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地球科学进展  2014, Vol. 29 Issue (5): 551-558    DOI: 10.11867/j.issn.1001-8166.2014.05.0551
综述与评述     
深海真核微生物多样性研究进展
赵峰, 徐奎栋
中国科学院海洋研究所海洋生物分类与系统演化实验室,山东 青岛 266071
Advances in the Diversity of Microbial Eukaryotes in Deep Sea
Zhao Feng, Xu Kuidong
Institute of Oceanology, Chinese Academy of Sciences, Department of Marine Organism Taxonomy & Phylogeny, Qingdao, 266071
 全文: PDF(942 KB)   HTML
摘要:

真核微生物是深海中数量占优势、多样性高且功能重要的微型生物类群。开展深海真核微生物多样性的研究,将为理解深海生态系统结构以及微型生物多样性及其地理分布提供科学依据。迄今,深海真核微生物多样性的研究明显滞后于原核微生物,对于其形态多样性的认识仍局限于有孔虫等无需培养且通过壳体可直接鉴定的少数类群。分子生物学技术的广泛应用,极大地拓展了对深海真核微生物群落结构和多样性的认识,发现了深海中存在的大量未知的新阶元,揭示了较之形态多样性更高的分子多样性。在综述国内外研究进展的基础上,针对真核微生物多样性的研究策略、存在的问题及未来研究应关注的问题提出了建议。

关键词: 原生生物分子多样性形态多样性原生动物    
Abstract:

Microbial eukaryotes are quantitatively predominant, highly diverse and functionally important groups of eukaryotes in the deep oceans. Investigations on the microbial eukaryotic diversity provide not only the base for elucidating the structure of deepsea ecosystems but also high support for better understanding the microbial diversity and their geographic distribution. So far, the biodiversity research on microbial eukaryotes obviously lags behind that of prokaryotes. Our knowledge of their morphological diversity mainly comes from groups (e.g. foraminiferans) that need not cultivate and are easily identified with external morphology. The application of molecular methods greatly extended our knowledge of the microbial eukaryotic diversity in deep sea, uncovering a much higher molecular than morphological diversity. More and more undescribed taxa and even novel evolutionary lineages of eukaryotes have been discovered from deep sea. By reviewing and summarizing literature data, the authors present the research progress and existing problems in the biodiversity of microbial eukaryotes in deep sea, and propose possible solutions and key issues for future research.

Key words: Protozoa    Protist    Molecular diversity    Morphological diversity.
出版日期: 2014-05-10
:  P735  
基金资助:

中国科学院战略性先导科技专项项目三“深海海洋环境与生态系统”(编号:XDA11030201); 中国科学院海洋研究所“一三五”专项“深海底栖生物生物多样性考察和分类”(编号:2012IO060105)资助.

通讯作者: 徐奎栋 (1969-),男,山东青岛人,研究员,主要从事海洋生物分类与多样性研究. E-mail: kxu@qdio.ac.cn     E-mail: kxu@qdio.ac.cn
作者简介: 赵峰 (1987-),男,黑龙江齐齐哈尔人,博士后,主要从事真核微生物分子生态学研究.E-mail:fzhao@qdio.ac.cn
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引用本文:

赵峰, 徐奎栋. 深海真核微生物多样性研究进展[J]. 地球科学进展, 2014, 29(5): 551-558.

Zhao Feng, Xu Kuidong. Advances in the Diversity of Microbial Eukaryotes in Deep Sea. Advances in Earth Science, 2014, 29(5): 551-558.

