron donor in biotechnological desulfurization of wastewaters and flue gases. Additionally, CO is a good alternative electron donor considering the recent isolation of a CO oxidizing, sulfate reducing bacterium. Here we review CO utilization by various anaerobic micro-organisms and their possible role in biotechnological processes, with a focus on hydrogen production and bio-desulfurization.
Changes in agricultural management drive the diversity of Burkholderia species isolated from soil on PCAT medium
Salles, J.F. ; Samyn, E. ; Vandamme, P.A. ; Veen, J.A. van; Elsas, J.D. van - \ 2006
Soil Biology and Biochemistry 38 (2006)4. - ISSN 0038-0717 - p. 661 - 673.
gradient gel-electrophoresis - cepacia complex infection - land-use history - sp-nov - cystic-fibrosis - bacterial communities - microbial diversity - maize-rhizosphere - genetic diversity - genomovar-iii
In order to assess the diversity of culturable Burkholderia populations in rhizosphere and bulk soil and to evaluate how different agricultural management regimes and land use history affect this diversity, four treatments were evaluated: permanent grassland; grassland converted into maize monoculture; arable land and arable land converted into grassland. Burkholderia isolates obtained on PCAT medium were grouped in 47 clusters using 16S ribosomal RNA gene based PCR-DGGE combined with BOX genomic fingerprinting (DGGE-BOX). The distribution of the isolates in the DGGE-BOX clusters was used to calculate the Shannon diversity index per treatment. Interestingly, we observed that the Burkholderia diversity was affected by changes in the agricultural management, since the highest diversity was observed in permanent grassland and in continuous arable land. In addition, the diversity tended to be higher in the rhizosphere than in the corresponding bulk soil. The use of species abundance models indicated that rhizosphere communities had more even distributions than communities collected from the bulk soil. Identification of isolates revealed that only 2% of these belonged to the B. cepacia complex and that the majority was assigned to either (1) new Burkholderia species or (2) Burkholderia species that had originally been isolated from soil. Isolates classified as B. hospita, B. caledonica and Burkholderia sp. LMG 22934' and `LMG 22936' were found mainly in the arable land, while isolates belonging to Burkholderia sp. `LMG 22929 and B. phytofirmans were associated with the grassland area. Another potentially new Burkholderia species, `LMG 22932'', was found in both areas, in close association with the maize rhizosphere
Multi-gene phylogeny for Ophiostoma spp. reveals two new species from Protea infructescences
Roets, F. ; Beer, Z.W. de; Dreyer, L.L. ; Zipfel, R. ; Crous, P.W. ; Wingfield, M.J. - \ 2006
Studies in Mycology 55 (2006). - ISSN 0166-0616 - p. 199 - 212.
mycangial fungi - bark beetles - south-africa - sp-nov - complex - scolytidae - coleoptera - symbiosis - survival - genus
Ophiostoma represents a genus of fungi that are mostly arthropod-dispersed and have a wide global distribution. The best known of these fungi are carried by scolytine bark beetles that infest trees, but an interesting guild of Ophiostoma spp. occurs in the infructescences of Protea spp. native to South Africa. Phylogenetic relationships between Ophiostoma spp. from Protea infructescences were studied using DNA sequence data from the P-tubulin, 5.8S ITS (including the flanking internal transcribed spacers 1 and 2) and the large subunit DNA regions. Two new species, O. phasma sp. nov. and O. paimiculminatum sp. nov. are described and compared with other Ophiostoma spp. occurring in the same niche. Results of this study have raised the number of Ophiostoma species from the infructescences of serotinous Protea spp. in South Africa to five. Molecular data also suggest that adaptation to the Protea infructescence niche by Ophiostoma spp. has occurred independently more than once.
Phylogenetic lineages in the Botryosphaeriaceae
Crous, P.W. ; Slippers, B. ; Wingfield, M.J. ; Rheeder, J. ; Marasas, W.F.O. ; Philips, A.J.L. ; Alves, A. ; Burgess, T. ; Barber, P. ; Groenewald, J.Z. - \ 2006
Studies in Mycology 55 (2006). - ISSN 0166-0616 - p. 235 - 253.
ribosomal dna-sequences - sp-nov - fruit rot - anamorphic fungi - north-america - south-africa - morphology - eucalyptus - dothidea - characters
Botryosphaeria is a species-rich genus with a cosmopolitan distribution, commonly associated with dieback and cankers of woody plants. As many as 18 anamorph genera have been associated with Botryosphaeria, most of which have been reduced to synonymy under Diplodia (conidia mostly ovoid, pigmented, thick-walled), or Fusicoccum (conidia mostly fusoid, hyaline, thin-walled). However, there are numerous conidial anamorphs having morphological characteristics intermediate between Diplodia and Fusicoccum, and there are several records of species outside the Botryosphaeriaceae that have anamorphs apparently typical of Botryosphaeria s.str. Recent studies have also linked Botryosphaeria to species with pigmented, septate ascospores, and Dothiorella anamorphs, or Fusicoccum anamorphs with Dichomera synanamorphs. The aim of this study was to employ DNA sequence data of the 28S rDNA to resolve apparent lineages within the Botryosphaeriaceae. From these data, 12 clades are recognised. Two of these lineages clustered outside the Botryosphaeriaceae, namely Diplodia-like anamorphs occurring on maize, which are best accommodated in Stenocarpella (Diaporthales), as well as an unresolved clade including species of Camarosporium/Microdiplodia. We recognise 10 lineages within the Botryosphaeriaceae, including an unresolved clade (Diplodia/Lasiodiplodia/Tiarosporella), Botryosphaeria s.str. (Fusicoccum anamorphs), Macrophomina, Neoscytalidium gen. nov., Dothidotthia (Dothiorella anamorphs), Neofusicoccum gen. nov. (Botryosphaeria-like teleomorphs, Dichomera-like synanamorphs), Pseudofusicoccum gen. nov., Saccharata (Fusicoccum- and Diplodia-like synanamorphs), "Botryosphaeria" quercuum (Diplodia-like anamorph), and Guignardia (Phyllosticta anamorphs). Separate teleomorph and anamorph names are not provided for newly introduced genera, even where both morphs are known. The taxonomy of some clades and isolates (e.g. B. mamane) remains unresolved due to the absence of ex-type cultures.
