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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    Characterization of the bacterial community involved in the bioflocculation process of wastewater organic matter in high loaded MBRs
    Faust, L. ; Szendy, M. ; Plugge, C.M. ; Brink, P.F. van den; Temmink, H. ; Rijnaarts, H.H.M. - \ 2015
    Applied Microbiology and Biotechnology 99 (2015)12. - ISSN 0175-7598 - p. 5327 - 5337.
    solids retention time - 16s ribosomal-rna - gradient gel-electrophoresis - improved energy recovery - in-situ hybridization - activated-sludge - microbial community - membrane bioreactor - identification - stability
    High-loaded membrane bioreactors (HL-MBRs), i.e., bioreactors equipped with a membrane for biomass retention and operated at extremely short sludge and hydraulic retention times, can concentrate sewage organic matter to facilitate subsequent energy and chemical recovery from these organics. Bioflocculation, accomplished by microorganisms that produce extracellular polymers, is a very important mechanism in these reactors. Bacterial diversity of the sludge and supernatant fraction of HL-MBRs operated at very short sludge retention times (0.125, 0.5, and 1 day) were determined using a PCR-denaturing gradient gel electrophoresis (DGGE) and clone library approach and compared to the diversity in sewage. Already at a sludge retention time (SRT) of 0.125 day, a distinct bacterial community developed compared to the community in sewage. Bioflocculation, however, was low and the majority of the bacteria, especially Arcobacter, were present in the supernatant fraction. Upon increasing SRT from 0.125 to 1 day, a much stronger bioflocculation was accompanied by an increased abundance of Bacteroidetes in the (solid) sludge fraction: 27.5 % at an SRT of 0.5 day and 46.4 % at an SRT of 1 day. Furthermore, cluster analysis of DGGE profiles revealed that the bacterial community structure in the sludge was different from that in the supernatant. To localize specific bacterial classes in the sludge flocs, fluorescence in situ hybridization (FISH) was carried out with three different bacterial probes. This showed that Betaproteobacteria formed clusters in the sludge flocs whereas Alphaproteobacteria and Gammaproteobacteria were mainly present as single cells
    Soil health indicators and Fusarium wilt suppression in organically managed greenhouse soils
    Bruggen, A.H.C. van; Sharma, K. ; Kaku, E. ; Karfopoulos, S. ; Zelenev, V.V. ; Blok, W.J. - \ 2015
    Applied Soil Ecology 86 (2015). - ISSN 0929-1393 - p. 192 - 201.
    gradient gel-electrophoresis - escherichia-coli o157-h7 - wave-like dynamics - 16s ribosomal-rna - bacterial-populations - microbial-populations - pythium-ultimum - nutrient input - wheat roots - corky root
    Soil health has been associated with internal cycling of nutrients, microbial activity and diversity as well as root disease suppression, which are frequently greater in organically than in conventionally managed soils. Resistance and resilience, measured as amplitude and frequency of oscillations in bacterial communities after a disturbance, were suggested as integral indicators of soil health, but until now there is little proof for this hypothesis. In this study, resistance and resilience of microbial communities and 24 soil chemical and biological parameters were analyzed and correlated to suppression of flax wilt (caused by Fusarium oxysporum f.sp. lini) in three experiments. Soil samples were collected on three different dates from a recently converted organic greenhouse and a similar, neighboring greenhouse under conventional management. The dynamics of copiotrophic and oligotrophic bacteria after a disturbance were monitored, and the resistance and resilience were calculated. The organic soil showed significantly higher water-holding capacity, organic matter content, total C and N contents, C: N ratio of the small particulate organic matter fraction, microbial biomass carbon, oxygen uptake rate, copiotrophic and oligotrophic bacterial communities and suppression of flax wilt incidence. After incorporation of a grass-clover mixture in both soils, the densities of copiotrophic and oligotrophic bacteria oscillated over time. The relative amplitudes of the oscillations (in grass-clover amended over non- amended soil) and the frequencies of the oscillations of both trophic groups were lower for the organic soil, indicating that the resistance and resilience of the microbial community were greater in this soil. These results support the hypothesis that the bacterial response to a disturbance can serve as an integral indicator for soil health, including disease suppressiveness. (C) 2014 Elsevier B.V. All rights reserved.