链接本文:

http://www.adearth.ac.cn/CN/10.11867/j.issn.1001-8166.2014.05.0551        http://www.adearth.ac.cn/CN/Y2014/V29/I5/551

[1]Ramirez-Llodra E, Brandt A, Danovaro R, et al. Deep, diverse and definitely different: Unique attributes of the world’s largest ecosystem[J]. Biogeosciences, 2010, 7: 2 851-2 899.
[2]Yesson C, Clark M R, Taylor M L, et al. The global distribution of seamounts based on 30 arc seconds bathymetry data[J]. Deep Sea Research Part I: Oceanographic Research Papers, 2011, 58: 442-453.
[3]Zhang Junlong, Xu Kuidong. Progress and prospects in seamount biodiversity[J]. Advances in Earth Science, 2013, 28(11): 1 209-1 216.[张均龙, 徐奎栋. 海山生物多样性研究进展与展望[J]. 地球科学进展, 2013, 28(11): 1 209-1 216.]
[4]Snelgrove P V R, Smith C R. A riot of species in an environmental calm: The paradox of the species-rich deep-sea floor[J]. Oceanography and Marine Biology, 2002, 40: 311-342.
[5]Bik H M, Sung W, De Ley P, et al. Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments[J]. Molecular Ecology, 2012, 21: 1 048-1 059.
[6]Worden A Z, Allen A E. The voyage of the microbial eukaryote[J]. Current Opinion in Microbiology,2010, 13: 652-660.
[7]Scheckenbach F, Hausmann K, Wylezich C, et al. Large-scale patterns in biodiversity of microbial eukaryotes from the abyssal sea floor[J]. Proceedings of the National Academy of Sciences of the United States of America, 2010, 107: 115-120.
[8]Lampitt R S, Salter I, Johns D. Radiolaria: Major exporters of organic carbon to the deep ocean[J]. Global Biogeochemical Cycles, 2009, 23(1),doi:10.1029/2008GB003221.
[9]Gudmundsson G, von Schmalensee M, Svavarsson J. Are foraminifers (Protozoa) important food for small isopods (Crustacea) in the deep sea?[J]. Deep Sea Research Part I:Oceanographic Research Papers, 2000, 47: 2 093-2 109.
[10]Wang Chunsheng, Yang Junyi, Zhang Dongsheng, et al. A review on deep-sea hydrothermal vent communities[J]. Journal of Xiamen University (Natural Science), 2006, 45 (Suppl.2): 141-149.[王春生, 杨俊毅, 张东声, 等.深海热液生物群落研究综述[J]. 厦门大学学报:自然科学版, 2006, 45(增刊2): 141-149.]
[11]Dang Hongyue, Li Tiegang, Zeng Zhigang, et al. Microbiological studies on sub seafloor deep biosphere[J]. Studia Marina Sinica, 2006, 47: 41-60.[党宏月, 李铁刚, 曾志刚, 等.深海极端环境深部生物圈微生物学研究综述[J]. 海洋科学集刊, 2006, 47: 41-60.]
[12]Xi Feng, Zheng Tianling, Jiao Nianzhi, et al. A preliminary analysis of mechanism of deep sea microorganisms diversity[J]. Advances in Earth Science, 2004, 19(1): 38-45.[席峰, 郑天凌, 焦念志, 等.深海微生物多样性形成机制浅析[J]. 地球科学进展, 2004, 19(1): 38-45.]
[13]Xu Kuidong. Biodiversity and biogeography of marine microbenthos: Progress and prospect[J]. Biodiversity Science, 2011, 19(6): 661-675.[徐奎栋. 海洋微型底栖生物的多样性和地理分布[J]. 生物多样性, 2011, 19(6): 661-675.]
[14]Gooday A J, Jorissen F J. Benthic foraminiferal biogeography: Controls on global distribution patterns in deep-water settings[J]. Annual Review of Marine Science, 2012, 4: 237-262.
[15]Gooday A J. Organic-walled allogromiids: Aspects of their occurrence, diversity and ecology in marine habitats[J]. Journal of Foraminiferal Research, 2002, 32: 384-399.
[16]Lecroq B, Lejzerowicz F, Bachar D, et al. Ultra-deep sequencing of foraminiferal microbarcodes unveils hidden richness of early monothalamous lineages in deep-sea sediments[J]. Proceedings of the National Academy of Sciences of the United States of America, 2011, 108: 13 177-13 182.
[17]Sen Gupta B K, Smith L E. Modern benthic foraminifera of the Gulf of Mexico: A census report[J]. Journal of Foraminiferal Research, 2010, 40: 247-265.