How many species of fungi are there at the tip of Africa?
Crous, P.W. ; Rong, I.H. ; Wood, A. ; Lee, S. ; Glen, H. ; Botha, W. ; Slippers, B. ; Beer, W.Z. de; Wingfield, M.J. ; Hawksworth, D.L. - \ 2006
Studies in Mycology 55 (2006). - ISSN 0166-0616 - p. 13 - 33.
dna-sequence data - eucalyptus leaf fungi - south-africa - sp-nov - root-rot - interesting records - cercosporoid fungi - protea infructescences - lichen genus - rust fungi
Several recent studies have reviewed the extent of fungal biodiversity, and have used these data as basis for revised estimates of species numbers based on known numbers of plants and insects. None of these studies, however, have focused on fungal biodiversity in South Africa. Coinciding with the 100th anniversary of the National Collection of Fungi (PREM) in South Africa in 2005, it is thus timely to reflect on the taxonomic research that has been conducted in South Africa over the past Century. Information is presented on the extent of fungal collections preserved at PREM, and the associated research publications that have largely resulted from this resource. These data are placed in context of the known plant and insect biodiversity, and used as basis to estimate the potential number of fungi that could be expected in South Africa. The conservative estimate is of approximately 200 000 species without taking into account those associated with a substantial insect biodiversity.
Carbon monoxide conversion by thermophilic sulfate-reducing bacteria in pure culture and in co-culture with Carboxydothermus hydrogenoformans
Parshina, S.N. ; Kijlstra, S. ; Henstra, A.M. ; Sipma, J. ; Plugge, C.M. ; Stams, A.J.M. - \ 2005
Applied Microbiology and Biotechnology 68 (2005)3. - ISSN 0175-7598 - p. 390 - 396.
desulfovibrio-vulgaris hildenborough - anaerobic bioreactor sludges - sp-nov - gen.-nov. - methanogenic bacteria - growth - reduction - energy - gas - hydrogenases
Biological sulfate (SO4) reduction with carbon monoxide (CO) as electron donor was investigated. Four thermophilic SO4-reducing bacteria, Desulfotomaculum thermoacetoxidans (DSM 5813), Thermodesulfovibrio yellowstonii (ATCC 51303), Desulfotomaculum kuznetsovii (DSM 6115; VKM B-1805), and Desulfotomaculum thermobenzoicum subsp. thermosyntrophicum (DSM 14055), were studied in pure culture and in co-culture with the thermophilic carboxydotrophic bacterium Carboxydothermus hydrogenoformans (DSM 6008). D. thermoacetoxidans and T. yellowstonii were extremely sensitive to CO: their growth on pyruvate was completely inhibited at CO concentrations above 2% in the gas phase. D. kuznetsovii and D. thermobenzoicum subsp. thermosyntrophicum were less sensitive to CO. In pure culture, D. kuznetsovii and D. thermobenzoicum subsp. thermosyntrophicum were able to grow on CO as the only electron donor and, in particular in the presence of hydrogen/carbon dioxide, at CO concentrations as high as 50-70%. The latter SO4 reducers coupled CO oxidation to SO4 reduction, but a large part of the CO was converted to acetate. In co-culture with C. hydrogenoformans, D. kuznetsovii and D. thermobenzoicum subsp. thermosyntrophicum could even grow with 100% CO (P CO=120 kPa).
Preliminary studies on Botryosphaeria species from Southern Hemisphere conifers in Australasia and South Africa
Slippers, B. ; Summerbell, B.A. ; Crous, P.W. ; Coutinho, T.A. ; Wingfield, B.D. ; Wingfield, M.J. - \ 2005
Australasian Plant Pathology 34 (2005)2. - ISSN 0815-3191 - p. 213 - 220.
wollemia-nobilis - genetic-variation - sp-nov - eucalyptus - dothidea - characters - pathogens - sequences - cankers - ribis
Wollemia nobilis is an ancient coniferous tree species that was recently discovered in eastern Australia. This tree is highly threatened due to its limited distribution. No genetic variation has been detected within the wild populations of ~100 adult plants. A recent study has revealed that a species of Botryosphaeria is highly pathogenic to W. nobilis. The aim of the present study was to identify this fungus, as well as Botryosphaeria isolates of unknown identity from other Southern Hemisphere coniferous hosts, Araucaria from New Zealand and Widdringtonia from South Africa. To facilitate their identification, sequence data for the ITS rDNA, as well as the ß-tubulin and translation elongation factor 1-¿ genes were combined to determine the phylogenetic relationship of these isolates with those of known Botryosphaeria spp. Isolates from W. nobilis included two Botryosphaeria spp. The first is closely related to B. ribis, but also shares some unique sequence polymorphisms with B. parva. One isolate grouped with B. australis, but also varied slightly from this taxon in the gene regions analysed. Additional isolates will be needed to determine whether these sequence variations represent speciation events or merely variation within populations of B. ribis and B. australis. In addition to this, B. parva was identified from Araucaria in New Zealand, and B. australis was found on Widdringtonia trees in South Africa. All three reports of these fungi are new records for their various hosts and could represent important pathogens of these trees
Hosts, species and genotypes: opinions versus data
Crous, P.W. ; Groenewald, J.Z. - \ 2005
Australasian Plant Pathology 34 (2005)4. - ISSN 0815-3191 - p. 463 - 470.
south-africa - mycosphaerella-suberosa - botryosphaeria-dothidea - pyrenophora-teres - dna phylogeny - shoot blight - sp-nov - eucalyptus - phomopsis - phaeoacremonium
We are currently in the middle of a revolution in fungal taxonomy. Taxonomy is at the crossroads, where phenotypic data must be merged with DNA and other data to facilitate accurate identifications. These data, linked to open access journals and databases, will facilitate the stability of nomenclature in the future. To achieve this, however, plant pathologists must embrace new technologies, and implement these policies in their research programmes.
|Protea infructescences represent a unique fungal niche
Lee, S. ; Roets, F. ; Crous, P.W. - \ 2005
Fungal Diversity 19 (2005). - ISSN 1560-2745 - p. 69 - 78.
