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. 2019 Apr 11;14(4):e0215328.
doi: 10.1371/journal.pone.0215328. eCollection 2019.

Diversity of the microbial community and cultivable protease-producing bacteria in the sediments of the Bohai Sea, Yellow Sea and South China Sea

Jiang Zhang  1 , Ming Chen  2 , Jiafeng Huang  1 , Xinwu Guo  2 , Yanjiao Zhang  3 , Dan Liu  1 , Ribang Wu  1 , Hailun He  1 , Jun Wang  1   2
Affiliations

Diversity of the microbial community and cultivable protease-producing bacteria in the sediments of the Bohai Sea, Yellow Sea and South China Sea

Jiang Zhang et al. PLoS One. .

Abstract

The nitrogen (N) cycle is closely related to the stability of marine ecosystems. Microbial communities have been directly linked to marine N-cycling processes. However, systematic research on the bacterial community composition and diversity involved in N cycles in different seas is lacking. In this study, microbial diversity in the Bohai Sea (BHS), Yellow Sea (YS) and South China Sea (SCS) was surveyed by targeting the hypervariable V4 regions of the 16S rRNA gene using next-generation sequencing (NGS) technology. A total of 2,505,721 clean reads and 15,307 operational taxonomic units (OTUs) were obtained from 86 sediment samples from the three studied China seas. LEfSe analysis demonstrated that the SCS had more abundant microbial taxa than the BHS and YS. Diversity indices demonstrated that Proteobacteria and Planctomycetes were the dominant phyla in all three China seas. Canonical correspondence analysis (CCA) indicated that pH (P = 0.034) was the principal determining factors, while the organic matter content, depth and temperature had a minor correlated with the variations in sedimentary microbial community distribution. Cluster and functional analyses of microbial communities showed that chemoheterotrophic and aerobic chemoheterotrophic microorganisms widely exist in these three seas. Further research found that the cultivable protease-producing bacteria were mainly affiliated with the phyla Proteobacteria, Firmicutes and Bacteroidetes. It was very clear that Pseudoalteromonadaceae possessed the highest relative abundance in the three sea areas. The predominant protease-producing genera were Pseudoalteromonas and Bacillus. These results shed light on the differences in bacterial community composition, especially protease-producing bacteria, in these three China seas.

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Conflict of interest statement

The authors have the following interests: Ming Chen, Xinwu Guo and Jun Wang are employee of Sanway Gene Technology. There are no patents, products in development or marketed products to declare. This does not alter our adherence to all the PLOS ONE policies on sharing data and materials.

Figures

Fig 1
Fig 1. Geographic location of sampling sites in the YS (Yellow Sea), BHS (Bohai Sea) and SCS (South China Sea).
Fig 2
Fig 2
(a) Boxplot of Simpson indices calculated using the OTU data in the three sea areas. (b) Boxplot of Shannon indices calculated using the OTU data in the three sea areas. (c) Venn diagram denoting the number of unique and shared species in the different libraries at the 3% distance level. The yellow circle indicates the YS, the purple circle indicates the BHS, and the green circle indicates the SCS. (d) Diagram showing the relative abundance of bacterial composition in the three sea areas at the phylum level. The red star represents the specific bacterial taxa showing significant differences in one of the three groups.
Fig 3
Fig 3. Taxonomic cladogram produced from LEfSe analysis.
(A) Cladogram representing statistically significant differences in bacterial clades among the three sea areas. Small circles shaded with different colors in the diagram represent abundances of those taxa in the respective group (red, BHS; green, YS; blue, SCS; and yellow, nonsignificant). Each circle’s diameter is proportional to the taxon’s abundance. (B) Indicator of bacterial groups within the three seas of sediments with LDA score ≥ 4.
Fig 4
Fig 4. Histogram method for determining the relative abundance of microorganisms at different inshore sampling sites in the three China seas at the family level.
Fig 5
Fig 5
(a) Cluster analysis showing the similarity of bacterial communities recovered from 86 sampling sites in the SCS, YS and SCS based on the OTU numbers of each sampling station. Eighty-six sampling sites could be classified into seven clusters. (b) Functional analysis of microbial communities. Bubbleplot representing the functional microorganisms in the seven clusters from the three China Seas.
Fig 6
Fig 6
(a) Dot plots of relative abundance. The dot plots show the relative abundance of the four classes of Proteobacteria. (b) Dot plots of the relative abundances of the four genera of Gammaproteobacteria in the three seas. The bar represents the median.
Fig 7
Fig 7
(a) Histogram method for determining the relative abundance of microorganisms at 86 sampling sites in the three China seas at the class level. (b) Relative abundance of microorganisms at ten sites of particular interest. (c) Canonical correspondence analysis (CCA) biplot showing the OTU-level community structure of chosen sampling sites and the physicochemical characteristics.
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The work was supported by the National Natural Science Foundation of China (31370104, 31300005), the Hunan Provincial Natural Science Foundation of China (2018JJ2497), the Opening Foundation of the Chinese National Engineering Research Center for Control and Treatment of Heavy Metal Pollution (No. 2015CNERC-CTHMP-07), the Hunan Provincial Innovation Foundation for Postgraduates (CX2017B074) and the Fundamental Research Funds for the Central Universities of Central South University (2018zzts119, 2018zzts392, 2017zzts076, 2017zzts351). The sediments of the BHS and YS were collected during the Bohai and Yellow Sea oceanological comprehensive scientific investigation organized by the National Nature Science Foundation of China (41349901). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Authors Ming Chen, Xinwu Guo and Jun Wang are employed by Sanway Gene Technology Inc.. Sanway Gene Technology Inc. provided support in the form of salaries for authors MC, XG and JW, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.