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ISME Journal

Sabrina Beckmann, Alison W S Luk, Maria-Luisa Gutierrez-Zamora, Nur Hazlin Hazrin Chong, Torsten Thomas, Matthew Lee, Michael Manefield
Despite the significance of biogenic methane generation in coal beds, there has never been a systematic long-term evaluation of the ecological response to biostimulation for enhanced methanogenesis in situ. Biostimulation tests in a gas-free coal seam were analysed over 1.5 years encompassing methane production, cell abundance, planktonic and surface associated community composition and chemical parameters of the coal formation water. Evidence is presented that sulfate reducing bacteria are energy limited whilst methanogenic archaea are nutrient limited...
October 15, 2018: ISME Journal
Hugo Berthelot, Solange Duhamel, Stéphane L'Helguen, Jean-Francois Maguer, Seaver Wang, Ivona Cetinić, Nicolas Cassar
Nitrogen (N) is a limiting nutrient in vast regions of the world's oceans, yet the sources of N available to various phytoplankton groups remain poorly understood. In this study, we investigated inorganic carbon (C) fixation rates and nitrate (NO3 - ), ammonium (NH4 + ) and urea uptake rates at the single cell level in photosynthetic pico-eukaryotes (PPE) and the cyanobacteria Prochlorococcus and Synechococcus. To that end, we used dual 15 N and 13 C-labeled incubation assays coupled to flow cytometry cell sorting and nanoSIMS analysis on samples collected in the North Pacific Subtropical Gyre (NPSG) and in the California Current System (CCS)...
October 15, 2018: ISME Journal
Christian Rinke, Francesco Rubino, Lauren F Messer, Noha Youssef, Donovan H Parks, Maria Chuvochina, Mark Brown, Thomas Jeffries, Gene W Tyson, Justin R Seymour, Philip Hugenholtz
Marine Group II (MGII) archaea represent the most abundant planktonic archaeal group in ocean surface waters, but our understanding of the group has been limited by a lack of cultured representatives and few sequenced genomes. Here, we conducted a comparative phylogenomic analysis of 270 recently available MGII metagenome-assembled genomes (MAGs) to investigate their evolution and ecology. Based on a rank-normalised genome phylogeny, we propose that MGII is an order-level lineage for which we propose the name Candidatus Poseidoniales (after Gr...
October 15, 2018: ISME Journal
Benoit J Kunath, Francesco Delogu, Adrian E Naas, Magnus Ø Arntzen, Vincent G H Eijsink, Bernard Henrissat, Torgeir R Hvidsten, Phillip B Pope
Microbial communities that degrade lignocellulosic biomass are typified by high levels of species- and strain-level complexity, as well as synergistic interactions between both cellulolytic and non-cellulolytic microorganisms. Coprothermobacter proteolyticus frequently dominates thermophilic, lignocellulose-degrading communities with wide geographical distribution, which is in contrast to reports that it ferments proteinaceous substrates and is incapable of polysaccharide hydrolysis. Here we deconvolute a highly efficient cellulose-degrading consortium (SEM1b) that is co-dominated by Clostridium (Ruminiclostridium) thermocellum and multiple heterogenic strains affiliated to C...
October 12, 2018: ISME Journal
Nathan A Ahlgren, Clara A Fuchsman, Gabrielle Rocap, Jed A Fuhrman
Much of the diversity of prokaryotic viruses has yet to be described. In particular, there are no viral isolates that infect abundant, globally significant marine archaea including the phylum Thaumarchaeota. This phylum oxidizes ammonia, fixes inorganic carbon, and thus contributes to globally significant nitrogen and carbon cycles in the oceans. Metagenomics provides an alternative to culture-dependent means for identifying and characterizing viral diversity. Some viruses carry auxiliary metabolic genes (AMGs) that are acquired via horizontal gene transfer from their host(s), allowing inference of what host a virus infects...
October 12, 2018: ISME Journal
Tomislav Cernava, Ines Aline Aschenbrenner, Jung Soh, Christoph W Sensen, Martin Grube, Gabriele Berg
The role of host-associated microbiota in enduring dehydration and drought is largely unknown. We have used lichens to study this increasingly important problem because they are the organisms that are optimally adapted to reoccurring hydration/dehydration cycles, and they host a defined and persistent bacterial community. The analysis of metatranscriptomic datasets from bacterial communities of the lung lichen (Lobaria pulmonaria (L.) Hoffm.), sampled under representative hydration stages, revealed significant structural shifts and functional specialization to host conditions...
