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TranscriptomicsMetagenomic, metatranscriptomic and metaproteomic study of enrichment culture of M. oxyfera (denitrifying methanotroph)
DNA, RNA and protein were extracted from the culture and subjected to massive parallel sequencing and nano-LC-MS-MS respectively Combination of these methods enabled the reconstruction of the complete genome sequence of M oxyfera from the metagenome and identification of the functionally relevant en...
ORGANISM(S): Candidatus Methylomirabilis oxyfera 
2010-03-25 | E-GEOD-18535 | biostudies-arrayexpress
ProteomicsIn serach of the pH limit of growth in halo-alkaliphilic cyanobacteria
We cultivated two halo-alkaliphilic cyanobacteria consortia in chemostats at pH 10.2-11.4. One consortium was dominated by Ca. Sodalinema alkaliphilum, the other by a species of Nodosilinea. These two cyanobacteria dominate natural communities in Canadian and Asian alkaline soda lakes. We show that ...
ORGANISM(S): Sodalinema sp. PMC 1182.19 Nodosilinea sp. ATA3-4Q-CV33 
2024-10-17 | PXD052563 | Pride
Halo-alkaliphilic cyanobacteria  chemostat  alkaline soda lakes  ph limit  extremophile  nodosilinea  ca. sodalinema alkaliphilum 
ProteomicsPhysiology, functional genomics and proteomics of Verruconatronum alginilyticum gen. nov., sp. nov., a first haloalkaliphilic representative of the phylum Verrucomicrobiota from soda habitats
Despite cultivation of many representatives of rich bacterial communities inhabiting alkaline soda lakes, members of the bacterial phylum Verrucomicrobiota have so far been detected only by molecular techniques. Here, we used alginate as a selective substrate to enrich and isolate two strains of hal...
ORGANISM(S): Homo sapiens (Human) 
2026-04-17 | PXD071159 | Pride
Alginate Verrucomicrobiota Alkaline soda lake 
UnknownProteomic evidence for aerobic methane production in groundwater by methylotrophic Methylotenera.
Not available
S-EPMC11978286 | biostudies-literature
TranscriptomicsMetatranscriptomic analysis of an anaerobic ammonium oxidizing community dominated by Kuenenia stuttgartiensis
We compiled a metatranscriptome by extracting total RNA (including ribosomes), reverse transcription and solexa sequencing. We obtained quantitative data on the transcription of each orf to assess the importance of each orf to the metabolism of Kuenenia stuttgartiensis The transcriptomic data are co...
ORGANISM(S): Candidatus Kuenenia stuttgartiensis 
2010-03-25 | E-GEOD-15408 | biostudies-arrayexpress
ProteomicsMetaproteomes of cyanobacterial consortium collected from photobioreactors enriched from soda lake microbial mats in BC, Canada
In this work we used metaproteomics to study the effect of pH and nitrogen source on cyanobacterial growth of the laboratory cultures. The database for protein identification was obtained from assembled metagenomes.
ORGANISM(S): Oscillatoriaceae cyanobacterium 
2021-11-02 | PXD024393 | Pride
Cyanobacteria Soda lake 
ProteomicsDifferential proteomics of Lenisia limosa (Breviatea) and its epibiotic Arcobacter symbiont
The Breviatea form a lineage of free-living protists that emerged over 800 million years ago as a sister clade to opistokonta, comprising animals and fungi. Breviates conserved the ability to thrive in absence of oxygen which was an important adaptation to the low oceanic oxygen-levels that prevaile...
ORGANISM(S): Alteromonas macleodii ATCC 27126 Breviatea Arcobacter 
2016-05-25 | PXD003275 | Pride
Symbiosis Q exactive plus Microbial community Easy nlc 1000 Lenisia limosa Lc-ms/ms Metaproteomics 
ProteomicsStable isotope probing with 13C-labeled bicarbonate/proteomics of cyanobacterial consortium collected from photobioreactors enriched from soda lake microbial mats in BC, Canada
In this work we used stable isotope probing/proteomics to study uptake of carbon sources by members of the cyanobacterial consortium. The database for protein identification was obtained from assembled metagenomes.
ORGANISM(S): Phormidium sp. OSCR 
2022-01-21 | PXD028578 | Pride
Heterotrophs Stable isotope probing Cyanobacteria 
ProteomicsProteomics of groundwater microbiomes collected from five wells in Alberta, Canada
Groundwater samples were collected from five wells in Alberta, Canada. The sampling location and time are indicated in the table below. 13 to 29 genomes were assembled from each metagenome. Proteomic analyses were performed to investigate which genomes and genes were expressed in each well. Sample I...
ORGANISM(S): uncultured Methylotenera sp. 
2024-05-21 | PXD044305 | Pride
Metaproteomics Metagenome-assembled-genomes Metaproteome Groundwater 
ProteomicsMetaproteomics of phototrophic biomats from two soda lakes in the Canadian Rocky Mountains
This data is a case study done in the context of developing methods for assessing the taxonomic composition of microbial communities using metaproteomics. For this study with analyzed phototrophic biomats from two Soda Lakes in the Canadian Rocky Mountains using metaproteomics. For protein identific...
ORGANISM(S): Eukaryota (eucaryotes) Bacteria Archaea Viruses 
2017-05-12 | PXD006343 | Pride
1d-lc Metaproteome Metagenomics Biomass assessment Metaproteomics 
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