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ISME Journal

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https://www.readbyqxmd.com/read/27922602/elevated-temperature-increases-carbon-and-nitrogen-fluxes-between-phytoplankton-and-heterotrophic-bacteria-through-physical-attachment
#1
Nestor Arandia-Gorostidi, Peter K Weber, Laura Alonso-Sáez, Xosé Anxelu G Morán, Xavier Mayali
Quantifying the contribution of marine microorganisms to carbon and nitrogen cycles and their response to predicted ocean warming is one of the main challenges of microbial oceanography. Here we present a single-cell NanoSIMS isotope analysis to quantify C and N uptake by free-living and attached phytoplankton and heterotrophic bacteria, and their response to short-term experimental warming of 4 °C. Elevated temperature increased total C fixation by over 50%, a small but significant fraction of which was transferred to heterotrophs within 12 h...
December 6, 2016: ISME Journal
https://www.readbyqxmd.com/read/27922601/the-effect-of-extrinsic-mortality-on-genome-size-evolution-in-prokaryotes
#2
Piotr Bentkowski, Cock van Oosterhout, Ben Ashby, Thomas Mock
Mortality has a significant role in prokaryotic ecology and evolution, yet the impact of variations in extrinsic mortality on prokaryotic genome evolution has received little attention. We used both mathematical and agent-based models to reveal how variations in extrinsic mortality affect prokaryotic genome evolution. Our results suggest that the genome size of bacteria increases with increased mortality. A high extrinsic mortality increases the pool of free resources and shortens life expectancy, which selects for faster reproduction, a phenotype we called 'scramblers'...
December 6, 2016: ISME Journal
https://www.readbyqxmd.com/read/27922600/vibrio-crassostreae-a-benign-oyster-colonizer-turned-into-a-pathogen-after-plasmid-acquisition
#3
Maxime Bruto, Adèle James, Bruno Petton, Yannick Labreuche, Sabine Chenivesse, Marianne Alunno-Bruscia, Martin F Polz, Frédérique Le Roux
Vibrios are frequently associated with oyster mortality; however whether they are the primary causative agent or secondary opportunistic colonizers is not well understood. Here we combine analysis of natural infection dynamics, population genomics and molecular genetics to ask (i) to what extent oysters are passively colonized by Vibrio population present in the surrounding water, (ii) how populations turn over during pathogenicity events and (iii) what genetic factors are responsible for pathogenicity. We identified several populations of Vibrio preferentially associated with oyster tissues...
December 6, 2016: ISME Journal
https://www.readbyqxmd.com/read/27922599/direct-single-cell-biomass-estimates-for-marine-bacteria-via-archimedes-principle
#4
Nathan Cermak, Jamie W Becker, Scott M Knudsen, Sallie W Chisholm, Scott R Manalis, Martin F Polz
Microbes are an essential component of marine food webs and biogeochemical cycles, and therefore precise estimates of their biomass are of significant value. Here, we measured single-cell biomass distributions of isolates from several numerically abundant marine bacterial groups, including Pelagibacter (SAR11), Prochlorococcus and Vibrio using a microfluidic mass sensor known as a suspended microchannel resonator (SMR). We show that the SMR can provide biomass (dry mass) measurements for cells spanning more than two orders of magnitude and that these estimates are consistent with other independent measures...
December 6, 2016: ISME Journal
https://www.readbyqxmd.com/read/27911440/the-prey-s-scent-volatile-organic-compound-mediated-interactions-between-soil-bacteria-and-their-protist-predators
#5
Kristin Schulz-Bohm, Stefan Geisen, E R Jasper Wubs, Chunxu Song, Wietse de Boer, Paolina Garbeva
Protists are major predators of bacteria in soils. However, it remains unknown how protists sense their prey in this highly complex environment. Here, we investigated whether volatile organic compounds (VOCs) of six phylogenetic distinct soil bacteria affect the performance of three different soil protists and how that relates to direct feeding interactions. We observed that most bacteria affected protist activity by VOCs. However, the response of protists to the VOCs was strongly dependent on both the bacterial and protist interacting partner...