    Growth of anaerobic methane oxidizing archaea and sulfate reducing bacteria in a high pressure membrane-capsule bioreactor
    Timmers, P.H.A. ; Gieteling, J. ; Widjaja-Greefkes, H.C.A. ; Plugge, C.M. ; Stams, A.J.M. ; Lens, P.N.L. ; Meulepas, R.J.W. - \ 2015
    Applied and Environmental Microbiology 81 (2015)4. - ISSN 0099-2240 - p. 1286 - 1296.
    cold-seep sediments - 16s ribosomal-rna - gradient gel-electrophoresis - guaymas basin - hydrothermal sediments - microbial diversity - marine-sediments - population-dynamics - community structure - gene database
    Anaerobic methane oxidizing communities of archaea (ANME) and sulfate reducing bacteria (SRB) grow slowly, which limits physiological studies. High methane partial pressure was previously successfully applied to stimulate growth, but it is not clear how different ANME subtypes and associated sulfate reducing bacteria (SRB) are affected by it. Here, we report growth of ANME/SRB in a membrane-capsule bioreactor inoculated with Eckernförde Bay sediment that combines high pressure incubation (10.1 MPa methane) and thorough mixing (100 rpm) with complete cell retention by a 0.2 µm membrane. Results were compared to previously obtained data from an ambient-pressure (0.101 MPa methane) bioreactor inoculated with the same sediment. Labelled-methane oxidation rates were not higher at 10.1 MPa, likely because measurements were done at ambient pressure. The subtype ANME-2a/b was abundant in both reactors, but subtype ANME-2c was only enriched at 10.1 MPa. SRB at 10.1 MPa mainly belonged to the SEEP-SRB2, Eel-1 group and Desulforomonadales and not to the typically found SEEP-SRB1. Increase of ANME-2a/b occurred in parallel with increase of SEEP-SRB2 which was previously only found associated with ANME-2c. Our results imply that the syntrophic association is flexible and that methane pressure and sulfide concentration influence growth of different ANME-SRB consortia. We also studied the effect of elevated methane pressure on methane production and oxidation by a mixture of methanogenic and sulfate-reducing sludge. Here, methane oxidation rates decreased and were not coupled to sulfide production, indicating trace methane oxidation during net methanogenesis and not anaerobic methane oxidation, even at high methane partial pressure.
    Inulin-type fructans modulate intestinal Bifidobacterium species populations and decrease fecal short-chain fatty acids in obese women
    Salazar, N. ; Dewulf, E.M. ; Neyrinck, A.M. ; Bindels, L.B. ; Cani, P.D. ; Mahillon, J. ; Vos, W.M. de; Thissen, J.P. ; Gueimonde, M. ; Reyes-Gavilán, C.G. de los; Delzenne, N.M. - \ 2015
    Clinical Nutrition 34 (2015)3. - ISSN 0261-5614 - p. 501 - 507.
    gradient gel-electrophoresis - protein-coupled receptor - gut microbiota - mice - prebiotics - increases - glucose - diet - pcr - fermentation
    Background & aims : Inulin-type fructans (ITF) prebiotics promote changes in the composition and activity of the gut microbiota. The aim of this study was to determine variations on fecal short chain fatty acids (SCFA) concentration in obese women treated with ITF and to explore associations between Bifidobacterium species, SCFA and host biological markers of metabolism. Methods Samples were obtained in a randomized, double blind, parallel, placebo-controlled trial, with 30 obese women randomly assigned to groups that received either 16 g/day ITF (n = 15) or maltodextrin (n = 15) for 3 months. The qualitative and quantitative analysis of Bifidobacterium spp. was performed in feces by PCR-DGGE and q-PCR, and SCFA profile was analyzed by gas chromatography. Spearman correlation analysis was performed between the different variables analyzed. Results The species Bifidobacterium longum, Bifidobacterium pseudocatenulatum and Bifidobacterium adolescentis were significantly increased at the end of the treatment in the prebiotic group (p <0.01) with being B. longum negatively correlated with serum lipopolysaccharide (LPS) endotoxin (p <0.01). Total SCFA, acetate and propionate, that positively correlated with BMI, fasting insulinemia and homeostasis model assessment (HOMA) (p <0.05), were significantly lower in prebiotic than in placebo group after the treatment period. Conclusions ITF consumption selectively modulates Bifidobacterium spp. and decreases fecal SCFA concentration in obese women. ITF could lessen metabolic risk factors associated with higher fecal SCFA concentration in obese individuals.
    Determinants of the microbial community structure of eutrophic, hyporheic river sediments polluted with chlorinated aliphatic hydrocarbons
    Hamonts, K. ; Ryngaert, A. ; Smidt, H. ; Springael, D. ; Dejonghe, W. - \ 2014
    FEMS microbiology ecology 87 (2014)3. - ISSN 0168-6496 - p. 715 - 732.
