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

Date Published: April 11, 2019

Publisher: Public Library of Science

Author(s): Jiang Zhang, Ming Chen, Jiafeng Huang, Xinwu Guo, Yanjiao Zhang, Dan Liu, Ribang Wu, Hailun He, Jun Wang, Marie-Joelle Virolle.


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.

Partial Text

Marine sediment, an important part of the aquatic environment, is a mixture of material deposited on the seafloor that mainly originates from the erosion of continents and the deposition of biological products [1]. Marine sediments are nutrient-rich habitats that harbor diverse microbial communities because of the reservoirs of absorbed nutrients, pesticides, and marine high-molecular-weight organic nitrogen (HMWON) [2, 3]. Subseafloor sediments accumulate large amounts of organic and inorganic materials and contain a highly diverse microbial ecosystem. Sediment microorganisms are very efficient at cycling nutrients, metabolizing foreign compounds in marine ecosystems and colonizing new ecological niches [4]. Among them, heterotrophic bacteria in marine environments are responsible for the degradation of organic biopolymers and the redistribution of organic matter, which have ecological significance in carbon and nitrogen cycling [4]. In recent years, many studies have focused on the microbial diversity of marine sediments. Quaiser et al. reported that the Marmara sediment clustered with the soil metagenome, highlighting the common ecological role of both types of microbial communities in the degradation of organic matter and the completion of biogeochemical cycles [1, 4]. Moreover, Heebok et al. found that the microbial communities in the surface sediments were distinct from those in the subsurface sediments in Jeju Island. Furthermore, this study also provided fundamental information on the potential interactions mediated by microorganisms driving different biogeochemical cycles in coastal sediments [5]. Zeng et al. found that diverse microbial communities inhabit panarctic marine sediments and highlighted the potential roles for Archaea and Bacteria in global biogeochemical cycles in Arctic Kongsfjorden and Sub-Arctic Northern Bering Sea sediments [6]. The nitrogen cycle is an important part of material circulation in the marine ecological system, and many N-cycling processes are microbially mediated [7]. In the marine nitrogen cycle, particulate organic nitrogen (PON) is first decomposed into dissolved inorganic nitrogen (DON) and then ammonified, nitrified, and denitrified, mainly performed by microbial enzymes, especially proteases [8]. Many cultivated bacteria from marine sediments, such as Pseudomonas, Pseudoalteromonas, Alkalimonas collagenimarina, Colwellia, Planococcus, Alteromonas, Marinobacter, Idiomarina, Halomonas, Vibrio, Shewanella and Rheinheimera, have been demonstrated to be protease-producing bacteria [1, 9]. China is a maritime country containing four large offshore seas across the tropical, subtropical and temperate climate zones. There are many untapped microbial resources in the China offshore seas. The China coastal aquaculture is large, and the marine environment has been seriously affected by humans, causing nitrogen enrichment. Thus, the microbial ecosystem, especially protease-producing bacteria of the China offshore seas, has been greatly affected [10]. Research on microbial diversity and protease-producing bacteria in China’s offshore seas will aid in the study of environmental pollution in coastal areas and will help to develop the environmental microbial resources in China. Based on pyrosequencing 16S rRNA gene clone libraries, Zheng et al. observed that the sediment median grain size and dissolved oxygen were major factors regulating bacterial community in the sediment of Liaodong Bay [11]. Protease-producing bacteria belonging to Photobacterium, Bacillus, and Vibrio were the richest cultivated protease-producing bacteria in Jiaozhou Bay marine sediments [7]. Research on the East China Sea showed that most bacteria were present in the 3–5 cm or 5–8 cm sediment layers and Proteobacteria, Chloroflexi, and Planctomycetacia were the dominant cultivable bacteria [10].

Investigating the diversity of microorganisms and protease-producing bacteria in sediments is essential for understanding the ecological role of microorganisms in these habitats; thus, research examining how global biogeochemical cycles function, in which protease-producing bacteria are indispensable participants, is vital to the understanding of organic nitrogen decomposition and recycling processes in marine ecosystems. However, information on the bacterial diversity and the biogeochemical cycles present in most regions is lacking, particularly in Chinese marginal seas where there is intense nitrogen biogeochemical cycling [1, 13]. In this study, using next-generation sequencing technology, the diversity of bacteria in three offshore seas in China were systematically analyzed, collecting a total of 86 sediments from the BHS, YS and SCS. The microbial community composition in different international sea areas showed different phyla distributions. As shown in Table 3, Proteobacteria, as the dominant phylum appeared widely in most marine sediments, which agreed with the results of our study. Many other major phyla mentioned in other marine sediments were abundant in the three China seas as well, such as Planctomycetes, Acidobacteria, Firmicutes, Chloroflexi, Bacteroidetes, Actinobacteria and Gemmatimonadetes, which revealed a similar microbial community composition between the three China seas and other seas.