[18]Duros P, Fontanier C, Metzger E, et al. Live (stained) benthic foraminifera in the Whittard Canyon, Celtic margin (NE Atlantic)[J]. Deep Sea Research Part I:Oceanographic Research Papers, 2011, 58: 128-146.
[19]Ohkushi K, Natori H. Living benthic foraminifera of the Hess Rise and Suiko Seamount, central North Pacific[J]. Deep Sea Research Part I: Oceanographic Research Papers, 2001, 48: 1 309-1 324.
[20]Corliss B H, Brown C W, Sun X, et al. Deep-sea benthic diversity linked to seasonality of pelagic productivity[J]. Deep Sea Research Part I: Oceanographic Research Papers, 2009, 56: 835-841.
[21]Yasuhara M, Hunt G, van Dijken G, et al. Patterns and controlling factors of species diversity in the Arctic Ocean[J]. Journal of Biogeography, 2012, 39: 2 081-2 088.
[22]Nishimura A, Nakaseko K. Characterization of radiolarian assemblages in the surface sediments of the Antarctic Ocean[J]. Palaeoworld, 2011, 20: 232-251.
[23]Aranda da Silva A, Gooday A J. Large organic-walled Protista (Gromia) in the Arabian Sea: Density, diversity, distribution and ecology[J]. Deep Sea Research Part II:Topical Studies in Oceanography, 2009, 56: 422-433.
[24]Rother N, Gooday A J, Cedhagen T, et al. Biodiversity and distribution of the genus Gromia (Protista, Rhizaria) in the deep Weddell Sea (Southern Ocean)[J]. Polar Biology,2011, 34: 69-81.
[25]Hausmann K, Hulsmann N, Polianski I, et al. Composition of benthic protozoan communities along a depth transect in the eastern Mediterranean Sea[J]. Deep Sea Research Part I:Oceanographic Research Papers, 2002, 49: 1 959-1 970.
[26]Orsi W, Edgcomb V, Faria J, et al. Class Cariacotrichea, a novel ciliate taxon from the anoxic Cariaco Basin, Venezuela[J]. International Journal of Systematic and Evolutionary Microbiology, 2012, 62: 1 425-1 433.
[27]Kudryavtsev A, Pawlowski J. Squamamoeba japonica n. g. n. sp (Amoebozoa): A deep-sea amoeba from the Sea of Japan with a novel cell coat structure[J]. Protist, 2013, 164: 13-23.
[28]Pawlowski J, Christen R, Lecroq B, et al. Eukaryotic richness in the abyss: Insights from pyrotag sequencing[J]. PLoS One, 2011, 6(4):e18169.
[29]Edgcomb V, Orsi W, Bunge J, et al. Protistan microbial observatory in the Cariaco Basin, Caribbean. I. Pyrosequencing vs Sanger insights into species richness[J]. ISME Journal, 2011, 5: 1 344-1 356.
[30]Sauvad A L, Gobet A, Guillou L. Comparative analysis between protist communities from the deep-sea pelagic ecosystem and specific deep hydrothermal habitats[J]. Environmental Microbiology, 2010, 12: 2 946-2 964.
[31]Takishita K, Kakizoe N, Yoshida T, et al. Molecular evidence that phylogenetically diverged ciliates are active in microbial mats of deep-sea cold-seep sediment[J]. Journal of Eukaryotic Microbiology, 2010, 57: 76-86.
[32]Noguchi F, Kawato M, Yoshida T, et al. A novel alveolate in bivalves with chemosynthetic bacteria inhabiting deep-sea methane seeps[J]. Journal of Eukaryotic Microbiology, 2013, 60: 158-165.
[33]Sogin M L, Morrison H G, Huber J A, et al. Microbial diversity in the deep sea and the underexplored "rare biosphere"[J]. Proceedings of the National Academy of Sciences of the United States of America, 2006, 103: 12 115-12 120.
[34]Gong J, Dong J, Liu X, et al. Extremely high copy numbers and polymorphisms of the rDNA operon estimated from single cell analysis of Oligotrich and Peritrich ciliates[J]. Protist, 2013, 164: 369-379.
