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Freshwater sediment metagenome

ABSTRACT: Methane enrichments of freshwater lake sediment (16S)

PROVIDER: PRJNA253595 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1503560.fastq.gz	Fastqsanger.gz
	SRR1503570.fastq.gz	Fastqsanger.gz
	SRR1503580.fastq.gz	Fastqsanger.gz
	SRR1503590.fastq.gz	Fastqsanger.gz
	SRR1503561.fastq.gz	Fastqsanger.gz

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freshwater sediment metagenome

Project description:Methane enrichments of freshwater lake sediment

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Project description:Methane enrichments of freshwater lake sediment (16S) across a range of oxygen tensions Targeted Locus (Loci)

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A transcriptomics approach to compare transcriptomes of individual methylotrophs from Lake Washington sediment in artificial communities and in pure cultures.

Project description:We established simple synthetic microbial communities in a microcosm model system to determine the mechanisms that underlay cross-feeding in microbial methane-consuming communities. Co-occurring strains from Lake Washington sediment were used that are involved in methane consumption, a methanotroph and two non-methanotrophic methylotrophs.

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QUORUM SENSING IN A METHANE-OXIDIZING BACTERIUM

Project description:Aerobic methanotrophic bacteria use methane as their sole source of carbon and energy and serve as a major sink for the potent greenhouse gas methane in freshwater ecosystems. Despite this important environmental role, little is known about the molecular details of how these organisms interact in the environment. Many bacterial species use quorum sensing systems to regulate gene expression in a density-dependent manner. We have identified a quorum sensing system in the genome of Methylobacter tundripaludum, a dominant methane-oxidizer in methane enrichments of sediment from Lake Washington (Seattle, WA, USA). We determined that M. tundripaludum primarily produces N-3-hydroxydecanoyl-L-homoserine lactone (3-OH-C10-HSL) and that production is governed by a positive feedback loop. We then further characterized this system by determining which genes are regulated by quorum sensing in this methane-oxidizer using RNA-seq, and discovered this system regulates the expression of a novel nonribosomal peptide synthetase biosynthetic gene cluster. These results identify and characterize a mode of cellular communication in an aerobic methane-oxidizing bacterium.

2016-08-16 | GSE85617 | GEO

freshwater sediment metagenome

Project description:Enrichments of ferruginous lake sediment

| PRJNA505658 | ENA

QUORUM SENSING IN A METHANE-OXIDIZING BACTERIUM

Project description:Aerobic methanotrophic bacteria use methane as their sole source of carbon and energy and serve as a major sink for the potent greenhouse gas methane in freshwater ecosystems. Despite this important environmental role, little is known about the molecular details of how these organisms interact in the environment. Many bacterial species use quorum sensing systems to regulate gene expression in a density-dependent manner. We have identified a quorum sensing system in the genome of Methylobacter tundripaludum, a dominant methane-oxidizer in methane enrichments of sediment from Lake Washington (Seattle, WA, USA). We determined that M. tundripaludum primarily produces N-3-hydroxydecanoyl-L-homoserine lactone (3-OH-CÂ10-HSL) and that production is governed by a positive feedback loop. We then further characterized this system by determining which genes are regulated by quorum sensing in this methane-oxidizer using RNA-seq, and discovered this system regulates the expression of a novel nonribosomal peptide synthetase biosynthetic gene cluster. These results identify and characterize a mode of cellular communication in an aerobic methane-oxidizing bacterium. Samples are 2 sets of biological replicates of a Methylobacter tundripaludum strain 21/22 mutant where the acyl-homoserine lactone (AHL) synthase gene mbaI (T451DRAFT_0796) has been deleted. The mutant strain was grown to log (48 hours) or stationary (68 hours) phase in the absence or presence of the AHL 3-OH-C10-HSL.

2016-08-16 | E-GEOD-85617 | biostudies-arrayexpress

sediment metagenome

Project description:Lake Washington sediment enrichments

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Project description:Freshwater metagenome from Lake Washington (methane SIP enrichment)

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Project description:Freshwater sediment microbial communities from Lake Washington, Seattle, for methane and nitrogen Cycles - SIP 13C-methane anaerobic+nitrate metagenome

| PRJNA337721 | ENA

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Project description:Freshwater sediment microbial communities from Lake Washington, Seattle, for methane and nitrogen Cycles - SIP 13C methane aerobic+nitrate metagenome

| PRJNA337722 | ENA

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