December 2, 2016: ISME Journal
https://www.readbyqxmd.com/read/27911439/evidence-for-a-role-of-viruses-in-the-thermal-sensitivity-of-coral-photosymbionts
#6
Rachel Ashley Levin, Christian Robert Voolstra, Karen Dawn Weynberg, Madeleine Josephine Henriette van Oppen
Symbiodinium, the dinoflagellate photosymbiont of corals, is posited to become more susceptible to viral infections when heat-stressed. To investigate this hypothesis, we mined transcriptome data of a thermosensitive and a thermotolerant type C1 Symbiodinium population at ambient (27 °C) and elevated (32°C) temperatures. We uncovered hundreds of transcripts from nucleocytoplasmic large double-stranded DNA viruses (NCLDVs) and the genome of a novel positive-sense single-stranded RNA virus (+ssRNAV). In the transcriptome of the thermosensitive population only, +ssRNAV transcripts had remarkable expression levels in the top 0...
December 2, 2016: ISME Journal
https://www.readbyqxmd.com/read/27911438/evolutionary-convergence-in-experimental-pseudomonas-populations
#7
Peter A Lind, Andrew D Farr, Paul B Rainey
Model microbial systems provide opportunity to understand the genetic bases of ecological traits, their evolution, regulation and fitness contributions. Experimental populations of Pseudomonas fluorescens rapidly diverge in spatially structured microcosms producing a range of surface-colonising forms. Despite divergent molecular routes, wrinkly spreader (WS) niche specialist types overproduce a cellulosic polymer allowing mat formation at the air-liquid interface and access to oxygen. Given the range of ways by which cells can form mats, such phenotypic parallelism is unexpected...
December 2, 2016: ISME Journal
https://www.readbyqxmd.com/read/27898054/refined-experimental-annotation-reveals-conserved-corrinoid-autotrophy-in-chloroform-respiring-dehalobacter-isolates
#8
Po-Hsiang Wang, Shuiquan Tang, Kayla Nemr, Robert Flick, Jun Yan, Radhakrishnan Mahadevan, Alexander F Yakunin, Frank E Löffler, Elizabeth A Edwards
Two novel chlorinated alkane-respiring Dehalobacter restrictus strains CF and DCA were isolated from the same enrichment culture, ACT-3, and characterized. The closed genomes of these highly similar sister strains were previously assembled from metagenomic sequence data and annotated. The isolation of the strains enabled experimental verification of predicted annotations, particularly focusing on irregularities or predicted gaps in central metabolic pathways and cofactor biosynthesis. Similar to D. restrictus strain PER-K23, strains CF and DCA require arginine, histidine and threonine for growth, although the corresponding biosynthesis pathways are predicted to be functional...
November 29, 2016: ISME Journal
https://www.readbyqxmd.com/read/27898053/microbial-mutualism-dynamics-governed-by-dose-dependent-toxicity-of-cross-fed-nutrients
#9
Breah LaSarre, Alexandra L McCully, Jay T Lennon, James B McKinlay
Microbial interactions, including mutualistic nutrient exchange (cross-feeding), underpin the flow of energy and materials in all ecosystems. Metabolic exchanges are difficult to assess within natural systems. As such, the impact of exchange levels on ecosystem dynamics and function remains unclear. To assess how cross-feeding levels govern mutualism behavior, we developed a bacterial coculture amenable to both modeling and experimental manipulation. In this coculture, which resembles an anaerobic food web, fermentative Escherichia coli and photoheterotrophic Rhodopseudomonas palustris obligately cross-feed carbon (organic acids) and nitrogen (ammonium)...
November 29, 2016: ISME Journal
https://www.readbyqxmd.com/read/27898052/complex-n-acquisition-by-soil-diazotrophs-how-the-ability-to-release-exoenzymes-affects-n-fixation-by-terrestrial-free-living-diazotrophs
#10
Jeffrey S Norman, Maren L Friesen
Terrestrial systems support a variety of free-living soil diazotrophs, which can fix nitrogen (N) outside of plant associations. However, owing to the metabolic costs associated with N fixation, free-living soil diazotrophs likely rely on soil N to satisfy the majority of cellular N demand and only fix atmospheric N under certain conditions. Culture-based studies and genomic data show that many free-living soil diazotrophs can access high-molecular weight organic soil N by releasing N-acquiring enzymes such as proteases and chitinases into the extracellular environment...
