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Adamo M, Voyron S, Girlanda M, Marmeisse R. RNA extraction from decaying wood for (meta)transcriptomic analyses. Can J Microbiol 2017; 63:841-850. [PMID: 28793203 DOI: 10.1139/cjm-2017-0230] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Wood decomposition is a key step of the terrestrial carbon cycle and is of economic importance. It is essentially a microbiological process performed by fungi and to an unknown extent by bacteria. To gain access to the genes expressed by the diverse microbial communities participating in wood decay, we developed an RNA extraction protocol from this recalcitrant material rich in polysaccharides and phenolic compounds. This protocol was implemented on 22 wood samples representing as many tree species from 11 plant families in the Angiosperms and Gymnosperms. RNA was successfully extracted from all samples and converted into cDNAs from which were amplified both fungal and bacterial protein coding genes, including genes encoding hydrolytic enzymes participating in lignocellulose hydrolysis. This protocol applicable to a wide range of decomposing wood types represents a first step towards a metatranscriptomic analysis of wood degradation under natural conditions.
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Affiliation(s)
- Martino Adamo
- a Università degli Studi di Torino, Dipartimento di Scienze della Vita e Biologia dei Sistemi, Viale Mattioli 25, 10125 Torino, Italy.,b Ecologie Microbienne, Université de Lyon, UCBL, CNRS, INRA, 43 boulevard du 11 Novembre 1918, F-69622 Villeurbanne Cedex, France
| | - Samuele Voyron
- a Università degli Studi di Torino, Dipartimento di Scienze della Vita e Biologia dei Sistemi, Viale Mattioli 25, 10125 Torino, Italy
| | - Mariangela Girlanda
- a Università degli Studi di Torino, Dipartimento di Scienze della Vita e Biologia dei Sistemi, Viale Mattioli 25, 10125 Torino, Italy
| | - Roland Marmeisse
- a Università degli Studi di Torino, Dipartimento di Scienze della Vita e Biologia dei Sistemi, Viale Mattioli 25, 10125 Torino, Italy.,b Ecologie Microbienne, Université de Lyon, UCBL, CNRS, INRA, 43 boulevard du 11 Novembre 1918, F-69622 Villeurbanne Cedex, France
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Trujillo-Esquivel E, Franco B, Flores-Martínez A, Ponce-Noyola P, Mora-Montes HM. Purification of Single-Stranded cDNA Based on RNA Degradation Treatment and Adsorption Chromatography. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2016; 35:404-9. [PMID: 27352216 DOI: 10.1080/15257770.2016.1184277] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Analysis of gene expression is a common research tool to study networks controlling gene expression, the role of genes with unknown function, and environmentally induced responses of organisms. Most of the analytical tools used to analyze gene expression rely on accurate cDNA synthesis and quantification to obtain reproducible and quantifiable results. Thus far, most commercial kits for isolation and purification of cDNA target double-stranded molecules, which do not accurately represent the abundance of transcripts. In the present report, we provide a simple and fast method to purify single-stranded cDNA, exhibiting high purity and yield. This method is based on the treatment with RNase H and RNase A after cDNA synthesis, followed by separation in silica spin-columns and ethanol precipitation. In addition, our method avoids the use of DNase I to eliminate genomic DNA from RNA preparations, which improves cDNA yield. As a case report, our method proved to be useful in the purification of single-stranded cDNA from the pathogenic fungus Sporothrix schenckii.
