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ISME Journal

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https://www.readbyqxmd.com/read/28644444/energy-and-carbon-metabolisms-in-a-deep-terrestrial-subsurface-fluid-microbial-community
#1
Lily Momper, Sean P Jungbluth, Michael D Lee, Jan P Amend
The terrestrial deep subsurface is a huge repository of microbial biomass, but in relation to its size and physical heterogeneity, few sites have been investigated in detail. Here, we applied a culture-independent metagenomic approach to characterize the microbial community composition in deep (1500 meters below surface) terrestrial fluids. Samples were collected from a former gold mine in Lead, South Dakota, USA, now Sanford Underground Research Facility (SURF). We reconstructed 74 genomes from metagenomes (MAGs), enabling the identification of common metabolic pathways...
June 23, 2017: ISME Journal
https://www.readbyqxmd.com/read/28644443/unexpected-genomic-features-in-widespread-intracellular-bacteria-evidence-for-motility-of-marine-chlamydiae
#2
Astrid Collingro, Stephan Köstlbacher, Marc Mussmann, Ramunas Stepanauskas, Steven J Hallam, Matthias Horn
Chlamydiae are obligate intracellular bacteria comprising important human pathogens and symbionts of protists. Molecular evidence indicates a tremendous diversity of chlamydiae particularly in marine environments, yet our current knowledge is based mainly on terrestrial representatives. Here we provide first insights into the biology of marine chlamydiae representing three divergent clades. Our analysis of single-cell amplified genomes revealed hallmarks of the chlamydial lifestyle, supporting the ancient origin of their characteristic developmental cycle and major virulence mechanisms...
June 23, 2017: ISME Journal
https://www.readbyqxmd.com/read/28644442/linking-the-development-and-functioning-of-a-carnivorous-pitcher-plant-s-microbial-digestive-community
#3
David W Armitage
Ecosystem development theory predicts that successional turnover in community composition can influence ecosystem functioning. However, tests of this theory in natural systems are made difficult by a lack of replicable and tractable model systems. Using the microbial digestive associates of a carnivorous pitcher plant, I tested hypotheses linking host age-driven microbial community development to host functioning. Monitoring the yearlong development of independent microbial digestive communities in two pitcher plant populations revealed a number of trends in community succession matching theoretical predictions...
June 23, 2017: ISME Journal
https://www.readbyqxmd.com/read/28622287/a-niche-for-cyanobacteria-producing-chlorophyll-f-within-a-microbial-mat
#4
Satoshi Ohkubo, Hideaki Miyashita
Acquisition of additional photosynthetic pigments enables photosynthetic organisms to survive in particular niches. To reveal the ecological significance of chlorophyll (Chl) f, we investigated the distribution of Chl and cyanobacteria within two microbial mats. In a 7-mm-thick microbial mat beneath the running water of the Nakabusa hot spring, Japan, Chl f was only distributed 4.0-6.5 mm below the surface, where the intensity of far-red light (FR) was higher than that of photosynthetically active radiation (PAR)...
June 16, 2017: ISME Journal
https://www.readbyqxmd.com/read/28585941/ubiquity-and-quantitative-significance-of-bacterioplankton-lineages-inhabiting-the-oxygenated-hypolimnion-of-deep-freshwater-lakes
#5
Yusuke Okazaki, Shohei Fujinaga, Atsushi Tanaka, Ayato Kohzu, Hideo Oyagi, Shin-Ichi Nakano
The oxygenated hypolimnion accounts for a volumetrically significant part of the global freshwater systems. Previous studies have proposed the presence of hypolimnion-specific bacterioplankton lineages that are distinct from those inhabiting the epilimnion. To date, however, no consensus exists regarding their ubiquity and abundance, which is necessary to evaluate their ecological importance. The present study investigated the bacterioplankton community in the oxygenated hypolimnia of 10 deep freshwater lakes...
