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ISME Journal

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https://www.readbyqxmd.com/read/28820506/physiological-and-ecological-implications-of-an-iron-or-hydrogen-oxidizing-member-of-the-zetaproteobacteria-ghiorsea-bivora-gen-nov-sp-nov
#1
Jiro F Mori, Jarrod J Scott, Kevin W Hager, Craig L Moyer, Kirsten Küsel, David Emerson
Chemosynthetic Fe-oxidizing communities are common at diffuse-flow hydrothermal vents throughout the world's oceans. The foundational members of these communities are the Zetaproteobacteria, a class of Proteobacteria that is primarily associated with ecosystems fueled by ferrous iron, Fe(II). We report here the discovery of two new isolates of Zetaproteobacteria isolated from the Mid-Atlantic Ridge (TAG-1), and the Mariana back-arc (SV-108), that are unique in that they can utilize either Fe(II) or molecular hydrogen (H2) as sole electron donor and oxygen as terminal electron acceptor for growth...
August 18, 2017: ISME Journal
https://www.readbyqxmd.com/read/28809851/grape-pomace-compost-harbors-organohalide-respiring-dehalogenimonas-species-with-novel-reductive-dehalogenase-genes
#2
Yi Yang, Steven A Higgins, Jun Yan, Burcu Şimşir, Karuna Chourey, Ramsunder Iyer, Robert L Hettich, Brett Baldwin, Dora M Ogles, Frank E Löffler
Organohalide-respiring bacteria have key roles in the natural chlorine cycle; however, most of the current knowledge is based on cultures from contaminated environments. We demonstrate that grape pomace compost without prior exposure to chlorinated solvents harbors a Dehalogenimonas (Dhgm) species capable of using chlorinated ethenes, including the human carcinogen and common groundwater pollutant vinyl chloride (VC) as electron acceptors. Grape pomace microcosms and derived solid-free enrichment cultures were able to dechlorinate trichloroethene (TCE) to less chlorinated daughter products including ethene...
August 15, 2017: ISME Journal
https://www.readbyqxmd.com/read/28809850/function-related-replacement-of-bacterial-siderophore-pathways
#3
Hilke Bruns, Max Crüsemann, Anne-Catrin Letzel, Mohammad Alanjary, James O McInerney, Paul R Jensen, Stefan Schulz, Bradley S Moore, Nadine Ziemert
Bacterial genomes are rife with orphan biosynthetic gene clusters (BGCs) associated with secondary metabolism of unrealized natural product molecules. Often up to a tenth of the genome is predicted to code for the biosynthesis of diverse metabolites with mostly unknown structures and functions. This phenomenal diversity of BGCs coupled with their high rates of horizontal transfer raise questions about whether they are really active and beneficial, whether they are neutral and confer no advantage, or whether they are carried in genomes because they are parasitic or addictive...
August 15, 2017: ISME Journal
https://www.readbyqxmd.com/read/28800138/phylogenetically-conserved-resource-partitioning-in-the-coastal-microbial-loop
#4
Samuel Bryson, Zhou Li, Francisco Chavez, Peter K Weber, Jennifer Pett-Ridge, Robert L Hettich, Chongle Pan, Xavier Mayali, Ryan S Mueller
Resource availability influences marine microbial community structure, suggesting that population-specific resource partitioning defines discrete niches. Identifying how resources are partitioned among populations, thereby characterizing functional guilds within the communities, remains a challenge for microbial ecologists. We used proteomic stable isotope probing (SIP) and NanoSIMS analysis of phylogenetic microarrays (Chip-SIP) along with 16S rRNA gene amplicon and metagenomic sequencing to characterize the assimilation of six (13)C-labeled common metabolic substrates and changes in the microbial community structure within surface water collected from Monterey Bay, CA...
August 11, 2017: ISME Journal
https://www.readbyqxmd.com/read/28800137/chemical-dispersants-enhance-the-activity-of-oil-and-gas-condensate-degrading-marine-bacteria
#5
Julien Tremblay, Etienne Yergeau, Nathalie Fortin, Susan Cobanli, Miria Elias, Thomas L King, Kenneth Lee, Charles W Greer
Application of chemical dispersants to oil spills in the marine environment is a common practice to disperse oil into the water column and stimulate oil biodegradation by increasing its bioavailability to indigenous bacteria capable of naturally metabolizing hydrocarbons. In the context of a spill event, the biodegradation of crude oil and gas condensate off eastern Canada is an essential component of a response strategy. In laboratory experiments, we simulated conditions similar to an oil spill with and without the addition of chemical dispersant under both winter and summer conditions and evaluated the natural attenuation potential for hydrocarbons in near-surface sea water from the vicinity of crude oil and natural gas production facilities off eastern Canada...