south-africa - species richness - cape fynbos - sp-nov - ophiostoma - genus - restionaceae - biodiversity - key
The biodiversity of the saprobic microfungi occurring in Protea infructescences (flowerheads) was investigated. A total of 28 fungal species including 14 ascomycetes and 14 anamorphic fungi were collected from 2000-2001. The mycoflora of the infructescences, especially the flowers, were found to differ totally from that of the bracts and other Protea tissues. This indicates their uniqueness as fungal micro-habitat. Furthermore, the majority of ascomycete species isolated from these flowers were characterised by having long ostiolar necks. This finding indicates that insects play a major role in the dispersal of the ascomycetes that occur on these infructescences, which is further corroborated by the unusually high number of insects that frequent these flowers. From these data it is clear that the saprobic fungal flora of Protea infructescences have a unique ecological role. However, the exact nature of this interaction will only become clear once further studies are conducted monitoring the individual components of this ecosystem.
High rate sulfate reduction in a submerged anaerobic membrane bioreactor (SAMBaR) at high salinity
Vallero, M.V.G. ; Lettinga, G. ; Lens, P.N.L. - \ 2005
Journal of Membrane Science 253 (2005)1-2. - ISSN 0376-7388 - p. 217 - 232.
methanogenic bacteria - thermophilic sulfate - waste-water - reducing bacterium - sulfite reduction - sp-nov - reactor - acetate - environments - degradation
Sulfate reduction in salt rich wastewaters (50 g NaCl L¿1 and 1 g MgCl2·6H2O L¿1; conductivity 60¿70 mS cm¿1) was investigated in a 6 L submerged anaerobic membrane bioreactor (SAMBaR) and inoculated solely with the halotolerant sulfate reducing bacterium Desulfobacter halotolerans. The SAMBaR was fed with acetate and ethanol at organic loading rates up to 14 g COD L¿1 day¿1 in excess of sulfate (COD/SO42¿ of 0.5) and operated at pH 7.2 ± 0.2 and a hydraulic retention time (HRT) from 8 to 36 h. A sulfate reduction rate up to 6.6 g SO42¿ L¿1 day¿1 was achieved in the SAMBaR operating at a flux of 17.1 L m¿2 h¿1, which resulted in a HRT of 9 h including the backflow of permeate used for backflushing. The fairly constant very high specific sulfate reduction rate of 5.5 g SO42¿ g VSS¿1 day¿1 showed that the performance of the SAMBaR was limited by the low amount of biomass (0.85 g VSS L¿1) present in the reactor at the end of the experiment. It was shown that sulfate reducing submerged anaerobic membrane bioreactors can be operated over extended periods of time without chemical cleaning of the membranes at a certain fixed flux if this flux is substantially below the nominal critical flux determined experimentally (18¿21 L m¿2 h¿1). Intermittent operation as well as backflush of the membranes were shown to slow the fouling in the membranes. Frequent backflush (e.g. 1 min each 10 min) is the suggested operational strategy to minimize fouling in anaerobic MBRs.
Bacterial mechanisms to overcome inhibitory effects of dietary tannins
Smith, A.H. ; Zoetendal, E.G. ; Mackie, R.I. - \ 2005
Microbial Ecology 50 (2005)2. - ISSN 0095-3628 - p. 197 - 205.
c-14-labeled condensed tannins - east-african ruminants - mulga acacia-aneura - sp-nov - streptococcus-gallolyticus - lotus-corniculatus - in-vitro - eubacterium-oxidoreducens - antimicrobial properties - gastrointestinal-tract
High concentrations of tannins in fodder plants inhibit gastrointestinal bacteria and reduce ruminant performance. Increasing the proportion of tannin-resistant bacteria in the rumen protects ruminants from antinutritional effects. The reason for the protective effect is unclear, but could be elucidated if the mechanism(s) by which tannins inhibit bacteria and the mechanisms of tannin resistance were understood. A review of the literature indicates that the ability of tannins to complex with polymers and minerals is the basis of the inhibitory effect on gastrointestinal bacteria. Mechanisms by which bacteria can overcome inhibition include tannin modification/degradation, dissociation of tannin¿substrate complexes, tannin inactivation by high-affinity binders, and membrane modification/repair and metal ion sequestration. Understanding the mechanism of action of tannins and the mechanism(s) bacteria use to overcome the inhibitory effects will allow better management of the rumen ecosystem to reduce the antinutritional effects of tannin-rich fodder plants and thereby improve ruminant production.
Structure and topology of microbial communities in the major gut compartments of Melolontha melolontha larvae (Coleoptera: Scarabaeidae)
Egert, M.G.G. ; Stingl, U. ; Dyhrberg Bruun, L. ; Pommerenke, B. ; Brune, A. ; Friedrich, M.W. - \ 2005
Applied and Environmental Microbiology 71 (2005)8. - ISSN 0099-2240 - p. 4556 - 4566.
sulfate-reducing bacteria - pachnoda-ephippiata coleoptera - termite mastotermes-darwiniensis - targeted oligonucleotide probes - humus-feeding larva - reticulitermes-flavipes - sp-nov - hindgut - oxygen - hybridization
Physicochemical gut conditions and the composition and topology of the intestinal microbiota in the major gut compartments of the root-feeding larva of the European cockchafer (Melolontha melolontha) were studied. Axial and radial profiles of pH, O2, H2, and redox potential were measured with microsensors. Terminal restriction fragment length polymorphism (T-RFLP) analysis of bacterial 16S rRNA genes in midgut samples of individual larvae revealed a simple but variable and probably nonspecific community structure. In contrast, the T-RFLP profiles of the hindgut samples were more diverse but highly similar, especially in the wall fraction, indicating the presence of a gut-specific community involved in digestion. While high acetate concentrations in the midgut and hindgut (34 and 15 mM) corroborated the presence of microbial fermentation in both compartments, methanogenesis was confined to the hindgut. Methanobrevibacter spp. were the only methanogens detected and were restricted to this compartment. Bacterial 16S rRNA gene clone libraries of the hindgut were dominated by clones related to the Clostridiales. Clones related to the Actinobacteria, Bacillales, Lactobacillales, and -Proteobacteria were restricted to the lumen, whereas clones related to the ß- and -Proteobacteria were found only on the hindgut wall. Results of PCR-based analyses and fluorescence in situ hybridization of whole cells with group-specific oligonucleotide probes documented that Desulfovibrio-related bacteria comprise 10 to 15% of the bacterial community at the hindgut wall. The restriction of the sulfate-reducer-specific adenosine-5'-phosphosulfate reductase gene apsA to DNA extracts of the hindgut wall in larvae from four other populations in Europe suggested that sulfate reducers generally colonize this habitat.
