Bacterial and Archaeal Communities in Sediments from the Adjacent Waters of Rushan Bay (China) Revealed by Illumina Sequencing

Abstract

In this study, bacterial and archaeal communities in sediments from the adjacent waters of Rushan Bay were studied based on 16S ribosomal RNA (rRNA) gene. Illumina sequencing and quantitative PCR (qPCR) analyses were used to analyze the bacterial and archaeal community characteristics. The ecological analyses of sequences revealed that the diversity of bacterial communities was higher than that of archaeal communities. The abundance of bacterial 16S rRNA genes was observed to be greater than that of archaeal 16S rRNA genes. Proteobacteria and Piscirickettsiaceae were the most abundant bacterial phylum and family; Thaumarchaeota dominated the archaeal communities, and MGI in Thaumarchaeota and Halobacteria in Euryarchaeota were prevalent and the predominant archaeal class in this study. Temperature and ammonium concentration were related to the bacterial communities, whereas the nitrite concentration and ammonium concentration had a correlation with the archaeal communities; meanwhile, a complex combination of environmental factors might shape the bacterial and archaeal communities in this dynamic environment. Functional Annotation of Prokaryotic Taxa (FAPROTAX) analysis showed that most bacterial sequences were involved in chemoheterotrophy, sulfate respiration, respiration of sulfur compounds, aerobic nitrite oxidation and nitrification; for the archaeal communities, the essential ecological functions were chemoheterotrophy, other ecological functions such as aerobic ammonia oxidation and methanogenesis, were also predicted to be present in this study. The comparison of bacterial and archaeal communities in different environments suggest that similar conditions are hypothesized to give rise to similar microbial communities, and environmental conditions may contribute significantly to the bacterial and archaeal community structure.

Keywords:

• Illumina sequencing
• microbial community
• 16S rRNA gene
• Rushan Bay
• sediment

Acknowledgments

The authors are grateful to Dr Xianbin Ran, Dr Jun Liu, and Dr Hualong Wang for their assistance with the collection of samples and geochemical data during the cruises. The authors also thank the Marine Ecology Research Center of the First Institute of Oceanography, State Oceanic Administration, People’s Republic of China for the determination of environmental factors.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was supported by the National Natural Science Foundation of China [41620104001 and 41521064]; the Scientific and Technological Innovation Project of the Qingdao National Laboratory for Marine Science and Technology [2016ASKJ02]; and the Open Fund of Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, and Laboratory for Marine Ecology and Environmental Science, National Laboratory for Marine Science and Technology (Qingdao) [KLMEES201601].