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Ecological functions of uncultured microorganisms in the cobalt-rich ferromanganese crust of a seamount in the central Pacific are elucidated by fosmid sequencing

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Abstract

Cobalt-rich ferromanganese is an important seafloor mineral and is abundantly present in the seamount crusts. Such crusts form potential hotspots for biogeochemical activity and microbial diversity, yet our understanding of their microbial communities is lacking. In this study, a cultivation-independent approach was used to recover genomic information and derive ecological functions of the microbes in a sediment sample collected from the cobalt-rich ferromanganese crust of a seamount region in the central Pacific. A total of 78 distinct clones were obtained by fosmid library screening with a 16S rRNA based PCR method. Proteobacteria and MGI Thaumarchaeota dominated the bacterial and archaeal 16S rRNA gene sequence results in the microbial community. Nine fosmid clones were sequenced and annotated. Numerous genes encoding proteins involved in metabolic functions and heavy metal resistance were identified, suggesting alternative metabolic pathways and stress responses that are essential for microbial survival in the cobalt-rich ferromanganese crust. In addition, genes that participate in the synthesis of organic acids and exoploymers were discovered. Reconstruction of the metabolic pathways revealed that the nitrogen cycle is an important biogeochemical process in the cobalt-rich ferromanganese crust. In addition, horizontal gene transfer (HGT) events have been observed, and most of them came from bacteria, with some occurring in archaea and plants. Clone W4-93a, belonging to MGI Thaumarchaeota, contained a region of gene synteny. Comparative analyses suggested that a high frequency of HGT events as well as genomic divergence play important roles in the microbial adaption to the deep-sea environment.

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Authors and Affiliations

  1. Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, 310012, China

    Yingyi Huo, Chunsheng Wang & Xuewei Xu

  2. State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Hangzhou, 310012, China

    Yingyi Huo, Chunsheng Wang & Xuewei Xu

  3. College of Life Sciences, Zhejiang University, Hangzhou, 310058, China

    Hong Cheng, Jie Pan & Min Wu

  4. Marine Biology Laboratory, The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Woods Hole, MA, 02543, USA

    Anton F. Post

  5. State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China

    Xiawei Jiang

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  1. Yingyi Huo
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Correspondence to Xuewei Xu.

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Foundation item: China Ocean Mineral Resources R & D Association COMRA Special Foundation under contract Nos DY125-15-R-03 and DY125-13-E-01; the National Natural Science Foundation of China under contract No. 41276173; the Zhejiang Provincial Natural Science Foundation of China under contract No. LQ13D060002; the Scientific Research Fund of the Second Institute of Oceanography, SOA under contract No. JT1305.

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Huo, Y., Cheng, H., Post, A.F. et al. Ecological functions of uncultured microorganisms in the cobalt-rich ferromanganese crust of a seamount in the central Pacific are elucidated by fosmid sequencing. Acta Oceanol. Sin. 34, 92–113 (2015). https://doi.org/10.1007/s13131-015-0650-7

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