Characterisation and mode of action of an exopolygalacturonase from the hyperthermophilic bacterium Thermotoga maritime
Kluskens, L.D. ; Alebeek, G.J.W.M. van; Walther, J. ; Voragen, A.G.J. ; Vos, W.M. de; Oost, J. van der - \ 2005
FEBS Journal 272 (2005)21. - ISSN 1742-464X - p. 5464 - 5473.
site-directed mutagenesis - aspergillus-niger - crystal-structure - butyrivibrio-fibrisolvens - endopolygalacturonase ii - subsite affinities - genome sequence - bovine rumen - sp-nov - pectin
An intracellular pectinolytic enzyme, PelB (TM0437), from the hyperthermophilic bacterium Thermotoga maritima was functionally produced in Escherichia coli and purified to homogeneity. PelB belongs to family 28 of the glycoside hydrolases, consisting of pectin-hydrolysing enzymes. As one of the few bacterial exopolygalacturonases, it is able to remove monogalacturonate units from the nonreducing end of polygalacturonate. Detailed characterization of the enzyme showed that PelB is highly thermo-active and thermostable, with a melting temperature of 105 °C and a temperature optimum of 80 °C, the highest described to date for hydrolytic pectinases. PelB showed increasing activity on oligosaccharides with an increasing degree of polymerization. The highest activity was found on the pentamer (1000 U·mg1). In addition, the affinity increased in conjunction with the length of the oligoGalpA chain. PelB displayed specificity for saturated oligoGalpA and was unable to degrade unsaturated or methyl-esterified oligoGalpA. Analogous to the exopolygalacturonase from Aspergillus tubingensis, it showed low activity with xylogalacturonan. Calculations on the subsite affinity revealed the presence of four subsites and a high affinity for GalpA at subsite +1, which is typical of exo-active enzymes. The physiological role of PelB and the previously characterized exopectate lyase PelA is discussed.
Cryptococcus allantoinivorans sp.nov., an anamorphic basidiomycetous yeast (Tremellales) physiologicallt resembling other species of the Cryptococcus laurentii complex that degrade polysaccharides and C2 compounds
Middelhoven, W.J. - \ 2005
Antonie van Leeuwenhoek: : Nederlandsch tijdschrift voor hygiëne, microbiologie en serologie 87 (2005)2. - ISSN 0003-6072 - p. 101 - 108.
sole source - uric-acid - sp-nov - normal-alkylamines - aromatic-compounds - energy - carbon - systematics - putrescine - nitrogen
A novel Cryptococcus species is proposed to accommodate a yeast strain (CBS 9604) able to assimilate allantoin as sole carbon source, a characteristic very uncommon among yeasts. By traditional methods, the strain could not be distinguished from Cryptococcus laurentii, but nucleotide sequences of the D1D2 region of the large subunit (26S) and of the ITS region of ribosomal DNA showed relationship to the Bulleromyces clade of the genus Cryptococcus (order Tremellales) with some Tremella spp. as the closest relatives. A traditional morphological and physiological description of the strain is given. Data on the assimilation of some C2 compounds and polysaccharides are provided and compared with those of other type strains of novel species of the C. laurentii complex
Novel physiological features of Carboxydothermus hydrogenoformans and Thermoterrabacterium ferrireducens
Henstra, A.M. ; Stams, A.J.M. - \ 2004
Applied and Environmental Microbiology 70 (2004)12. - ISSN 0099-2240 - p. 7236 - 7240.
gradient gel-electrophoresis - sp-nov - thermophilic-bacterium - purification - reveals
Carboxydothermus hydrogenoformans is able to grow by conversion of CO to H2 and CO2. Besides CO, only pyruvate was described as serving as an energy source. Based on 16S rRNA gene sequence similarity, C. hydrogenoformans is closely related to Thermoterrabacterium ferrireducens. T. ferrireducens is like C. hydrogenoformans a gram-positive, thermophilic, strict anaerobic bacterium. However, it is capable of using various electron donors and acceptors for growth. Growth of C. hydrogenoformans with multiple electron donors and acceptors was tested. C. hydrogenoformans oxidized formate, lactate, glycerol, CO, and H2 with 9,10-anthraquinone-2,6-disulfonate as an electron acceptor. Sulfite, thiosulfate, sulfur, nitrate, and fumarate were reduced with lactate as an electron donor. T. ferrireducens oxidized CO with 9,10-anthraquinone-2,6-disulfonate as an electron acceptor but did not produce H2 from CO. In contrast to what was published before, T. ferrireducens was able to grow on lactate with sulfite, sulfur, and nitrate as electron acceptors
Speciation and distribution of Botryosphaeria spp. on native and introduced Eucalyptus trees in Australia and South Africa
Slippers, B. ; Fourie, G. ; Crous, P.W. ; Coutinho, T.A. ; Wingfield, B.D. ; Carnegie, A.J. ; Wingfield, M.J. - \ 2004
Studies in Mycology 50 (2004)2. - ISSN 0166-0616 - p. 343 - 358.
