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Community Structure and Function of Planktonic Crenarchaeota: Changes with Depth in the South China Sea

  • Environmental Microbiology
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Abstract

Marine Crenarchaeota represent a widespread and abundant microbial group in marine ecosystems. Here, we investigated the abundance, diversity, and distribution of planktonic Crenarchaeota in the epi-, meso-, and bathypelagic zones at three stations in the South China Sea (SCS) by analysis of crenarchaeal 16S rRNA gene, ammonia monooxygenase gene amoA involved in ammonia oxidation, and biotin carboxylase gene accA putatively involved in archaeal CO2 fixation. Quantitative PCR analyses indicated that crenarchaeal amoA and accA gene abundances varied similarly with archaeal and crenarchaeal 16S rRNA gene abundances at all stations, except that crenarchaeal accA genes were almost absent in the epipelagic zone. Ratios of the crenarchaeal amoA gene to 16S rRNA gene abundances decreased ~2.6 times from the epi- to bathypelagic zones, whereas the ratios of crenarchaeal accA gene to marine group I crenarchaeal 16S rRNA gene or to crenarchaeal amoA gene abundances increased with depth, suggesting that the metabolism of Crenarchaeota may change from the epi- to meso- or bathypelagic zones. Denaturing gradient gel electrophoresis profiling of the 16S rRNA genes revealed depth partitioning in archaeal community structures. Clone libraries of crenarchaeal amoA and accA genes showed two clusters: the “shallow” cluster was exclusively derived from epipelagic water and the “deep” cluster was from meso- and/or bathypelagic waters, suggesting that niche partitioning may take place between the shallow and deep marine Crenarchaeota. Overall, our results show strong depth partitioning of crenarchaeal populations in the SCS and suggest a shift in their community structure and ecological function with increasing depth.

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Acknowledgments

We thank the captain and crew of the RV “Dongfanghong” #2, L. Wang and R. Zong for assistance in collecting the samples, Z. Y. Sun and J. Zhu for providing the temperature and salinity data, and M. H. Dai for providing the dissolved oxygen data. The manuscript benefits from careful reading and constructive comments by James T. Hollibaugh. N. Jiao was supported by MOST (2007CB815900), NSFC (40632013 and 40821063), and SOA (200805068). C. Zhang was supported by NSFC (91028005) and the State Key Laboratory of Marine Geology Lecturer Professorship at Tongji University. A. Hu was supported by the MEL Young Scientist Visiting Fellowship (MELRS1026) from the State Key Laboratory of Marine Environmental Science at Xiamen University.

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  1. State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361005, People’s Republic of China

    Anyi Hu & Nianzhi Jiao

  2. State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, People’s Republic of China

    Chuanlun L. Zhang

  3. Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA

    Chuanlun L. Zhang

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  1. Anyi Hu
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Table S1

Thermocycling condition and efficiency of individual qPCR assay in this study (DOC 39 kb)

Table S2

Summary for qPCR estimates of gene abundance in the samples from the SCS (DOC 71 kb)

Table S3

Summary for qPCR estimates of gene abundance in the particle-associated samples from station Y23 in the SCS (DOC 31 kb)

Fig. S1

Theta-S diagram of the water masses at the sampling stations S2, Z97 and Y23. Locations of water samples used to qPCR analysis are marked with symbols (S2, circles; Z97, rectangles; and Y23, triangles) and samples used to the clone library and DGGE analysis are indicated by arrows. The epipelagia is defined as <200 m depth, the mesopelagia 200–1,000 m depth, and the bathypelagia >1,000 m depth (Arístegui et al. 2009) (DOC 236 kb)

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Hu, A., Jiao, N. & Zhang, C.L. Community Structure and Function of Planktonic Crenarchaeota: Changes with Depth in the South China Sea. Microb Ecol 62, 549–563 (2011). https://doi.org/10.1007/s00248-011-9866-z

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