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ISME Journal

Chen Cai, Andy O Leu, Guo-Jun Xie, Jianhua Guo, Yuexing Feng, Jian-Xin Zhao, Gene W Tyson, Zhiguo Yuan, Shihu Hu
Microbially mediated anaerobic oxidation of methane (AOM) is a key process in the regulation of methane emissions to the atmosphere. Iron can serve as an electron acceptor for AOM, and it has been suggested that Fe(III)-dependent AOM potentially comprises a major global methane sink. Although it has been proposed that anaerobic methanotrophic (ANME) archaea can facilitate this process, their active metabolic pathways have not been confirmed. Here we report the enrichment and characterisation of a novel archaeon in a laboratory-scale bioreactor fed with Fe(III) oxide (ferrihydrite) and methane...
April 16, 2018: ISME Journal
Kyle M Meyer, Hervé Memiaghe, Lisa Korte, David Kenfack, Alfonso Alonso, Brendan J M Bohannan
Analysis of patterns in the distribution of taxa can provide important insights into ecological and evolutionary processes. Microbial biogeographic patterns almost always appear to be weaker than those reported for plant and animal taxa. It is as yet unclear why this is the case. Some argue that microbial diversity scales differently over space because microbial taxa are fundamentally different in their abundance, longevity and dispersal abilities. Others have argued that differences in scaling are an artifact of how we assess microbial biogeography, driven, for example, by differences in taxonomic resolution, spatial scale, sampling effort or community activity/dormancy...
April 16, 2018: ISME Journal
Angela M Oliverio, Jean F Power, Alex Washburne, S Craig Cary, Matthew B Stott, Noah Fierer
Decades of research into the Bacteria and Archaea living in geothermal spring ecosystems have yielded great insight into the diversity of life and organismal adaptations to extreme environmental conditions. Surprisingly, while microbial eukaryotes (protists) are also ubiquitous in many environments, their diversity across geothermal springs has mostly been ignored. We used high-throughput sequencing to illuminate the diversity and structure of microbial eukaryotic communities found in 160 geothermal springs with broad ranges in temperature and pH across the Taupō Volcanic Zone in New Zealand...
April 16, 2018: ISME Journal
Anirban Chakraborty, Emily Ellefson, Carmen Li, Daniel Gittins, James M Brooks, Bernie B Bernard, Casey R J Hubert
Dormant endospores of thermophilic bacteria (thermospores) can be detected in cold marine sediments following high-temperature incubation. Thermospores in the cold seabed may be explained by a dispersal history originating in deep biosphere oil reservoir habitats where upward migration of petroleum fluids at hydrocarbon seeps transports viable cells into the overlying ocean. We assessed this deep-to-shallow dispersal hypothesis through geochemical and microbiological analyses of 111 marine sediments from the deep water Eastern Gulf of Mexico...
March 29, 2018: ISME Journal
Alberto Amato, Valeria Sabatino, Göran M Nylund, Johanna Bergkvist, Swaraj Basu, Mats X Andersson, Remo Sanges, Anna Godhe, Thomas Kiørboe, Erik Selander, Maria I Ferrante
Diatoms and copepods are main actors in marine food webs. The prey-predator interactions between them affect bloom dynamics, shape marine ecosystems and impact the energy transfer to higher trophic levels. Recently it has been demonstrated that the presence of grazers may affect the diatom prey beyond the direct effect of grazing. Here, we investigated the response of the chain-forming centric diatom Skeletonema marinoi to grazer cues, including changes in morphology, gene expression and metabolic profile. S...
March 29, 2018: ISME Journal
Ri-Qing Yu, John R Reinfelder, Mark E Hines, Tamar Barkay
Exposure to dietary sources of methylmercury (MeHg) is the focus of public health concerns with environmental mercury (Hg) contamination. MeHg is formed in anoxic environments by anaerobic microorganisms. This process has been studied mostly with single-species culture incubations, although the relevance of such studies to Hg(II)-methylation in situ is limited because microbial activities in the environment are critically modulated by interactions among microbial functional groups. Here we describe experiments in which Hg(II)-methylation was examined within the context of various microbial syntrophies...
March 29, 2018: ISME Journal
Claude-Alexandre Gustave, Anne Tristan, Patricia Martins-Simões, Marc Stegger, Yvonne Benito, Paal Skytt Andersen, Michèle Bes, Typhanie Le Hir, Binh An Diep, Anne-Catrin Uhlemann, Philippe Glaser, Frédéric Laurent, Thierry Wirth, François Vandenesch
Community-acquired (CA)- as opposed to hospital acquired- methicillin-resistant Staphylococcus aureus (MRSA) lineages arose worldwide during the 1990s. To determine which factors, including selective antibiotic pressure, govern the expansion of two major lineages of CA-MRSA, namely "USA300" in Northern America and "European ST80" in North Africa, Europe and Middle-East, we explored virulence factor expression, and fitness levels with or without antibiotics. The sampled strains were collected in a temporal window representing various steps of the epidemics, reflecting predicted changes in effective population size as inferred from whole-genome analysis...