multiple gene genealogies - sphaeropsis-sapinea - primer sets - sp-nov - fungi - dothidea - sequences - cankers - ribis - characters
Botryosphaeria spp. are important canker and die-back pathogens that affect Eucalyptus spp. They also occur endophytically in Eucalyptus leaves and stems. For the purpose of this study, Botryosphaeria strains were isolated from diseased and symptomless Eucalyptus material from Australia and South Africa. These isolates were induced to sporulate in culture, and compared with known species of Botryosphaeria. Selected isolates were also compared with authentic isolates of known Botryosphaeria spp. based on nuclear DNA sequence data of the ITS rDNA, P-tubulin and elongation factor l-alpha regions. Five Botryosphaeria spp. were identified from Eucalyptus plants. The ITS rDNA sequence data were then used to develop a PCR RFLP technique that could distinguish these species. Botryosphaeria eucalyptorum and a new species, B. eucalypticola, were the most common species on Eucalyptus in eastern Australia. These species also occur on Eucalyptus in South Africa, where they have most likely been introduced. Botryosphaeria parva was common on Eucalyptus in exotic environments, but rare on this host in Australia. Although B. dothidea was previously thought to be common on eucalypts, only one isolate of each of B. dothidea and B. australis were found in all the areas surveyed. No isolates of B. ribis, which was also commonly reported from Eucalyptus, were identified during this survey from Eucalyptus. Data from the present study provide the first holistic overview of the species of Botryosphaeria associated with Eucalyptus in both native and exotic environments.
|Diversity of saprobic hyphomycetes on Proteaceae and Restionaceae from South Africa
Lee, S. ; Mel'nik, V. ; Taylor, J.E. ; Crous, P.W. - \ 2004
Fungal Diversity 17 (2004). - ISSN 1560-2745 - p. 91 - 114.
fungal succession - leaf-litter - interesting records - sp-nov - microfungi - fynbos - soils - decomposition - biodiversity - thailand
To assess the diversity of saprobic microfungi occurring on the Proteaceae and Restionaceae of the Western Cape province of South Africa, samples of leaf, stem, flowerhead and culm litter were collected from the year 2000 until the end of 2002. About 1 000 fungal collections were made, 117 of which were hyphomycetes, representing 66 species in 53 genera. Of these, 49 species were newly recorded from South Africa, and 64 occurred on previously unreported host substrates. The diversity of hyphomycetes on Proteaceae and Restionaceae is discussed, together with a list of the hyphomycetes.
Isolation and biodiversity of hitherto undescribed soil bacteria related to Bacillus niacini
Felske, A. ; Tzeneva, V.A. ; Heyrman, J. ; Langeveld, M.A. ; Akkermans, A.D.L. ; Vos, P. - \ 2004
Microbial Ecology 48 (2004)1. - ISSN 0095-3628 - p. 111 - 119.
16s ribosomal-rna - genus bacillus - culturable bacteria - agricultural soil - paddy soil - sp-nov - diversity - sequences - dna - identification
The hitherto largely not described phylogenetic neighborhood of Bacillus niacini has been explored by a comprehensive cultivation experiment and genomic variety studies. Previous culture-independent studies demonstrated that similar to15% of all Bacillus 16S rDNA directly extracted from soils worldwide was affiliated to B. niacini. Seven different media were inoculated with soil suspensions in serial dilutions and incubated at different temperatures. Then, bacterial colonies were picked and analyzed by sequencing. A mineral medium with acetate as carbon source yielded a B. niacini rate of >3% of all picked colonies. Other media were less efficient but also successful. Applying this culturing approach, we succeeded in obtaining 64 isolates from different Dutch soils. The isolates turned out to be diverse, although closely related to B. niacini as revealed by 16S rDNA sequencing. Close matches with environmental clones were also found, thus demonstrating much more diversity beyond previously known 16S rDNA sequences. The rep-PCR fingerprinting method revealed a high genomic variety, redundancy could not be observed among our isolates. Hence, the hitherto neglected B. niacini lineage, apparently among the most abundant soil Bacillus, was accessible to our cultivation approach.
Methanol utilization in defined mixed cultures of thermophilic anaerobes in the presence sulfate
Goorissen, H.P. ; Stams, A.J.M. ; Hansen, T.A. - \ 2004
FEMS microbiology ecology 49 (2004)3. - ISSN 0168-6496 - p. 489 - 494.
sp-nov - reducing bacterium - reactor - reduction - hydrogen - sulfide - strains
We studied thermophilic sulfate reduction with methanol as electron donor in continuous cultures. Mixed cultures of selected microorganisms were used, representing different methanol degrading pathways followed by various trophic groups of microorganisms. Our results show that direct competition for methanol between a homoacetogen, Moorella thermoautotrophica, and a sulfate reducer, Desulfotomaculum kuzrietsovii, is in favour of the sulfate reducer due to its affinity for methanol. Methanogenesis as a result of interspecies hydrogen transfer between D. kuznetsovii and a hydrogen-consuming methanogenic archaeon, Methanothermobacter thermoautotrophicus occurred only below 5 mM total sulfide. A similar result was obtained when M. thermoautotrophica was grown on methanol in the presence of Mb. thermoautotrophicus. Interestingly, D. kuznetsovii could coexist with a non-methanolutilizing sulfate reducer (Thermodesulfovibrio species). Our data show that it is possible to maintain a dominant sulfate-reducing process with methanol as electron donor at 60 degreesC in mixed continuous cultures. (C) 2004 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved.
Interspecies electron transfer in methanogenic propionate degrading consortia
Bok, F.A.M. de; Plugge, C.M. ; Stams, A.J.M. - \ 2004
Water Research 38 (2004)6. - ISSN 0043-1354 - p. 1368 - 1375.
sulfate-reducing bacterium - syntrophobacter-wolinii - oxidizing bacterium - granular sludge - sp-nov - methanospirillum-hungatei - formate dehydrogenases - anaerobic degradation - phylogenetic analysis - smithella-propionica
Propionate is a key intermediate in the conversion of complex organic matter under methanogenic conditions. Oxidation of this compound requires obligate syntrophic consortia of acetogenic proton- and bicarbonate reducing bacteria and methanogenic archaea. Although H-2 acts as an electron-carrier in these consortia, evidence accumulates that formate plays an even more important role. To make energy yield from propionate oxidation energetically feasible for the bacteria and archaea involved, the concentrations of H-2 and formate have to be extremely low. On the other hand, the diffusion distance of these carriers has to be small to allow high propionate conversion rates. Accordingly, the high conversion rates observed in methanogenic bioreactors are due to the fact that the propionate-oxidizing bacteria and their methanogenic partners form micro-colonies within the densely packed granules. (C) 2003 Elsevier Ltd. All rights reserved.
