Advertisement

Springer Nature is making Coronavirus research free. View research | View latest news | Sign up for updates

Metatranscriptomics: an approach for retrieving novel eukaryotic genes from polluted and related environments

Abstract

Metatranscriptomics, a subset of metagenomics, provides valuable information about the whole gene expression profiling of complex microbial communities of an ecosystem. Metagenomic studies mainly focus on the genomic content and identification of microbes present within a community, while metatranscriptomics provides the diversity of the active genes within such community, their expression profile and how these levels change due to change in environmental conditions. Metatranscriptomics has been applied to different types of environments, from the study of human microbiomes, to those found in plants, animals, within soils and in aquatic systems. Metatranscriptomics, based on the utilization of mRNA isolated from environmental samples, is a suitable approach to mine the eukaryotic gene pool for genes of biotechnological relevance. Also, it is imperative to develop different bioinformatic pipelines to analyse the data obtained from metatranscriptomic analysis. In the present review, we summarise the metatranscriptomics applied to soil environments to study the functional diversity, and discuss approaches for isolating the genes involved in organic matter degradation and providing tolerance to toxic metals, role of metatranscriptomics in microbiome research, various bioinformatics pipelines used in data analysis and technical challenges for gaining biologically meaningful insight of this approach.

This is a preview of subscription content, log in to check access.

Fig. 1
Fig. 2

Modified from Bragalini et al. (2014)

Fig. 3

Adapted from Lehembre et al. (2013) and Ziller et al. (2017)

Fig. 4
Fig. 5

References

  1. Abubucker S, Segata N, Gol J, Schubert AM, Izard J, Cantarel BL, Rodriguez-Mueller B, Zucker J, Thiagarajan M, Henrissat B, White O (2012) Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol 8:e1002358. https://doi.org/10.1371/journal.pcbi.1002358

  2. Allison SD, Martiny JB (2008) Resistance, resilience, and redundancy in microbial communities. Proc Natl Acad Sci USA 105(Supplement 1):11512–11519. https://doi.org/10.1073/pnas.0801925105

  3. Azizan MS, Zamani AI, Stahmann KP, Ng CL (2016) Fungal metabolites and their industrial importance: a brief review. Malays J Biochem Mol Biol 19:15–23

  4. Bailly J, Fraissinet-Tachet L, Verner MC, Debaud JC, Lemaire M, Wésolowski-Louvel MR (2007) Soil eukaryotic functional diversity, a metatranscriptomic approach. ISME J 17:632–642. https://doi.org/10.1038/ismej.2007.68

  5. Bashiardes S, Zilberman-Schapira G, Elinav E (2016) Use of metatranscriptomics in microbiome research. Bioinform Biol insights. https://doi.org/10.4137/BBI.S34610

  6. Bending GD, Rodriguez-Cruz MS, Lincoln SD (2007) Fungicide impacts on microbial communities in soils with contrasting management histories. Chemosphere 69:82–88. https://doi.org/10.1016/j.chemosphere.2007.04.042

  7. Biddle JF, Fitz-Gibbon S, Schuster SC, Brenchley JE, House CH (2008) Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment. Proc Natl Acad Sci USA 105:10583–10588. https://doi.org/10.1073/pnas.0709942105

  8. Binz PA, Kägi JHR (1999) Metallothionein: molecular evolution and classification. In: Klaassen CD (ed) Metallothionein IV. Advances in life sciences. Birkhäuser, Basel, pp 7–13

  9. Blindauer CA (2013) Lessons on the critical interplay between zinc binding and protein structure and dynamics. J Inorg Biochem 121:145–155. https://doi.org/10.1016/j.jinorgbio.2013.01.005

  10. Boekel J, Chilton JM, Cooke IR, Horvatovich PL, Jagtap PD, Käll L, Lehtiö J, Lukasse P, Moerland PD, Griffin TJ (2015) Multi-omic data analysis using Galaxy. Nat Biotechnol 33:137–139. https://doi.org/10.1038/nbt.3134

  11. Botero LM, D’imperio S, Burr M, McDermott TR, Young M, Hassett DJ (2005) Poly (A) polymerase modification and reverse transcriptase PCR amplification of environmental RNA. Appl Environ Microbiol 71:1267–1275. https://doi.org/10.1128/AEM.71.3.1267-1275.2005

