| HUO Yingyi,CHENG Hong,Anton F. Post,WANG Chunsheng,JIANG Xiawei,PAN Jie,WU Min,XU Xuewei. 2015. Ecological functions of uncultured microorganisms in the cobaltrich ferromanganese crust of a seamount in the central Pacific are elucidated by fosmid sequencing. Acta Oceanologica Sinica, 34(4):92－113 |
| Ecological functions of uncultured microorganisms in the cobaltrich ferromanganese crust of a seamount in the central Pacific are elucidated by fosmid sequencing |
| 基于宏基因组测序研究中太平洋海山富钴结壳区非培养微生物生态功能 |
| Received:January 03, 2014 Revised:July 05, 2014 |
| DOI：10.1007/s13131-015-0650-7 |
| Key words:seamount cobalt-rich ferromanganese crust metagenome horizontal gene transfer |
| 中文关键词: 海山 富钴结壳 宏基因组 水平基因转移 |
| 基金项目: |
| Author Name | Affiliation | E-mail | | HUO Yingyi | Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, China
State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Hangzhou 310012, China | | | CHENG Hong | College of Life Sciences, Zhejiang University, Hangzhou 310058, China | | | Anton F. Post | The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biology Laboratory, Woods Hole, MA 02543, USA | | | WANG Chunsheng | Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, China
State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Hangzhou 310012, China | | | JIANG Xiawei | State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China | | | PAN Jie | College of Life Sciences, Zhejiang University, Hangzhou 310058, China | | | WU Min | College of Life Sciences, Zhejiang University, Hangzhou 310058, China | | | XU Xuewei | Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, China
State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Hangzhou 310012, China | xuxw@sio.org.cn |
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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. |
| 中文摘要: |
| 富钴结壳是一种重要的海底矿产资源.富钴结壳是生物地球化学和微生物学的研究热点,但目前我们对富钴结壳区的微生物群落结构仍缺乏认识.本研究针对中太平洋海山富钴结壳区沉积物,采用非培养方法获得微生物基因组信息并分析其生态学功能.采用PCR的方法筛选得到78个带有16S rRNA基因的克隆.变形杆菌门和奇古菌门MGI类群分别为古菌和细菌的主要类群.测序并分析了9个带有16S rRNA 基因的fosmid克隆.这些克隆中含有较多的代谢相关和重金属抗性相关基因,表明多样的代谢和抗逆途径在微生物适应富钴结壳环境中发挥了重要作用.代谢途径分析表明,氮循环是富钴结壳区一种重要的生物地球化学过程.此外,发现多个水平基因转移事件,这些基因大部分转移自细菌,少量转移自古菌或植物.比较基因组分析表明,属于奇古菌门MGI类群的克隆W4-93包含一段共线性的基因簇.以上结果说明水平基因转移和基因组分歧进化在微生物适应深海环境过程中发挥了重要作用. |
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