Soil eukaryotic functional diversity, a metatranscriptomic approach

被引:129
作者
Bailly, Julie
Fraissinet-Tachet, Laurence
Verner, Marie-Christine
Debaud, Jean-Claude
Lemaire, Marc
Wesolowski-Louvel, Micheline
Marmeisse, Roland [1 ]
机构
[1] Univ Lyon 1, Univ Lyon, USC INRA, CNRS,UMR,Ecol Microbienne, Batiment Lwoff,43 Blvd 11 Novembre 1918, F-69622 Villeurbanne, France
[2] Univ Lyon 1, Univ Lyon, BCS, INSA,UCBL,CNRS,UMR, Villeurbanne, France
关键词
cDNA; eukaryotic micro-organisms; metatranscriptome; soil RNA;
D O I
10.1038/ismej.2007.68
中图分类号
Q14 [生态学(生物生态学)];
学科分类号
071012 ; 0713 ;
摘要
To appreciate the functional diversity of communities of soil eukaryotic micro-organisms we evaluated an experimental approach based on the construction and screening of a cDNA library using polyadenylated mRNA extracted from a forest soil. Such a library contains genes that are expressed by each of the different organisms forming the community and represents its metatranscriptome. The diversity of the organisms that contributed to this library was evaluated by sequencing a portion of the 18S rDNA gene amplified from either soil DNA or reverse-transcribed RNA. More than 70% of the sequences were from fungi and unicellular eukaryotes (protists) while the other most represented group was the metazoa. Calculation of richness estimators suggested that more than 180 species could be present in the soil samples studied. Sequencing of 119 cDNA identified genes with no homologues in databases (32%) and genes coding proteins involved in different biochemical and cellular processes. Surprisingly, the taxonomic distribution of the cDNA and of the 18S rDNA genes did not coincide, with a marked under-representation of the protists among the cDNA. Specific genes from such an environmental cDNA library could be isolated by expression in a heterologous microbial host, Saccharomyces cerevisiae. This is illustrated by the functional complementation of a histidine auxotrophic yeast mutant by two cDNA originating possibly from an ascomycete and a basidiomycete fungal species. Study of the metatranscriptome has the potential to uncover adaptations of whole microbial communities to local environmental conditions. It also gives access to an abundant source of genes of biotechnological interest.
引用
收藏
页码:632 / 642
页数:11
相关论文
共 37 条
  • [31] Comparative metagenomics of microbial communities
    Tringe, SG
    von Mering, C
    Kobayashi, A
    Salamov, AA
    Chen, K
    Chang, HW
    Podar, M
    Short, JM
    Mathur, EJ
    Detter, JC
    Bork, P
    Hugenholtz, P
    Rubin, EM
    [J]. SCIENCE, 2005, 308 (5721) : 554 - 557
  • [32] Community structure and metabolism through reconstruction of microbial genomes from the environment
    Tyson, GW
    Chapman, J
    Hugenholtz, P
    Allen, EE
    Ram, RJ
    Richardson, PM
    Solovyev, VV
    Rubin, EM
    Rokhsar, DS
    Banfield, JF
    [J]. NATURE, 2004, 428 (6978) : 37 - 43
  • [33] Environmental genome shotgun sequencing of the Sargasso Sea
    Venter, JC
    Remington, K
    Heidelberg, JF
    Halpern, AL
    Rusch, D
    Eisen, JA
    Wu, DY
    Paulsen, I
    Nelson, KE
    Nelson, W
    Fouts, DE
    Levy, S
    Knap, AH
    Lomas, MW
    Nealson, K
    White, O
    Peterson, J
    Hoffman, J
    Parsons, R
    Baden-Tillson, H
    Pfannkoch, C
    Rogers, YH
    Smith, HO
    [J]. SCIENCE, 2004, 304 (5667) : 66 - 74
  • [34] Prospecting for novel biocatalysts in a soil metagenome
    Voget, S
    Leggewie, C
    Uesbeck, A
    Raasch, C
    Jaeger, KE
    Streit, WR
    [J]. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2003, 69 (10) : 6235 - 6242
  • [35] The genome sequence of Schizosaccharomyces pombe
    Wood, V
    Gwilliam, R
    Rajandream, MA
    Lyne, M
    Lyne, R
    Stewart, A
    Sgouros, J
    Peat, N
    Hayles, J
    Baker, S
    Basham, D
    Bowman, S
    Brooks, K
    Brown, D
    Brown, S
    Chillingworth, T
    Churcher, C
    Collins, M
    Connor, R
    Cronin, A
    Davis, P
    Feltwell, T
    Fraser, A
    Gentles, S
    Goble, A
    Hamlin, N
    Harris, D
    Hidalgo, J
    Hodgson, G
    Holroyd, S
    Hornsby, T
    Howarth, S
    Huckle, EJ
    Hunt, S
    Jagels, K
    James, K
    Jones, L
    Jones, M
    Leather, S
    McDonald, S
    McLean, J
    Mooney, P
    Moule, S
    Mungall, K
    Murphy, L
    Niblett, D
    Odell, C
    Oliver, K
    O'Neil, S
    Pearson, D
    [J]. NATURE, 2002, 415 (6874) : 871 - 880
  • [36] The Sorcerer II Global Ocean Sampling expedition:: Expanding the universe of protein families
    Yooseph, Shibu
    Sutton, Granger
    Rusch, Douglas B.
    Halpern, Aaron L.
    Williamson, Shannon J.
    Remington, Karin
    Eisen, Jonathan A.
    Heidelberg, Karla B.
    Manning, Gerard
    Li, Weizhong
    Jaroszewski, Lukasz
    Cieplak, Piotr
    Miller, Christopher S.
    Li, Huiying
    Mashiyama, Susan T.
    Joachimiak, Marcin P.
    van Belle, Christopher
    Chandonia, John-Marc
    Soergel, David A.
    Zhai, Yufeng
    Natarajan, Kannan
    Lee, Shaun
    Raphael, Benjamin J.
    Bafna, Vineet
    Friedman, Robert
    Brenner, Steven E.
    Godzik, Adam
    Eisenberg, David
    Dixon, Jack E.
    Taylor, Susan S.
    Strausberg, Robert L.
    Frazier, Marvin
    Venter, J. Craig
    [J]. PLOS BIOLOGY, 2007, 5 (03) : 432 - 466
  • [37] Characterization of a novel amylolytic enzyme encoded by a gene from a soil-derived metagenomic library
    Yun, J
    Kang, S
    Park, S
    Yoon, H
    Kim, MJ
    Heu, S
    Ryu, S
    [J]. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2004, 70 (12) : 7229 - 7235