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ISME Journal

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https://www.readbyqxmd.com/read/28338677/integrated-metabolism-in-sponge-microbe-symbiosis-revealed-by-genome-centered-metatranscriptomics
#1
Lucas Moitinho-Silva, Cristina Díez-Vives, Giampiero Batani, Ana Is Esteves, Martin T Jahn, Torsten Thomas
Despite an increased understanding of functions in sponge microbiomes, the interactions among the symbionts and between symbionts and host are not well characterized. Here we reconstructed the metabolic interactions within the sponge Cymbastela concentrica microbiome in the context of functional features of symbiotic diatoms and the host. Three genome bins (CcPhy, CcNi and CcThau) were recovered from metagenomic data of C. concentrica, belonging to the proteobacterial family Phyllobacteriaceae, the Nitrospira genus and the thaumarchaeal order Nitrosopumilales...
March 24, 2017: ISME Journal
https://www.readbyqxmd.com/read/28338676/dirhamnolipids-secreted-from-pseudomonas-aeruginosa-modify-anjpegungal-susceptibility-of-aspergillus-fumigatus-by-inhibiting-%C3%AE-1-3-glucan-synthase-activity
#2
Benoit Briard, Vero Rasoldier, Perrine Bomme, Noureddine ElAouad, Catherine Guerreiro, Pierre Chassagne, Laetitia Muszkieta, Jean-Paul Latgé, Laurence Mulard, Anne Beauvais
Pseudomonas aeruginosa and Aspergillus fumigatus are the two microorganisms responsible for most of the chronic infections in cystic fibrosis patients. P. aeruginosa is known to produce quorum-sensing controlled rhamnolipids during chronic infections. Here we show that the dirhamnolipids secreted from P. aeruginosa (i) induce A. fumigatus to produce an extracellular matrix, rich in galactosaminogalactan, 1,8-dihydroxynaphthalene (DHN)- and pyo-melanin, surrounding their hyphae, which facilitates P. aeruginosa binding and (ii) inhibit A...
March 24, 2017: ISME Journal
https://www.readbyqxmd.com/read/28338675/biogeography-and-diversity-of-collodaria-radiolaria-in-the-global-ocean
#3
Tristan Biard, Estelle Bigeard, Stéphane Audic, Julie Poulain, Andres Gutierrez-Rodriguez, Stéphane Pesant, Lars Stemmann, Fabrice Not
Collodaria are heterotrophic marine protists that exist either as large colonies composed of hundreds of cells or as large solitary cells. All described species so far harbour intracellular microalgae as photosymbionts. Although recent environmental diversity surveys based on molecular methods demonstrated their consistently high contribution to planktonic communities and their worldwide occurrence, our understanding of their diversity and biogeography is still very limited. Here we estimated the 18S ribosomal DNA (rDNA) gene copies per collodarian cell for solitary (5770±1960 small subunit (SSU) rDNA copies) and colonial specimens (37 474±17 799 SSU rDNA copies, for each individual cell within a colony) using single-specimen quantitative PCR...
March 24, 2017: ISME Journal
https://www.readbyqxmd.com/read/28338674/biofilm-formation-enables-free-living-nitrogen-fixing-rhizobacteria-to-fix-nitrogen-under-aerobic-conditions
#4
Di Wang, Anming Xu, Claudine Elmerich, Luyan Z Ma
The multicellular communities of microorganisms known as biofilms are of high significance in agricultural setting, yet it is largely unknown about the biofilm formed by nitrogen-fixing bacteria. Here we report the biofilm formation by Pseudomonas stutzeri A1501, a free-living rhizospheric bacterium, capable of fixing nitrogen under microaerobic and nitrogen-limiting conditions. P. stutzeri A1501 tended to form biofilm in minimal media, especially under nitrogen depletion condition. Under such growth condition, the biofilms formed at the air-liquid interface (termed as pellicles) and the colony biofilms on agar plates exhibited nitrogenase activity in air...