  12. Bragalini C, Ribiere C, Parisot N, Vallon L, Prudent E, Peyretaillade E, Girlanda M, Peyret P, Marmeisse R, Luis P (2014) Solution hybrid selection capture for the recovery of functional full-length eukaryotic cDNAs from complex environmental samples. DNA Res. 21:685–694. https://doi.org/10.1093/dnares/dsu030

  13. Brim H, Heyndrickx M, De Vos P, Wilmotte A, Springael D, Schlegel HG, Mergeay M (1999) Amplified rDNA restriction analysis and further genotypic characterisation of metal-resistant soil bacteria and related facultative hydrogenotrophs. Syst Appl Microbiol 22:258–268. https://doi.org/10.1016/S0723-2020(99)80073-3

  14. Capdevila M, Atrian S (2011) Metallothionein protein evolution: a miniassay. J Biol Inorg Chem 16:977–989. https://doi.org/10.1007/s00775-011-0798-3

  15. Carvalhais LC, Dennis PG, Tyson GW, Schenk PM (2012) Application of metatranscriptomics to soil environments. J Microbiol Meth 91:246–251. https://doi.org/10.1016/j.mimet.2012.08.011

  16. Cervantes C, Gutierrez-Corona F (1994) Copper resistance mechanisms in bacteria and fungi. FEMS Microbiol Rev 14:121–137. https://doi.org/10.1111/j.1574-6976.1994.tb00083.x

  17. Chao-Rong GE, Zhang QC (2011) Microbial community structure and enzyme activities in a sequence of copper-polluted soils. Pedosphere 21:164–169. https://doi.org/10.1016/S1002-0160(11)60114-8

  18. Chenchik A, Zhu YY, Diatchenko L, Li R, Hill J, Siebert PD (1998) Generation and use of high-quality cDNA from small amounts of total RNA by SMART PCR. In: Siebert PD, Larrick JW (eds) RT-PCR Methods for gene cloning and analysis. Eaton Publishing, Natick, MA, pp 305–319

  19. Clarke J, Wu HC, Jayasinghe L, Patel A, Reid S, Bayley H (2009) Continuous base identification for single-molecule nanopore DNA sequencing. Nat Nanotechnol 4:265–270. https://doi.org/10.1038/nnano.2009.12

  20. Clement BG, Kehl LE, DeBord KL, Kitts CL (1998) Terminal restriction fragment patterns (TRFPs), a rapid, PCR-based method for the comparison of complex bacterial communities. J Microbiol Meth 31:135–142. https://doi.org/10.1016/S0167-7012(97)00105-X

  21. Comtet-Marre S, Parisot N, Lepercq P, Chaucheyras-Durand F, Mosoni P, Peyretaillade E, Bayat AR, Shingfield KJ, Peyret P, Forano E (2017) Metatranscriptomics reveals the active bacterial and eukaryotic fibrolytic communities in the rumen of dairy cow fed a mixed diet. Front Microbiol 8:67. https://doi.org/10.3389/fmicb.2017.00067

  22. D’Alessio JM, Gerard GF (1988) Second-strand cDNA synthesis with E. coli DNA polymerase I and RNase H: the fate of information at the mRNA 5'terminus and the effect of E. coli DNA ligase. Nucleic Acids Res 16:1999–2014. https://doi.org/10.1093/nar/16.5.1999

  23. Dai X, Tian Y, Li J, Su X, Wang X, Zhao S, Liu L, Luo Y, Liu D, Zheng H, Wang J, Dong Z, Hu S, Huang L (2015) Metatranscriptomic analyses of plant cell wall polysaccharide degradation by microorganisms in the cow rumen. Appl Environ Microbiol 81:1375–1386. https://doi.org/10.1128/AEM.03682-14

  24. Damon C, Vallon L, Zimmermann S, Haider MZ, Galeote V, Dequin S, Luis P, Fraissinet-Tachet L, Marmeisse R (2011) A novel fungal family of oligopeptide transporters identified by functional metatranscriptomics of soil eukaryotes. ISME J 5:1871–1880. https://doi.org/10.1038/ismej.2011.67

