The acclimation process of phytoplankton biomass, carbon fixation and respiration to the combined effects of elevated temperature and pCO2 in the northern South China Sea

ABSTRACTMetagenomics of marine sediments has uncovered a broad diversity of new uncultured taxa and provided insights into their metabolic capabilities. Here, we detected microbial lineages from a sediment core near the Jiulong methane reef of the northern South China Sea (at 1,100-m depth). Assembly and binning of the metagenomes resulted in 11 genomes (>85% complete) that represented nine distinct phyla, including candidate phyla TA06 and LCP-89,Lokiarchaeota,Heimdallarchaeota, and a newly described globally distributed phylum (B38). The genome of LCP-89 has pathways for nitrate, selenate, and sulfate reduction, suggesting that they may be involved in mediating these important processes. B38 are able to participate in the cycling of hydrogen and selenocompounds. Many of these uncultured microbes may also be capable of autotrophic CO2fixation, as exemplified by identification of the Wood-Ljungdahl (W-L) pathway. Genes encoding carbohydrate degradation, W-L pathway, Rnf-dependent energy conservation, and Ni/Fe hydrogenases were detected in the transcriptomes of these novel members. Characterization of these new lineages provides insight to the undescribed branches in the tree of life.IMPORTANCESedimentary microorganisms in the South China Sea (SCS) remain largely unknown due to the complexity of sediment communities impacted by continent rifting and extension. Distinct geochemical environments may breed special microbial communities including microbes that are still enigmatic. Functional inference of their metabolisms and transcriptional activity provides insight in the ecological roles and substrate-based interactivity of these unculturedArchaeaandBacteria. These microorganisms play different roles in utilizing inorganic carbon and scavenging diverse organic compounds involved in the deep-sea carbon cycle. The genomes recovered here contributed undescribed species to the tree of life and laid the foundation for future study on these novel phyla persisting in marginal sediments of the SCS.

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Thaumarchaeotal Signature Gene Distribution in Sediments of the Northern South China Sea: an Indicator of the Metabolic Intersection of the Marine Carbon, Nitrogen, and Phosphorus Cycles?

Applied and Environmental Microbiology ◽

10.1128/aem.03204-12 ◽

2013 ◽

Vol 79 (7) ◽

pp. 2137-2147 ◽

Cited By ~ 40

Author(s):

Hongyue Dang ◽

Haixia Zhou ◽

Jinying Yang ◽

Huangmin Ge ◽

Nianzhi Jiao ◽

...

Keyword(s):

Community Structure ◽

South China Sea ◽

Pore Water ◽

Marine Sediments ◽

South China ◽

Carbon Fixation ◽

Northern South China Sea ◽

Nitrogen And Phosphorus ◽

China Sea ◽

Lipid Biomarker

ABSTRACTThaumarchaeota are abundant and active in marine waters, where they contribute to aerobic ammonia oxidation and light-independent carbon fixation. The ecological function of thaumarchaeota in marine sediments, however, has rarely been investigated, even though marine sediments constitute the majority of the Earth's surface. Thaumarchaeota in the upper layer of sediments may contribute significantly to the reservoir of nitrogen oxides in ocean waters and thus to productivity, including the assimilation of carbon. We tested this hypothesis in the northern South China Sea (nSCS), a section of a large oligotrophic marginal sea with limited influx of nutrients, including nitrogen, by investigating the diversity, abundance, community structure, and spatial distribution of thaumarchaeotal signatures in surface sediments. Quantitative real-time PCR using primers designed to detect 16S rRNA andamoAgenes in sediment community DNA revealed a significantly higher abundance of pertinent thaumarchaeotal than betaproteobacterial genes. This finding correlates with high levels ofhcdgenes, a signature of thaumarchaeotal autotrophic carbon fixation. Thaumarchaeol, a signature lipid biomarker for thaumarchaeota, constituted the majority of archaeal lipids in marine sediments. Sediment temperature and organic P and silt contents were identified as key environmental factors shaping the community structure and distribution of the monitored thaumarchaeotalamoAgenes. When the pore water PO43−concentration was controlled for via partial-correlation analysis, thaumarchaeotalamoAgene abundance significantly correlated with the sediment pore water NO2−concentration, suggesting that theamoA-bearing thaumarchaeota contribute to nitrite production. Statistical analyses also suggest that thaumarchaeotal metabolism could serve as a pivotal intersection of the carbon, nitrogen, and phosphorus cycles in marine sediments.

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