Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics.
Kristin BergauerAntonio Fernandez-GuerraJuan A L GarciaRichard R SprengerRamunas StepanauskasMaria G PachiadakiOle Nørregaard JensenGerhard J HerndlPublished in: Proceedings of the National Academy of Sciences of the United States of America (2017)
The phylogenetic composition of the heterotrophic microbial community is depth stratified in the oceanic water column down to abyssopelagic layers. In the layers below the euphotic zone, it has been suggested that heterotrophic microbes rely largely on solubilized particulate organic matter as a carbon and energy source rather than on dissolved organic matter. To decipher whether changes in the phylogenetic composition with depth are reflected in changes in the bacterial and archaeal transporter proteins, we generated an extensive metaproteomic and metagenomic dataset of microbial communities collected from 100- to 5,000-m depth in the Atlantic Ocean. By identifying which compounds of the organic matter pool are absorbed, transported, and incorporated into microbial cells, intriguing insights into organic matter transformation in the deep ocean emerged. On average, solute transporters accounted for 23% of identified protein sequences in the lower euphotic and ∼39% in the bathypelagic layer, indicating the central role of heterotrophy in the dark ocean. In the bathypelagic layer, substrate affinities of expressed transporters suggest that, in addition to amino acids, peptides and carbohydrates, carboxylic acids and compatible solutes may be essential substrates for the microbial community. Key players with highest expression of solute transporters were Alphaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria, accounting for 40%, 11%, and 10%, respectively, of relative protein abundances. The in situ expression of solute transporters indicates that the heterotrophic prokaryotic community is geared toward the utilization of similar organic compounds throughout the water column, with yet higher abundances of transporters targeting aromatic compounds in the bathypelagic realm.
Keyphrases
- organic matter
- microbial community
- amino acid
- antibiotic resistance genes
- poor prognosis
- binding protein
- liquid chromatography
- optical coherence tomography
- induced apoptosis
- healthcare
- protein protein
- mental health
- solid phase extraction
- cancer therapy
- wastewater treatment
- drug delivery
- cell cycle arrest
- long non coding rna
- high resolution
- mass spectrometry
- endoplasmic reticulum stress
- tandem mass spectrometry