March 24, 2017: ISME Journal
https://www.readbyqxmd.com/read/28338673/environmental-fluctuation-governs-selection-for-plasticity-in-biofilm-production
#5
Jing Yan, Carey D Nadell, Bonnie L Bassler
Bacteria can grow in a free-swimming state, as planktonic cells, or in surface-attached communities, termed biofilms. The planktonic and biofilm growth modes differ dramatically with respect to spatial constraints, nutrient access, population density and cell-cell interactions. Fitness trade-offs underlie how successfully bacteria compete in each of these environments. Accordingly, some bacteria have evolved to be specialists in biofilm formation, while others specialize in planktonic growth. There are species, however, that possess flexible strategies: they can transition between the molecular programs required for biofilm formation and for planktonic growth...
March 24, 2017: ISME Journal
https://www.readbyqxmd.com/read/28323281/chance-and-necessity-in-the-genome-evolution-of-endosymbiotic-bacteria-of-insects
#6
Beatriz Sabater-Muñoz, Christina Toft, David Alvarez-Ponce, Mario A Fares
An open question in evolutionary biology is how does the selection-drift balance determine the fates of biological interactions. We searched for signatures of selection and drift in genomes of five endosymbiotic bacterial groups known to evolve under strong genetic drift. Although most genes in endosymbiotic bacteria showed evidence of relaxed purifying selection, many genes in these bacteria exhibited stronger selective constraints than their orthologs in free-living bacterial relatives. Remarkably, most of these highly constrained genes had no role in the host-symbiont interactions but were involved in either buffering the deleterious consequences of drift or other host-unrelated functions, suggesting that they have either acquired new roles or their role became more central in endosymbiotic bacteria...
March 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28323280/defining-the-functional-traits-that-drive-bacterial-decomposer-community-productivity
#7
Rachael Evans, Anna M Alessi, Susannah Bird, Simon J McQueen-Mason, Neil C Bruce, Michael A Brockhurst
Microbial communities are essential to a wide range of ecologically and industrially important processes. To control or predict how these communities function, we require a better understanding of the factors which influence microbial community productivity. Here, we combine functional resource use assays with a biodiversity-ecosystem functioning (BEF) experiment to determine whether the functional traits of constituent species can be used to predict community productivity. We quantified the abilities of 12 bacterial species to metabolise components of lignocellulose and then assembled these species into communities of varying diversity and composition to measure their productivity growing on lignocellulose, a complex natural substrate...
March 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28323279/spontaneous-mutations-of-a-model-heterotrophic-marine-bacterium
#8
Ying Sun, Kate E Powell, Way Sung, Michael Lynch, Mary Ann Moran, Haiwei Luo
Heterotrophic marine bacterioplankton populations display substantive genomic diversity that is commonly explained to be the result of selective forces imposed by resource limitation or interactions with phage and predators. Here we use a mutation-accumulation experiment followed by whole-genome sequencing of mutation lines to determine an unbiased rate and molecular spectrum of spontaneous mutations for a model heterotrophic marine bacterium in the globally important Roseobacter clade, Ruegeria pomeroyi DSS-3...
March 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28323278/acceptable-symbiont-cell-size-differs-among-cnidarian-species-and-may-limit-symbiont-diversity
#9
Elise Biquand, Nami Okubo, Yusuke Aihara, Vivien Rolland, David C Hayward, Masayuki Hatta, Jun Minagawa, Tadashi Maruyama, Shunichi Takahashi
Reef-building corals form symbiotic relationships with dinoflagellates of the genus Symbiodinium. Symbiodinium are genetically and physiologically diverse, and corals may be able to adapt to different environments by altering their dominant Symbiodinium phylotype. Notably, each coral species associates only with specific Symbiodinium phylotypes, and consequently the diversity of symbionts available to the host is limited by the species specificity. Currently, it is widely presumed that species specificity is determined by the combination of cell-surface molecules on the host and symbiont...
March 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28323277/an-alternative-polysaccharide-uptake-mechanism-of-marine-bacteria
#10
Greta Reintjes, Carol Arnosti, Bernhard M Fuchs, Rudolf Amann
Heterotrophic microbial communities process much of the carbon fixed by phytoplankton in the ocean, thus having a critical role in the global carbon cycle. A major fraction of the phytoplankton-derived substrates are high-molecular-weight (HMW) polysaccharides. For bacterial uptake, these substrates must initially be hydrolysed to smaller sizes by extracellular enzymes. We investigated polysaccharide hydrolysis by microbial communities during a transect of the Atlantic Ocean, and serendipitously discovered-using super-resolution structured illumination microscopy-that up to 26% of total cells showed uptake of fluorescently labelled polysaccharides (FLA-PS)...
