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The metabolic core of the prokaryotic community from deep-sea sediments of the southern Gulf of Mexico shows different functional signatures between the continental slope and abyssal plain.

ABSTRACT: Marine sediments harbor an outstanding level of microbial diversity supporting diverse metabolic activities. Sediments in the Gulf of Mexico (GoM) are subjected to anthropic stressors including oil pollution with potential effects on microbial community structure and function that impact biogeochemical cycling. We used metagenomic analyses to provide significant insight into the potential metabolic capacity of the microbial community in Southern GoM deep sediments. We identified genes for hydrocarbon, nitrogen and sulfur metabolism mostly affiliated with Alpha and Betaproteobacteria, Acidobacteria, Chloroflexi and Firmicutes, in relation to the use of alternative carbon and energy sources to thrive under limiting growth conditions, and metabolic strategies to cope with environmental stressors. In addition, results show amino acids metabolism could be associated with sulfur metabolism carried out by Acidobacteria, Chloroflexi and Firmicutes, and may play a crucial role as a central carbon source to favor bacterial growth. We identified the tricarboxylic acid cycle (TCA) and aspartate, glutamate, glyoxylate and leucine degradation pathways, as part of the core carbon metabolism across samples. Further, microbial communities from the continental slope and abyssal plain show differential metabolic capacities to cope with environmental stressors such as oxidative stress and carbon limiting growth conditions, respectively. This research combined taxonomic and functional information of the microbial community from Southern GoM sediments to provide fundamental knowledge that links the prokaryotic structure to its potential function and which can be used as a baseline for future studies to model microbial community responses to environmental perturbations, as well as to develop more accurate mitigation and conservation strategies.

SUBMITTER: Torres-Beltran M

PROVIDER: S-EPMC8679910 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:The prokaryote community activity and structural characteristics within marine sediment sampled across a continental shelf area located off eastern Antarctica (66 degrees S, 143 degrees E; depth range, 709 to 964 m) were studied. Correlations were found between microbial biomass and aminopeptidase and chitinase rates, which were used as proxies for microbial activity. Biomass and activity were maximal within the 0- to 3-cm depth range and declined rapidly with sediment depths below 5 cm. Most-probable-number counting using a dilute carbohydrate-containing medium recovered 1.7 to 3.8% of the sediment total bacterial count, with mostly facultatively anaerobic psychrophiles cultured. The median optimal growth temperature for the sediment isolates was 15 degrees C. Many of the isolates identified belonged to genera characteristic of deep-sea habitats, although most appear to be novel species. Phospholipid fatty acid (PLFA) and isoprenoid glycerol dialkyl glycerol tetraether analyses indicated that the samples contained lipid components typical of marine sediments, with profiles varying little between samples at the same depth; however, significant differences in PLFA profiles were found between depths of 0 to 1 cm and 13 to 15 cm, reflecting the presence of a different microbial community. Denaturing gradient gel electrophoresis (DGGE) analysis of amplified bacterial 16S rRNA genes revealed that between samples and across sediment core depths of 1 to 4 cm, the community structure appeared homogenous; however, principal-component analysis of DGGE patterns revealed that at greater sediment depths, successional shifts in community structure were evident. Sequencing of DGGE bands and rRNA probe hybridization analysis revealed that the major community members belonged to delta proteobacteria, putative sulfide oxidizers of the gamma proteobacteria, Flavobacteria, Planctomycetales, and Archaea. rRNA hybridization analyses also indicated that these groups were present at similar levels in the top layer across the shelf region.

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The metabolic core of the prokaryotic community from deep-sea sediments of the southern Gulf of Mexico shows different functional signatures between the continental slope and abyssal plain.

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