November 29, 2016: ISME Journal
https://www.readbyqxmd.com/read/27858931/tick-microbiome-and-pathogen-acquisition-altered-by-host-blood-meal
#11
Andrea Swei, Jessica Y Kwan
Lyme disease, a zoonotic disease, is the most prevalent vector-borne disease in the Northern Hemisphere. Diversity of the vector (tick) microbiome can impact pathogen transmission, yet the biotic and abiotic factors that drive microbiome diversity are largely unresolved, especially under natural, field conditions. We describe the microbiome of Ixodes pacificus ticks, the vector for Lyme disease in the western United States, and show a strong impact of host blood meal identity on tick microbiome species richness and composition...
November 18, 2016: ISME Journal
https://www.readbyqxmd.com/read/27858930/environmental-spread-of-microbes-impacts-the-development-of-metabolic-phenotypes-in-mice-transplanted-with-microbial-communities-from-humans
#12
Li Zhang, Martin Iain Bahl, Henrik Munch Roager, Cilius Esmann Fonvig, Lars I Hellgren, Henrik Lauritz Frandsen, Oluf Pedersen, Jens-Christian Holm, Torben Hansen, Tine Rask Licht
Microbiota transplantation to germ-free animals is a powerful method to study involvement of gut microbes in the aetiology of metabolic syndrome. Owing to large interpersonal variability in gut microbiota, studies with broad coverage of donors are needed to elucidate the establishment of human-derived microbiotas in mice, factors affecting this process and resulting impact on metabolic health. We thus transplanted faecal microbiotas from humans (16 obese and 16 controls) separately into 64 germ-free Swiss Webster mice caged in pairs within four isolators, with two isolators assigned to each phenotype, thereby allowing us to explore the extent of microbial spread between cages in a well-controlled environment...
November 18, 2016: ISME Journal
https://www.readbyqxmd.com/read/27834945/assessment-of-the-bimodality-in-the-distribution-of-bacterial-genome-sizes
#13
Hyun S Gweon, Mark J Bailey, Daniel S Read
Bacterial genome sizes have previously been shown to exhibit a bimodal distribution. This phenomenon has prompted discussion regarding the evolutionary forces driving genome size in bacteria and its ecological significance. We investigated the level of inherent redundancy in the public database and the effect it has on the shape of the apparent bimodal distribution. Our study reveals that there is a significant bias in the genome sequencing efforts towards a certain group of species, and that correcting the bias using species nomenclature and clustering of the 16S rRNA gene, results in a unimodal rather than the previously published bimodal distribution...
November 11, 2016: ISME Journal
https://www.readbyqxmd.com/read/27824344/catch-me-if-you-can-dispersal-and-foraging-of-bdellovibrio-bacteriovorus-109j-along-mycelia
#14
Sally Otto, Estelle P Bruni, Hauke Harms, Lukas Y Wick
To cope with heterogeneous environments and resource distributions, filamentous fungi have evolved a spatially extensive growth enabling their hyphae to penetrate air-water interfaces and pass through air-filled pores. Such mycelia are also known to act as dispersal networks for the mobilisation of bacteria ('fungal highways') and connection of microbial microhabitats. Hitherto, however, nothing is known about the effect of mycelia-based dispersal on interactions between bacterial predators and their prey and concomitant effects on biomass formation...
November 8, 2016: ISME Journal
https://www.readbyqxmd.com/read/27824343/membrane-vesicles-in-sea-water-heterogeneous-dna-content-and-implications-for-viral-abundance-estimates
#15
Steven J Biller, Lauren D McDaniel, Mya Breitbart, Everett Rogers, John H Paul, Sallie W Chisholm
Diverse microbes release membrane-bound extracellular vesicles from their outer surfaces into the surrounding environment. Vesicles are found in numerous habitats including the oceans, where they likely have a variety of functional roles in microbial ecosystems. Extracellular vesicles are known to contain a range of biomolecules including DNA, but the frequency with which DNA is packaged in vesicles is unknown. Here, we examine the quantity and distribution of DNA associated with vesicles released from five different bacteria...
