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MetabolomicsCandidatus Alkanophaga archaea from Guaymas Basin hydrothermal vent sediment oxidize petroleum alkanes
Methanogenic and methanotrophic archaea produce and consume the greenhouse gas methane, respectively, using the reversible enzyme methyl-coenzyme M reductase (Mcr). Recently, Mcr variants that can activate multi-carbon alkanes have been recovered from archaeal cultures. These enzymes, called alkyl-c...
2025-07-07 | MTBLS7727 | MetaboLights
MetabolomicsSeagrass excretes sugars to their rhizosphere making them the sweet spots in the sea (Sediment porewater; GC-MS assay)

Seagrasses are one of the most efficient natural sinks of carbon dioxide (CO2) on Earth. Despite covering less than 0.1% of coastal regions, they have the capacity to bury up to 10% of marine organic matter and can bury the same amount of carbon 35 times faster than tropical rainforests. On land,...

2022-01-28 | MTBLS1610 | MetaboLights
TranscriptomicsGene expression profiling as a tool for sediment risk assessment: a pilot study using Caenorhabditis elegans whole genome microarrays
Toxicity of river sediments are assessed using whole sediment toxicity tests with benthic organisms. The challenge, however, is the differentiation between multiple effects caused by complex contaminant mixtures and the unspecific toxicity endpoints such as survival, growth or reproduction. Moreover...
ORGANISM(S): Caenorhabditis elegans 
2008-06-25 | E-GEOD-11837 | biostudies-arrayexpress
ProteomicsImproving protein extraction for metaproteomic analysis of marine sediment with high clay content
Marine sediments harbor highly diverse microbial communities that contribute to global biodiversity and play essential roles in the ecosystem functioning. However, the metaproteome of marine sediments remains poorly understood. Extracting proteins from environmental samples can be challenging, espec...
ORGANISM(S): unclassified Bacteria (miscellaneous) 
2025-05-12 | PXD054260 | Pride
Metaproteomics  marine sediment  protein extraction 
ProteomicsInfluence of seagrass decline on the metabolic profile of sediment microbial communities
Seagrass meadows are highly productive ecosystems that are considered hotspots for carbon sequestration. The decline of seagrass meadows of various species has been documented worldwide, including that of Cymodocea nodosa, a widespread seagrass in the Mediterranean Sea. To assess the influence of se...
ORGANISM(S): Escherichia coli 
2025-08-04 | PXD054602 | Pride
Marine microbial metaproteome 
MetabolomicsViral lysis and host reprogramming impact carbohydrate, amino acid, and osmolyte cycling in salt marsh tidal creek sediments

Salt marshes are highly productive ecosystems where microbial communities drive key

transformations of organic matter at rates often exceeding those of oceanic and inland

environments. Viruses are recognised as important drivers and regulators of global

biogeochemical cycling, y...

2026-06-26 | MTBLS12630 | MetaboLights
TranscriptomicsSediment Series Upper Danube River (Sediment Extract and Freeze-Dried)
The zebrafish embryo has repeatedly proved to be a useful model for the analysis of effects by environmental toxicants. This study was performed to investigate if an approach combining mechanism-specific bioassays with microarray techniques can obtain more in-depth insights into the ecotoxicity of c...
ORGANISM(S): Danio rerio 
2012-12-31 | E-GEOD-31400 | biostudies-arrayexpress
TranscriptomicsHigh-throughput 16S rRNA amplicon pyrosequencing of contaminated aquifer sediment
Contaminated aquifer (Dusseldorf-Flinger, Germany) templates extracted from 5 sediment depths ranging between 6.4 and 8.4 m below ground and over 3 years of sampling were amplified for amplicon pyrosequencing using the primers Ba27f (5’-aga gtt tga tcm tgg ctc ag-3’) and Ba519r (5’- tat tac cgc ggc ...
ORGANISM(S): unidentified 
2012-11-11 | E-GEOD-25345 | biostudies-arrayexpress
TranscriptomicsGene expression analysis of urine sediment: evaluation for potential noninvasive markers of interstitial cystitis/bladder pain syndrome
Purpose: Determine if gene expression profiles in urine sediment could provide non-invasive candidate markers for painful bladder syndrome (PBS) with and/or without Hunner lesions. Materials and Methods: Fresh catheterized urine was collected and centrifuged from control (n = 5), lesion-free (n = 5)...
ORGANISM(S): Homo sapiens 
2012-02-06 | E-GEOD-28242 | biostudies-arrayexpress
TranscriptomicsSediment Extract Series River Rhine
The zebrafish embryo has repeatedly proved to be a useful model for the analysis of effects by environmental toxicants. This proof-of-concept study was performed to investigate if an approach combining mechanism-specific bioassays with microarray techniques can obtain more in-depth insights into the...
ORGANISM(S): Danio rerio 
2012-12-31 | E-GEOD-30594 | biostudies-arrayexpress
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