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ISME Journal

Lennart Kappelmann, Karen Krüger, Jan-Hendrik Hehemann, Jens Harder, Stephanie Markert, Frank Unfried, Dörte Becher, Nicole Shapiro, Thomas Schweder, Rudolf I Amann, Hanno Teeling
Marine algae convert a substantial fraction of fixed carbon dioxide into various polysaccharides. Flavobacteriia that are specialized on algal polysaccharide degradation feature genomic clusters termed polysaccharide utilization loci (PULs). As knowledge on extant PUL diversity is sparse, we sequenced the genomes of 53 North Sea Flavobacteriia and obtained 400 PULs. Bioinformatic PUL annotations suggest usage of a large array of polysaccharides, including laminarin, α-glucans, and alginate as well as mannose-, fucose-, and xylose-rich substrates...
August 15, 2018: ISME Journal
Alastair F Smith, Branko Rihtman, Rachel Stirrup, Eleonora Silvano, Michaela A Mausz, David J Scanlan, Yin Chen
Marine microorganisms employ multiple strategies to cope with transient and persistent nutrient limitation, one of which, for alleviating phosphorus (P) stress, is to substitute membrane glycerophospholipids with non-P containing surrogate lipids. Such a membrane lipid remodelling strategy enables the most abundant marine phytoplankton and heterotrophic bacteria to adapt successfully to nutrient scarcity in marine surface waters. An important group of non-P lipids, the aminolipids which lack a diacylglycerol backbone, are poorly studied in marine microbes...
August 14, 2018: ISME Journal
Amanda C Perofsky, Rebecca J Lewis, Lauren Ancel Meyers
The gut microbiomes of mammals appear to mirror their hosts' phylogeny, suggesting host-driven microbial community assembly. Yet, much of this evidence stems from comparative studies of distinct wild or captive populations that lack data for disentangling the relative influences of shared phylogeny and environment. Here, we present phylogenetic and multivariate analyses of gut microbiomes from six sympatric (i.e., co-occurring) mammal species inhabiting a 1-km2 area in western Madagascar-three lemur and three non-primate species-that consider genetic, dietary, and ecological predictors of microbiome functionality and composition...
August 14, 2018: ISME Journal
Subhendu Chakraborty, Marina Pančić, Ken H Andersen, Thomas Kiørboe
Many species of phytoplankton produce toxins that may provide protection from grazing. In that case one would expect toxin production to be costly; else all species would evolve toxicity. However, experiments have consistently failed to show any costs. Here, we show that costs of toxin production are environment dependent but can be high. We develop a fitness optimization model to estimate rate, costs, and benefits of toxin production, using PST (paralytic shellfish toxin) producing dinoflagellates as an example...
August 14, 2018: ISME Journal
Roland C Wilhelm
For the past 60 years Caulobacter spp. have been commonly attributed an aquatic and oligotrophic lifestyle yet are not uncommon in nutrient-rich or soil environments. This study evaluates the environmental and ecological associations of Caulobacter to reconcile past evidence, largely limited to culturing and microscopy, with currently available metagenomic and genomic data. The distribution of Caulobacter species and their characteristic adhesion-conferring genes, holdfast (hfaAB), were determined using collections of 10,641 16S rRNA gene libraries (196 studies) and 2625 shotgun metagenomes (190 studies) from a range of terrestrial and aquatic environments...
August 14, 2018: ISME Journal
Olivia Molenda, Shuiquan Tang, Line Lomheim, Vasu K Gautam, Sofia Lemak, Alexander F Yakunin, Karen L Maxwell, Elizabeth A Edwards
Dehalococcoides mccartyi are obligate organohalide-respiring bacteria that play an important detoxifying role in the environment. They have small genomes (~1.4 Mb) with a core region interrupted by two high plasticity regions (HPRs) containing dozens of genes encoding reductive dehalogenases involved in organohalide respiration. The genomes of eight new strains of D. mccartyi were closed from metagenomic data from a related set of enrichment cultures, bringing the total number of genomes to 24. Two of the newly sequenced strains and three previously sequenced strains contain CRISPR-Cas systems...
August 13, 2018: ISME Journal
Olga A Lastovetsky, Ezekiel Ahn, Stephen J Mondo, Kevin H Toomer, Aolin Zhang, Lynn M Johnson, Teresa E Pawlowska
Arbuscular mycorrhizal fungi (AMF, Glomeromycotina), in addition to forming symbioses with the majority of land plants, harbor vertically transmitted endosymbiotic bacteria 'Candidatus Glomeribacter gigasporarum' (CaGg) and 'Candidatus Moeniiplasma glomeromycotorum' (CaMg). CaGg is a nonessential mutualist of AMF, whereas the lifestyle of CaMg is unknown. To start unraveling the interactions between AMF and their endosymbionts in nature, we examined diversity and distribution of AMF-associated endobacteria in North Atlantic dunes at Cape Cod...
