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Jordan C Angle, Timothy H Morin, Lindsey M Solden, Adrienne B Narrowe, Garrett J Smith, Mikayla A Borton, Camilo Rey-Sanchez, Rebecca A Daly, Golnazalsdat Mirfenderesgi, David W Hoyt, William J Riley, Christopher S Miller, Gil Bohrer, Kelly C Wrighton
The current paradigm, widely incorporated in soil biogeochemical models, is that microbial methanogenesis can only occur in anoxic habitats. In contrast, here we show clear geochemical and biological evidence for methane production in well-oxygenated soils of a freshwater wetland. A comparison of oxic to anoxic soils reveal up to ten times greater methane production and nine times more methanogenesis activity in oxygenated soils. Metagenomic and metatranscriptomic sequencing recover the first near-complete genomes for a novel methanogen species, and show acetoclastic production from this organism was the dominant methanogenesis pathway in oxygenated soils...
November 16, 2017: Nature Communications
Alyse K Hawley, Masaru K Nobu, Jody J Wright, W Evan Durno, Connor Morgan-Lang, Brent Sage, Patrick Schwientek, Brandon K Swan, Christian Rinke, Monica Torres-Beltrán, Keith Mewis, Wen-Tso Liu, Ramunas Stepanauskas, Tanja Woyke, Steven J Hallam
Microbial communities drive biogeochemical cycles through networks of metabolite exchange that are structured along energetic gradients. As energy yields become limiting, these networks favor co-metabolic interactions to maximize energy disequilibria. Here we apply single-cell genomics, metagenomics, and metatranscriptomics to study bacterial populations of the abundant "microbial dark matter" phylum Marinimicrobia along defined energy gradients. We show that evolutionary diversification of major Marinimicrobia clades appears to be closely related to energy yields, with increased co-metabolic interactions in more deeply branching clades...
November 15, 2017: Nature Communications
Anastasia A Ivanova, Carl-Eric Wegner, Yongkyu Kim, Werner Liesack, Svetlana N Dedysh
Members of the phylum Planctomycetes are common inhabitants of northern Sphagnum-dominated wetlands. Evidence is accumulating that, in these environments, some planctomycetes may be involved in degrading polymeric organic matter. The experimental data, however, remain scarce due to the low number of characterized representatives of this phylum. In a previous study, we used metatranscriptomics to assess the activity response of peat-inhabiting microorganisms to biopolymers abundantly present in native peat. The community responses to cellulose, xylan, pectin, and chitin availability were analysed relative to unamended controls...
November 13, 2017: Antonie Van Leeuwenhoek
Bastian Herzog, Andreas Dötsch, Hilde Lemmer, Harald Horn, Elisabeth Müller
Efficient biodegradation of 5-tolyltriazole (5-TTri) in wastewater treatment would minimize its potential detrimental effects on aquatic systems. Therefore, in order to profile 5-TTri biodegrading activated sludge communities (ASC) by DGGE and NGS, acclimation experiments with (i) easily degradable substrates, and (ii) various complex substrates mimicking wastewater conditions were performed. DGGE revealed four genera: Aminobacter (family Phyllobacteriaceae), Flavobacterium (family Flavobacteriaceae), Pseudomonas (family Pseudomonaceae), and Hydrogenophaga (family Comamonadaceae)...
November 3, 2017: Systematic and Applied Microbiology
Bruno L Mello, Anna M Alessi, Diego M Riaño-Pachón, Eduardo R deAzevedo, Francisco E G Guimarães, Melissa C Espirito Santo, Simon McQueen-Mason, Neil C Bruce, Igor Polikarpov
Background: Using globally abundant crop residues as a carbon source for energy generation and renewable chemicals production stand out as a promising solution to reduce current dependency on fossil fuels. In nature, such as in compost habitats, microbial communities efficiently degrade the available plant biomass using a diverse set of synergistic enzymes. However, deconstruction of lignocellulose remains a challenge for industry due to recalcitrant nature of the substrate and the inefficiency of the enzyme systems available, making the economic production of lignocellulosic biofuels difficult...
2017: Biotechnology for Biofuels
Tim H Mauchline, Rifat Hayat, Ian M Clark, Penny R Hirsch
Metagenomics and metatranscriptomics provide insights into biological processes in complex substrates such as soil, but linking the presence and expression of genes with functions can be difficult. Here we obtain traditional most probable number estimates (MPN) of Rhizobium abundance in soil as a form of sample validation. Our work shows that in the Highfield experiment at Rothamsted, which has three contrasting conditions (> 50 years continual bare fallow, wheat and grassland), MPN based on host plant nodulation assays corroborate metagenomic and metatranscriptomic estimates for R...
