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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/28798361/increased-sporadic-extremes-decrease-the-intraseasonal-variability-in-the-indian-summer-monsoon-rainfall
#10
Nirupam Karmakar, Arindam Chakraborty, Ravi S Nanjundiah
The Indian summer monsoon (ISM) shows quasi-rhythmic intraseasonal oscillations (ISO) manifested as alternate 'active' phases of copious rainfall and quiescent phases of 'break'. Within these periodic phases, the daily rainfall shows large variability and exhibits spatiotemporally sporadic extreme rainfall events. The recent decades have witnessed a significant increase in the number of these extreme rainfall events, especially in the quiescent phases. This increase is accompanied by a decreasing trend in the mean monsoon rainfall and a weakening variance of its low-frequency ISO (LF-ISO) cycle...
August 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28783619/fully-automated-segmentation-of-fluid-cyst-regions-in-optical-coherence-tomography-images-with-diabetic-macular-edema-using-neutrosophic-sets-and-graph-algorithms
#11
Abdolreza Rashno, Dara D Koozekanani, Paul M Drayna, Behzad Nazari, Saeed Sadri, Hossein Rabbani, Keshab K Parhi
This paper presents a fully-automated algorithm to segment fluid-associated (fluid-filled) and cyst regions in optical coherence tomography (OCT) retina images of the subjects with diabetic macular edema (DME). The OCT image is segmented using a novel neutrosophic transformation and a graph-based shortest path method. In neutrosophic domain, an image g is transformed into three sets: T (true), I (indeterminate) that represents noise, and F (false). This paper makes four key contributions. First, a new method is introduced to compute the indeterminacy set I, and a new λ-correction operation is introduced to compute the set T in neutrosophic domain...
July 31, 2017: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/28780163/online-monitoring-of-cell-concentration-in-high-cell-density-escherichia-coli-cultivations-using-in-situ-microscopy
#12
D Marquard, C Schneider-Barthold, S Düsterloh, T Scheper, P Lindner
In situ Microscopy (ISM) is an optical non-invasive technique to monitor cells in bioprocesses in real-time. Escherichia coli is the most studied and used organism in biotechnology. In this article the cell density in Escherichia coli cultivations was monitored by applying ISM in these cultivations. The acquired images were analyzed with an image processing algorithm to determine the turbidity of the cultivation medium. In three cultivations the cell density was monitored with the algorithm and offline samples were taken to determine the dry cell mass (DCM)...
August 2, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28777382/the-growing-tree-of-archaea-new-perspectives-on-their-diversity-evolution-and-ecology
#13
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
#14
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
#15
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
#16
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/28763108/biodegradation-of-anthracene-by-a-newly-isolated-bacterial-strain-bacillus-thuringiensis-at-ism-1-isolated-from-a-fly-ash-deposition-site
#17
Abhrajyoti Tarafdar, Alok Sinha, Reginald E Masto
Current study is aimed to evaluate the mechanism of anthracene degradation by a bacterial strain isolated from fly ash deposition site near Jamadoba Coal Preparation Plant, Jharkhand, India. The Bushnell-Haas media cultured (containing anthracene as sole carbon source) bacterial isolate was identified by 16S rRNA gene sequence coding as the Bacillus thuringiensis strain, which showed the efficiency to degrade anthracene. The degradation efficiency of the strain has been estimated around 91% (for 40 mgL(-1) of anthracene concentration) after two weeks of incubation period at temperature 33-36°C and initial pH of 6...
August 1, 2017: Letters in Applied Microbiology
https://www.readbyqxmd.com/read/28763056/methanethiol-dependent-dimethylsulfide-production-in-soil-environments
#18
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/28759607/comparison-of-soil-sampling-and-analytical-methods-for-asbestos-at-the-sumas-mountain-asbestos-site-working-towards-a-toolbox-for-better-assessment
#19
Julie Wroble, Timothy Frederick, Alicia Frame, Daniel Vallero
Established soil sampling methods for asbestos are inadequate to support risk assessment and risk-based decision making at Superfund sites due to difficulties in detecting asbestos at low concentrations and difficulty in extrapolating soil concentrations to air concentrations. Environmental Protection Agency (EPA)'s Office of Land and Emergency Management (OLEM) currently recommends the rigorous process of Activity Based Sampling (ABS) to characterize site exposures. The purpose of this study was to compare three soil analytical methods and two soil sampling methods to determine whether one method, or combination of methods, would yield more reliable soil asbestos data than other methods...
2017: PloS One
https://www.readbyqxmd.com/read/28756240/frequency-specific-modulation-of-connectivity-in-the-ipsilateral-sensorimotor-cortex-by-different-forms-of-movement-initiation
#20
Bin A Wang, Shivakumar Viswanathan, Rouhollah O Abdollahi, Nils Rosjat, Svitlana Popovych, Silvia Daun, Christian Grefkes, Gereon R Fink
A consistent finding in motor EEG research is a bilateral attenuation of oscillatory activity over sensorimotor regions close to the onset of an upcoming unilateral hand movement. In contrast, little is known about how movement initiation affects oscillatory activity, especially in the hemisphere ipsilateral to the moving hand. We here investigated the neural mechanisms modulating oscillatory activity in the ipsilateral motor cortex prior to movement onset under the control of two different initiating networks, namely, Self-initiated and Visually-cued actions...
July 26, 2017: NeuroImage
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