Variability of Microbial Community Structure Distribution in Marine Shallow Surface Sediments in Shenhu Area

Abstract

Due to the frequent exchange of matter and energy between living and non-living matter in seawater, the surface layer, particularly the distribution of microorganisms in centimeter-scale and element concentrations in surface sediments, demonstrates the important message of the local biogeochemical environment. This work probed the differences in microbial communities between two sampling cores obtained from the same area and the possible environmental factors, e.g., in situ component and concentration in porewater. Here, high-throughput sequencing (16S rRNA, Illumina sequencing) and quantitative PCR analysis were used to investigate the diversity of microorganisms in sediments of two push cores of L1 and S8 from Shenhu Area, South China Sea. Porewater concentration of components and isotopic fractionation were also obtained to explore the possible correlation between the microbial community and the chemical compositions of porewater. Q-PCR revealed bacteria play an important role in the geochemical cycle in the surface sediments, and archaea may be the main community in response to environmental changes and maintain the local marine ecosystem. The total gene copies of microorganisms in the study area were lower than nearby marine sediments. Microbial community compositions showed the dominant microbial phyla were similar on Phylum level in L1 and S8, with only different abundances. Firmicutes and Proteobacter were the main bacterial phyla, while Thaumarchaeota, Lokiarchaeota and Bathyarchaeota dominated the archaeal community. The abundance of the dominant class varied significantly between L1 and S8. Bacilli in Firmicutes and Gammaproteobacteria in Proteobacter were prevalent bacterial class, MGI in Thaumarchaeota was the predominant archaeal class in L1, while Thermoplasmata and Group-C3 dominated in S8. PCoA results showed a clear diversity of bacterial and archaeal communities between these two sites, as well as significant geographic variation in microbial communities. RDA results revealed that a complex combination of environmental factors might correlate to microbial communities in a marine dynamic environment. Here, δ¹³C_DIC, DIC and SO₄^2– were strongly correlated to the bacterial communities, whereas δ¹³C_DIC, Fe²⁺ and SO₄^2– concentration linked to archaeal communities. Microbial communities and RDA results suggested carbon may be the main factor related to the microbial community in L1, while Fe²⁺ correlated with microbial community composition in S8. SO₄^2– concentration and the distribution of Gammaproteobacteria indicated that the sulfur cycle is probably active in this area.

Keywords:

• Shenhu area
• sediments
• porewater
• microorganisms

Acknowledgments

We thank the crew and scientists of the Dongfanghong exploration ship for their supports in sediment samples.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

Both the original pore water data and gene sequencing data are stored in the corresponding public database. The SRA records (sequencing data) will be accessible with the following link after the indicated release date: https://www.ncbi.nlm.nih.gov/sra/SRP145537. And the accession number was PRJNA474456.

Additional information

Funding

This research was supported by NSF program [Grant No. 417760711], Guangdong Provincial Special Fund for Economic Development in 2019 [Grant No. GDOE [2019] A41], Institute of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences [Grant No. ISEE2020YB05], Guangdong Ocean Science and Technology Collaborative Innovation Center [Grant No. 20180207].