Composition and distribution of methane metabolic archaea in oceanic surface sediments
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摘要: 海洋沉积物中的甲烷代谢微生物是甲烷循环的关键参与者，其代谢过程对大气甲烷浓度及全球气候变化具有显著影响，研究其在全球大洋沉积物中的组成及分布特征是探究微生物介导甲烷循环的基础。采用焦磷酸454高通量测序测定甲烷代谢保守功能基因mcrA（Methyl coenzyme–M reductase A）分析全球大洋沉积物中甲烷代谢微生物群落的组成和多样性；结合荧光实时定量PCR技术检测了古菌和甲烷代谢古菌的丰度分布特征。与其他海洋生境对比，大洋沉积物中甲烷代谢古菌群落结构单一，大西洋和印度洋的α多样性指数显著高于太平洋（p<0.05）。在大洋沉积物样品中鉴定到3个目的甲烷代谢古菌，即甲烷杆菌目（Methanobacteriales）、甲烷八叠球菌目（Methanosarcinales）和甲烷微菌目（Methanomicrobiales），其中甲烷微菌目占绝对优势，并主要由一簇未知类群（暂名Oceanic Sediments Dominant group，OSD group）组成。大洋沉积物的古菌16S rRNA基因丰度（湿重，下同）平均为8.81×106 copies/g，大西洋的低于印度洋和太平洋；马里亚纳海沟基因丰度低于南海北部，且随着采样深度增加而呈降低趋势。大洋沉积物的mcrA基因丰度为1.38×103～8.25×104 copies/g。基因丰度大西洋最高，太平洋次之，印度洋最低；马里亚纳海沟略高于南海。本研究发现，相较于冷泉、热液、近海河口等海洋生境，大洋沉积物中甲烷代谢古菌丰度低且群落结构单一，不同海区样品间具有极高的相似性；同时发现OSD group是全球大洋沉积物样品的绝对优势类群，其与已知类群序列亲缘关系均较远，分类进化地位尚不明晰，值得进一步研究。Abstract: The microorganisms that generate and utilize methane are recognized as the key parts of global methane cycle, and their metabolic process has significant effects on global climate change. The knowledge upon composition and distribution characteristics of these methane metabolic microorganisms in global ocean sediments is the basis to understand the participation of methane metabolizing microorganisms in marine sediments in methane cycle. Pyrosequencing based on functional gene mcrA (methyl coenzyme-M reductase A) was applied to study the community composition and abundance of methane metabolic microbes in global ocean sediments, and their abundance together with those of archaea were estimated with fluorescence real-time quantitative PCR. Compared with other marine habitats, the methane metabolic archaeal communities in the deep ocean sediments had a much lower diversity and simpler community structure. The α-diversity in Atlantic Ocean and Indian Ocean was significantly higher than that in the Pacific Ocean (p<0.05). Methanogens revealed from this study belong to three orders, Methanobacteriales, Methanosarcinales, and Methanomicrobiales. Methanomicrobiales as the dominant one was predominated by an unknown OSD group. The average abundance (wet weight, the same below) of archaeal 16S rRNA gene in all sediments was 8.81×106 copies/g. Those in Atlantic Ocean was lower than the other two oceans; while those in the Mariana Trench was lower than in the northern part of the South China Sea, and tended to decrease with the increase of sediment depth. The abundance of mcrA gene in all sediment samples was 1.38×103–8.25×104 copies/g. Those in Atlantic Ocean was the highest. It revealed that low abundance and diversity of methane metabolic archaea in the deep-sea sediments, and the high similarities among different communities among samples in different oceans. In addition, the OSD group recovered as the predominant group in this study had no close relationship with any other known genotypes in the GenBank, therefore, its taxonomic status was unknown and deserve further study.
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图 2 大洋沉积物甲烷代谢古菌群落的α多样性指数
*代表 p<0.05
Fig. 2 α-diversity index of the methane metabolic microbes in different ocean sediments
* Represents p<0.05
图 3 大洋沉积物样品中甲烷代谢古菌的群落结构
Fig. 3 Community structure of methane metabolic archaea in different ocean sediments
图 4 基于甲烷代谢古菌mcrA基因核酸序列构建的系统进化树
Fig. 4 The phylogenetic tree based on nucleic acid sequence of mcrA gene of methane metabolizing archaea
图 5 大洋沉积物中的古菌16S rRNA和甲烷代谢古菌mcrA基因的丰度分布
Fig. 5 Distribution of abundance of the archaeal 16S rRNA gene and methane metabolic mcrA gene in different marine sediments
表 1 沉积物样品的采样环境参数
Tab. 1 Sampling parameters in different ocean sediments
编号 海区 纬度 经度 站位深度/m 采样时间 A1 南大西洋中脊 13.589 6°S 14.519 3°W 3 203 2012年7月25日 A2 南大西洋中脊 13.355 1°S 14.311 1°W 3 142 2012年7月26日 A3 南大西洋中脊 13.593 5°S 14.519 2°W 3 149 2012年7月27日 A4 南大西洋中脊 13.594 6°S 14.517 7°W 3 073 2012年7月29日 A5 南大西洋中脊 14.056 6°S 14.354 8°W 1 598 2012年8月8日 A6 南大西洋中脊 19.347 3°S 11.923 2°W 2 597 2012年9月25日 A7 南大西洋中脊 19.260 7°S 11.919 8°W 2 621 2012年9月27日 A8 南大西洋中脊 19.408 5°S 11.885 1°W 2 400 2012年9月27日 A9 南大西洋中脊 19.260 7°S 11.930 2°W 2 559 2012年9月30日 I10 西北印度洋脊 3.710 6°N 63.657 3°E 3 690 2013年4月24日 I11 西北印度洋脊 5.716 8°N 61.462 1°E 4 071 2013年4月28日 I12 西北印度洋脊 6.363 2°N 60.525 5°E 2 989 2013年5月1日 I13 西北印度洋脊 9.066 1°N 58.252 7°E 2 844 2013年5月6日 I14 西北印度洋脊 9.774 7°N 57.581 9°E 2 088 2013年5月9日 P15 西太平洋 11.006 5°N 141.952 2°E 7 015 2012年6月30日 P16 西太平洋 11.006 5°N 141.952 2°E 7 015 2012年6月30日 P17 西太平洋 11.006 5°N 141.952 2°E 7 015 2012年6月30日 P18 西太平洋 18.989 1°N 113.924 1°E 1 015 2015年6月29日 P19 西太平洋 18.464 1°N 113.998 1°E 3 681 2015年6月30日 P20 西太平洋 18.563 9°N 113.674 3°E 3 743 2015年7月2日 注：P15–P17号样品，沉积物采集深度分别为0～2 cm、2～5 cm、5～10 cm；其余表层沉积物采集深度均为0～5 cm。 
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