October 11, 2018: ISME Journal
Anja Kombrink, Annageldi Tayyrov, Andreas Essig, Martina Stöckli, Sebastian Micheller, John Hintze, Yasemin van Heuvel, Natalia Dürig, Chia-Wei Lin, Pauli T Kallio, Markus Aebi, Markus Künzler
Bacteria are the main nutritional competitors of saprophytic fungi during colonization of their ecological niches. This competition involves the mutual secretion of antimicrobials that kill or inhibit the growth of the competitor. Over the last years it has been demonstrated that fungi respond to the presence of bacteria with changes of their transcriptome, but the significance of these changes with respect to competition for nutrients is not clear as functional proof of the antibacterial activity of the induced gene products is often lacking...
October 9, 2018: ISME Journal
Karen Grace V Bondoc, Christine Lembke, Stefan N Lang, Sebastian Germerodt, Stefan Schuster, Wim Vyverman, Georg Pohnert
Microorganisms encounter a diversity of chemical stimuli that trigger individual responses and influence population dynamics. However, microbial behavior under the influence of different incentives and microbial decision-making is poorly understood. Benthic marine diatoms that react to sexual attractants as well as to nutrient gradients face such multiple constraints. Here, we document and model behavioral complexity and context-sensitive responses of these motile unicellular algae to sex pheromones and the nutrient silicate...
October 9, 2018: ISME Journal
Kristy L Hentchel, Leila M Reyes Ruiz, Patrick D Curtis, Aretha Fiebig, Maureen L Coleman, Sean Crosson
Bacterial genomes evolve in complex ecosystems and are best understood in this natural context, but replicating such conditions in the lab is challenging. We used transposon sequencing to define the fitness consequences of gene disruption in the bacterium Caulobacter crescentus grown in natural freshwater, compared with axenic growth in common laboratory media. Gene disruptions in amino-acid and nucleotide sugar biosynthesis pathways and in metabolic substrate transport machinery impaired fitness in both lake water and defined minimal medium relative to complex peptone broth...
October 8, 2018: ISME Journal
Yue Wang, Ji Lu, Likai Mao, Jie Li, Zhiguo Yuan, Philip L Bond, Jianhua Guo
Antibiotic resistance is a severe global threat for public health, causing around 700,000 deaths per year. Horizontal gene transfer (HGT) is one of the most significant pathways to disseminate antibiotic resistance. It is commonly acknowledged that sub-minimum inhibition concentrations of antibiotics are major contributors in promoting antibiotic resistance through HGT. Pharmaceuticals are occurring in our environments at increased levels, yet little is known whether non-antibiotic pharmaceuticals cause or accelerate the dissemination of antibiotic resistance...
October 5, 2018: ISME Journal
Lars Möller, Peeter Laas, Andreas Rogge, Florian Goetz, Rainer Bahlo, Thomas Leipe, Matthias Labrenz
The central Baltic Sea is characterized by a pelagic redox zone exhibiting high dark CO2 fixation rates below the chemocline. These rates are mainly driven by chemolithoautotrophic and denitrifying Sulfurimonas GD17 subgroup cells which are motile and fast-reacting r-strategists. Baltic Sea redox zones are unstable and a measurable overlap of nitrate and reduced sulfur, essential for chemosynthesis, is often only available on small scales and short times due to local mixing events. This raises the question of how GD17 cells gain access to electron donors or acceptors over longer term periods and under substrate deficiency...
October 5, 2018: ISME Journal
Sheila Podell, Jessica M Blanton, Alexander Neu, Vinayak Agarwal, Jason S Biggs, Bradley S Moore, Eric E Allen
Candidatus Poribacteria is a little-known bacterial phylum, previously characterized by partial genomes from a single sponge host, but never isolated in culture. We have reconstructed multiple genome sequences from four different sponge genera and compared them to recently reported, uncharacterized Poribacteria genomes from the open ocean, discovering shared and unique functional characteristics. Two distinct, habitat-linked taxonomic lineages were identified, designated Entoporibacteria (sponge-associated) and Pelagiporibacteria (free-living)...
October 5, 2018: ISME Journal
Xihui Xu, Raphy Zarecki, Shlomit Medina, Shany Ofaim, Xiaowei Liu, Chen Chen, Shunli Hu, Dan Brom, Daniella Gat, Seema Porob, Hanan Eizenberg, Zeev Ronen, Jiandong Jiang, Shiri Freilich
Microbial communities play a vital role in biogeochemical cycles, allowing the biodegradation of a wide range of pollutants. The composition of the community and the interactions between its members affect degradation rate and determine the identity of the final products. Here, we demonstrate the application of sequencing technologies and metabolic modeling approaches towards enhancing biodegradation of atrazine-a herbicide causing environmental pollution. Treatment of agriculture soil with atrazine is shown to induce significant changes in community structure and functional performances...