August 10, 2018: ISME Journal
Alvaro San Millan, Macarena Toll-Riera, Qin Qi, Alex Betts, Richard J Hopkinson, James McCullagh, R Craig MacLean
Horizontal gene transfer (HGT) mediated by the spread of plasmids fuels evolution in prokaryotes. Although plasmids provide bacteria with new adaptive genes, they also produce physiological alterations that often translate into a reduction in bacterial fitness. The fitness costs associated with plasmids represent an important limit to plasmid maintenance in bacterial communities, but their molecular origins remain largely unknown. In this work, we combine phenomics, transcriptomics and metabolomics to study the fitness effects produced by a collection of diverse plasmids in the opportunistic pathogen Pseudomonas aeruginosa PAO1...
August 10, 2018: ISME Journal
Rok Krašovec, Huw Richards, Danna R Gifford, Roman V Belavkin, Alastair Channon, Elizabeth Aston, Andrew J McBain, Christopher G Knight
Evolution depends on mutations. For an individual genotype, the rate at which mutations arise is known to increase with various stressors (stress-induced mutagenesis-SIM) and decrease at high final population density (density-associated mutation-rate plasticity-DAMP). We hypothesised that these two forms of mutation-rate plasticity would have opposing effects across a nutrient gradient. Here we test this hypothesis, culturing Escherichia coli in increasingly rich media. We distinguish an increase in mutation rate with added nutrients through SIM (dependent on error-prone polymerases Pol IV and Pol V) and an opposing effect of DAMP (dependent on MutT, which removes oxidised G nucleotides)...
August 7, 2018: ISME Journal
Jérôme Comte, Alexander I Culley, Connie Lovejoy, Warwick F Vincent
Aquatic ecosystems in the High Arctic are facing unprecedented changes as a result of global warming effects on the cryosphere. Snow pack is a central feature of northern landscapes, but the snow microbiome and its microbial connectivity to adjacent and downstream habitats have been little explored. To evaluate these aspects, we sampled along a hydrologic continuum at Ward Hunt Lake (latitude 83°N) in the Canadian High Arctic, from snow banks, water tracks in the permafrost catchment, the upper and lower strata of the lake, and the lake outlet and its coastal marine mixing zone...
August 7, 2018: ISME Journal
Maxime Bruto, Yannick Labreuche, Adèle James, Damien Piel, Sabine Chenivesse, Bruno Petton, Martin F Polz, Frédérique Le Roux
Diseases of marine animals caused by bacteria of the genus Vibrio are on the rise worldwide. Understanding the eco-evolutionary dynamics of these infectious agents is important for predicting and managing these diseases. Yet, compared to Vibrio infecting humans, knowledge of their role as animal pathogens is scarce. Here we ask how widespread is virulence among ecologically differentiated Vibrio populations, and what is the nature and frequency of virulence genes within these populations? We use a combination of population genomics and molecular genetics to assay hundreds of Vibrio strains for their virulence in the oyster Crassostrea gigas, a unique animal model that allows high-throughput infection assays...
August 2, 2018: ISME Journal
Miguel A Redondo, Johanna Boberg, Jan Stenlid, Jonàs Oliva
Diversity of microbial organisms is linked to global climatic gradients. The genus Phytophthora includes both aquatic and terrestrial plant pathogenic species that display a large variation of functional traits. The extent to which the physical environment (water or soil) modulates the interaction of microorganisms with climate is unknown. Here, we explored the main environmental drivers of diversity and functional trait composition of Phytophthora communities. Communities were obtained by a novel metabarcoding setup based on PacBio sequencing of river filtrates in 96 river sites along a geographical gradient...
August 2, 2018: ISME Journal
Emily C Hoedt, Donovan H Parks, James G Volmer, Carly P Rosewarne, Stuart E Denman, Christopher S McSweeney, Jane G Muir, Peter R Gibson, Páraic Ó Cuív, Philip Hugenholtz, Gene W Tyson, Mark Morrison
The genus Methanosphaera is a well-recognized but poorly characterized member of the mammalian gut microbiome, and distinctive from Methanobrevibacter smithii for its ability to induce a pro-inflammatory response in humans. Here we have used a combination of culture- and metagenomics-based approaches to expand the representation and information for the genus, which has supported the examination of their phylogeny and physiological capacity. Novel isolates of the genus Methanosphaera were recovered from bovine rumen digesta and human stool, with the bovine isolate remarkable for its large genome size relative to other Methanosphaera isolates from monogastric hosts...