    16s ribosomal-rna - gradient gel-electrophoresis - sulfate-reducing bacteria - dehalococcoides sp strain - reductive dehalogenase genes - vinyl-chloride reductase - contaminated groundwater - seasonal dynamics - running waters - lake sediment
    Chlorinated aliphatic hydrocarbons (CAHs) often discharge into rivers as contaminated groundwater baseflow. As biotransformation of CAHs in the impacted river sediments might be an effective remediation strategy, we investigated the determinants of the microbial community structure of eutrophic, CAH-polluted sediments of the Zenne River. Based on PCR-DGGE analysis, a high diversity of Bacteria, sulfate-reducing bacteria, Geobacteraceae, methanogenic archaea, and CAH-respiring Dehalococcoides was found. Depth in the riverbed, organic carbon content, CAH content and texture of the sediment, pore water temperature and conductivity, and concentrations of toluene and methane significantly contributed to the variance in the microbial community structure. On a meter scale, CAH concentrations alone explained only 6% of the variance in the Dehalococcoides and sulfate-reducing communities. On a cm-scale, however, CAHs explained 14.5-35% of the variation in DGGE profiles of Geobacteraceae, methanogens, sulfate-reducing bacteria, and Bacteria, while organic carbon content explained 2-14%. Neither the presence of the CAH reductive dehalogenase genes tceA, bvcA, and vcrA, nor the community structure of the targeted groups significantly differed between riverbed locations showing either no attenuation or reductive dechlorination, indicating that the microbial community composition was not a limiting factor for biotransformation in the Zenne sediments.
    Assessing effects of the fungicide tebuconazole to heterotrophic microbes in aquatic microcosms
    Dimitrov, M.R. ; Kosol, Sujitra ; Smidt, H. ; Brink, P.J. van den; Wijngaarden, R.P.A. van; Brock, T.C.M. ; Maltby, L. - \ 2014
    Science of the Total Environment 490 (2014). - ISSN 0048-9697 - p. 1002 - 1011.
    gradient gel-electrophoresis - leaf-litter decomposition - fresh-water microcosms - coal-mine effluent - decaying leaves - gammarus-pulex - community composition - fungal communities - primary producers - stream fungi
    Aquatic ecological risk assessment of fungicides in Europe under Regulation 1107/2009/EC does not currently assess risk to non-target bacteria and fungi. Rather, regulatory acceptable concentrations based on ecotoxicological data obtained from studies with fish, invertebrates and primary producers (including algae) are assumed to be protective to all other aquatic organisms. Here we explore the validity of this assumption by investigating the effects of a fungicide (tebuconazole) applied at its "non-microbial" HC5 concentration (the concentration that is hazardous to 5% of the tested taxa) and derived from acute single species toxicity tests on fish, invertebrates and primary producers (including algae) on the community structure and functioning of heterotrophic microbes (bacteria and aquatic fungi) in a semi-field study, using novel molecular techniques. In our study, a treatment-related effect of tebuconazole (238 µg/L) on either fungal biomass associated with leaf material or leaf decomposition or the composition of the fungal community associated with sediment could not be demonstrated. Moreover, treatment-related effects on bacterial communities associated with sediment and leaf material were not detected. However, tebuconazole exposure did significantly reduce conidia production and altered fungal community composition associated with leaf material. An effect on a higher trophic level was observed when Gammarus pulex were fed tebuconazole-exposed leaves, which caused a significant decrease in their feeding rate. Therefore, tebuconazole may affect aquatic fungi and fungally mediated processes even when applied at its "non-microbial" HC5 concentration.
    The first thousand days – intestinal microbiology of early life: establishing a symbiosis
    Wopereis, H. ; Oozeer, R. ; Knipping, K. ; Belzer, C. ; Knol, J. - \ 2014
    Pediatric Allergy and Immunology 25 (2014)5. - ISSN 0905-6157 - p. 428 - 438.
    gradient gel-electrophoresis - infant gut microbiota - fecal microbiota - atopic-dermatitis - allergic diseases - immune-system - galacto-oligosaccharides - fructo-oligosaccharides - reduced diversity - human-milk
    The development of the intestinal microbiota in the first years of life is a dynamic process significantly influenced by early-life nutrition. Pioneer bacteria colonizing the infant intestinal tract and the gradual diversification to a stable climax ecosystem plays a crucial role in establishing host–microbe interactions essential for optimal symbiosis. This colonization process and establishment of symbiosis may profoundly influence health throughout life. Recent developments in microbiologic cultivation-independent methods allow a detailed view of the key players and factors involved in this process and may further elucidate their roles in a healthy gut and immune maturation. Aberrant patterns may lead to identifying key microbial signatures involved in developing immunologic diseases into adulthood, such as asthma and atopic diseases. The central role of early-life nutrition in the developmental human microbiota, immunity, and metabolism offers promising strategies for prevention and treatment of such diseases. This review provides an overview of the development of the intestinal microbiota, its bidirectional relationship with the immune system, and its role in impacting health and disease, with emphasis on allergy, in early life.
