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"study-abstract": "The present study determines the microbes involved in biofilm formation on polyethylene plastic which was pre-incubated for 6 months in marine conditions and to know the plastic degrading microbial communities, their function, and their role in quorum sensing.",
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"study-abstract": "The anaerobic digestion microbiome has been puzzling us since the dawn of molecular methods for mixed microbial community analysis. Monitoring of the anaerobic digestion microbiome can either take place via a non-targeted holistic evaluation of the microbial community through fingerprinting or by targeted monitoring of selected taxa. Here, we compared four different microbial community fingerprinting methods, i.e., amplicon sequencing, metaproteomics, metabolomics and cytomics, in their ability to characterise the full-scale anaerobic digestion microbiome. Cytometric fingerprinting through cytomics reflects a, for anaerobic digestion, novel, single cell-based approach of direct microbial community fingerprinting by flow cytometry. Three different digester types, i.e., sludge digesters, digesters treating agro-industrial waste and dry anaerobic digesters, each reflected different operational parameters. The alpha-diversity analysis yielded inconsistent results, especially for richness, across the different methods. In contrast, beta-diversity analysis resulted in comparable profiles, even when translated into phyla or functions, with clear separation of the three digester types. In-depth analysis of each method's features i.e., operational taxonomic units, metaproteins, metabolites, and cytometric traits, yielded certain similar features, yet, also some clear differences between the different methods, which was related to the complexity of the anaerobic digestion process. In conclusion, cytometric fingerprinting through flow cytometry is a reliable, fast method for holistic monitoring of the anaerobic digestion microbiome, and the complementary identification of key features through other methods could give rise to a direct interpretation of anaerobic digestion process performance.",
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"study-abstract": "We evaluated the efficacy of mycobiome analysis strategies using three NGS techniques, Illumina MiSeq, Life Technologies IonPGM, and Pacific Biosciences PacBio RS II sequencing to characterize a mock fungal community consisting of 26 species representing 15 genera.",
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"study-abstract": "We established a novel laboratory system to investigate biodegradation of Macondo oil dispersions (10 m or 30 m median droplet sizes) at low oil concentrations (2 mg L-1) in coastal Norwegian seawater at a temperature of 4-5C. Metagenomic analyses were performed on 0.5 - 1 g whole extracted DNA using Illumina HiSeq 100 bp paired end reads.",
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"study-abstract": "Marine minimum medium was amended with brown algal biomass and antibiotics (kanamycin and streptomycin), and inoculated with a WT or alyA1-deficient strain of Z. galactanivorans. Bacterial communities were characterized by Miseq 16S rRNA-gene sequencing.",
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"centre-name": "University of Manchester",
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"study-abstract": "Safe disposal of nuclear waste necessitates a thorough understanding of the role microorganisms play on the fate of the waste materials over time. In this study we conducted enrichment experiments to assess the potential for plasticised PVC, commonly used in the nuclear industry, to fuel nitrate reduction by a high pH-adapted microbial community at pH 10. Non-plasticised PVC powder served as an additive-free control, and samples of both materials were gamma irradiated (1 MGy) under hyperalkaline conditions, representative of conditioned nuclear waste, to assess the effect of irradiation on bioavailability.",
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"study-abstract": "Difficulties in studying growth dynamics of marine sediment microbial populations in a natural setting limits the ability to identify functions in novel populations, assess competition mechanisms, and extrapolate from growth dynamics in pure cultures. We used qPCR and 16S rRNA gene tag libraries to measure relative growth rates of a microbial community from Cape Lookout Bight, NC, in a laboratory mesocosm. Homogenized sediments were incubated for 122 days, hydrogen concentrations were consistent with thermodynamic control by sulfate-reducing prokaryotes during the sulfate-reducing phase and methanogenesis commenced when hydrogen increased above the methanogen thermodynamic maintenance. Uncultured clades of Methanosarcinales and Methanomicrobiales grew during the methanogenic phase with doubling times ranging from 15-46 days, considerably slower than those grown in pure cultures. An uncultured archaeal group, Kazan-3A-21, also increased with methane production. The majority of the population were from deeply-branching uncultured groups and, like the majority of the putative sulfate reducers, were mostly unresponsive to the shift from sulfate reduction to methanogenesis. We conclude that marine sediment methanogens grow more slowly than cultures, once thermodynamic inhibition by sulfate reducers is alleviated; and the majority of the diversity present in marine sediments grow or die more slowly than could be observed in our 122 day incubation.",
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