August 1, 2018: ISME Journal
Lisa Sundqvist, Anna Godhe, Per R Jonsson, Josefin Sefbom
Understanding the genetic structure of populations is key to revealing past and present demographic and evolutionary processes in a species. In the past decade high genetic differentiation has been observed in many microbial species challenging the previous view of cosmopolitan distribution. Populations have displayed high genetic differentiation, even at small spatial scales, despite apparent high dispersal. Numerous species of microalgae have a life-history strategy that includes a long-term resting stage, which can accumulate in sediments and serve as refuge during adverse conditions...
August 1, 2018: ISME Journal
Takashi Yoshida, Yosuke Nishimura, Hiroyasu Watai, Nana Haruki, Daichi Morimoto, Hiroto Kaneko, Takashi Honda, Keigo Yamamoto, Pascal Hingamp, Yoshihiko Sako, Susumu Goto, Hiroyuki Ogata
The original version of this Article contained an error in the main text citations and reference list. These errors have now been corrected in both the PDF and HTML versions of the Article.
August 1, 2018: ISME Journal
Elisa T Granato, Christoph Ziegenhain, Rasmus L Marvig, Rolf Kümmerli
Bacterial opportunistic pathogens are feared for their difficult-to-treat nosocomial infections and for causing morbidity in immunocompromised patients. Here, we study how such a versatile opportunist, Pseudomonas aeruginosa, adapts to conditions inside and outside its model host Caenorhabditis elegans, and use phenotypic and genotypic screens to identify the mechanistic basis of virulence evolution. We found that virulence significantly dropped in unstructured environments both in the presence and absence of the host, but remained unchanged in spatially structured environments...
July 31, 2018: ISME Journal
Valentina Laclare McEneany, Michael J Coyne, Maria Chatzidaki-Livanis, Laurie E Comstock
The ability to antagonize competing strains and species is often important for bacterial fitness in microbial communities. The extent to which intra-species antagonism drives phenotypic diversity of bacterial species is rarely examined in a comprehensive manner at both the genetic and phenotypic levels. Here we show that for nine abundant human gut Bacteroides species examined, there are only a few LPS glycan genetic types. We show that for a given Bacteroides species, there is a predominant lipopolysaccharide (LPS) glycan locus present in the majority of strains...
July 31, 2018: ISME Journal
Frank Unfried, Stefan Becker, Craig S Robb, Jan-Hendrik Hehemann, Stephanie Markert, Stefan E Heiden, Tjorven Hinzke, Dörte Becher, Greta Reintjes, Karen Krüger, Burak Avcı, Lennart Kappelmann, Richard L Hahnke, Tanja Fischer, Jens Harder, Hanno Teeling, Bernhard Fuchs, Tristan Barbeyron, Rudolf I Amann, Thomas Schweder
Polysaccharide degradation by heterotrophic microbes is a key process within Earth's carbon cycle. Here, we use environmental proteomics and metagenomics in combination with cultivation experiments and biochemical characterizations to investigate the molecular details of in situ polysaccharide degradation mechanisms during microalgal blooms. For this, we use laminarin as a model polysaccharide. Laminarin is a ubiquitous marine storage polymer of marine microalgae and is particularly abundant during phytoplankton blooms...
July 30, 2018: ISME Journal
Wasimuddin, Stefan Dominik Brändel, Marco Tschapka, Rachel Page, Andrea Rasche, Victor M Corman, Christian Drosten, Simone Sommer
Astroviruses (AstV) are a major cause of diarrhoea in children. Interestingly, some wildlife species, including bats, remain phenotypically asymptomatic after infection. Disease symptoms, however, may only be less visible in bats and enteric viruses may indeed perturb their gut microbial communities. Gut microbiomes represent an important driver of immune defence mechanisms but potential effects of enteric virus-host microbiome interactions are largely unexplored. Using bats as a natural model system, we show that AstV-infections affect the gut microbiome, with the strength of the effect depending on host age...
July 30, 2018: ISME Journal
Andrew M Boddicker, Annika C Mosier
Nitrite-oxidizing bacteria (NOB) play a critical role in the mitigation of nitrogen pollution by metabolizing nitrite to nitrate, which is removed via assimilation, denitrification, or anammox. Recent studies showed that NOB are phylogenetically and metabolically diverse, yet most of our knowledge of NOB comes from only a few cultured representatives. Using cultivation and genomic sequencing, we identified four putative Candidatus Nitrotoga NOB species from freshwater sediments and water column samples in Colorado, USA...
July 26, 2018: ISME Journal
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