November 8, 2017: Letters in Applied Microbiology
Sara Beier, Dandan Shen, Thomas Schott, Klaus Jürgens
The assessment of functional redundancy (FR) is essential to understand community structure-function relationships because FR buffers the functional performance of communities against changes in community composition. We introduce a novel metatranscriptome-based approach to quantify FR, which permits multifunctional aspects to be addressed. FR among prokaryotes was ranked in water samples after exposure to changing salinity. FR was higher for functional categories with mostly broad functions shared among many taxa than for functional categories containing many narrow functions...
November 7, 2017: Molecular Ecology
Divyashri Baraniya, Paolo Nannipieri, Susanne Kublik, Gisle Vestergaard, Michael Schloter, Anne Schöler
While root exudation follows diurnal rhythms, little is known about the consequences for the microbiome of the rhizosphere. In this study, we used a metatranscriptomic approach to analyze the active microbial communities, before and after sunrise, in the rhizosphere of barley. We detected increased activities of many prokaryotic microbial taxa and functions at the pre-dawn stage, compared to post-dawn. Actinomycetales, Planctomycetales, Rhizobiales, and Burkholderiales were the most abundant and therefore the most active orders in the barley rhizosphere...
November 6, 2017: Microbial Ecology
Craig W Herbold, Laura E Lehtovirta-Morley, Man-Young Jung, Nico Jehmlich, Bela Hausmann, Ping Han, Alexander Loy, Michael Pester, Luis A Sayavedra-Soto, Sung-Keun Rhee, James I Prosser, Graeme W Nicol, Michael Wagner, Cécile Gubry-Rangin
Obligate acidophilic members of the thaumarchaeotal genus Candidatus Nitrosotalea play an important role in nitrification in acidic soils, but their evolutionary and physiological adaptations to acidic environments are still poorly understood, with only a single member of this genus (Ca. N. devanaterra) having its genome sequenced. In this study, we sequenced the genomes of two additional cultured Ca. Nitrosotalea strains, extracted an almost complete Ca. Nitrosotalea metagenome-assembled genome from an acidic fen, and performed comparative genomics of the four Ca...
November 2, 2017: Environmental Microbiology
Samir A Shah, Sukirth M Ganesan, Saradhadevi Varadharaj, Shareef M Dabdoub, John D Walters, Purnima S Kumar
We have previously reported that oral biofilms in clinically healthy smokers are pathogen-rich, and that this enrichment occurs within 24 h of biofilm formation. The present investigation aimed to identify a mechanism by which smoking creates this altered community structure. By combining in vitro microbial-mucosal interface models of commensal (consisting of Streptococcus oralis, Streptococcus sanguis, Streptococcus mitis, Actinomyces naeslundii, Neisseria mucosa and Veillonella parvula) and pathogen-rich (comprising S...
2017: NPJ Biofilms and Microbiomes
Lauren B Stadler, Jeseth Delgado Vela, Sunit Jain, Gregory J Dick, Nancy G Love
In addition to removing organics and other nutrients, the microorganisms in wastewater treatment plants (WWTPs) biotransform many pharmaceuticals present in wastewater. The objective of this study was to examine the relationship between pharmaceutical biotransformation and biodiversity in WWTP bioreactor microbial communities and identify taxa and functional genes that were strongly associated with biotransformation. Dilution-to-extinction of an activated sludge microbial community was performed to establish cultures with a gradient of microbial biodiversity...
October 27, 2017: Microbial Biotechnology
Emilie E L Muller, Shaman Narayanasamy, Myriam Zeimes, Cédric C Laczny, Laura A Lebrun, Malte Herold, Nathan D Hicks, John D Gillece, James M Schupp, Paul Keim, Paul Wilmes
The Gram-negative beta-proteobacterium Zoogloea sp. LCSB751 (LMG 29444) was newly isolated from foaming activated sludge of a municipal wastewater treatment plant. Here, we describe its draft genome sequence and annotation together with a general physiological and genomic analysis, as the first sequenced representative of the Zoogloea genus. Moreover, Zoogloea sp. gene expression in its environment is described using metatranscriptomic data obtained from the same treatment plant. The presented genomic and transcriptomic information demonstrate a pronounced capacity of this genus to synthesize poly-β-hydroxyalkanoate within wastewater...