Anaerobic microbial dehalogenation
Smidt, H. ; Vos, W.M. de - \ 2004
Annual Review of Microbiology 58 (2004). - ISSN 0066-4227 - p. 43 - 73.
desulfitobacterium-frappieri pcp-1 - polymerase-chain-reaction - reductively dechlorinates tetrachloroethene - bacterium rhodopseudomonas-palustris - chloroethene-contaminated sites - chlorinated aliphatic-compounds - sp strain cbdb1 - vinyl-chloride - sp-nov - de
The natural production and anthropogenic release of halogenated hydrocarbons into the environment has been the likely driving force for the evolution of an unexpectedly high microbial capacity to dehalogenate different classes of xenobiotic haloorganics. This contribution provides an update on the current knowledge on metabolic and phylogenetic diversity of anaerobic microorganisms that are capable of dehalogenating-or completely mineralizing-halogenated hydrocarbons by fermentative, oxidative, or reductive pathways. In particular, research of the past decade has focused on halorespiring anaerobes, which couple the dehalogenation by dedicated enzyme systems to the generation of energy by electron transport-driven phosphorylation. Significant advances in the biochemistry and molecular genetics of degradation pathways have revealed mechanistic and structural similarities between dehalogenating enzymes from phylogenetically distinct anaerobes. The availability of two almost complete genome sequences of halorespiring isolates recently enabled comparative and functional genomics approaches, setting the stage for the further exploitation of halorespiring and other anaerobic dehalogenating microbes as dedicated degraders in biological remediation processes.
Anaerobic reduction and oxidation of quinine moieties and the reduction of oxidized metals by halorespiring and related organisms
Luijten, M.L.G.C. ; Weelink, S.A.B. ; Godschalk, B. ; Langenhoff, A.A.M. ; Eekert, M.H.A. van; Schraa, G. ; Stams, A.J.M. - \ 2004
FEMS microbiology ecology 49 (2004)1. - ISSN 0168-6496 - p. 145 - 150.
sp-nov - gen-nov - dehalospirillum-multivorans - electron-acceptors - humic substances - desulfitobacterium - bacterium - tetrachloroethene - sulfurospirillum - dechlorination
Halorespiring microorganisms have been detected in soils that were not polluted with chlorinated compounds. In this study, we describe alternative electron acceptor utilization by some halorespiring bacteria and phylogenetically related bacteria. It appears that oxidized metals like selenate, arsenate and manganese are rather common electron acceptors for halorespiring species of Desulfitobacterium and Sulfurospirillum and related bacteria. All tested microorganisms are able to reduce anthraquinone-2,6-disulfonate (AQDS) and four tested organisms (Desulfobacterium hafniense DP7, Sulfurospirillum barnesii, Sulfurospirillum deleyianum and Sulfurospirillum arsenophilum) are able to oxidize reduced anthrahydroquinone-2,6,-disulfonate (AH(2)QDS) as well. The characteristic to reduce oxidized metals, and to reduce and oxidize quinone moieties coupled to energy conservation is a likely explanation for the presence of halorespiring microorganisms in unpolluted soils. (C) 2004 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved.
Analysis of 16S rDNA reveals bacterial shift during in vitro fermentation of fermentable carbohydrate using piglet faeces as inoculum
Zhu Wei-Yun, ; Williams, B.A. ; Konstantinov, S.R. ; Tamminga, S. ; Vos, W.M. de; Akkermans, A.D.L. - \ 2003
Anaerobe 9 (2003)4. - ISSN 1075-9964 - p. 175 - 180.
gradient gel-electrophoresis - ribosomal-rna - grassland soils - gas-production - sp-nov - intestine - pigs - dna - communities - microbiota
In vitro fermentation of sugar beet pulp (SBP) was carried out to determine which bacterial species would be enriched by use of this carbohydrate source. Faeces from four weaning piglets as a source of inoculum was also compared. The microbial diversity of the prominent bacteria before and after this in vitro fermentation was analysed using denaturing gradient gel electrophoresis (DGGE) of PCR amplicons of 16S rDNA. Before fermentation, the DGGE profiles showed differences between cultures inoculated with faeces from different piglets, though some bands were common to all piglets. After fermentation of SBP, three dominant bands appeared, of which two bands appeared in all samples and one for both replicates of one piglet. Sequences of the corresponding 16S rDNA of two bands showed 92% similarity to Eubacterium eligens and 96% similarity to Lachnospira pectinoschiza, and that of the third band 95% to L. pectinoschiza. (C) 2003 Elsevier Ltd. All rights reserved.
Development of a novel Process for the Biological conversion of H2S and Methanethiol to Elemental Sulfur
Sipma, J. ; Janssen, A.J.H. ; Hulshoff Pol, L.W. ; Lettinga, G. - \ 2003
Biotechnology and Bioengineering 82 (2003)1. - ISSN 0006-3592 - p. 1 - 11.
