Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Chloroflexi Dominate the Deep-Sea Golf Ball Sponges Craniella zetlandica and Craniella infrequens Throughout Different Life Stages
    Busch, Kathrin ; Wurz, Erik ; Rapp, Hans Tore ; Bayer, Kristina ; Franke, Andre ; Hentschel, Ute - \ 2020
    Frontiers in Marine Science 7 (2020). - ISSN 2296-7745
    amplicon sequencing - Chloroflexi - Craniella - early life stages - fluorescence in situ hybridization - sponges - symbiosis - vulnerable marine ecosystems

    Deep-sea sponge grounds are underexplored ecosystems that provide numerous goods and services to the functioning of the deep-sea. This study assessed the prokaryotic diversity in embryos, recruits, and adults of Craniella zetlandica and Craniella infrequens, common and abundant representatives of deep-sea sponge grounds in the North Atlantic. Our results reveal that symbiont transmission in the two Craniella sponge species likely occurs vertically, as highly similar microbial consortia have been identified in adults, embryos, and recruits. Moreover, transmission electron microscopy revealed high abundances of sponge-associated microorganisms, among which Chloroflexi (SAR202) were identified as common representatives by amplicon sequencing and fluorescence in situ hybridization (FISH). Equal diversity metrices, a similar overall prokaryotic community composition and a distinct dominance of the phylum Chloroflexi within all life stages are the key findings of our analyses. Information such as presented here provide understanding on the recruitment of deep-sea sponge holobionts which is needed to develop integrated management tools of such vulnerable marine ecosystems.

    Roadmap for naming uncultivated Archaea and Bacteria
    Murray, Alison E. ; Freudenstein, John ; Gribaldo, Simonetta ; Hatzenpichler, Roland ; Hugenholtz, Philip ; Kämpfer, Peter ; Konstantinidis, Konstantinos T. ; Lane, Christopher E. ; Papke, R.T. ; Parks, Donovan H. ; Rossello-Mora, Ramon ; Stott, Matthew B. ; Sutcliffe, Iain C. ; Thrash, J.C. ; Venter, Stephanus N. ; Whitman, William B. ; Acinas, Silvia G. ; Amann, Rudolf I. ; Anantharaman, Karthik ; Armengaud, Jean ; Baker, Brett J. ; Barco, Roman A. ; Bode, Helge B. ; Boyd, Eric S. ; Brady, Carrie L. ; Carini, Paul ; Chain, Patrick S.G. ; Colman, Daniel R. ; DeAngelis, Kristen M. ; Rios, Maria Asuncion de los; Estrada-de los Santos, Paulina ; Dunlap, Christopher A. ; Eisen, Jonathan A. ; Emerson, David ; Ettema, Thijs J.G. ; Eveillard, Damien ; Girguis, Peter R. ; Hentschel, Ute ; Hollibaugh, James T. ; Hug, Laura A. ; Inskeep, William P. ; Ivanova, Elena P. ; Klenk, Hans Peter ; Li, Wen Jun ; Lloyd, Karen G. ; Löffler, Frank E. ; Makhalanyane, Thulani P. ; Moser, Duane P. ; Nunoura, Takuro ; Palmer, Marike ; Parro, Victor ; Pedrós-Alió, Carlos ; Probst, Alexander J. ; Smits, Theo H.M. ; Steen, Andrew D. ; Steenkamp, Emma T. ; Spang, Anja ; Stewart, Frank J. ; Tiedje, James M. ; Vandamme, Peter ; Wagner, Michael ; Wang, Feng Ping ; Hedlund, Brian P. ; Reysenbach, Anna Louise - \ 2020
    Nature Microbiology 5 (2020). - ISSN 2058-5276 - p. 987 - 994.

    The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as ‘type material’, thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity.

    Antibiotics-induced monodominance of a novel gut bacterial order
    Hildebrand, Falk ; Moitinho-Silva, Lucas ; Blasche, Sonja ; Jahn, Martin Thomas Thomas ; Gossmann, Toni Ingolf ; Heuerta Cepas, Jaime ; Hercog, Rajna ; Luetge, Mechthild ; Bahram, Mohammad ; Pryszlak, Anna ; Alves, Renato J. ; Waszak, Sebastian M. ; Zhu, Ana ; Ye, Lumeng ; Costea, Paul Igor ; Aalvink, Steven ; Belzer, Clara ; Forslund, Sofia K. ; Sunagawa, Shinichi ; Hentschel, Ute ; Merten, Christoph ; Patil, Kiran Raosaheb ; Benes, Vladimir ; Bork, Peer - \ 2019
    Gut 68 (2019)10. - ISSN 0017-5749
    antibiotics - bacterial overgrowth - intestinal microbiology - molecular genetics