June 6, 2017: ISME Journal
https://www.readbyqxmd.com/read/28585940/identifying-the-core-seed-bank-of-a-complex-boreal-bacterial-metacommunity
#6
Clara Ruiz-González, Juan Pablo Niño-García, Steven W Kembel, Paul A Del Giorgio
Seed banks are believed to contribute to compositional changes within and across microbial assemblages, but the application of this concept to natural communities remains challenging. Here we describe the core seed bank of a bacterial metacommunity from a boreal watershed, using the spatial distribution of bacterial operational taxonomic units (OTUs) across 223 heterogeneous terrestrial, aquatic and phyllosphere bacterial assemblages. Taxa were considered potential seeds if they transitioned from rare to abundant somewhere within the metacommunity and if they were ubiquitous and able to persist under unfavorable conditions, the latter assessed by checking their presence in three deeply sequenced samples (one soil, one river and one lake, 2...
June 6, 2017: ISME Journal
https://www.readbyqxmd.com/read/28585939/linking-rhizosphere-microbiome-composition-of-wild-and-domesticated-phaseolus-vulgaris-to-genotypic-and-root-phenotypic-traits
#7
Juan E Pérez-Jaramillo, Víctor J Carrión, Mirte Bosse, Luiz F V Ferrão, Mattias de Hollander, Antonio A F Garcia, Camilo A Ramírez, Rodrigo Mendes, Jos M Raaijmakers
Plant domestication was a pivotal accomplishment in human history, but also led to a reduction in genetic diversity of crop species compared to their wild ancestors. How this reduced genetic diversity affected plant-microbe interactions belowground is largely unknown. Here, we investigated the genetic relatedness, root phenotypic traits and rhizobacterial community composition of modern and wild accessions of common bean (Phaseolus vulgaris) grown in agricultural soil from the highlands of Colombia, one of the centers of common bean diversification...
June 6, 2017: ISME Journal
https://www.readbyqxmd.com/read/28585938/genomics-and-metagenomics-of-trimethylamine-utilizing-archaea-in-the-human-gut-microbiome
#8
Guillaume Borrel, Angela McCann, Jennifer Deane, Marta C Neto, Denise B Lynch, Jean-François Brugère, Paul W O'Toole
The biological significance of Archaea in the human gut microbiota is largely unclear. We recently reported genomic and biochemical analyses of the Methanomassiliicoccales, a novel order of methanogenic Archaea dwelling in soil and the animal digestive tract. We now show that these Methanomassiliicoccales are present in published microbiome data sets from eight countries. They are represented by five Operational Taxonomic Units present in at least four cohorts and phylogenetically distributed into two clades...
June 6, 2017: ISME Journal
https://www.readbyqxmd.com/read/28585937/nitrogen-cost-minimization-is-promoted-by-structural-changes-in-the-transcriptome-of-n-deprived-prochlorococcus-cells
#9
Robert W Read, Paul M Berube, Steven J Biller, Iva Neveux, Andres Cubillos-Ruiz, Sallie W Chisholm, Joseph J Grzymski
Prochlorococcus is a globally abundant marine cyanobacterium with many adaptations that reduce cellular nutrient requirements, facilitating growth in its nutrient-poor environment. One such genomic adaptation is the preferential utilization of amino acids containing fewer N-atoms, which minimizes cellular nitrogen requirements. We predicted that transcriptional regulation might further reduce cellular N budgets during transient N limitation. To explore this, we compared transcription start sites (TSSs) in Prochlorococcus MED4 under N-deprived and N-replete conditions...
June 6, 2017: ISME Journal
https://www.readbyqxmd.com/read/28585936/letting-go-bacterial-genome-reduction-solves-the-dilemma-of-adapting-to-predation-mortality-in-a-substrate-restricted-environment
#10
Michael Baumgartner, Stefan Roffler, Thomas Wicker, Jakob Pernthaler
Resource limitation and predation mortality are major determinants of microbial population dynamics, and optimization for either aspect is considered to imply a trade-off with respect to the other. Adaptation to these selective factors may, moreover, lead to disadvantages at rich growth conditions. We present an example of a concomitant evolutionary optimization to both, substrate limitation and predation in an aggregate-forming freshwater bacterial isolate, and we elucidate an underlying genomic mechanism...