August 11, 2017: ISME Journal
https://www.readbyqxmd.com/read/28800136/feathermoss-and-epiphytic-nostoc-cooperate-differently-expanding-the-spectrum-of-plant-cyanobacteria-symbiosis
#6
Denis Warshan, Josh L Espinoza, Rhona K Stuart, R Alexander Richter, Sea-Yong Kim, Nicole Shapiro, Tanja Woyke, Nikos C Kyrpides, Kerrie Barry, Vasanth Singan, Erika Lindquist, Charles Ansong, Samuel O Purvine, Heather M Brewer, Philip D Weyman, Christopher L Dupont, Ulla Rasmussen
Dinitrogen (N2)-fixation by cyanobacteria in symbiosis with feathermosses is the primary pathway of biological nitrogen (N) input into boreal forests. Despite its significance, little is known about the cyanobacterial gene repertoire and regulatory rewiring needed for the establishment and maintenance of the symbiosis. To determine gene acquisitions and regulatory changes allowing cyanobacteria to form and maintain this symbiosis, we compared genomically closely related symbiotic-competent and -incompetent Nostoc strains using a proteogenomics approach and an experimental set up allowing for controlled chemical and physical contact between partners...
August 11, 2017: ISME Journal
https://www.readbyqxmd.com/read/28800135/network-analysis-of-gut-microbiota-literature-an-overview-of-the-research-landscape-in-non-human-animal-studies
#7
Emily L Pascoe, Heidi C Hauffe, Julian R Marchesi, Sarah E Perkins
A wealth of human studies have demonstrated the importance of gut microbiota to health. Research on non-human animal gut microbiota is now increasing, but what insight does it provide? We reviewed 650 publications from this burgeoning field (2009-2016) and determined that animals driving this research were predominantly 'domestic' (48.2%), followed by 'model' (37.5%), with least studies on 'wild' (14.3%) animals. Domestic studies largely experimentally perturbed microbiota (81.8%) and studied mammals (47.9%), often to improve animal productivity...
August 11, 2017: ISME Journal
https://www.readbyqxmd.com/read/28800134/bacterial-volatile-ammonia-regulates-the-consumption-sequence-of-d-pinitol-and-d-glucose-in-a-fungus-associated-with-an-invasive-bark-beetle
#8
Fangyuan Zhou, Letian Xu, Shanshan Wang, Bo Wang, Qiaozhe Lou, Min Lu, Jianghua Sun
Interactions among microbial symbionts have multiple roles in the maintenance of insect-microbe symbiosis. However, signals mediating microbial interactions have been scarcely studied. In the classical model system of bark beetles and fungal associates, fungi increase the fitness of insects. However, not all interactions are mutualistic, some of these fungal symbionts compete for sugars with beetle larvae. How this antagonistic effect is alleviated is unknown, and recent research suggests potential roles of bacterial symbionts...
August 11, 2017: ISME Journal
https://www.readbyqxmd.com/read/28800133/adaptive-evolution-of-rhizobial-symbiotic-compatibility-mediated-by-co-evolved-insertion-sequences
#9
Ran Zhao, Li Xue Liu, Yun Zeng Zhang, Jian Jiao, Wen Jing Cui, Biliang Zhang, Xiao Lin Wang, Meng Lin Li, Yi Chen, Zhu Qing Xiong, Wen Xin Chen, Chang Fu Tian
Mutualism between bacteria and eukaryotes has essential roles in the history of life, but the evolution of their compatibility is poorly understood. Here we show that different Sinorhizobium strains can form either nitrogen-fixing nodules or uninfected pseudonodules on certain cultivated soybeans, while being all effective microsymbionts of some wild soybeans. However, a few well-infected nodules can be found on a commercial soybean using inocula containing a mixed pool of Tn5 insertion mutants derived from an incompatible strain...
August 11, 2017: ISME Journal
https://www.readbyqxmd.com/read/28786973/modeling-time-series-data-from-microbial-communities
#10
Benjamin J Ridenhour, Sarah L Brooker, Janet E Williams, James T Van Leuven, Aaron W Miller, M Denise Dearing, Christopher H Remien
As sequencing technologies have advanced, the amount of information regarding the composition of bacterial communities from various environments (for example, skin or soil) has grown exponentially. To date, most work has focused on cataloging taxa present in samples and determining whether the distribution of taxa shifts with exogenous covariates. However, important questions regarding how taxa interact with each other and their environment remain open thus preventing in-depth ecological understanding of microbiomes...
