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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Insights into the ecology and evolution of the mucus-dwelling gut bacterium Mucispirillum schaedleri
Berry, David ; Pfann, Carina ; Steinberger, Michaela ; Hanson, Buck ; Herp, Simone ; Brugiroux, Sandrine ; Gomes Neto, João Carlos ; Boekschoten, M.V. ; Schwab, Clarissa ; Urich, Tim ; Ramer-Tait, Amanda E. ; Rattei, Thomas ; Stecher, Bärbel ; Loy, Alexander - \ 2017
Mus musculus - GSE83625 - PRJNA326520
Mucispirillum schaedleri is an abundant inhabitant of the intestinal mucus layer of rodents and other animals. To gain insights into its lifestyle, we analyzed the genome and transcriptome of M. schaedleri ASF 457 and tested for traits predicted by the genome using physiological experiments. Although thought to be a mucus degrader, its genome surprisingly predicts that M. schaedleri has limited capacity for degrading host-derived mucosal glycans or other complex polysaccharides. Rather, it may utilize small compounds such as peptides, amino acids, glycerol, and short chain fatty acids. Additionally, it can reduce nitrate and has systems for scavenging oxygen and reactive oxygen species, which accounts for its presence close to the mucosal tissue and during inflammation. Also of note, M. schaedleri harbors a type VI secretion system (T6SS) and several putative effector proteins containing eukaryotic domains, which suggest intimate interactions with the host and a role in inflammation. Examination of the individual phylogenies of all genes in the M. schaedleri genome revealed extensive horizontal gene transfer, primarily from intestinal Epsilon- and Deltaproteobacteria. Though M. schaedleri utilizes non-horizontally-transferred pathways (e.g. nitrate reduction), horizontally-acquired pathways from gut organisms (e.g. T6SS and glycerol-P utilization) are also likely also important for its survival in the intestine, suggesting that lateral gene transfer may have played a key role in facilitating its establishment in the gut ecosystem.
Lifestyle and Horizontal Gene Transfer-Mediated Evolution of Mucispirillum schaedleri, a Core Member of the Murine Gut Microbiota
Loy, Alexander ; Pfann, Carina ; Steinberger, Michaela ; Hanson, Buck ; Herp, Simone ; Brugiroux, Sandrine ; Gomes Neto, João Carlos ; Boekschoten, Mark V. ; Schwab, Clarissa ; Urich, Tim ; Ramer-Tait, Amanda E. ; Rattei, Thomas ; Stecher, Bärbel ; Berry, David ; Lozupone, Catherine - \ 2017
mSystems 2 (2017)1. - ISSN 2379-5077 - 15 p.
Mucispirillum schaedleri is an abundant inhabitant of the intestinal mucus layer of rodents and other animals and has been suggested to be a pathobiont, a commensal that plays a role in disease. In order to gain insights into its lifestyle, we analyzed the genome and transcriptome of M. schaedleri ASF 457 and performed physiological experiments to test traits predicted by its genome. Although described as a mucus inhabitant, M. schaedleri has limited capacity for degrading host-derived mucosal glycans and other complex polysaccharides. Additionally, M. schaedleri reduces nitrate and expresses systems for scavenging oxygen and reactive oxygen species in vivo, which may account for its localization close to the mucosal tissue and expansion during inflammation. Also of note, M. schaedleri harbors a type VI secretion system and putative effector proteins and can modify gene expression in mucosal tissue, suggesting intimate interactions with its host and a possible role in inflammation. The M. schaedleri genome has been shaped by extensive horizontal gene transfer, primarily from intestinal Epsilon- and Deltaproteobacteria, indicating that horizontal gene transfer has played a key role in defining its niche in the gut ecosystem.
Genome and transcriptome of Mucispirillum schaedleri ASF457 (MCS)
Loy, Alexander ; Pfann, Carina ; Steinberger, Michaela ; Hanson, Buck ; Herp, Simone ; Brugiroux, Sandrine ; Gomes Neto, João Carlos ; Boekschoten, M.V. ; Schwab, Clarissa ; Urich, Tim ; Ramer-Tait, Amanda E. ; Rattei, Thomas ; Stecher, Bärbel ; Berry, David ; Lozupone, Catherine - \ 2016
PRJEB13534 - ERP015095 - Mucispirillum schaedleri
Mucispirillum schaedleri is an abundant inhabitant of the intestinal mucus layer of rodents and other animals. We analyzed the genome and transcriptome of M. schaedleri ASF 457 to gain insights into its lifestyle and tested traits predicted by the genome with physiological experiments. Surprisingly, though thought to be a mucus degrader its genome predicts that M. schaedleri has limited capacity for degrading host-derived mucosal glycans or other complex polysaccharides. It may rather utilize small compounds such as peptides, amino acids, glycerol, and short chain fatty acids. Additionally, it can reduce nitrate and has systems for scavenging oxygen and reactive oxygen species, which accounts for its survival close to the mucosal tissue blooms during inflammation. Interestingly, M. schaedleri harbors a type VI secretion system (T6SS) and several putative effector proteins containing eukaryotic domains, which may be involved in interacting with the host and may play a role in inflammation. An examination of individual phylogenies of all genes in the M. schaedleri genome indicated extensive lateral gene transfer, primarily from intestinal Epsilon- and Deltaproteobacteria. Though M. schaedleri utilizes non-laterally-transferred pathways (e.g. nitrate reduction), laterally acquired pathways from gut organisms (e.g. T6SS and glycerol-P utilization) are likely also important for its survival in the intestine, suggesting that lateral gene transfer may have played a key role in facilitating its establishment in the gut ecosystem.
The soil food web revisited: Diverse and widespread mycophagous soil protists
Geisen, Stefan ; Koller, R. ; Hünninghaus, M. ; Dumack, K. ; Urich, T. ; Bonkowski, M. - \ 2016
Soil Biology and Biochemistry 94 (2016). - ISSN 0038-0717 - p. 10 - 18.
Soil protists are commonly suggested being solely bacterivorous, serving together with bacterivorous nematodes as the main controllers of the bacterial energy channel in soil food webs. In contrast, the fungal energy channel is assumed to be controlled by arthropods and mycophagous nematodes. This perspective accepted by most soil biologists is, however, challenged by functional studies conducted by taxonomists that revealed a range of mycophagous protists. In order to increase the knowledge on the functional importance of mycophagous protists we isolated and initiated cultures of protist taxa and tested eight for facultative feeding on diverse fungi in microcosm experiments. Two different flagellate species of the genus Cercomonas, the testate amoeba Cryptodifflugia operculata and four genera of naked amoebae (Acanthamoeba sp., Leptomyxa sp., two Mayorella spp. and Thecamoeba spp.) fed and grew on yeasts with four taxa (Cercomonas sp., Leptomyxa sp., Mayorella sp., and Thecamoeba sp.) also thriving on spores of the plant pathogenic hyphal-forming fungus Fusarium culmorum.