    Objective: The composition of the healthy human adult gut microbiome is relatively stable over prolonged periods, and representatives of the most highly abundant and prevalent species have been cultured and described. However, microbial abundances can change on perturbations, such as antibiotics intake, enabling the identification and characterisation of otherwise low abundant species. Design: Analysing gut microbial time-series data, we used shotgun metagenomics to create strain level taxonomic and functional profiles. Community dynamics were modelled postintervention with a focus on conditionally rare taxa and previously unknown bacteria. Results: In response to a commonly prescribed cephalosporin (ceftriaxone), we observe a strong compositional shift in one subject, in which a previously unknown species, UBorkfalki ceftriaxensis, was identified, blooming to 92% relative abundance. The genome assembly reveals that this species (1) belongs to a so far undescribed order of Firmicutes, (2) is ubiquitously present at low abundances in at least one third of adults, (3) is opportunistically growing, being ecologically similar to typical probiotic species and (4) is stably associated to healthy hosts as determined by single nucleotide variation analysis. It was the first coloniser after the antibiotic intervention that led to a long-lasting microbial community shift and likely permanent loss of nine commensals. Conclusion: The bloom of UB. ceftriaxensis and a subsequent one of Parabacteroides distasonis demonstrate the existence of monodominance community states in the gut. Our study points to an undiscovered wealth of low abundant but common taxa in the human gut and calls for more highly resolved longitudinal studies, in particular on ecosystem perturbations.

    Erratum to: The sponge microbiome project
    Moitinho-Silva, Lucas ; Nielsen, Shaun ; Amir, Amnon ; Gonzalez, Antonio ; Ackermann, Gail L. ; Cerrano, Carlo ; Astudillo-Garcia, Carmen ; Easson, Cole ; Sipkema, Detmer ; Liu, Fang ; Steinert, Georg ; Kotoulas, Giorgos ; McCormack, Grace P. ; Feng, Guofang ; Bell, James J. ; Vicente, Jan ; Björk, Johannes R. ; Montoya, Jose M. ; Olson, Julie B. ; Reveillaud, Julie ; Steindler, Laura ; Pineda, Mari Carmen ; Marra, Maria V. ; Ilan, Micha ; Taylor, Michael W. ; Polymenakou, Paraskevi ; Erwin, Patrick M. ; Schupp, Peter J. ; Simister, Rachel L. ; Knight, Rob ; Thacker, Robert W. ; Costa, Rodrigo ; Hill, Russell T. ; Lopez-Legentil, Susanna ; Dailianis, Thanos ; Ravasi, Timothy ; Hentschel, Ute ; Li, Zhiyong ; Webster, Nicole S. ; Thomas, Torsten - \ 2018
    GigaScience 7 (2018)12. - ISSN 2047-217X
    The sponge microbiome project
    Moitinho-Silva, Lucas ; Nielsen, Shaun ; Amir, Amnon ; Gonzalez, Antonio ; Ackermann, Gail L. ; Cerrano, Carlo ; Astudillo-Garcia, Carmen ; Easson, Cole ; Sipkema, Detmer ; Liu, Fang ; Steinert, Georg ; Kotoulas, Giorgos ; McCormack, Grace P. ; Feng, Guofang ; Bell, James J. ; Vicente, Jan ; Björk, Johannes R. ; Montoya, Jose M. ; Olson, Julie B. ; Reveillaud, Julie ; Steindler, Laura ; Pineda, Mari Carmen ; Marra, Maria V. ; Ilan, Micha ; Taylor, Michael W. ; Polymenakou, Paraskevi ; Erwin, Patrick M. ; Schupp, Peter J. ; Simister, Rachel L. ; Knight, Rob ; Thacker, Robert W. ; Costa, Rodrigo ; Hill, Russell T. ; Lopez-Legentil, Susanna ; Dailianis, Thanos ; Ravasi, Timothy ; Hentschel, Ute ; Li, Zhiyong ; Webster, Nicole S. ; Thomas, Torsten - \ 2017
    GigaScience 6 (2017)10. - ISSN 2047-217X
    16S rRNA gene - Archaea - Bacteria - Marine sponges - Microbial diversity - Microbiome - Symbiosis
    Marine sponges (phylum Porifera) are a diverse, phylogenetically deep-branching clade known for forming intimate partnerships with complex communities of microorganisms. To date, 16S rRNA gene sequencing studies have largely utilised different extraction and amplification methodologies to target the microbial communities of a limited number of sponge species, severely limiting comparative analyses of sponge microbial diversity and structure. Here, we provide an extensive and standardised dataset that will facilitate sponge microbiome comparisons across large spatial, temporal, and environmental scales. Samples from marine sponges (n = 3569 specimens), seawater (n = 370), marine sediments (n = 65) and other environments (n = 29) were collected from different locations across the globe. This dataset incorporates at least 268 different sponge species, including several yet unidentified taxa. The V4 region of the 16S rRNA gene was amplified and sequenced from extracted DNA using standardised procedures. Raw sequences (total of 1.1 billion sequences) were processed and clustered with (i) a standard protocol using QIIME closed-reference picking resulting in 39 543 operational taxonomic units (OTU) at 97% sequence identity, (ii) a de novo clustering using Mothur resulting in 518 246 OTUs, and (iii) a new high-resolution Deblur protocol resulting in 83 908 unique bacterial sequences. Abundance tables, representative sequences, taxonomic classifications, and metadata are provided. This dataset represents a comprehensive resource of sponge-associated microbial communities based on 16S rRNA gene sequences that can be used to address overarching hypotheses regarding host-associated prokaryotes, including host specificity, convergent evolution, environmental drivers of microbiome structure, and the sponge-associated rare biosphere.
    Predicting the HMA-LMA status in marine sponges by machine learning
    Moitinho-Silva, Lucas ; Steinert, Georg ; Nielsen, Shaun ; Hardoim, Cristiane C.P. ; Wu, Yu Chen ; McCormack, Grace P. ; López-Legentil, Susanna ; Marchant, Roman ; Webster, Nicole ; Thomas, Torsten ; Hentschel, Ute - \ 2017
    Frontiers in Microbiology 8 (2017). - ISSN 1664-302X - 14 p.
    16S rRNA gene - Marine sponges - Microbial diversity - Microbiome - Random forest - Symbiosis