March 29, 2018: ISME Journal
Lyria Berdjeb, Alma Parada, David M Needham, Jed A Fuhrman
We examined the short-term variability, by daily to weekly sampling, of protist assemblages from March to July in surface water of the San Pedro Ocean Time-series station (eastern North Pacific), by V4 Illumina sequencing of the 18S rRNA gene. The sampling period encompassed a spring bloom followed by progression to summer conditions. Several protistan taxa displayed sharp increases and declines, with whole community Bray-Curtis dissimilarities of adjacent days being 66% in March and 40% in May. High initial abundance of parasitic Cercozoa Cryothecomonas longipes and Protaspis grandis coincided with a precipitous decline of blooming Pseudo-nitzschia diatoms, possibly suggesting their massive infection by these parasites; these cercozoans were hardly detectable afterwards...
March 29, 2018: ISME Journal
Michael W Henson, V Celeste Lanclos, Brant C Faircloth, J Cameron Thrash
Evolutionary transitions between fresh and salt water happen infrequently among bacterioplankton. Within the ubiquitous and highly abundant heterotrophic Alphaproteobacteria order Pelagibacterales (SAR11), most members live in marine habitats, but the LD12 subclade has evolved as a unique freshwater lineage. LD12 cells occur as some of the most dominant freshwater bacterioplankton, yet this group has remained elusive to cultivation, hampering a more thorough understanding of its biology. Here, we report the first successful isolation of an LD12 representative, strain LSUCC0530, using high-throughput dilution-to-extinction cultivation methods, and its complete genome sequence...
March 29, 2018: ISME Journal
Fangqiong Ling, Rachel Whitaker, Mark W LeChevallier, Wen-Tso Liu
What happens to tap water when you are away from home? Day-to-day water stagnation in building plumbing can potentially result in water quality deterioration (e.g., lead release or pathogen proliferation), which is a major public health concern. However, little is known about the microbial ecosystem processes in plumbing systems, hindering the development of biological monitoring strategies. Here, we track tap water microbiome assembly in situ, showing that bacterial community composition changes rapidly from the city supply following ~6-day stagnation, along with an increase in cell count from 103 cells/mL to upwards of 7...
March 27, 2018: ISME Journal
Tian'an Zhang, Han Y H Chen, Honghua Ruan
Soil microbes comprise a large portion of the genetic diversity on Earth and influence a large number of important ecosystem processes. Increasing atmospheric nitrogen (N) deposition represents a major global change driver; however, it is still debated whether the impacts of N deposition on soil microbial biomass and respiration are ecosystem-type dependent. Moreover, the extent of N deposition impacts on microbial composition remains unclear. Here we conduct a global meta-analysis using 1408 paired observations from 151 studies to evaluate the responses of soil microbial biomass, composition, and function to N addition...
March 27, 2018: ISME Journal
Wei Lin, Wensi Zhang, Xiang Zhao, Andrew P Roberts, Greig A Paterson, Dennis A Bazylinski, Yongxin Pan
The origin and evolution of magnetoreception, which in diverse prokaryotes and protozoa is known as magnetotaxis and enables these microorganisms to detect Earth's magnetic field for orientation and navigation, is not well understood in evolutionary biology. The only known prokaryotes capable of sensing the geomagnetic field are magnetotactic bacteria (MTB), motile microorganisms that biomineralize intracellular, membrane-bounded magnetic single-domain crystals of either magnetite (Fe3 O4 ) or greigite (Fe3 S4 ) called magnetosomes...
March 26, 2018: ISME Journal
Xue Jiang, Christian Zerfaß, Song Feng, Ruth Eichmann, Munehiro Asally, Patrick Schäfer, Orkun S Soyer
A key prerequisite to achieve a deeper understanding of microbial communities and to engineer synthetic ones is to identify the individual metabolic interactions among key species and how these interactions are affected by different environmental factors. Deciphering the physiological basis of species-species and species-environment interactions in spatially organized environments requires reductionist approaches using ecologically and functionally relevant species. To this end, we focus here on a defined system to study the metabolic interactions in a spatial context among the plant-beneficial endophytic fungus Serendipita indica, and the soil-dwelling model bacterium Bacillus subtilis...