November 8, 2016: ISME Journal
https://www.readbyqxmd.com/read/27824342/systems-level-metabolism-of-the-altered-schaedler-flora-a-complete-gut-microbiota
#16
Matthew B Biggs, Gregory L Medlock, Thomas J Moutinho, Hannah J Lees, Jonathan R Swann, Glynis L Kolling, Jason A Papin
The altered Schaedler flora (ASF) is a model microbial community with both in vivo and in vitro relevance. Here we provide the first characterization of the ASF community in vitro, independent of a murine host. We compared the functional genetic content of the ASF to wild murine metagenomes and found that the ASF functionally represents wild microbiomes better than random consortia of similar taxonomic composition. We developed a chemically defined medium that supported growth of seven of the eight ASF members...
November 8, 2016: ISME Journal
https://www.readbyqxmd.com/read/27824341/critical-decisions-in-metaproteomics-achieving-high-confidence-protein-annotations-in-a-sea-of-unknowns
#17
Emma Timmins-Schiffman, Damon H May, Molly Mikan, Michael Riffle, Chris Frazar, H R Harvey, William S Noble, Brook L Nunn
No abstract text is available yet for this article.
November 8, 2016: ISME Journal
https://www.readbyqxmd.com/read/27801910/trade-offs-between-microbiome-diversity-and-productivity-in-a-stratified-microbial-mat
#18
Hans C Bernstein, Colin Brislawn, Ryan S Renslow, Karl Dana, Beau Morton, Stephen R Lindemann, Hyun-Seob Song, Erhan Atci, Haluk Beyenal, James K Fredrickson, Janet K Jansson, James J Moran
Productivity is a major determinant of ecosystem diversity. Microbial ecosystems are the most diverse on the planet yet very few relationships between diversity and productivity have been reported as compared with macro-ecological studies. Here we evaluated the spatial relationships of productivity and microbiome diversity in a laboratory-cultivated photosynthetic mat. The goal was to determine how spatial diversification of microorganisms drives localized carbon and energy acquisition rates. We measured sub-millimeter depth profiles of net primary productivity and gross oxygenic photosynthesis in the context of the localized microenvironment and community structure, and observed negative correlations between species richness and productivity within the energy-replete, photic zone...
November 1, 2016: ISME Journal
https://www.readbyqxmd.com/read/27801909/genome-of-ca-desulfovibrio-trichonymphae-an-h2-oxidizing-bacterium-in-a-tripartite-symbiotic-system-within-a-protist-cell-in-the-termite-gut
#19
Hirokazu Kuwahara, Masahiro Yuki, Kazuki Izawa, Moriya Ohkuma, Yuichi Hongoh
The cellulolytic protist Trichonympha agilis in the termite gut permanently hosts two symbiotic bacteria, 'Candidatus Endomicrobium trichonymphae' and 'Candidatus Desulfovibrio trichonymphae'. The former is an intracellular symbiont, and the latter is almost intracellular but still connected to the outside via a small pore. The complete genome of 'Ca. Endomicrobium trichonymphae' has previously been reported, and we here present the complete genome of 'Ca. Desulfovibrio trichonymphae'. The genome is small (1 410 056 bp), has many pseudogenes, and retains biosynthetic pathways for various amino acids and cofactors, which are partially complementary to those of 'Ca...
November 1, 2016: ISME Journal
https://www.readbyqxmd.com/read/27801908/metabolic-and-physiological-interdependencies-in-the-bathymodiolus-azoricus-symbiosis
#20
Ruby Ponnudurai, Manuel Kleiner, Lizbeth Sayavedra, Jillian M Petersen, Martin Moche, Andreas Otto, Dörte Becher, Takeshi Takeuchi, Noriyuki Satoh, Nicole Dubilier, Thomas Schweder, Stephanie Markert
The hydrothermal vent mussel Bathymodiolus azoricus lives in an intimate symbiosis with two types of chemosynthetic Gammaproteobacteria in its gills: a sulfur oxidizer and a methane oxidizer. Despite numerous investigations over the last decades, the degree of interdependence between the three symbiotic partners, their individual metabolic contributions, as well as the mechanism of carbon transfer from the symbionts to the host are poorly understood. We used a combination of proteomics and genomics to investigate the physiology and metabolism of the individual symbiotic partners...
November 1, 2016: ISME Journal
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