March 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28304370/identification-of-dimethylamine-monooxygenase-in-marine-bacteria-reveals-a-metabolic-bottleneck-in-the-methylated-amine-degradation-pathway
#11
Ian Lidbury, Michaela A Mausz, David J Scanlan, Yin Chen
Methylated amines (MAs) are ubiquitous in the marine environment and their subsequent flux into the atmosphere can result in the formation of aerosols and ultimately cloud condensation nuclei. Therefore, these compounds have a potentially important role in climate regulation. Using Ruegeria pomeroyi as a model, we identified the genes encoding dimethylamine (DMA) monooxygenase (dmmABC) and demonstrate that this enzyme degrades DMA to monomethylamine (MMA). Although only dmmABC are required for enzyme activity in recombinant Escherichia coli, we found that an additional gene, dmmD, was required for the growth of R...
March 17, 2017: ISME Journal
https://www.readbyqxmd.com/read/28304369/the-role-of-adaptive-immunity-as-an-ecological-filter-on-the-gut-microbiota-in-zebrafish
#12
Keaton Stagaman, Adam R Burns, Karen Guillemin, Brendan Jm Bohannan
All animals live in intimate association with communities of microbes, collectively referred to as their microbiota. Certain host traits can influence which microbial taxa comprise the microbiota. One potentially important trait in vertebrate animals is the adaptive immune system, which has been hypothesized to act as an ecological filter, promoting the presence of some microbial taxa over others. Here we surveyed the intestinal microbiota of 68 wild-type zebrafish, with functional adaptive immunity, and 61 rag1(-) zebrafish, lacking functional B- and T-cell receptors, to test the role of adaptive immunity as an ecological filter on the intestinal microbiota...
March 17, 2017: ISME Journal
https://www.readbyqxmd.com/read/28291233/lysogeny-in-nature-mechanisms-impact-and-ecology-of-temperate-phages
#13
Cristina Howard-Varona, Katherine R Hargreaves, Stephen T Abedon, Matthew B Sullivan
Viruses that infect bacteria (phages) can influence bacterial community dynamics, bacterial genome evolution and ecosystem biogeochemistry. These influences differ depending on whether phages establish lytic, chronic or lysogenic infections. Although the first two produce virion progeny, with lytic infections resulting in cell destruction, phages undergoing lysogenic infections replicate with cells without producing virions. The impacts of lysogeny are numerous and well-studied at the cellular level, but ecosystem-level consequences remain underexplored compared to those of lytic infections...
March 14, 2017: ISME Journal
https://www.readbyqxmd.com/read/28282042/divergent-extremes-but-convergent-recovery-of-bacterial-and-archaeal-soil-communities-to-an-ongoing-subterranean-coal-mine-fire
#14
Sang-Hoon Lee, Jackson W Sorensen, Keara L Grady, Tammy C Tobin, Ashley Shade
Press disturbances are stressors that are extended or ongoing relative to the generation times of community members, and, due to their longevity, have the potential to alter communities beyond the possibility of recovery. They also provide key opportunities to investigate ecological resilience and to probe biological limits in the face of prolonged stressors. The underground coal mine fire in Centralia, Pennsylvania has been burning since 1962 and severely alters the overlying surface soils by elevating temperatures and depositing coal combustion pollutants...
March 10, 2017: ISME Journal
https://www.readbyqxmd.com/read/28282041/habitat-specific-patterns-and-drivers-of-bacterial-%C3%AE-diversity-in-china-s-drylands
#15
Xiao-Bo Wang, Xiao-Tao Lü, Jing Yao, Zheng-Wen Wang, Ye Deng, Wei-Xin Cheng, Ji-Zhong Zhou, Xing-Guo Han
The existence of biogeographic patterns among most free-living microbial taxa has been well established, yet little is known about the underlying mechanisms that shape these patterns. Here, we examined soil bacterial β-diversity across different habitats in the drylands of northern China. We evaluated the relative importance of environmental factors versus geographic distance to a distance-decay relationship, which would be explained by the relative effect of basic ecological processes recognized as drivers of diversity patterns in macrobial theoretical models such as selection and dispersal...