    The dichotomy between high microbial abundance (HMA) and low microbial abundance (LMA) sponges has been observed in sponge-microbe symbiosis, although the extent of this pattern remains poorly unknown. We characterized the differences between the microbiomes of HMA (n = 19) and LMA (n = 17) sponges (575 specimens) present in the Sponge Microbiome Project. HMA sponges were associated with richer and more diverse microbiomes than LMA sponges, as indicated by the comparison of alpha diversity metrics. Microbial community structures differed between HMA and LMA sponges considering Operational Taxonomic Units (OTU) abundances and across microbial taxonomic levels, from phylum to species. The largest proportion of microbiome variation was explained by the host identity. Several phyla, classes, and OTUs were found differentially abundant in either group, which were considered "HMA indicators" and "LMA indicators." Machine learning algorithms (classifiers) were trained to predict the HMA-LMA status of sponges. Among nine different classifiers, higher performances were achieved by Random Forest trained with phylum and class abundances. Random Forest with optimized parameters predicted the HMA-LMA status of additional 135 sponge species (1,232 specimens) without a priori knowledge. These sponges were grouped in four clusters, from which the largest two were composed of species consistently predicted as HMA (n = 44) and LMA (n = 74). In summary, our analyses shown distinct features of the microbial communities associated with HMA and LMA sponges. The prediction of the HMA-LMA status based on the microbiome profiles of sponges demonstrates the application of machine learning to explore patterns of host-associated microbial communities.

    Breeding strategies of Antarctic Petrels Thalassoica antarctica and Southern Fulmars Fulmarus glacialoides in the high Antarctic and implications for reproductive success
    Creuwels, J.C.S. ; Franeker, J.A. van; Doust, S.J. ; Beinssen, A. ; Harding, B. ; Hentschel, O. - \ 2008
    Ibis 150 (2008)1. - ISSN 0019-1019 - p. 160 - 171.
    windmill islands - ice conditions - snow - procellariidae - incubation - abundance - survival - seabirds - growth - ardery
    Breeding strategies of two closely related fulmarine petrels were studied on Ardery Island, on the continental coast of East Antarctica, where short summers are expected to narrow the time-window for reproduction. Both species had a similar breeding period (97 days from laying to fledging) but Antarctic Petrels Thalassoica antarctica bred up to 16 days earlier than Southern Fulmars. During the pre-laying exodus, all Antarctic Petrels deserted the colony, whereas some Southern Fulmars Fulmarus glacialoides remained. Antarctic Petrels exhibited stronger synchronization in breeding, made longer foraging trips and spent less time guarding their chicks than Southern Fulmars. Overall breeding success of both species was similar but failures of Antarctic Petrels were concentrated in the early egg-phase and after hatching, when parents ceased guarding. Southern Fulmars lost eggs and chicks later in the breeding cycle and so wasted more parental investment in failed breeding attempts. Different breeding strategies may be imposed by flight characteristics; Southern Fulmars are less capable of crossing large expanses of pack ice and need to delay breeding until the sea ice retreats and breaks up. However, due to the short summer they risk chick failure when weather conditions deteriorate late in the season.
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