    The Colonization Dynamics of the Gut Microbiota in Tilapia Larvae
    Giatsis, C. ; Sipkema, D. ; Smidt, H. ; Verreth, J.A.J. ; Verdegem, M.C.J. - \ 2014
    PLoS ONE 9 (2014)7. - ISSN 1932-6203 - 15 p.
    gradient gel-electrophoresis - 16s ribosomal-rna - early-life stages - gadus-morhua - fish - populations - genes - determinant - communities - aquaculture
    The gut microbiota of fish larvae evolves fast towards a complex community. Both host and environment affect the development of the gut microbiota; however, the relative importance of both is poorly understood. Determining specific changes in gut microbial populations in response to a change in an environmental factor is very complicated. Interactions between factors are difficult to separate and any response could be masked due to high inter-individual variation even for individuals that share a common environment. In this study we characterized and quantified the spatio-temporal variation in the gut microbiota of tilapia larvae, reared in recirculating aquaculture systems (RAS) or active suspension tanks (AS). Our results showed that variation in gut microbiota between replicate tanks was not significantly higher than within tank variation, suggesting that there is no tank effect on water and gut microbiota. However, when individuals were reared in replicate RAS, gut microbiota differed significantly. The highest variation was observed between individuals reared in different types of system (RAS vs. AS). Our data suggest that under experimental conditions in which the roles of deterministic and stochastic factors have not been precisely determined, compositional replication of the microbial communities of an ecosystem is not predictable.
    The first 1000 cultured species of the human gastrointestinal microbiota
    Rajilic-Stojanovic, M. ; Vos, W.M. de - \ 2014
    FEMS Microbiology Reviews 38 (2014)5. - ISSN 0168-6445 - p. 996 - 1047.
    irritable-bowel-syndrome - 16s ribosomal-rna - human gut microbiota - gradient gel-electrophoresis - human intestinal microbiota - human fecal samples - mucin-degrading bacterium - equol-producing bacterium - diet-induced obesity - bottle-fed infants
    The microorganisms that inhabit the human gastrointestinal tract comprise a complex ecosystem with functions that significantly contribute to our systemic metabolism and have an impact on health and disease. In line with its importance, the human gastrointestinal microbiota has been extensively studied. Despite the fact that a significant part of the intestinal microorganisms has not yet been cultured, presently over 1000 different microbial species that can reside in the human gastrointestinal tract have been identified. This review provides a systematic overview and detailed references of the total of 1057 intestinal species of Eukarya (92), Archaea (8) and Bacteria (957), based on the phylogenetic framework of their small subunit ribosomal RNA gene sequences. Moreover, it unifies knowledge about the prevalence, abundance, stability, physiology, genetics and the association with human health of these gastrointestinal microorganisms, which is currently scattered over a vast amount of literature published in the last 150 years. This detailed physiological and genetic information is expected to be instrumental in advancing our knowledge of the gastrointestinal microbiota. Moreover, it opens avenues for future comparative and functional metagenomic and other high-throughput approaches that need a systematic and physiological basis to have an impact.
    Recovery of microbial diversity and activity during bioremediation following chemical oxidation of diesel contaminated soils
    Sutton, N.B. ; Langenhoff, A.A.M. ; Hidalgo Lasso, D. ; Zaan, B.M. van der; Gaans, P. van; Maphosa, F. ; Smidt, H. ; Grotenhuis, J.T.C. ; Rijnaarts, H.H.M. - \ 2014
    Applied Microbiology and Biotechnology 98 (2014)6. - ISSN 0175-7598 - p. 2751 - 2764.
    polycyclic aromatic-hydrocarbons - gradient gel-electrophoresis - in-situ ozonation - real-time pcr - crude-oil - fentons reagent - biological remediation - community composition - organic-matter - ribosomal-rna
    To improve the coupling of in situ chemical oxidation and in situ bioremediation, a systematic analysis was performed of the effect of chemical oxidation with Fenton's reagent, modified Fenton's reagent, permanganate, or persulfate, on microbial diversity and activity during 8 weeks of incubation in two diesel-contaminated soils (peat and fill). Chemical oxidant and soil type affected the microbial community diversity and biodegradation activity; however, this was only observed following treatment with Fenton's reagent and modified Fenton's reagent, and in the biotic control without oxidation. Differences in the highest overall removal efficiencies of 69 % for peat (biotic control) and 59 % for fill (Fenton's reagent) were partially explained by changes in contaminant soil properties upon oxidation. Molecular analysis of 16S rRNA and alkane monooxygenase (alkB) gene abundances indicated that oxidation with Fenton's reagent and modified Fenton's reagent negatively affected microbial abundance. However, regeneration occurred, and final relative alkB abundances were 1–2 orders of magnitude higher in chemically treated microcosms than in the biotic control. 16S rRNA gene fragment fingerprinting with DGGE and prominent band sequencing illuminated microbial community composition and diversity differences between treatments and identified a variety of phylotypes within Alpha-, Beta-, and Gammaproteobacteria. Understanding microbial community dynamics during coupled chemical oxidation and bioremediation is integral to improved biphasic field application.
    Normal Operating Range of Bacterial Communities in Soil Used for Potato Cropping
    Inceoglu, O. ; Overbeek, L.S. van; Salles, J.F. ; Elsas, J.D. van - \ 2013
    Applied and Environmental Microbiology 79 (2013)4. - ISSN 0099-2240 - p. 1160 - 1170.
