Browse
Submit Data
Databases
API
Help

Dataset Information

64 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Metagenome-Assembled Genome Sequences Recovered from Epilithic River Biofilm in the Tama River, Japan.

ABSTRACT: Draft genome sequences of putatively novel bacteria were assembled from the metagenome of epilithic biofilm samples collected from the Tama River (Tokyo, Japan). The metagenome contains 44,630,724 sequences, 44,792 contigs, and 48% G+C content. Binning resulted in 31 metagenome-assembled genomes (MAGs) with ≥50% completeness.

SUBMITTER: Martinez JN

PROVIDER: S-EPMC8459653 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Metagenome-Assembled Genome Sequences Recovered from Epilithic River Biofilm in the Tama River, Japan.

Martinez Joval N JN Nishihara Arisa A Haruta Shin S

Microbiology resource announcements 20210923 38

Draft genome sequences of putatively novel bacteria were assembled from the metagenome of epilithic biofilm samples collected from the Tama River (Tokyo, Japan). The metagenome contains 44,630,724 sequences, 44,792 contigs, and 48% G+C content. Binning resulted in 31 metagenome-assembled genomes (MAGs) with ≥50% completeness. ...[more]

PMID: 34554005

Similar Datasets

Diversity of purple phototrophic bacteria, inferred from pufM gene, within epilithic biofilm in Tama River, Japan.

Project description:The diversity of purple phototrophic bacteria in algae-dominated biofilm of a streambed in Tama River, Japan was investigated. Clone library analysis of the pufM gene encoding a subunit of the photochemical reaction center of purple bacteria detected 18 operational taxonomic units (OTUs) in several classes of Proteobacteria. Most of the OTUs showed less than 85% identity to the PufM amino acid sequences of known phototrophic bacteria. These results suggest that phylogenetically divergent and unknown purple phototrophic bacteria are present in the epilithic biofilm of the river.

| S-EPMC4036046 | biostudies-literature

Phylogenetically Diverse Aerobic Anoxygenic Phototrophic Bacteria Isolated from Epilithic Biofilms in Tama River, Japan.

Project description:The diversity of aerobic anoxygenic phototrophic (AAP) bacteria in freshwater environments, particularly in rivers, has not been examined in as much detail as in ocean environments. In the present study, we investigated the phylogenetic and physiological diversities of AAP bacteria in biofilms that developed on submerged stones in a freshwater river using culture methods. The biofilms collected were homogenized and inoculated on solid media and incubated aerobically in the dark. Sixty-eight red-, pink-, yellow-, orange-, or brown-colored colonies were isolated, and, of these, 28 isolates contained the photosynthetic pigment, bacteriochlorophyll (BChl) a. Phylogenetic analyses based on 16S rRNA gene sequences showed that the isolates were classified into 14 groups in 8 operational taxonomic units (OTUs) and distributed in the orders Rhodospirillales, Rhodobacterales, and Sphingomonadales of Alphaproteobacteria and in Betaproteobacteria. Physiological analyses confirmed that none of the representative isolates from any of the groups grew under anaerobic phototrophic conditions. Seven isolates in 4 OTUs showed a 16S rRNA gene sequence identity of 98.0% or less with any established species, suggesting the presence of previously undescribed species of AAP bacteria. Six isolates in 2 other OTUs had the closest relatives, which have not been reported to be AAP bacteria. Physiological comparisons among the isolates revealed differences in preferences for nutrient concentrations, BChl contents, and light-harvesting proteins. These results suggest that diverse and previously unknown AAP bacteria inhabit river biofilms.

| S-EPMC5017807 | biostudies-literature

Metagenome-Assembled Genome Sequences of a Biofilm Derived from Marsberg Copper Mine.

Project description:We sequenced the metagenome of a biofilm collected near a leachate stream of the Marsberg copper mine (Germany) and reconstructed eight metagenome-assembled genomes. These genomes yield copper resistance through Cu(I) oxidation via multiple copper oxidases and extrusion through copper-exporting P-type ATPases.

| S-EPMC7849705 | biostudies-literature

Genome Sequences and Metagenome-Assembled Genome Sequences of Microbial Communities Enriched on Phytoplankton Exometabolites.

Project description:We report 11 bacterial draft genome sequences and 38 metagenome-assembled genomes (MAGs) from marine phytoplankton exometabolite enrichments. The genomes and MAGs represent marine bacteria adapted to the metabolite environment of phycospheres, organic matter-rich regions surrounding phytoplankton cells, and are useful for exploring functional and taxonomic attributes of phytoplankton-associated bacterial communities.

| S-EPMC7378039 | biostudies-literature

Bacterial and Archaeal Metagenome-Assembled Genome Sequences from Svalbard Permafrost.

Project description:Permafrost contains one of the least known soil microbiomes, where microbial populations reside in an ice-locked environment. Here, 56 prokaryotic metagenome-assembled genome (MAG) sequences from 13 phyla are reported. These MAGs will provide information on metabolic pathways that could mediate biogeochemical cycles in Svalbard permafrost.

| S-EPMC6606907 | biostudies-literature

Draft Metagenome-Assembled Genome Sequences of Three Novel Ammonia-Oxidizing <i>Nitrososphaera</i> Strains Recovered from Agricultural Soils in Western Colorado.

Project description:Microbial nitrification is critical to nitrogen loss from agricultural soils. Here, we report three thaumarchaeotal metagenome-assembled genomes (MAGs) representing a new species of Nitrososphaera. These genomes expand the representation of archaeal nitrifiers recovered from arid, agricultural soils.

| S-EPMC9476989 | biostudies-literature

Archaeal and Bacterial Metagenome-Assembled Genome Sequences Derived from Pig Feces.

Project description:We report the recovery of metagenome-assembled genomes (MAGs) from fecal samples collected in 2018 from five healthy adult female pigs in southeast England. The resulting nonredundant catalog of 192 MAGs encompasses 102 metagenomic species, 41 of them novel, spanning 10 bacterial and 2 archaeal phyla.

| S-EPMC8772591 | biostudies-literature

Metagenomes and Metagenome-Assembled Genome Sequences from Nitrogen-Fixing Alder Nodules.

Project description:Bacterial nitrogen (N) fixation in alder nodules is a key process providing nitrogen to nutrient-limited arctic biomes. Here, 45 prokaryotic metagenome-assembled genome (MAG) sequences from root nodules of arctic alder are reported.

| S-EPMC10190285 | biostudies-literature

Metagenome-Assembled Genome Sequences from Different Wastewater Treatment Stages in Germany.

Project description:Metagenome-assembled genome sequences (MAGs) were generated from two wastewater treatment systems in two German cities (Göttingen and Greifswald), based on metagenomes derived from hospital effluent, different wastewater treatment stages, and adjacent water bodies. The MAGs mainly originated from bacterial members of Proteobacteria, Bacteroidota, Firmicutes, "Candidatus Patescibacteria," Actinobacteriota, Chloroflexota, Desulfobacterota, and Verrucomicrobiota.

| S-EPMC8265224 | biostudies-literature

Reconstruction of Bacterial Metagenome-Assembled Genome Sequences from Alpine Bog Vegetation.

Project description:Bacteria are essential constituents of bog ecosystems. Here, we report 44 bacterial genome sequences reconstructed from metagenomes sampled across 12 plant species representing Alpine bog vegetation. This resource will facilitate further exploration of the genetic potential of these bacteria and allow researchers to refine their ecological roles in association with their plant hosts.

| S-EPMC7453291 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data