October 5, 2018: ISME Journal
Bhusan K Kuntal, Pranjal Chandrakar, Sudipta Sadhu, Sharmila S Mande
The combined effect of mutual association within the co-inhabiting microbes in human body is known to play a major role in determining health status of individuals. The differential taxonomic abundance between healthy and disease are often used to identify microbial markers. However, in order to make a microbial community based inference, it is important not only to consider microbial abundances, but also to quantify the changes observed among inter microbial associations. In the present study, we introduce a method called 'NetShift' to quantify rewiring and community changes in microbial association networks between healthy and disease...
October 4, 2018: ISME Journal
Yuniar Devi Utami, Hirokazu Kuwahara, Katsura Igai, Takumi Murakami, Kaito Sugaya, Takahiro Morikawa, Yuichi Nagura, Masahiro Yuki, Pinsurang Deevong, Tetsushi Inoue, Kumiko Kihara, Nathan Lo, Akinori Yamada, Moriya Ohkuma, Yuichi Hongoh
We investigated the phylogenetic diversity, localisation and metabolism of an uncultured bacterial clade, Termite Group 2 (TG2), or ZB3, in the termite gut, which belongs to the candidate phylum 'Margulisbacteria'. We performed 16S rRNA amplicon sequencing analysis and detected TG2/ZB3 sequences in 40 out of 72 termite and cockroach species, which exclusively constituted a monophyletic cluster in the TG2/ZB3 clade. Fluorescence in situ hybridisation analysis in lower termites revealed that these bacteria are specifically attached to ectosymbiotic spirochetes of oxymonad gut protists...
October 4, 2018: ISME Journal
Alyssa G Kent, Steven E Baer, Céline Mouginot, Jeremy S Huang, Alyse A Larkin, Michael W Lomas, Adam C Martiny
The globally abundant marine Cyanobacteria Prochlorococcus and Synechococcus share many physiological traits but presumably have different evolutionary histories and associated phylogeography. In Prochlorococcus, there is a clear phylogenetic hierarchy of ecotypes, whereas multiple Synechococcus clades have overlapping physiologies and environmental distributions. However, microbial traits are associated with different phylogenetic depths. Using this principle, we reclassified diversity at different phylogenetic levels and compared the phylogeography...
October 3, 2018: ISME Journal
Roland C Wilhelm, Rahul Singh, Lindsay D Eltis, William W Mohn
Delignification, or lignin-modification, facilitates the decomposition of lignocellulose in woody plant biomass. The extant diversity of lignin-degrading bacteria and fungi is underestimated by culture-dependent methods, limiting our understanding of the functional and ecological traits of decomposers populations. Here, we describe the use of stable isotope probing (SIP) coupled with amplicon and shotgun metagenomics to identify and characterize the functional attributes of lignin, cellulose and hemicellulose-degrading fungi and bacteria in coniferous forest soils from across North America...
September 26, 2018: ISME Journal
Stefan Lambert, Margot Tragin, Jean-Claude Lozano, Jean-François Ghiglione, Daniel Vaulot, François-Yves Bouget, Pierre E Galand
Seasonality in marine microorganisms has been classically observed in phytoplankton blooms, and more recently studied at the community level in prokaryotes, but rarely investigated at the scale of individual microbial taxa. Here we test if specific marine eukaryotic phytoplankton, bacterial and archaeal taxa display yearly rhythms at a coastal site impacted by irregular environmental perturbations. Our seven-year study in the Bay of Banyuls (North Western Mediterranean Sea) shows that despite some fluctuating environmental conditions, many microbial taxa displayed significant yearly rhythms...
September 25, 2018: ISME Journal
Shao-Peng Li, Jiaqi Tan, Xian Yang, Chao Ma, Lin Jiang
There is increasing awareness of invasion in microbial communities worldwide, but the mechanisms behind microbial invasions remain poorly understood. Specifically, we know little about how the evolutionary and ecological differences between invaders and natives regulate invasion success and impact. Darwin's naturalization hypothesis suggests that the phylogenetic distance between invaders and natives could be a useful predictor of invasion, and modern coexistence theory proposes that invader-native niche and fitness differences combine to determine invasion outcome...
September 25, 2018: ISME Journal
Sandra V Flechas, Alejandro Acosta-González, Laura A Escobar, Jordan G Kueneman, Zilpa Adriana Sánchez-Quitian, Claudia M Parra-Giraldo, Louise A Rollins-Smith, Laura K Reinert, Vance T Vredenburg, Adolfo Amézquita, Douglas C Woodhams
Management of hyper-virulent generalist pathogens is an emergent global challenge, yet for most disease systems we lack a basic understanding as to why some host species suffer mass mortalities, while others resist epizootics. We studied two sympatric species of frogs from the Colombian Andes, which coexist with the amphibian pathogen Batrachochytrium dendrobatidis (Bd), to understand why some species did not succumb to the infection. We found high Bd prevalence in juveniles for both species, yet infection intensities remained low...
September 25, 2018: ISME Journal
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