August 8, 2017: ISME Journal
https://www.readbyqxmd.com/read/28777382/the-growing-tree-of-archaea-new-perspectives-on-their-diversity-evolution-and-ecology
#11
Panagiotis S Adam, Guillaume Borrel, Céline Brochier-Armanet, Simonetta Gribaldo
The Archaea occupy a key position in the Tree of Life, and are a major fraction of microbial diversity. Abundant in soils, ocean sediments and the water column, they have crucial roles in processes mediating global carbon and nutrient fluxes. Moreover, they represent an important component of the human microbiome, where their role in health and disease is still unclear. The development of culture-independent sequencing techniques has provided unprecedented access to genomic data from a large number of so far inaccessible archaeal lineages...
August 4, 2017: ISME Journal
https://www.readbyqxmd.com/read/28777381/mixotrophy-drives-niche-expansion-of-verrucomicrobial-methanotrophs
#12
Carlo R Carere, Kiel Hards, Karen M Houghton, Jean F Power, Ben McDonald, Christophe Collet, Daniel J Gapes, Richard Sparling, Eric S Boyd, Gregory M Cook, Chris Greening, Matthew B Stott
Aerobic methanotrophic bacteria have evolved a specialist lifestyle dependent on consumption of methane and other short-chain carbon compounds. However, their apparent substrate specialism runs contrary to the high relative abundance of these microorganisms in dynamic environments, where the availability of methane and oxygen fluctuates. In this work, we provide in situ and ex situ evidence that verrucomicrobial methanotrophs are mixotrophs. Verrucomicrobia-dominated soil communities from an acidic geothermal field in Rotokawa, New Zealand rapidly oxidised methane and hydrogen simultaneously...
August 4, 2017: ISME Journal
https://www.readbyqxmd.com/read/28777380/sulfide-production-and-oxidation-by-heterotrophic-bacteria-under-aerobic-conditions
#13
Yongzhen Xia, Chuanjuan Lü, Ningke Hou, Yufeng Xin, Jihua Liu, Honglei Liu, Luying Xun
Sulfide (H2S, HS(-) and S(2-)) oxidation to sulfite and thiosulfate by heterotrophic bacteria, using sulfide:quinone oxidoreductase (SQR) and persulfide dioxygenase (PDO), has recently been reported as a possible detoxification mechanism for sulfide at high levels. Bioinformatic analysis revealed that the sqr and pdo genes were common in sequenced bacterial genomes, implying the sulfide oxidation may have other physiological functions. SQRs have previously been classified into six types. Here we grouped PDOs into three types and showed that some heterotrophic bacteria produced and released H2S from organic sulfur into the headspace during aerobic growth, and others, for example, Pseudomonas aeruginosa PAO1, with sqr and pdo did not release H2S...
August 4, 2017: ISME Journal
https://www.readbyqxmd.com/read/28777379/metabolic-and-spatio-taxonomic-response-of-uncultivated-seafloor-bacteria-following-the-deepwater-horizon-oil-spill
#14
K M Handley, Y M Piceno, P Hu, L M Tom, O U Mason, G L Andersen, J K Jansson, J A Gilbert
The release of 700 million liters of oil into the Gulf of Mexico over a few months in 2010 produced dramatic changes in the microbial ecology of the water and sediment. Here, we reconstructed the genomes of 57 widespread uncultivated bacteria from post-spill deep-sea sediments, and recovered their gene expression pattern across the seafloor. These genomes comprised a common collection of bacteria that were enriched in heavily affected sediments around the wellhead. Although rare in distal sediments, some members were still detectable at sites up to 60 km away...
August 4, 2017: ISME Journal
https://www.readbyqxmd.com/read/28763056/methanethiol-dependent-dimethylsulfide-production-in-soil-environments
#15
Ornella Carrión, Jennifer Pratscher, Andrew R J Curson, Beth T Williams, Wayne G Rostant, J Colin Murrell, Jonathan D Todd
Dimethylsulfide (DMS) is an environmentally important trace gas with roles in sulfur cycling, signalling to higher organisms and in atmospheric chemistry. DMS is believed to be predominantly produced in marine environments via microbial degradation of the osmolyte dimethylsulfoniopropionate (DMSP). However, significant amounts of DMS are also generated from terrestrial environments, for example, peat bogs can emit ~6 μmol DMS m(-2) per day, likely via the methylation of methanethiol (MeSH). A methyltransferase enzyme termed 'MddA', which catalyses the methylation of MeSH, generating DMS, in a wide range of bacteria and some cyanobacteria, may mediate this process, as the mddA gene is abundant in terrestrial metagenomes...