To identify the potential importance of mycophagous protists in the environment we applied a data-mining approach targeting small subunit (SSU) rRNA data obtained in metatranscriptomes of five fundamentally different terrestrial samples. We focused our analyses on the distribution and relative abundances of two well-studied mycophagous protist groups, vampyrellid amoebae and grossglockneriid ciliates. Both groups were detected in all of the highly contrasting terrestrial samples, comprising up to 3% of all protist SSU rRNA transcripts. SSU transcripts of these two groups, in contrast to all remaining protist SSU transcripts, showed strong correlations with the relative abundance of fungal sequences indicating close direct trophic interactions.

Taken together, this study provides evidence that mycophagy among soil protists is common and might be of substantial but hitherto overlooked ecological importance in terrestrial ecosystems. Future studies should aim at evaluating taxon-specific (facultative) mycophagy, decipher changes caused in the fungal community and quantitatively evaluate the functional importance of this trophic position in soil ecosystems.
Metatranscriptomic census of active protists in soils
Geisen, Stefan ; Tveit, A.T. ; Clark, I.M. ; Richter, A. ; Svenning, M. ; Bonkowski, M. ; Urich, T. - \ 2015
ISME Journal 9 (2015). - ISSN 1751-7362 - p. 2178 - 2190.
The high numbers and diversity of protists in soil systems have long been presumed, but their true diversity and community composition have remained largely concealed. Traditional cultivation-based methods miss a majority of taxa, whereas molecular barcoding approaches employing PCR introduce significant biases in reported community composition of soil protists. Here, we applied a metatranscriptomic approach to assess the protist community in 12 mineral and organic soil samples from different vegetation types and climatic zones using small subunit ribosomal RNA transcripts as marker. We detected a broad diversity of soil protists spanning across all known eukaryotic supergroups and revealed a strikingly different community composition than shown before. Protist communities differed strongly between sites, with Rhizaria and Amoebozoa dominating in forest and grassland soils, while Alveolata were most abundant in peat soils. The Amoebozoa were comprised of Tubulinea, followed with decreasing abundance by Discosea, Variosea and Mycetozoa. Transcripts of Oomycetes, Apicomplexa and Ichthyosporea suggest soil as reservoir of parasitic protist taxa. Further, Foraminifera and Choanoflagellida were ubiquitously detected, showing that these typically marine and freshwater protists are autochthonous members of the soil microbiota. To the best of our knowledge, this metatranscriptomic study provides the most comprehensive picture of active protist communities in soils to date, which is essential to target the ecological roles of protists in the complex soil system.
Pack hunting by a common soil amoeba on nematodes
Geisen, Stefan ; Rosengarten, J. ; Koller, R. ; Mulder, Christian ; Urich, T. ; Bonkowski, M. - \ 2015
Environmental Microbiology 17 (2015)11. - ISSN 1462-2912 - p. 4538 - 4546.
Soils host the most complex communities on Earth,
including the most diverse and abundant eukaryotes,
i.e. heterotrophic protists. Protists are generally con-
sidered as bacterivores, but evidence for negative
interactions with nematodes both from laboratory and
field studies exist. However, direct impacts of protists
on nematodes remain unknown. We isolated the soil-
borne testate amoeba
Cryptodifflugia operculata and
found a highly specialized and effective pack-hunting
strategy to prey on bacterivorous nematodes.
Enhanced reproduction in presence of prey nema-
todes suggests a beneficial predatory life history of
these omnivorous soil amoebae.
Cryptodifflugia
operculata appears to selectively impact the nema-
tode community composition as reductions of nema-
tode numbers were species specific. Furthermore, we
investigated 12 soil metatranscriptomes from five dis-
tinct locations throughout Europe for 18S ribosomal
RNA transcripts of C. operculata. The presence of
C. operculata transcripts in all samples, representing
up to 4% of the active protist community, indicates a
potential ecological importance of nematophagy per-
formed by
C. operculata in soil food webs. The unique
pack-hunting strategy on nematodes that was previously unknown from protists, together with molecular
evidence that these pack hunters are likely to be
abundant and widespread in soils, imply a consider-
able importance of the hitherto neglected trophic link
‘nematophagous protists’ in soil food webs

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