afvalwaterbehandeling - anaërobe behandeling - zwavel - rioolafvalwater - slib - methanol - reductie - bioreactoren - waste water treatment - anaerobic treatment - sulfur - sewage effluent - sludges - methanol - reduction - bioreactors - granular sludge reactor - methylotrophic methanogen - sp-nov - waste-water - estuarine methanogen - sulfide - degradation - sediments - dimethylsulfide - bacterium
The feasibility of anaerobic treatment of wastewater containing methanethiol (MT), an extremely volatile and malodorous sulfur compound, was investigated in lab-scale bioreactors. Inoculum biomass originating from full-scale anaerobic wastewater treatment facilities was used. Several sludges were tested for their ability to degrade MT
The feasibility of anaerobic treatment of wastewater containing methanethiol (MT), an extremely volatile and malodorous sulfur compound, was investigated in lab-scale bioreactors. Inoculum biomass originating from full-scale anaerobic wastewater treatment facilities was used. Several sludges, tested for their ability to degrade MT, revealed the presence of organisms capable of metabolizing MT as their sole source of energy. Furthermore, batch tests were executed to gain a better understanding of the inhibition potential of MT. It was found that increasing MT concentrations affected acetotrophic organisms more dramatically than methylotrophic organisms. Continuous reactor experiments, using two lab-scale upflow anaerobic sludge bed (UASB) reactors (R1 and R2), aimed to determine the maximal MT load and the effect of elevated sulfide concentrations on MT conversion. Both reactors were operated at a hydraulic retention time (HRT) of about 7 hours, a temperature of 30degreesC, and a pH of between 7.3 and 7.6. At the highest influent MT concentration applied, 14 mM in R1, corresponding to a volumetric loading rate of about 50 mM MT per day, 87% of the organic sulfur was recovered as hydrogen sulfide (12.2 mM) and the remainder as volatile organic sulfur compounds (VOSCs). Upon decreasing the HRT to 3.5 to 4.0 h at a constant MT loading rate, the sulfide concentration in the reactor decreased to 8 mM and MT conversion efficiency increased to values near 100%. MT conversion was apparently inhibited by the high sulfide concentrations in the reactor. The specific MT degradation rate, as determined after 120 days of operation in R1, was 2.83 +/- 0.27 mmol MT g VSS-1 day(-1). During biological desulfurization of liquid hydrocarbon phases, such as with liquefied petroleum gas (LPG), the combined removal of hydrogen sulfide and MT is desired. In R2, the simultaneous addition of sodium sulfide and MT was therefore studied and the effect of elevated sulfide concentrations was investigated. The addition of sodium sulfide resulted in enhanced disintegration of sludge granules, causing significant washout of biomass. Additional acetate, added to stimulate growth of methanogenic bacteria to promote granulation, was hardly converted at the termination of the experimental period. (C) 2003 Wiley Periodicals, Inc.
Effect of NaCl on thermophilic (55°C) methanol degradation in sulfate reducing granular sludge reactors
Vallero, M.V.G. ; Hulshoff Pol, L.W. ; Lettinga, G. ; Lens, P.N.L. - \ 2003
Water Research 37 (2003)10. - ISSN 0043-1354 - p. 2269 - 2280.
anaërobe behandeling - afvalwaterbehandeling - methanol - reductie - natriumchloride - sulfaten - rioolafvalwater - slib - anaerobic treatment - waste water treatment - methanol - reduction - sodium chloride - sulfates - sewage effluent - sludges - sp-nov - processing wastewaters - sodium inhibition - bacteria - methanogenesis - temperature - antagonism - digestion
The effect of NaCl on thermophilic (55degreesC) methanol conversion in the presence of excess of sulfate (COD/SO42-=0.5) was investigated in two 6.5L lab-scale upflow anaerobic sludge bed reactors inoculated with granular sludge previously not adapted to NaCl
The effect of NaCl on thermophilic (55degreesC) methanol conversion in the presence of excess of sulfate (COD/SO42-=0.5) was investigated in two 6.5L lab-scale upflow anaerobic sludge bed reactors inoculated with granular sludge previously not adapted to NaCl. Methanol was almost completely used for sulfate reduction in the absence of NaCl when operating at an organic loading rate of 5 g COD L-1 day(-1) and a hydraulic retention time of 10 h. The almost fully sulfidogenic sludge consisted of both granules and flocs developed after approximately 100 days in both reactors. Sulfate reducing bacteria (SRB) outcompeted methane producing archaea (MPA) for methanol, but acetate represented a side-product, accounting for maximal 25% of the total COD converted. Either MPA or SRB did not use acetate as substrate in activity tests. High NaCl concentrations (25 g L-1) completely inhibited methanol degradation, whereas low salt concentrations (2.5 g NaCl L-1) provoked considerable changes in the metabolic fate of methanol. The MPA were most sensitive towards the NaCl shock (25 g L-1). In contrast, the addition of 2.5 g L-1 of NaCl stimulated MPA and homoacetogenic bacteria. (C) 2003 Elsevier Science Ltd. All rights reserved.
Crystal structure of Pyrococcus furiosus phosphoglucose isomerase: Implications for substrate binding and catalysis
Berrisford, J.M. ; Akerboom, A.P. ; Turnbull, A.P. ; Geus, D. de; Sedelnikova, S.E. ; Staton, I. ; McLeod, C.W. ; Verhees, C.H. ; Oost, J. van der; Rice, D.W. ; Baker, P.J. - \ 2003
Journal of Biological Chemistry 278 (2003). - ISSN 0021-9258 - p. 33290 - 33297.
cupin superfamily - thermococcus-litoralis - angstrom resolution - sugar fermentation - protein structures - sp-nov - pathway - enzyme - archaebacteria - evolution
Phosphoglucose isomerase (PGI) catalyzes the reversible isomerization between D-fructose 6-phosphate and D-glucose 6-phosphate as part of the glycolytic pathway. PGI from the Archaea Pyrococcus furiosus (Pfu) was crystallized, and its structure was determined by x-ray diffraction to a 2-Angstrom resolution. Structural comparison of this archaeal PGI with the previously solved structures of bacterial and eukaryotic PGIs reveals a completely different structure. Each subunit of the homodimeric Pfu PGI consists of a cupin domain, for which the overall structure is similar to other cupin domain-containing proteins, and includes a conserved transition metal-binding site. Biochemical data on the recombinant enzyme suggests that Fe2+ is bound to Pfu PGI. However, as catalytic activity is not strongly influenced either by the replacement of Fe2+ by a range of transition metals or by the presence or absence of the bound metal ion, we suggest that the metal may not be directly involved in catalysis but rather may be implicated in substrate recognition.