August 1, 2017: ISME Journal
https://www.readbyqxmd.com/read/28753210/biogeography-and-organic-matter-removal-shape-long-term-effects-of-timber-harvesting-on-forest-soil-microbial-communities
#16
Roland C Wilhelm, Erick Cardenas, Kendra R Maas, Hilary Leung, Larisa McNeil, Shannon Berch, William Chapman, Graeme Hope, J M Kranabetter, Stephane Dubé, Matt Busse, Robert Fleming, Paul Hazlett, Kara L Webster, David Morris, D Andrew Scott, William W Mohn
The growing demand for renewable, carbon-neutral materials and energy is leading to intensified forest land-use. The long-term ecological challenges associated with maintaining soil fertility in managed forests are not yet known, in part due to the complexity of soil microbial communities and the heterogeneity of forest soils. This study determined the long-term effects of timber harvesting, accompanied by varied organic matter (OM) removal, on bacterial and fungal soil populations in 11- to 17-year-old reforested coniferous plantations at 18 sites across North America...
July 28, 2017: ISME Journal
https://www.readbyqxmd.com/read/28753209/drought-and-host-selection-influence-bacterial-community-dynamics-in-the-grass-root-microbiome
#17
Dan Naylor, Stephanie DeGraaf, Elizabeth Purdom, Devin Coleman-Derr
Root endophytes have been shown to have important roles in determining host fitness under periods of drought stress, and yet the effect of drought on the broader root endosphere bacterial community remains largely uncharacterized. In this study, we present phylogenetic profiles of bacterial communities associated with drought-treated root and rhizosphere tissues of 18 species of plants with varying degrees of drought tolerance belonging to the Poaceae family, including important crop plants. Through 16S rRNA gene profiling across two distinct watering regimes and two developmental time points, we demonstrate that there is a strong correlation between host phylogenetic distance and the microbiome dissimilarity within root tissues, and that drought weakens this correlation by inducing conserved shifts in bacterial community composition...
July 28, 2017: ISME Journal
https://www.readbyqxmd.com/read/28753208/ice-nucleation-active-bacteria-in-precipitation-are-genetically-diverse-and-nucleate-ice-by-employing-different-mechanisms
#18
K C Failor, D G Schmale, B A Vinatzer, C L Monteil
A growing body of circumstantial evidence suggests that ice nucleation active (Ice(+)) bacteria contribute to the initiation of precipitation by heterologous freezing of super-cooled water in clouds. However, little is known about the concentration of Ice(+) bacteria in precipitation, their genetic and phenotypic diversity, and their relationship to air mass trajectories and precipitation chemistry. In this study, 23 precipitation events were collected over 15 months in Virginia, USA. Air mass trajectories and water chemistry were determined and 33 134 isolates were screened for ice nucleation activity (INA) at -8 °C...
July 28, 2017: ISME Journal
https://www.readbyqxmd.com/read/28742073/biological-nitrogen-fixation-in-the-oxygen-minimum-region-of-the-eastern-tropical-north-pacific-ocean
#19
Amal Jayakumar, Bonnie X Chang, Brittany Widner, Peter Bernhardt, Margaret R Mulholland, Bess B Ward
Biological nitrogen fixation (BNF) was investigated above and within the oxygen-depleted waters of the oxygen-minimum zone of the Eastern Tropical North Pacific Ocean. BNF rates were estimated using an isotope tracer method that overcame the uncertainty of the conventional bubble method by directly measuring the tracer enrichment during the incubations. Highest rates of BNF (~4 nM day(-1)) occurred in coastal surface waters and lowest detectable rates (~0.2 nM day(-1)) were found in the anoxic region of offshore stations...
July 25, 2017: ISME Journal
https://www.readbyqxmd.com/read/28742072/phaeoviruses-discovered-in-kelp-laminariales
#20
Dean A McKeown, Kim Stevens, Akira F Peters, Peter Bond, Glenn M Harper, Colin Brownlee, Murray T Brown, Declan C Schroeder
Phaeoviruses are latent double-stranded DNA viruses that insert their genomes into those of their brown algal (Phaeophyceae) hosts. So far these viruses are known only from members of the Ectocarpales, which are small and short-lived macroalgae. Here we report molecular and morphological evidence for a new Phaeovirus cluster, referred to as sub-group C, infecting kelps (Laminariales) of the genera Laminaria and Saccharina, which are ecologically and commercially important seaweeds. Epifluorescence and TEM observations indicate that the Laminaria digitata Virus (LdigV), the type species of sub-group C, targets the host nucleus for its genome replication, followed by gradual degradation of the chloroplast and assembly of virions in the cytoplasm of both vegetative and reproductive cells...
July 25, 2017: ISME Journal
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