[35]Bachy C, Dolan J R, Lopez-Garcia P, et al. Accuracy of protist diversity assessments: Morphology compared with cloning and direct pyrosequencing of 18S rRNA genes and ITS regions using the conspicuous tintinnid ciliates as a case study[J]. ISME Journal, 2013, 7: 244-255.
[36]Finlay B J. Global dispersal of free-living microbial eukaryote species[J]. Science, 2002, 296: 1 061-1 063.
[37]Foissner W. Protist diversity and distribution: Some basic considerations[J]. Biodiversity and Conservation, 2008, 17: 235-242.
[38]López-García P, Rodriguez-Valera F, Pedrós-Alió C, et al. Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton[J]. Nature,2001, 409: 603-607.
[39]Quaiser A, Zivanovic Y, Moreira D, et al. Comparative metagenomics of bathypelagic plankton and bottom sediment from the Sea of Marmara[J]. ISME Journal, 2011, 5: 285-304.
[40]Alexander E, Stock A, Breiner H W, et al. Microbial eukaryotes in the hypersaline anoxic L’Atalante deep-sea basin[J]. Environmental Microbiology,2009, 11: 360-381.
[41]Edgcomb V, Orsi W, Leslin C, et al. Protistan community patterns within the brine and halocline of deep hypersaline anoxic basins in the eastern Mediterranean Sea[J]. Extremophiles, 2009, 13: 151-167.
[42]Stock A, Edgcomb V, Orsi W, et al. Evidence for isolated evolution of deepsea ciliate communities through geological separation and environmental selection[J]. BMC Microbiology, 2013, 13:150.
[43]Creer S, Sinniger F. Cosmopolitanism of microbial eukaryotes in the global deep seas[J]. Molecular Ecology, 2012, 21: 1 033-1 035.
[44]Zhao Feng, Xu Kuidong. Methodological advances in soil protozoa research[J]. Chinese Journal of Ecology, 2010, 29(5):1 028-1 034.[赵峰, 徐奎栋. 土壤原生动物研究方法[J]. 生态学杂志, 2010, 29(5):1 028-1 034.]
[45]Countway P D, Gast R J, Savai P, et al. Protistan diversity estimates based on 18S rDNA from seawater incubations in the western North Atlantic[J]. Journal of Eukaryotic Microbiology, 2005, 52: 95-106.
[46]Takishita K, Yubuki N, Kakizoe N, et al. Diversity of microbial eukaryotes in sediment at a deep-sea methane cold seep: Surveys of ribosomal DNA libraries from raw sediment samples and two enrichment cultures[J]. Extremophiles, 2007, 11: 563-576.
[47]Stoeck T, Bass D, Nebel M, et al. Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water[J]. Molecular Ecology, 2010, 19: 21-31.
[48]Lara E, Berney C, Harms H, et al. Cultivation-independent analysis reveals a shift in ciliate 18S rRNA gene diversity in a polycyclic aromatic hydrocarbon-polluted soil[J]. FEMS Microbiology Ecology, 2007,62: 365-373.
[49]Bass D, Cavalier-Smith T. Phylum-specific environmental DNA analysis reveals remarkably high global biodiversity of Cercozoa (Protozoa)[J]. International Journal of Systematic and Evolutionary Microbiology, 2004, 54: 2 393-2 404.
[50]Mardis E R. The impact of next-generation sequencing technology on genetics[J]. Trends in Genetics, 2008, 24: 133-141.
[51]Stoeck T, Zuendorf A, Breiner H W, et al. A molecular approach to identify active microbes in environmental eukaryote clone libraries[J]. Microbial Ecology, 2007, 53: 328-339.
[52]Wang Pinxian.Oceanography from inside the ocean[J]. Advances in Earth Science, 2013, 28(5):517-520.[汪品先. 从海洋内部研究海洋[J].地球科学进展, 2013, 28(5):517-520.]
[53]Qin Yunshan, Yin Hong. Western Pacific: The strategic priority in China deep sea research[J]. Advances in Earth Science, 2011, 26 (3):245-248.[秦蕴珊, 尹宏. 西太平洋——我国深海科学研究的优先战略选区[J]. 地球科学进展, 2011, 26(3):245-248.]
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