Molecular and biochemical characterisation of the thermoactive family 1 pectase lyase from the hyperthermophilic bacterium Thermotoga maritima
Kluskens, L.D. ; Alebeek, G.J.W.M. van; Voragen, A.G.J. ; Vos, W.M. de; Oost, J. van der - \ 2003
Biochemical Journal 370 (2003). - ISSN 0264-6021 - p. 651 - 659.
aspergillus-niger - sp-nov - sequence - enzymes - pectin - purification - oligogalacturonides - protopectinase - inhibitors - archaea
The ability of the hyperthermophilic bacterium Thermotoga maritima to grow on pectin as a sole carbon source coincides with the secretion of a pectate lyase A (PeplA) in the extracellular medium. The pe/A gene of T. maritima was functionally expressed in Escherichia coli as the first heterologously produced thermophilic pectinase, and purified to homogeneity. Gel filtration indicated that the native form of PelA is tetrameric. Highest activity (422 units/mg, with a K-m of 0.06 mM) was demonstrated on polygalacturonic acid (PGA), whereas pectins with an increasing degree of methylation were degraded at a decreasing rate. In the tradition of pectate lyases, PelA demonstrated full dependency on Ca2+ for stability and activity. The enzyme is highly thermoactive and thermostable, operating optimally at 90 degreesC and pH 9.0, with a half-life for thermal inactivation of almost 2 h at 95 degreesC and an apparent melting temperature of 102.5 degreesC. Detailed characterization of the product formation with PGA indicated that PelA has a unique eliminative exo-cleavage pattern liberating unsaturated trigalacturonate as the major product, in contrast with unsaturated digalacturonate for other exopectate lyases known. The unique exo-acting mode of action was supported by progression profiles of PelA on oligo-galacturonides (degree of polymerization, 3-8) and the examination of the bond cleavage frequencies.
Two W-containing formate dehydrogenase (CO2 reductases) involved in syntrophic propionate oxidation by Syntrophobacter fumaroxidans
Bok, F.A.M. de; Hagedoorn, P.L. ; Silva, P.J. ; Hagen, W.R. ; Schiltz, E. ; Fritsche, K. ; Stams, A.J.M. - \ 2003
European Journal of Biochemistry 270 (2003)11. - ISSN 0014-2956 - p. 2476 - 2485.
sulfate-reducing bacterium - desulfovibrio-gigas - oxidizing bacterium - spectroscopic characterization - clostridium-thermoaceticum - phylogenetic analysis - escherichia-coli - pure culture - sp-nov - purification
Two formate dehydrogenases (CO2-reductases) (FDH-1 and FDH-2) were isolated from the syntrophic propionate-oxidizing bacterium Syntrophobacter fumaroxidans. Both enzymes were produced in axenic fumarate-grown cells as well as in cells which were grown syntrophically on propionate with Methanospirillum hungatei as the H2 and formate scavenger. The purified enzymes exhibited extremely high formate-oxidation and CO2-reduction rates, and low Km values for formate. For the enzyme designated FDH-1, a specific formate oxidation rate of 700 U·mg-1 and a Km for formate of 0.04 mm were measured when benzyl viologen was used as an artificial electron acceptor. The enzyme designated FDH-2 oxidized formate with a specific activity of 2700 U·mg-1 and a Km of 0.01 mm for formate with benzyl viologen as electron acceptor. The specific CO2-reduction (to formate) rates measured for FDH-1 and FDH-2, using dithionite-reduced methyl viologen as the electron donor, were 900 U·mg-1 and 89 U·mg-1, respectively. From gel filtration and polyacrylamide gel electrophoresis it was concluded that FDH-1 is composed of three subunits (89 ± 3, 56 ± 2 and 19 ± 1 kDa) and has a native molecular mass of approximately 350 kDa. FDH-2 appeared to be a heterodimer composed of a 92 ± 3 kDa and a 33 ± 2 kDa subunit. Both enzymes contained tungsten and selenium, while molybdenum was not detected. EPR spectroscopy suggested that FDH-1 contains at least four [2Fe-2S] clusters per molecule and additionally paramagnetically coupled [4Fe-4S] clusters. FDH-2 contains at least two [4Fe-4S] clusters per molecule. As both enzymes are produced under all growth conditions tested, but with differences in levels, expression may depend on unknown parameters.
Carbon monoxide conversion by anaerobic bioreactor sludges
Sipma, J. ; Stams, A.J.M. ; Lens, P.N.L. ; Lettinga, G. - \ 2003
FEMS microbiology ecology 44 (2003)2. - ISSN 0168-6496 - p. 271 - 277.
slib - anaërobe behandeling - afvalwaterbehandeling - rioolafvalwater - reductie - koolmonoxide - bioreactoren - sludges - anaerobic treatment - waste water treatment - sewage effluent - reduction - carbon monoxide - bioreactors - carboxydothermus-hydrogenoformans - methanogenic bacteria - sulfate reduction - synthesis-gas - sp-nov - growth - metabolism - oxidation - reactor - energy
Seven different anaerobic sludges from wastewater treatment reactors were screened for their ability to convert carbon monoxide (CO) at 30 and 55degreesC
Seven different anaerobic sludges from wastewater treatment reactors were screened for their ability to convert carbon monoxide (CO) at 30 and 55degreesC. At 30degreesC, CO was converted to methane and/or acetate by all tested sludges. Inhibition experiments, using 2-bromoethanesulfonic acid and vancomycine, showed that CO conversion to methane at 30degreesC occurred via acetate, but not via H-2. At 55degreesC, four sludges originally cultivated at 30-35degreesC and one sludge cultivated at 55degreesC converted CO rapidly into hydrogen or into methane. In the latter case, inhibition experiments showed that methane was formed via hydrogen as the intermediate. (C) 2003 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.
Hydrogen production from paper sludge hydrolysate
Kádár, Z. ; Vrije, G.J. de; Budde, M.A.W. ; Szengyel, Z. ; Reczey, K. ; Claassen, P.A.M. - \ 2003
Applied Biochemistry and Biotechnology 107 (2003)1-3. - ISSN 0273-2289 - p. 557 - 566.
caldicellulosiruptor-saccharolyticus - thermotoga-elfii - sp-nov - bacterium
The main objective of this study was to develop a system for the production of 'renewable' hydrogen. Paper sludge is a solid industrial waste yielding mainly cellulose, which can be used, after hydrolysis, as a feedstock in anaerobic fermentation by (hyper)thermophilic organisms, such as Thermotoga elfii and Caldicellulosiruptor saccharolyticus. Tests on different medium compositions showed that both bacteria were able to produce hydrogen from paper sludge hydrolysate, but the amount of produced hydrogen and the requirement for other components differed. Hydrogen production by T. elfii strongly depended on the presence of yeast extract and salts. By contrast, C. saccharolyticus was less dependent on medium components but seemed to be inhibited by a component present in the sludge hydrolysate. Utilization of xylose was preferred over glucose by C. saccharolyticus.