    16s ribosomal-rna - gradient gel-electrophoresis - microbial communities - rhizosphere bacteria - plant genotype - diversity - dynamics - ecology - growth - populations
    In this study, the impacts of six potato (Solanum tuberosum) cultivars with different tuber starch allocations (including one genetically modified [GM] line) on the bacterial communities in field soil were investigated across two growth seasons interspersed with 1 year of barley cultivation, using quantitative PCR, clone library, and PCR-denaturing gradient gel electrophoresis (DGGE) analyses. It was hypothesized that the modifications in the tuber starch contents of these plants, yielding changed root growth rates and exudation patterns, might have elicited altered bacterial communities in the soil. The data showed that bacterial abundances in the bulk soil varied over about 2 orders of magnitude across the 3 years. As expected, across all cultivars, positive potato rhizosphere effects on bacterial abundances were noted in the two potato years. The bulk soil bacterial community structures revealed progressive shifts across time, and moving-window analysis revealed a 60% change over the total experiment. Consistent with previous findings, the community structures in the potato rhizosphere compartments were mainly affected by the growth stage of the plants and, to a lesser extent, by plant cultivar type. The data from the soil under the non-GM potato lines were then taken to define the normal operating range (NOR) of the microbiota under potatoes. Interestingly, the bacterial communities under the GM potato line remained within this NOR. In regard to the bacterial community compositions, particular bacterial species in the soil appeared to be specific to (i) the plant species under investigation (barley versus potato) or, with respect to potatoes, (ii) the plant growth stage. Members of the genera Arthrobacter, Streptomyces, Rhodanobacter, and Dokdonella were consistently found only at the flowering potato plants in both seasons, whereas Rhodoplanes and Sporosarcina were observed only in the soil planted to barley
    Ileal microbiota composition of broilers fed various commercial diet compositions
    Hoeven-Hangoor, E. van der; Vossen, J.M.B.M. ; Schuren, F.H.J. ; Verstegen, M.W.A. ; Oliveira, J.E. de; Montijn, R.C. ; Hendriks, W.H. - \ 2013
    Poultry Science 92 (2013)10. - ISSN 0032-5791 - p. 2713 - 2723.
    gradient gel-electrophoresis - fatty-acids - gut microflora - xylanase supplementation - bacterial community - enterococcus-hirae - chickens - performance - ileum - feed
    Microbiota plays a role in the release and absorption of nutrients from feed components, thereby affecting digesta composition and moisture content of the excreta. The objective of the current study was to determine the effects of 5 different diets varying in ingredients (medium-chain fatty acids, nonstarch polysaccharides, and starch) on the microbiota composition of ileal digesta of broiler chickens and excreta DM content. Each treatment was repeated 6 times in cages each containing 18 Ross 308 broilers, with growth performance measured from 0 to 34 d of age and excreta DM and ileal microbiota composition analyzed at 34 d of age. Microbiota composition was evaluated using a novel ribosomal RNA microarray technology containing 370 different probes covering various genera, groups of microbial species, and individual species of the chicken gut microbiota, of which 321 had a signal above the background threshold. Replacing part of the animal fat and soybean oil in the wheat-based diet with medium-chain fatty acids (MCFA; 0.3% C10 and 2.7% C12) improved feed efficiency compared with the other dietary treatments. This coincided with a suppression of gram-positive bacteria belonging to the phylum of the Firmicutes, including Lactobacillus species, and species belonging to the family of the Enterococcaceae and Micrococcaceae, whereas the gram-negative bacteria belonging to the family of the Enterobacteriaceae were promoted. None of the other diets used in the present study notably changed the ileal digesta bacteria composition. Excreta DM content was not affected by dietary treatment. The variation between individual birds per dietary treatment was more pronounced than variation caused by feed composition, with the exception of the digesta microbiota of the birds fed the MCFA diet. It is concluded that a diet with MCFA significantly changes the ileal microbiota composition, whereas the effect of the other diets on the composition of the microbiota and excreta DM content is small in broiler chickens.
    Monitoring the ecology of Bacillus during Daqu incubation, a fermentation starter, using culture-dependent and culture-independent methods
    Zheng, Y. ; Zheng, X. ; Han, B.Z. ; Han, J.S. ; Nout, M.J.R. ; Chen, J.Y. - \ 2013
    Journal of Microbiology and Biotechnology 23 (2013)5. - ISSN 1017-7825 - p. 614 - 622.