June 6, 2017: ISME Journal
https://www.readbyqxmd.com/read/28585935/shifts-in-rhizosphere-fungal-community-during-secondary-succession-following-abandonment-from-agriculture
#11
S Emilia Hannula, Elly Morriën, Mattias de Hollander, Wim H van der Putten, Johannes A van Veen, Wietse de Boer
Activities of rhizosphere microbes are key to the functioning of terrestrial ecosystems. It is commonly believed that bacteria are the major consumers of root exudates and that the role of fungi in the rhizosphere is mostly limited to plant-associated taxa, such as mycorrhizal fungi, pathogens and endophytes, whereas less is known about the role of saprotrophs. In order to test the hypothesis that the role of saprotrophic fungi in rhizosphere processes increases with increased time after abandonment from agriculture, we determined the composition of fungi that are active in the rhizosphere along a chronosequence of ex-arable fields in the Netherlands...
June 6, 2017: ISME Journal
https://www.readbyqxmd.com/read/28585934/crenothrix-are-major-methane-consumers-in-stratified-lakes
#12
Kirsten Oswald, Jon S Graf, Sten Littmann, Daniela Tienken, Andreas Brand, Bernhard Wehrli, Mads Albertsen, Holger Daims, Michael Wagner, Marcel Mm Kuypers, Carsten J Schubert, Jana Milucka
Methane-oxidizing bacteria represent a major biological sink for methane and are thus Earth's natural protection against this potent greenhouse gas. Here we show that in two stratified freshwater lakes a substantial part of upward-diffusing methane was oxidized by filamentous gamma-proteobacteria related to Crenothrix polyspora. These filamentous bacteria have been known as contaminants of drinking water supplies since 1870, but their role in the environmental methane removal has remained unclear. While oxidizing methane, these organisms were assigned an 'unusual' methane monooxygenase (MMO), which was only distantly related to 'classical' MMO of gamma-proteobacterial methanotrophs...
June 6, 2017: ISME Journal
https://www.readbyqxmd.com/read/28574490/capturing-the-genetic-makeup-of-the-active-microbiome-in-situ
#13
Esther Singer, Michael Wagner, Tanja Woyke
More than any other technology, nucleic acid sequencing has enabled microbial ecology studies to be complemented with the data volumes necessary to capture the extent of microbial diversity and dynamics in a wide range of environments. In order to truly understand and predict environmental processes, however, the distinction between active, inactive and dead microbial cells is critical. Also, experimental designs need to be sensitive toward varying population complexity and activity, and temporal as well as spatial scales of process rates...
June 2, 2017: ISME Journal
https://www.readbyqxmd.com/read/28548661/co-evolution-with-staphylococcus-aureus-leads-to-lipopolysaccharide-alterations-in-pseudomonas-aeruginosa
#14
Mikael Tognon, Thilo Köhler, Bartosz G Gdaniec, Youai Hao, Joseph S Lam, Marie Beaume, Alexandre Luscher, Angus Buckling, Christian van Delden
Detrimental and beneficial interactions between co-colonizing bacteria may influence the course of infections. In cystic fibrosis (CF) airways, Staphylococcus aureus prevails in childhood, whereas Pseudomonas aeruginosa progressively predominates thereafter. While a range of interactions has been identified, it is unclear if these represent specific adaptations or correlated responses to other aspects of the environment. Here, we investigate how P. aeruginosa adapts to S. aureus by evolving P. aeruginosa in the presence and absence of S...
May 26, 2017: ISME Journal
https://www.readbyqxmd.com/read/28548660/transcriptomic-and-micrornaomic-profiling-reveals-multi-faceted-mechanisms-to-cope-with-phosphate-stress-in-a-dinoflagellate
#15
Xinguo Shi, Xin Lin, Ling Li, Meizhen Li, Brian Palenik, Senjie Lin
Although gene regulation can occur at both transcriptional and epigenetic (microRNA) levels, combined transcriptomic and microRNAomic responses to environmental stress are still largely unexplored for marine plankton. Here, we conducted transcriptome and microRNAome sequencing for Prorocentrum donghaiense to understand the molecular mechanisms by which this dinoflagellate copes with phosphorus (P) deficiency. Under P-depleted conditions, G1/S specific cyclin gene was markedly downregulated, consistent with growth inhibition, and genes related to dissolved organic phosphorus (DOP) hydrolysis, carbon fixation, nitrate assimilation, glycolysis, and cellular motility were upregulated...
