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 - Metagenomics and metatranscriptomics as potential driving forces for the exploration of diversity and functions of micro-eukaryotes in soil.
Yadav BNS, Sharma P, Maurya S, Yadav RK. Yadav BNS, et al. 3 Biotech. 2023 Dec;13(12):423. doi: 10.1007/s13205-023-03841-3. Epub 2023 Nov 30. 3 Biotech. 2023. PMID: 38047037 Free PMC article. Review. - 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.
Cited by
- Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests.
Hesse CN, Mueller RC, Vuyisich M, Gallegos-Graves LV, Gleasner CD, Zak DR, Kuske CR. Hesse CN, et al. Front Microbiol. 2015 Apr 23;6:337. doi: 10.3389/fmicb.2015.00337. eCollection 2015. Front Microbiol. 2015. PMID: 25954263 Free PMC article. - Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome.
Urich T, Lanzén A, Qi J, Huson DH, Schleper C, Schuster SC. Urich T, et al. PLoS One. 2008 Jun 25;3(6):e2527. doi: 10.1371/journal.pone.0002527. PLoS One. 2008. PMID: 18575584 Free PMC article. - Detection of viable Cryptosporidium parvum in soil by reverse transcription-real-time PCR targeting hsp70 mRNA.
Liang Z, Keeley A. Liang Z, et al. Appl Environ Microbiol. 2011 Sep;77(18):6476-85. doi: 10.1128/AEM.00677-11. Epub 2011 Jul 29. Appl Environ Microbiol. 2011. PMID: 21803904 Free PMC article. - Structural and functional diversity of free-living microorganisms in reef surface, Kra island, Thailand.
Somboonna N, Wilantho A, Assawamakin A, Monanunsap S, Sangsrakru D, Tangphatsornruang S, Tongsima S. Somboonna N, et al. BMC Genomics. 2014 Jul 18;15:607. doi: 10.1186/1471-2164-15-607. BMC Genomics. 2014. PMID: 25037613 Free PMC article. - Targeted Metagenomics of Retting in Flax: The Beginning of the Quest to Harness the Secret Powers of the Microbiota.
Djemiel C, Goulas E, Badalato N, Chabbert B, Hawkins S, Grec S. Djemiel C, et al. Front Genet. 2020 Oct 27;11:581664. doi: 10.3389/fgene.2020.581664. eCollection 2020. Front Genet. 2020. PMID: 33193706 Free PMC article. Review.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Molecular Biology Databases