    gradient gel-electrophoresis - cocoa fermentation - chinese liquor - flavor liquor - fen liquor - identification - licheniformis - bacterial - subtilis - strains
    Daqu, a traditional fermentation starter, has been used to produce attractively flavored foods such as vinegar and Chinese liquor for thousands of years. Although Bacillus spp. are one of the dominant microorganisms in Daqu, more precise information is needed to reveal why and how Bacillus became dominant in Daqu, and next, to assess the impact of Bacillus sp. on Daqu and its derived products. We combined culture-dependent and culture-independent methods to study the ecology of Bacillus during Daqu incubation. Throughout the incubation, 67 presumptive Bacillus spp. isolates were obtained, 52 of which were confirmed by 16S rDNA sequencing. The identified organisms belonged to 8 Bacillus species: B. licheniformis, B. subtilis, B. amyloliquefaciens, B. cereus, B. circulans, B. megaterium, B. pumilus, and B. anthracis. A primer set specific for Bacillus and related genera was used in a selective PCR study, followed by a nested DGGE PCR targeting the V9 region of the 16S rDNA. Species identified from the PCR-DGGE fingerprints were related to B. licheniformis, B. subtilis, B. amyloliquefaciens, B. pumilus, B. benzoevorans, and B. foraminis. The predominant species was found to be B. licheniformis. Certain B. licheniformis strains exhibited potent antimicrobial activities. The greatest species diversity occurred at the Liangmei stage of Daqu incubation. To date, we lack sufficient knowledge of Bacillus distribution in Daqu. Elucidating the ecology of Bacillus during Daqu incubation would enable the impact of Bacillus on Daqu to be accessed, and the quality and stabilization of Daqu-derived products to be optimized. Keywords: microbial ecology, Bacillus, fermentation starter, Daqu, PCR-DGGE
    Microbial diversity and dynamics of microbial communities during black-slop soaking of soybeans as determined by PCR-DGGE and molecular cloning
    Yan, Y.Z. ; Wolkers-Rooijackers, J.C.M. ; Nout, M.J.R. ; Han, B.Z. - \ 2013
    World Journal of Microbiology and Biotechnology 29 (2013)10. - ISSN 0959-3993 - p. 1969 - 1974.
    gradient gel-electrophoresis - 16s ribosomal-rna - polymerase-chain-reaction - tempe production - temperature - water
    Tempe is a traditional fermented food in Indonesia. The manufacture process is quite complex, which comprises two stages, preparatory soaking of soybeans and fungal solid state fermentation. Daily addition of previous soak water (back-slopping) during the soybean soaking step is considered to be crucial in the manufacture of high quality tempe. The microbial diversity and dynamics of the microbial communities evolving during back-slop soaking of soybeans for tempe making was investigated by culture-independent PCR–DGGE and molecular cloning. Both DNA and total RNA were isolated and included in this study, to obtain a view on the succession of total and viable bacteria in the complex microbiota. DGGE profiles indicated that Enterobacter sp., Enterococcus sp., Pseudomonas putida, Leuconostoc fallax, Pediococcus pentosaceus, and Weissella cibaria, were the predominant bacteria. Their occurrence shifted dramatically during the back-slop soaking procedure. This study combined with previous culture-dependent studies could gain a better understanding of the complex microbiota of traditional fermented food and give useful information for its quality control.
    Effect of supplementing coconut or krabok oil, rich in medium-chain fatty acids on ruminal fermentation, protozoa and archaeal population of bulls
    Panyakaew, P. ; Boon, N. ; Goel, G. ; Yuangklang, C. ; Schonewille, J.T. ; Hendriks, W.H. ; Fievez, V. - \ 2013
    Animal 7 (2013)12. - ISSN 1751-7311 - p. 1950 - 1958.
    different hypervariable regions - gradient gel-electrophoresis - myristic acid - in-vitro - methane suppression - ciliate protozoa - energy-balance - lauric acid - dairy-cows - rumen
    Medium-chain fatty acids (MCFA), for example, capric acid (C10:0), myristic (C14:0) and lauric (C12:0) acid, have been suggested to decrease rumen archaeal abundance and protozoal numbers. This study aimed to compare the effect of MCFA, either supplied through krabok (KO) or coconut (CO) oil, on rumen fermentation, protozoal counts and archaeal abundance, as well as their diversity and functional organization. KO contains similar amounts of C12:0 as CO (420 and 458 g/kg FA, respectively), but has a higher proportion of C14:0 (464 v. 205 g/kg FA, respectively). Treatments contained 35 g supplemental fat per kg DM: a control diet with tallow (T); a diet with supplemental CO; and a diet with supplemental KO. A 4th treatment consisted of a diet with similar amounts of MCFA (i.e. C10:0+C12:0+C14:0) from CO and KO. To ensure isolipidic diets, extra tallow was supplied in the latter treatment (KO+T). Eight fistulated bulls (two bulls per treatment), fed a total mixed ration predominantly based on cassava chips, rice straw, tomato pomace, rice bran and soybean meal (1.5% of BW), were used. Both KO and CO increased the rumen volatile fatty acids, in particular propionate and decreased acetate proportions. Protozoal numbers were reduced through the supplementation of an MCFA source (CO, KO and KO+T), with the strongest reduction by KO. Quantitative real-time polymerase chain reaction assays based on archaeal primers showed a decrease in abundance of Archaea when supplementing with KO and KO+T compared with T and CO. The denaturing gradient gel electrophoresis profiles of the rumen archaeal population did not result in a grouping of treatments. Richness indices were calculated from the number of DGGE bands, whereas community organization was assessed from the Pareto–Lorenz eveness curves on the basis of DGGE band intensities. KO supplementation (KO and KO+T treatments) increased richness and evenness within the archaeal community. Further research including methane measurements and productive animals should elucidate whether KO could be used as a dietary methane mitigation strategy.
