ArticleMicrobial ecology2014
Metaproteomic survey of six aquatic habitats: discovering the identities of microbial populations active in biogeochemical cycling.
Article in Microbial ecology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 40 citations in OpenAlex.
- Hypoxia increases microbial carbon assimilation of taurine in a seasonally anoxic fjord.The ISME journal · 2026Article
- Unlocking Enzyme Discovery: Leveraging Multi-Omics, Machine Learning, and De Novo Design.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Diel cycle of lanthanide-dependent methylotrophy by TMED127/Methylaequorales bacteria in oligotrophic surface seawater.Applied and environmental microbiology · 2025Article
- Aerobic anoxygenic phototrophs play important roles in nutrient cycling within cyanobacterial Microcystis bloom microbiomes.Microbiome · 2024Article
- Tracking nitrogen allocation to proteome biosynthesis in a marine microbial community.Nature microbiology · 2023Article
- Comparative Genomics Provides Insight into the Function of Broad-Host Range Sponge Symbionts.mBio · 2021Article
- Illuminating Key Microbial Players and Metabolic Processes Involved in the Remineralization of Particulate Organic Carbon in the Ocean's Twilight Zone by Metaproteomics.Applied and environmental microbiology · 2021Article
- Bottom-Up Community Proteome Analysis of Saliva Samples and Tongue Swabs by Data-Dependent Acquisition Nano LC-MS/MS Mass Spectrometry.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Mesozooplankton taurine production and prokaryotic uptake in the northern Adriatic Sea.Limnology and oceanography · 2020Article
- Reducing the arbitrary: fuzzy detection of microbial ecotones and ecosystems - focus on the pelagic environment.Environmental microbiome · 2020Article
- Production of Dibromomethane and Changes in the Bacterial Community in Bromoform-Enriched Seawater.Microbes and environments · 2019Article
- MS analysis of a dilution series of bacteria:phytoplankton to improve detection of low abundance bacterial peptides.Scientific reports · 2018Article
- Environmental Microbial Community Proteomics: Status, Challenges and Perspectives.International journal of molecular sciences · 2016Review
- Comprehensive Genomic Analyses of the OM43 Clade, Including a Novel Species from the Red Sea, Indicate Ecotype Differentiation among Marine Methylotrophs.Applied and environmental microbiology · 2016Article
- A Metaproteomic Analysis of the Response of a Freshwater Microbial Community under Nutrient Enrichment.Frontiers in microbiology · 2016Article
- The ecology of pelagic freshwater methylotrophs assessed by a high-resolution monitoring and isolation campaign.The ISME journal · 2015Article
- Article
- A nonpyrrolysine member of the widely distributed trimethylamine methyltransferase family is a glycine betaine methyltransferase.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Our goal is to strengthen the foundations of metaproteomics as a microbial community analysis tool that links the functional identity of actively expressed gene products with host phylogeny. We used shotgun metaproteomics to survey waters in six disparate aquatic habitats (Cayuga Lake, NY; Oneida Lake, NY; Gulf of Maine; Chesapeake Bay, MD; Gulf of Mexico; and the South Pacific). Peptide pools prepared from filter-gathered microbial biomass, analyzed by nano-liquid chromatography-mass spectrometry (MS/MS) generating 9,693 ± 1,073 mass spectra identified 326 ± 107 bacterial proteins per sample. Distribution of proteobacterial (Alpha and Beta) and cyanobacterial (Prochlorococcus and Synechococcus spp.) protein hosts across all six samples was consistent with the previously published biogeography for these microorganisms. Marine samples were enriched in transport proteins (TRAP-type for dicarboxylates and ATP binding cassette (ABC)-type for amino acids and carbohydrates) compared with the freshwater samples. We were able to match in situ expression of many key proteins catalyzing C-, N-, and S-cycle processes with their bacterial hosts across all six habitats. Pelagibacter was identified as the host of ABC-type sugar-, organic polyanion-, and glycine betaine-transport proteins; this extends previously published studies of Pelagibacter's in situ biogeochemical role in marine C- and N-metabolism. Proteins matched to Ruegeria confirmed these organism's role in marine waters oxidizing both carbon monoxide and sulfide. By documenting both processes expressed in situ and the identity of host cells, metaproteomics tested several existing hypotheses about ecophysiological processes and provided fodder for new ones.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.