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Groundwater metagenome

ABSTRACT: Methane production mechanisms in deep subterrestrial environment in Southeastern Kyushu

PROVIDER: PRJDB4560 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR054745_1.fastq.gz	Fastqsanger.gz
	DRR054745_2.fastq.gz	Fastqsanger.gz
	DRR054746_1.fastq.gz	Fastqsanger.gz
	DRR054746_2.fastq.gz	Fastqsanger.gz
	DRR054747_1.fastq.gz	Fastqsanger.gz

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groundwater metagenome

Project description:Microbial methane production in the deep aquifer of accretionary prism in Okinawa Island

| PRJDB5276 | 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-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

groundwater metagenome

Project description:Regional variation of CH4 and N2 production processes in the deep aquifers of an accretionary prism

| PRJDB4666 | 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

lake water metagenome

Project description:Oligotrophication enhances contribution of oxic methane production to atmospheric methane flux from a deep lake (PRJCA026363)

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Interspecies chemical signalling in a methane-oxidizing bacterial community

Project description:Multiple species of bacteria oxidize methane in the environment after it is produced by anaerobic ecosystems. These organisms provide a carbon and energy source for species that cannot oxidize methane themselves, thereby serving a key role in these niches while also sequestering this potent greenhouse gas before it enters the atmosphere. Deciphering the molecular details of how methane-oxidizing bacteria interact in the environment enables us to understand an important aspect that shapes the structure and function these communities. Here we show that many members of the Methylomonas genus possess a LuxR-type acyl-homoserine lactone (acyl-HSL) receptor/transcription factor highly homologous to MbaR from the quorum sensing (QS) system of Methylobacter tundripaludum, another methane-oxidizer that has been isolated from the same environment. We reconstitute this detection system in Escherichia coli and also use mutant and transcriptomic analysis to show that the receptor from Methylomonas species strain LW13 (LW13) is active and alters LW13 gene expression in response to the acyl-HSL produced by M. tundripaludum. These findings provide a molecular mechanism for how two species of bacteria that may compete for resources in the environment can interact in a specific manner through a chemical signal.

2019-01-29 | GSE122293 | GEO

Groundwater Metagenome

Project description:Deep Subsurface Groundwater Metagenome

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Soil metagenome from avocado orchards in Channybearup, Western Australia in 2024

Project description:Metagenome data from soil samples were collected at 0 to 10cm deep from 2 avocado orchards in Channybearup, Western Australia, in 2024. Amplicon sequence variant (ASV) tables were constructed based on the DADA2 pipeline with default parameters.

2025-06-15 | GSE298403 | GEO

groundwater metagenome

Project description:Metagenome deep biosphere Raw sequence reads

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Characterization of the Tumor Immune Microenvironment in Gastric Cancer by Single-Cell RNA Sequencing Analysis

Project description:Gastric cancer tissues were obtained from patients who underwent gastrectomy at Kyushu University Hospital, and single-cell RNA sequencing was performed on the collected samples.

2025-03-24 | GSE268238 | GEO

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