    Effects of slurry from sulfadiazine- (SDZ) and difloxacin- (DIF) medicated pigs on the structural diversity of microorganisms in bulk and rhizosphere soil
    Reichel, R. ; Rosendahl, I. ; Peeters, E.T.H.M. ; Focks, A. ; Groeneweg, K.J.I. ; Bierl, R. - \ 2013
    Soil Biology and Biochemistry 62 (2013). - ISSN 0038-0717 - p. 82 - 91.
    microbial-community structure - gradient gel-electrophoresis - organic-matter - antibiotic sulfadiazine - agricultural soils - arable soils - manure - nitrogen - bacteria - impact
    Conventional farming still consumes considerable amounts of antibiotics such as sulfadiazine (SDZ) or difloxacin (DIF) to protect livestock from infectious diseases. Consequently, slurries from medicated animals are applied to arable soils. Antibiotics, co-applied with pig slurry, are increasingly reported to change soil microbial community structures in un-rooted bulk soil. The effects in rhizosphere soil, as well as the medication-derived direct and indirect effects of an altered slurry composition are poorly investigated. We evaluated the response of microorganisms to slurry of SDZ- and DIF-medicated pigs in a 63-d mesocosm experiment, considering the natural complexity of a typical agricultural pig slurry amendment and developing Zea mays L. root systems. Slurry-derived fecal bacteria were still present in mesosocosm soil 14 days after amendment. Medication with DIF and SDZ further altered the molecular-chemical pattern of the pig slurry, confounding the precise antibiotic effect. This has to be considered when investigating antimicrobial effects under ecological relevant conditions. Effects on the microbial community in mesocosm bulk soil widely matched results from previous studies on directly spiked soil. Effects were also found in the mesocosm rhizosphere soil, but not more pronounced than in bulk soil. This was also verified under laboratory conditions after application of artificially SDZ-spiked control slurry.
    Chitin amendment raises the suppressiveness of soil towards plant pathogens and modulates the actinobacterial and oxalobacteriaceal communities in an experimental agricultural field
    Cretoiu, M.S. ; Korthals, G.W. ; Visser, J.H.M. ; Elsas, J.D. van - \ 2013
    Applied and Environmental Microbiology 79 (2013)17. - ISSN 0099-2240 - p. 5291 - 5301.
    gradient gel-electrophoresis - bacterial communities - microbial community - janthinobacterium-lividum - phytopathogenic fungi - biological-control - ribosomal-rna - rhizosphere - genes - diversity
    A long-term experiment on the effect of chitin addition to soil on the suppression of soil-borne pathogens was set up and monitored for eight years in an experimental field, Vredepeel, the Netherlands. Chitinous matter obtained from shrimps was added to soil top layers at two different occasions and the suppressiveness of soil towards Verticillium dahliae as well as plant-pathogenic nematodes was assessed, in addition to analyses of the abundances and community structures of members of the soil microbiota. The data revealed that chitin amendment had raised the suppressiveness of soil, in particular towards Verticillium dahliae, 9 months after the (second) treatment, extending to two years following treatment. Moreover, major effects of the added chitin on the soil microbial communities were detected. First, shifts in both the abundances and structures of the chitin-treated soil microbial communities were found, both of total soil bacteria and fungi. In addition, the abundances and structures of soil actinobacteria and Oxalobacteriaceae were affected by chitin. At the functional gene level, the abundance of specific (family-18 glycoside hydrolase) chitinase genes carried by the soil bacteriota also revealed upshifts as a result of the added chitin. The effects of chitin noted for the Oxalobacteriaceae were specifically related to significant upshifts in the abundances of the species Duganella violaceinigra and Massilia plicata. These effects of chitin persisted over the time of the experiment.
    Soil microbial community structure of range-expanding plant species differs from co-occurring natives
    Morriën, W.E. ; Putten, W.H. van der - \ 2013
    Journal of Ecology 101 (2013)5. - ISSN 0022-0477 - p. 1093 - 1102.