March 10, 2017: ISME Journal
https://www.readbyqxmd.com/read/28282040/impact-of-water-heater-temperature-setting-and-water-use-frequency-on-the-building-plumbing-microbiome
#16
Pan Ji, William J Rhoads, Marc A Edwards, Amy Pruden
Hot water plumbing is an important conduit of microbes into the indoor environment and can increase risk of opportunistic pathogens (for example, Legionella pneumophila). We examined the combined effects of water heater temperature (39, 42, 48, 51 and 58 °C), pipe orientation (upward/downward), and water use frequency (21, 3 and 1 flush per week) on the microbial composition at the tap using a pilot-scale pipe rig. 16S rRNA gene amplicon sequencing indicated that bulk water and corresponding biofilm typically had distinct taxonomic compositions (R(2)Adonis=0...
March 10, 2017: ISME Journal
https://www.readbyqxmd.com/read/28282039/membrane-vesicle-mediated-bacterial-communication
#17
Masanori Toyofuku, Kana Morinaga, Yohei Hashimoto, Jenny Uhl, Hiroko Shimamura, Hideki Inaba, Philippe Schmitt-Kopplin, Leo Eberl, Nobuhiko Nomura
The classical quorum-sensing (QS) model is based on the assumption that diffusible signaling molecules accumulate in the culture medium until they reach a critical concentration upon which expression of target genes is triggered. Here we demonstrate that the hydrophobic signal N-hexadecanoyl-L-homoserine lactone, which is produced by Paracoccus sp., is released from cells by the aid of membrane vesicles (MVs). Packed into MVs, the signal is not only solubilized in an aqueous environment but is also delivered with varying propensities to different bacteria...
March 10, 2017: ISME Journal
https://www.readbyqxmd.com/read/28267153/seasonal-patterns-in-arctic-prasinophytes-and-inferred-ecology-of-bathycoccus-unveiled-in-an-arctic-winter-metagenome
#18
Nathalie Joli, Adam Monier, Ramiro Logares, Connie Lovejoy
Prasinophytes occur in all oceans but rarely dominate phytoplankton populations. In contrast, a single ecotype of the prasinophyte Micromonas is frequently the most abundant photosynthetic taxon reported in the Arctic from summer through autumn. However, seasonal dynamics of prasinophytes outside of this period are little known. To address this, we analyzed high-throughput V4 18S rRNA amplicon data collected from November to July in the Amundsen Gulf Region, Beaufort Sea, Arctic. Surprisingly during polar sunset in November and December, we found a high proportion of reads from both DNA and RNA belonging to another prasinophyte, Bathycoccus...
March 7, 2017: ISME Journal
https://www.readbyqxmd.com/read/28244978/origin-and-fate-of-methane-in-the-eastern-tropical-north-pacific-oxygen-minimum-zone
#19
Panagiota-Myrsini Chronopoulou, Felicity Shelley, William J Pritchard, Susanna T Maanoja, Mark Trimmer
Oxygen minimum zones (OMZs) contain the largest pools of oceanic methane but its origin and fate are poorly understood. High-resolution (<15 m) water column profiles revealed a 300 m thick layer of elevated methane (20-105 nM) in the anoxic core of the largest OMZ, the Eastern Tropical North Pacific. Sediment core incubations identified a clear benthic methane source where the OMZ meets the continental shelf, between 350 and 650 m, with the flux reflecting the concentration of methane in the overlying anoxic water...
February 28, 2017: ISME Journal
https://www.readbyqxmd.com/read/28244977/linking-the-community-structure-of-arbuscular-mycorrhizal-fungi-and-plants-a-story-of-interdependence
#20
Sebastian Horn, Stefan Hempel, Erik Verbruggen, Matthias C Rillig, Tancredi Caruso
Arbuscular mycorrhizal fungi (AMF) are crucial to plants and vice versa, but little is known about the factors linking the community structure of the two groups. We investigated the association between AMF and the plant community structure in the nearest neighborhood of Festuca brevipila in a semiarid grassland with steep environmental gradients, using high-throughput sequencing of the Glomeromycotina (former Glomeromycota). We focused on the Passenger, Driver and Habitat hypotheses: (i) plant communities drive AMF (passenger); (ii) AMF communities drive the plants (driver); (iii) the environment shapes both communities causing covariation...
February 28, 2017: ISME Journal
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