May 26, 2017: ISME Journal
https://www.readbyqxmd.com/read/28548659/metatranscriptomic-analysis-of-prokaryotic-communities-active-in-sulfur-and-arsenic-cycling-in-mono-lake-california-usa
#16
Christian F Edwardson, James T Hollibaugh
This study evaluates the transcriptionally active, dissimilatory sulfur- and arsenic-cycling components of the microbial community in alkaline, hypersaline Mono Lake, CA, USA. We sampled five depths spanning the redox gradient (10, 15, 18, 25 and 31 m) during maximum thermal stratification. We used custom databases to identify transcripts of genes encoding complex iron-sulfur molybdoenzyme (CISM) proteins, with a focus on arsenic (arrA, aioA and arxA) and sulfur cycling (dsrA, aprA and soxB), and assigned them to taxonomic bins...
May 26, 2017: ISME Journal
https://www.readbyqxmd.com/read/28548658/distinctive-microbiomes-and-metabolites-linked-with-weight-loss-after-gastric-bypass-but-not-gastric-banding
#17
Zehra Esra Ilhan, John K DiBaise, Nancy G Isern, David W Hoyt, Andrew K Marcus, Dae-Wook Kang, Michael D Crowell, Bruce E Rittmann, Rosa Krajmalnik-Brown
Roux-en-Y gastric bypass (RYGB) and laparoscopic adjustable gastric banding (LAGB) are anatomically different bariatric operations. RYGB achieves greater weight loss compared with LAGB. Changes in the gut microbiome have been documented after RYGB, but not LAGB, and the microbial contribution to sustainable surgical weight loss warrants further evaluation. We hypothesized that RYGB imposes greater changes on the microbiota and its metabolism than LAGB, and that the altered microbiota may contribute to greater weight loss...
May 26, 2017: ISME Journal
https://www.readbyqxmd.com/read/28548657/the-endobacterium-of-an-arbuscular-mycorrhizal-fungus-modulates-the-expression-of-its-toxin-antitoxin-systems-during-the-life-cycle-of-its-host
#18
Alessandra Salvioli di Fossalunga, Justine Lipuma, Francesco Venice, Laurence Dupont, Paola Bonfante
Arbuscular mycorrhizal fungi (AMF) are widespread root symbionts that perform important ecological services, such as improving plant nutrient and water acquisition. Some AMF from the Gigasporaceae family host a population of endobacteria, Candidatus Glomeribacter gigasporarum (Cagg). The analysis of the Cagg genome identified six putative toxin-antitoxin modules (TAs), consisting of pairs of stable toxins and unstable antitoxins that affect diverse physiological functions. Sequence analysis suggested that these TA modules were acquired by horizontal transfer...
May 26, 2017: ISME Journal
https://www.readbyqxmd.com/read/28534880/a-tale-of-two-risks-smoking-diabetes-and-the-subgingival-microbiome
#19
Sukirth M Ganesan, Vinayak Joshi, Megan Fellows, Shareef M Dabdoub, Haikady N Nagaraja, Benjamin O'Donnell, Neeta Rohit Deshpande, Purnima S Kumar
Although smoking and diabetes have been established as the only two risk factors for periodontitis, their individual and synergistic impacts on the periodontal microbiome are not well studied. The present investigation analyzed 2.7 million 16S sequences from 175 non-smoking normoglycemic individuals (controls), smokers, diabetics and diabetic smokers with periodontitis as well as periodontally healthy controls, smokers and diabetics to assess subgingival bacterial biodiversity and co-occurrence patterns. The microbial signatures of periodontally healthy smokers, but not diabetics, were highly aligned with the disease-associated microbiomes of their respective cohorts...
May 23, 2017: ISME Journal
https://www.readbyqxmd.com/read/28534879/epibionts-dominate-metabolic-functional-potential-of-trichodesmium-colonies-from-the-oligotrophic-ocean
#20
Kyle R Frischkorn, Mónica Rouco, Benjamin A S Van Mooy, Sonya T Dyhrman
Trichodesmium is a genus of marine diazotrophic colonial cyanobacteria that exerts a profound influence on global biogeochemistry, by injecting 'new' nitrogen into the low nutrient systems where it occurs. Colonies of Trichodesmium ubiquitously contain a diverse assemblage of epibiotic microorganisms, constituting a microbiome on the Trichodesmium host. Metagenome sequences from Trichodesmium colonies were analyzed along a resource gradient in the western North Atlantic to examine microbiome community structure, functional diversity and metabolic contributions to the holobiont...
May 23, 2017: ISME Journal
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