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Affiliation(s)
- Elías Trujillo-Esquivel
- a Departamento de Biología , División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n, col. Noria Alta , Guanajuato , Gto. , México
| | - Bernardo Franco
- a Departamento de Biología , División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n, col. Noria Alta , Guanajuato , Gto. , México
| | - Alberto Flores-Martínez
- a Departamento de Biología , División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n, col. Noria Alta , Guanajuato , Gto. , México
| | - Patricia Ponce-Noyola
- a Departamento de Biología , División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n, col. Noria Alta , Guanajuato , Gto. , México
| | - Héctor M Mora-Montes
- a Departamento de Biología , División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n, col. Noria Alta , Guanajuato , Gto. , México
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Hesse CN, Mueller RC, Vuyisich M, Gallegos-Graves LV, Gleasner CD, Zak DR, Kuske CR. Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests. Front Microbiol 2015; 6:337. [PMID: 25954263 PMCID: PMC4407611 DOI: 10.3389/fmicb.2015.00337] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 04/05/2015] [Indexed: 11/13/2022] Open
Abstract
Anthropogenic N deposition alters patterns of C and N cycling in temperate forests, where forest floor litter decomposition is a key process mediated by a diverse community of bacteria and fungi. To track forest floor decomposer activity we generated metatranscriptomes that simultaneously surveyed the actively expressed bacterial and eukaryote genes in the forest floor, to compare the impact of N deposition on the decomposers in two natural maple forests in Michigan, USA, where replicate field plots had been amended with N for 16 years. Site and N amendment responses were compared using about 74,000 carbohydrate active enzyme transcript sequences (CAZymes) in each metatranscriptome. Parallel ribosomal RNA (rRNA) surveys of bacterial and fungal biomass and taxonomic composition showed no significant differences in either biomass or OTU richness between the two sites or in response to N. Site and N amendment were not significant variables defining bacterial taxonomic composition, but they were significant for fungal community composition, explaining 17 and 14% of the variability, respectively. The relative abundance of expressed bacterial and fungal CAZymes changed significantly with N amendment in one of the forests, and N-response trends were also identified in the second forest. Although the two ambient forests were similar in community biomass, taxonomic structure and active CAZyme profile, the shifts in active CAZyme profiles in response to N-amendment differed between the sites. One site responded with an over-expression of bacterial CAZymes, and the other site responded with an over-expression of both fungal and different bacterial CAZymes. Both sites showed reduced representation of fungal lignocellulose degrading enzymes in N-amendment plots. The metatranscriptome approach provided a holistic assessment of eukaryote and bacterial gene expression and is applicable to other systems where eukaryotes and bacteria interact.
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Affiliation(s)
- Cedar N Hesse
- Bioscience Division, Los Alamos National Laboratory Los Alamos, NM, USA
| | - Rebecca C Mueller
- Bioscience Division, Los Alamos National Laboratory Los Alamos, NM, USA
| | - Momchilo Vuyisich
- Bioscience Division, Los Alamos National Laboratory Los Alamos, NM, USA
| | | | - Cheryl D Gleasner
- Bioscience Division, Los Alamos National Laboratory Los Alamos, NM, USA
| | - Donald R Zak
- Department of Ecology and Evolutionary Biology, School of Natural Resources and Environment, University of Michigan Ann Arbor, MI, USA
| | - Cheryl R Kuske
- Bioscience Division, Los Alamos National Laboratory Los Alamos, NM, USA
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Weber CF, Kuske CR. Comparative assessment of fungal cellobiohydrolase I richness and composition in cDNA generated using oligo(dT) primers or random hexamers. J Microbiol Methods 2011; 88:224-8. [PMID: 22178429 DOI: 10.1016/j.mimet.2011.11.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 11/28/2011] [Accepted: 11/28/2011] [Indexed: 11/30/2022]
Abstract
Understanding soil fungal distribution and activities, particularly at the level of gene expression, is important in unveiling mechanisms regulating their activities in situ. Recent identification of fungal genes involved in carbon cycling has provided the foundation for developing reverse-transcriptase PCR assays to monitor spatiotemporal gene expression patterns in soils and other complex microbial systems. The polyadenylated 3' ends of eukaryotic mRNA transcripts enables the use of oligo(dT) primers for cDNA synthesis, but this can result in the overrepresentation of the 3' end of transcripts in cDNA pools. In an effort to increase the uniformity of transcripts represented in cDNA pools, random hexamers have been used. The use of both priming methods is abundant in the literature, but we do not know how these methods perform relative to each other. We performed comparative richness and compositional analyses of the fungal glycosyl hydrolase family 7 cellobiohydrolase I gene cbhI amplified from soil cDNAs that had been generated using either oligo(dT) primers or random hexamers. Our results demonstrate that similar cbhI richness and composition were recovered using both approaches. Richness estimates and compositional profiles of cbhI sequence libraries generated from random hexamer-primed cDNA were more variable than from libraries generated from oligo(dT) primed cDNA. However, our overall results indicate that, on average, comparable richness and composition were recovered from soil cDNAs when either priming method was used.
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Affiliation(s)
- Carolyn F Weber
- Los Alamos National Laboratory, Bioscience Division, Mail Stop 888, Los Alamos, NM 87545, USA
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