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Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments
- Source :
- The ISME Journal, EPIC3The ISME Journal, 10(8), pp. 1939-1953, ISSN: 1751-7362
- Publication Year :
- 2016
- Publisher :
- Springer Science and Business Media LLC, 2016.
-
Abstract
- Marine sediments are the largest carbon sink on earth. Nearly half of dark carbon fixation in the oceans occurs in coastal sediments, but the microorganisms responsible are largely unknown. By integrating the 16S rRNA approach, single-cell genomics, metagenomics and transcriptomics with (14)C-carbon assimilation experiments, we show that uncultured Gammaproteobacteria account for 70-86% of dark carbon fixation in coastal sediments. First, we surveyed the bacterial 16S rRNA gene diversity of 13 tidal and sublittoral sediments across Europe and Australia to identify ubiquitous core groups of Gammaproteobacteria mainly affiliating with sulfur-oxidizing bacteria. These also accounted for a substantial fraction of the microbial community in anoxic, 490-cm-deep subsurface sediments. We then quantified dark carbon fixation by scintillography of specific microbial populations extracted and flow-sorted from sediments that were short-term incubated with (14)C-bicarbonate. We identified three distinct gammaproteobacterial clades covering diversity ranges on family to order level (the Acidiferrobacter, JTB255 and SSr clades) that made up >50% of dark carbon fixation in a tidal sediment. Consistent with these activity measurements, environmental transcripts of sulfur oxidation and carbon fixation genes mainly affiliated with those of sulfur-oxidizing Gammaproteobacteria. The co-localization of key genes of sulfur and hydrogen oxidation pathways and their expression in genomes of uncultured Gammaproteobacteria illustrates an unknown metabolic plasticity for sulfur oxidizers in marine sediments. Given their global distribution and high abundance, we propose that a stable assemblage of metabolically flexible Gammaproteobacteria drives important parts of marine carbon and sulfur cycles.
- Subjects :
- 0301 basic medicine
Geologic Sediments
Oceans and Seas
030106 microbiology
Biology
Microbiology
Carbon Cycle
Carbon cycle
03 medical and health sciences
Microbial ecology
Gammaproteobacteria
14. Life underwater
Ecology, Evolution, Behavior and Systematics
Geography
Ecology
Geomicrobiology
Gene Expression Profiling
Carbon fixation
Australia
Carbon sink
Sequence Analysis, DNA
15. Life on land
biology.organism_classification
Anoxic waters
Carbon
Europe
Microbial population biology
13. Climate action
Original Article
Metagenomics
Oxidation-Reduction
Sulfur
Subjects
Details
- ISSN :
- 17517370 and 17517362
- Volume :
- 10
- Database :
- OpenAIRE
- Journal :
- The ISME Journal
- Accession number :
- edsair.doi.dedup.....6f2829b98275357d24806f3c328d86ea