March 23, 2018: ISME Journal
Zhenhui Zhong, Meilian Chen, Lianyu Lin, Yijuan Han, Jiandong Bao, Wei Tang, Lili Lin, Yahong Lin, Rewish Somai, Lin Lu, Wenjing Zhang, Jian Chen, Yonghe Hong, Xiaofeng Chen, Baohua Wang, Wei-Chiang Shen, Guodong Lu, Justice Norvienyeku, Daniel J Ebbole, Zonghua Wang
We examined the genomes of 100 isolates of Magnaporthe oryzae (Pyricularia oryzae), the causal agent of rice blast disease. We grouped current field populations of M. oryzae into three major globally distributed groups. A genetically diverse group, clade 1, which may represent a group of closely related lineages, contains isolates of both mating types. Two well-separated clades, clades 2 and 3, appear to have arisen as clonal lineages distinct from the genetically diverse clade. Examination of genes involved in mating pathways identified clade-specific diversification of several genes with orthologs involved in mating behavior in other fungi...
March 22, 2018: ISME Journal
Cristina Howard-Varona, Katherine R Hargreaves, Natalie E Solonenko, Lye Meng Markillie, Richard Allen White, Heather M Brewer, Charles Ansong, Galya Orr, Joshua N Adkins, Matthew B Sullivan
Phage-host interactions are critical to ecology, evolution, and biotechnology. Central to those is infection efficiency, which remains poorly understood, particularly in nature. Here we apply genome-wide transcriptomics and proteomics to investigate infection efficiency in nature's own experiment: two nearly identical (genetically and physiologically) Bacteroidetes bacterial strains (host18 and host38) that are genetically intractable, but environmentally important, where phage infection efficiency varies. On host18, specialist phage phi18:3 infects efficiently, whereas generalist phi38:1 infects inefficiently...
March 22, 2018: ISME Journal
Ford Ballantyne Iv, Sharon A Billings
No abstract text is available yet for this article.
March 22, 2018: ISME Journal
Isabel Frost, William P J Smith, Sara Mitri, Alvaro San Millan, Yohan Davit, James M Osborne, Joe M Pitt-Francis, R Craig MacLean, Kevin R Foster
Bacteria commonly live in dense and genetically diverse communities associated with surfaces. In these communities, competition for resources and space is intense, and yet we understand little of how this affects the spread of antibiotic-resistant strains. Here, we study interactions between antibiotic-resistant and susceptible strains using in vitro competition experiments in the opportunistic pathogen Pseudomonas aeruginosa and in silico simulations. Selection for intracellular resistance to streptomycin is very strong in colonies, such that resistance is favoured at very low antibiotic doses...
March 21, 2018: ISME Journal
Seynabou Séne, Marc-André Selosse, Mathieu Forget, Josie Lambourdière, Khoudia Cissé, Abdala Gamby Diédhiou, Elsie Rivera-Ocasio, Hippolyte Kodja, Norikazu Kameyama, Kazuhide Nara, Lucie Vincenot, Jean-Louis Mansot, Jean Weber, Mélanie Roy, Samba Ndao Sylla, Amadou Bâ
Global trade increases plant introductions, but joint introduction of associated microbes is overlooked. We analyzed the ectomycorrhizal fungi of a Caribbean beach tree, seagrape (Coccoloba uvifera, Polygonacaeae), introduced pantropically to stabilize coastal soils and produce edible fruits. Seagrape displays a limited symbiont diversity in the Caribbean. In five regions of introduction (Brazil, Japan, Malaysia, Réunion and Senegal), molecular barcoding showed that seagrape mostly or exclusively associates with Scleroderma species (Basidiomycota) that were hitherto only known from Caribbean seagrape stands...
March 13, 2018: ISME Journal
Jonathan W Leff, Richard D Bardgett, Anna Wilkinson, Benjamin G Jackson, William J Pritchard, Jonathan R De Long, Simon Oakley, Kelly E Mason, Nicholas J Ostle, David Johnson, Elizabeth M Baggs, Noah Fierer
There are numerous ways in which plants can influence the composition of soil communities. However, it remains unclear whether information on plant community attributes, including taxonomic, phylogenetic, or trait-based composition, can be used to predict the structure of soil communities. We tested, in both monocultures and field-grown mixed temperate grassland communities, whether plant attributes predict soil communities including taxonomic groups from across the tree of life (fungi, bacteria, protists, and metazoa)...
March 9, 2018: ISME Journal
E D Graham, J F Heidelberg, B J Tully
Aerobic anoxygenic phototrophs (AAnPs) are common in marine environments and are associated with photoheterotrophic activity. To date, AAnPs that possess the potential for carbon fixation have not been identified in the surface ocean. Using the Tara Oceans metagenomic dataset, we have identified draft genomes of nine bacteria that possess the genomic potential for anoxygenic phototrophy, carbon fixation via the Calvin-Benson-Bassham cycle, and the oxidation of sulfite and thiosulfate. Forming a monophyletic clade within the Alphaproteobacteria and lacking cultured representatives, the organisms compose minor constituents of local microbial communities (0...
March 9, 2018: ISME Journal
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