2017: Standards in Genomic Sciences
Ines Krohn-Molt, Malik Alawi, Konrad U Förstner, Alena Wiegandt, Lia Burkhardt, Daniela Indenbirken, Melanie Thieß, Adam Grundhoff, Julia Kehr, Andreas Tholey, Wolfgang R Streit
Microalga are of high relevance for the global carbon cycling and it is well-known that they are associated with a microbiota. However, it remains unclear, if the associated microbiota, often found in phycosphere biofilms, is specific for the microalga strains and which role individual bacterial taxa play. Here we provide experimental evidence that Chlorella saccharophila, Scenedesmus quadricauda, and Micrasterias crux-melitensis, maintained in strain collections, are associated with unique and specific microbial populations...
2017: Frontiers in Microbiology
Julien Crovadore, Vice Soljan, Gautier Calmin, Romain Chablais, Bastien Cochard, François Lefort
Anaerobic digestion is a common method for reducing the amount of sludge solids in used waters and enabling biogas production. The wet oxidation process (WOX) improves anaerobic digestion by converting carbon into methane through oxidation of organic compounds. WOX produces effluents rich in ammonia, which must be removed to maintain the activity of methanogens. Ammonia removal from WOX could be biologically operated by aerobic granules. To this end, granulation experiments were conducted in 2 bioreactors containing an activated sludge (AS)...
October 2017: Heliyon
Heiner Klingenberg, Peter Meinicke
BACKGROUND: Differential expression analysis on the basis of RNA-Seq count data has become a standard tool in transcriptomics. Several studies have shown that prior normalization of the data is crucial for a reliable detection of transcriptional differences. Until now it has not been clear whether and how the transcriptomic approach can be used for differential expression analysis in metatranscriptomics. METHODS: We propose a model for differential expression in metatranscriptomics that explicitly accounts for variations in the taxonomic composition of transcripts across different samples...
2017: PeerJ
Michael D Lee, Eric A Webb, Nathan G Walworth, Fei-Xue Fu, Noelle A Held, Mak A Saito, David A Hutchins
Trichodesmium are globally distributed cyanobacteria whose nitrogen-fixing capabilities fuel primary production in warm, oligotrophic oceans. Like many photoautotrophs, Trichodesmium serve as hosts to various other microorganisms, yet little is known about how this associated community modulates fluxes of environmentally relevant chemical species into and out of the supraorganismal structure. Here we utilized metatranscriptomics to examine gene-expression activities of microbial communities associated with Trichodesmium erythraeum (strain IMS101) using laboratory-maintained enrichment cultures that have previously been shown to harbor similar microbial communities to those of natural populations...
October 20, 2017: Applied and Environmental Microbiology
Daniela Beisser, Nadine Graupner, Lars Grossmann, Henning Timm, Jens Boenigk, Sven Rahmann
BACKGROUND: High-throughput sequencing (HTS) technologies are increasingly applied to analyse complex microbial ecosystems by mRNA sequencing of whole communities, also known as metatranscriptome sequencing. This approach is at the moment largely limited to prokaryotic communities and communities of few eukaryotic species with sequenced genomes. For eukaryotes the analysis is hindered mainly by a low and fragmented coverage of the reference databases to infer the community composition, but also by lack of automated workflows for the task...
October 16, 2017: BMC Genomics
Yu Cao, Séamus Fanning, Sinéad Proos, Kieran Jordan, Shabarinath Srikumar
The development of next generation sequencing (NGS) techniques has enabled researchers to study and understand the world of microorganisms from broader and deeper perspectives. The contemporary advances in DNA sequencing technologies have not only enabled finer characterization of bacterial genomes but also provided deeper taxonomic identification of complex microbiomes which in its genomic essence is the combined genetic material of the microorganisms inhabiting an environment, whether the environment be a particular body econiche (e...
2017: Frontiers in Microbiology
Kevin Anthony Meyer, Timothy W Davis, Susan B Watson, Vincent J Denef, Michelle A Berry, Gregory J Dick
Blooms of the potentially toxic cyanobacterium Microcystis are increasing worldwide. In the Laurentian Great Lakes they pose major socioeconomic, ecological, and human health threats, particularly in western Lake Erie. However, the interpretation of "omics" data is constrained by the highly variable genome of Microcystis and the small number of reference genome sequences from strains isolated from the Great Lakes. To address this, we sequenced two Microcystis isolates from Lake Erie (Microcystis aeruginosa LE3 and M...
2017: PloS One
Chijioke O Elekwachi, Zuo Wang, Xiaofeng Wu, Alaa Rabee, Robert J Forster
Advances in high throughput, next generation sequencing technologies have allowed an in-depth examination of biological environments and phenomena, and are particularly useful for culture-independent microbial community studies. Recently the use of RNA for metatranscriptomic studies has been used to elucidate the role of active microbes in the environment. Extraction of RNA of appropriate quality is critical in these experiments and TRIzol reagent is often used for maintaining stability of RNA molecules during extraction...
2017: Frontiers in Microbiology
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