    gradient gel-electrophoresis - arbuscular mycorrhizal fungi - 16s ribosomal-rna - climate-change - litter decomposition - invasive plants - rhizosphere - diversity - ergosterol - feedback
    1. Due to global warming and other changes in the environment, many native and exotic plant species show range expansion from lower to higher latitudes. In the new range, the (in)ability of range-expanding plants to establish associations with local soil microbes can have important consequences for plant abundance; however, very little information exists on rhizosphere communities of range-expanding plant species. Here, we examine the rhizosphere microbial community composition of range-expanding plant species in comparison with phylogenetically related species that are native in the invaded range. 2. We tested the hypothesis that range-expanding plants species would promote fewer shifts in rhizosphere communities than congeneric natives would. In order to test this, soil was collected from the invaded habitat and six range-expanding and nine congeneric natives were planted individually in pots to condition soil microbial communities. 3. After harvesting, individuals of the same species were planted in conditioned own and control soils to test the legacy effects of soil conditioning on biomass production. The control soils were mixtures of soils conditioned by all other plant species, except congenerics. After 10 weeks of plant growth, we determined the rhizosphere community composition of bacteria, fungi, arbuscular mycorrhizal fungi (AMF) and Fusarium spp. 4. All groups of microbes were analysed qualitatively using denaturating gradient gel electrophoresis (DGGE). Ergosterol was determined as a quantitative measure of nonarbuscular mycorrhizal fungal biomass, and real-time PCR was applied to detect amounts of Fusarium spp. 5. Range-expanding plants had less fungal hyphal biomass and lower amounts of Fusarium spp. in the rhizosphere than congenerics. Bacterial community composition was influenced by a combination of soil conditioning and plant origin, whereas fungal communities, AMF and Fusarium spp. were less pronounced in their responses to the experimental treatments. 6. Synthesis. We conclude that the lack of legacy effects in range-expanding plant species compared with natives may be due to differences in bacterial rhizosphere community composition, or to different quantities of potential pathogenic fungi. If the range-expanding plant species were benefiting more from AMF, effects will not have been due to differences in community composition, but we cannot exclude other options, such as different effectiveness of AMF or other soil biota in the rhizosphere of range-expanding vs. native plant species. The greater accumulation of bacterial and fungal pathogens in the rhizosphere of natives in relation to range expanders might explain the successful establishment of range-expanding plants.
    Going back to the roots: the microbial ecology of the rhizosphere
    Philippot, L. ; Raaijmakers, J. ; Lemanceau, P. ; Putten, W.H. van der - \ 2013
    Nature Reviews Microbiology 11 (2013)11. - ISSN 1740-1526 - p. 789 - 799.
    arbuscular mycorrhizal fungi - bacterial community structure - disease-suppressive bacteria - gradient gel-electrophoresis - plant-herbivore interactions - elevated atmospheric co2 - soil-borne pathogens - medicago-truncatula - food webs - arabidopsis-thaliana
    The rhizosphere is the interface between plant roots and soil where interactions among a myriad of microorganisms and invertebrates affect biogeochemical cycling, plant growth and tolerance to biotic and abiotic stress. The rhizosphere is intriguingly complex and dynamic, and understanding its ecology and evolution is key to enhancing plant productivity and ecosystem functioning. Novel insights into key factors and evolutionary processes shaping the rhizosphere microbiome will greatly benefit from integrating reductionist and systems-based approaches in both agricultural and natural ecosystems. Here, we discuss recent developments in rhizosphere research in relation to assessing the contribution of the micro- and macroflora to sustainable agriculture, nature conservation, the development of bio-energy crops and the mitigation of climate change.
    Enrichment of anaerobic syngas converting bacteria from bioreactor sludges
    Alves, J.I. ; Stams, A.J.M. ; Plugge, C.M. ; Alves, M.M. ; Sousa, D.Z. - \ 2013
    FEMS microbiology ecology 86 (2013)3. - ISSN 0168-6496 - p. 590 - 597.
    carbon-monoxide conversion - gradient gel-electrophoresis - chain fatty-acids - 16s ribosomal-rna - sp nov. - methanogenic bacteria - gen. nov. - growth - sulfate - communities
    Thermophilic (55°C) anaerobic microbial communities were enriched with a synthetic syngas mixture (composed of CO, H2 and CO2 ) or with CO alone. Cultures T-Syn and T-CO were incubated and successively transferred with syngas (16 transfers) or CO (9 transfers), respectively, with increasing CO partial pressures from 0.09 to 0.88 bar. Culture T-Syn, after 4 successive transfers with syngas, was also incubated with CO and subsequently transferred (9 transfers) with solely this substrate - cultures T-Syn-CO. Incubation with syngas and CO caused a rapid decrease in the microbial diversity of the anaerobic consortium. T-Syn and T-Syn-CO showed identical microbial composition, and were dominated by Desulfotomaculum and Caloribacterium species. Incubation initiated with CO resulted in the enrichment of bacteria from the genera Thermincola and Thermoanaerobacter. Methane was detected in the first two to three transfers of T-Syn, but production ceased afterwards. Acetate was the main product formed by T-Syn and T-Syn-CO. Enriched T-CO cultures showed a two-phase conversion, in which H2 was formed first and then converted to acetate. This research provides insight into how thermophilic anaerobic communities develop using syngas/CO as sole energy and carbon source can be steered for specific end products and subsequent microbial synthesis of chemicals
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