Soil eukaryotic functional diversity, a metatranscriptomic approach - PubMed (original) (raw)
doi: 10.1038/ismej.2007.68. Epub 2007 Sep 20.
Affiliations
- PMID: 18043670
- DOI: 10.1038/ismej.2007.68
Free article
Soil eukaryotic functional diversity, a metatranscriptomic approach
Julie Bailly et al. ISME J. 2007 Nov.
Free article
Abstract
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.
Similar articles
- Molecular characterization of the spatial diversity and novel lineages of mycoplankton in Hawaiian coastal waters.
Gao Z, Johnson ZI, Wang G. Gao Z, et al. ISME J. 2010 Jan;4(1):111-20. doi: 10.1038/ismej.2009.87. Epub 2009 Jul 30. ISME J. 2010. PMID: 19641535 - Screening of a soil metatranscriptomic library by functional complementation of Saccharomyces cerevisiae mutants.
Kellner H, Luis P, Portetelle D, Vandenbol M. Kellner H, et al. Microbiol Res. 2011 Jul 20;166(5):360-8. doi: 10.1016/j.micres.2010.07.006. Epub 2010 Sep 23. Microbiol Res. 2011. PMID: 20869217 - Discovering Protein-Coding Genes from the Environment: Time for the Eukaryotes?
Marmeisse R, Kellner H, Fraissinet-Tachet L, Luis P. Marmeisse R, et al. Trends Biotechnol. 2017 Sep;35(9):824-835. doi: 10.1016/j.tibtech.2017.02.003. Epub 2017 Mar 7. Trends Biotechnol. 2017. PMID: 28279485 Review. - Soil protists: a fertile frontier in soil biology research.
Geisen S, Mitchell EAD, Adl S, Bonkowski M, Dunthorn M, Ekelund F, Fernández LD, Jousset A, Krashevska V, Singer D, Spiegel FW, Walochnik J, Lara E. Geisen S, et al. FEMS Microbiol Rev. 2018 May 1;42(3):293-323. doi: 10.1093/femsre/fuy006. FEMS Microbiol Rev. 2018. PMID: 29447350 Review.
Cited by
- rRNAFilter: A Fast Approach for Ribosomal RNA Read Removal Without a Reference Database.
Wang Y, Hu H, Li X. Wang Y, et al. J Comput Biol. 2017 Apr;24(4):368-375. doi: 10.1089/cmb.2016.0113. Epub 2016 Sep 9. J Comput Biol. 2017. PMID: 27610931 Free PMC article. - Drivers and assemblies of soil eukaryotic microbes among different soil habitat types in a semi-arid mountain in China.
Zhao H, Li X, Zhang Z, Zhao Y, Chen P, Zhu Y. Zhao H, et al. PeerJ. 2018 Dec 5;6:e6042. doi: 10.7717/peerj.6042. eCollection 2018. PeerJ. 2018. PMID: 30568857 Free PMC article. - Expanding the range of the respiratory infectome in Australian feedlot cattle with and without respiratory disease using metatranscriptomics.
Brito BP, Frost MJ, Anantanawat K, Jaya F, Batterham T, Djordjevic SP, Chang WS, Holmes EC, Darling AE, Kirkland PD. Brito BP, et al. Microbiome. 2023 Jul 25;11(1):158. doi: 10.1186/s40168-023-01591-1. Microbiome. 2023. PMID: 37491320 Free PMC article. - Subsurface cycling of nitrogen and anaerobic aromatic hydrocarbon biodegradation revealed by nucleic Acid and metabolic biomarkers.
Yagi JM, Suflita JM, Gieg LM, DeRito CM, Jeon CO, Madsen EL. Yagi JM, et al. Appl Environ Microbiol. 2010 May;76(10):3124-34. doi: 10.1128/AEM.00172-10. Epub 2010 Mar 26. Appl Environ Microbiol. 2010. PMID: 20348302 Free PMC article. - Metatranscriptomics: an approach for retrieving novel eukaryotic genes from polluted and related environments.
Mukherjee A, Reddy MS. Mukherjee A, et al. 3 Biotech. 2020 Feb;10(2):71. doi: 10.1007/s13205-020-2057-1. Epub 2020 Jan 27. 3 Biotech. 2020. PMID: 32030340 Free PMC article. Review.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Molecular Biology Databases