  25. Damon C, Lehembre F, Oger-Desfeux C, Luis P, Ranger J, Fraissinet-Tachet L, Marmeisse R (2012) Metatranscriptomics reveals the diversity of genes expressed by eukaryotes in forest soils. PLoS ONE 7:e28967. https://doi.org/10.1371/journal.pone.0028967

  26. Daniel R (2002) Construction of environmental libraries for functional screening of enzyme activity. In: Brakmann S, Johnsson K (eds) Directed molecular evolution of proteins: or how to improve enzymes for biocatalysis, Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, pp 63–78. https://doi.org/10.1002/3527600647.ch4

  27. Daniel R (2005) The metagenomics of soil. Nat Rev Microbiol 3:470–478. https://doi.org/10.1038/nrmicro1160

  28. Degens BP, Schipper LA, Sparling GP, Duncan LC (2001) Is the microbial community in a soil with reduced catabolic diversity less resistant to stress or disturbance? Soil Biol Biochem 33:1143–1153. https://doi.org/10.1016/S0038-0717(01)00018-9

  29. Dell’Amico E, Mazzocchi M, Cavalca L, Allievi L, Andreoni V (2008) Assessment of bacterial community structure in a long-term copper-polluted ex-vineyard soil. Microbiol Res 163:671–683. https://doi.org/10.1016/j.micres.2006.09.003

  30. Deng W, Xi D, Mao H, Wanapat M (2008) The use of molecular techniques based on ribosomal RNA and DNA for rumen microbial ecosystem studies: a review. Mol Biol Rep 35:265–274. https://doi.org/10.1007/s11033-007-9079-1

  31. Dominati E, Patterson M, Mackay A (2010) A framework for classifying and quantifying the natural capital and ecosystem services of soils. Ecol Eng 69:1858–1868. https://doi.org/10.1016/j.ecolecon.2010.05.002

  32. Doran JW, Zeiss MR (2000) Soil health and sustainability: managing the biotic component of soil quality. Appl Soil Ecol 15:3–11. https://doi.org/10.1016/S0929-1393(00)00067-6

  33. Eichner CA, Erb RW, Timmis KN, Wagner-Döbler I (1999) Thermal gradient gel electrophoresis analysis of bioprotection from pollutant shocks in the activated sludge microbial community. Appl Environ Microbiol 65:102–109

  34. Ferrer M, Martínez-Martínez M, Bargiela R, Streit WR, Golyshina OV, Golyshin PN (2016) Estimating the success of enzyme bioprospecting through metagenomics: current status and future trends. Microb Biotechnol 9:22–34. https://doi.org/10.1111/1751-7915.12309

  35. Fierer N, Breitbart M, Nulton J, Salamon P, Lozupone C, Jones R, Robeson M, Edwards RA, Felts B, Rayhawk S, Knight R (2007) Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol 73:7059–7066. https://doi.org/10.1128/AEM.00358-07

  36. Gelsomino A, Keijzer-Wolters AC, Cacco G, van Elsas JD (1999) Assessment of bacterial community structure in soil by polymerase chain reaction and denaturing gradient gel electrophoresis. J Microbiol Meth 38:1–15. https://doi.org/10.1016/S0167-7012(99)000548

  37. Gill SR, Pop M, DeBoy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, Gordon JI, Relman DA, Fraser-Liggett CM, Nelson KE (2006) Metagenomic analysis of the human distal gut microbiome. Science 312:1355–1359. https://doi.org/10.1126/science.1124234

  38. Giller KE, Witter E, Mcgrath SP (1998) Toxicity of heavy metals to microorganisms and microbial processes in agricultural soils: a review. Soil Biol Biochem 30:1389–1414. https://doi.org/10.1016/S0038-0717(97)00270-8

  39. Goldmann K, Schöning I, Buscot F, Wubet T (2015) Forest management type influences diversity and community composition of soil fungi across temperate forest ecosystems. Front Microbiol 6:1300. https://doi.org/10.3389/fmicb.2015.01300

  40. Grant S, Grant WD, Cowan DA, Jones BE, Ma Y, Ventosa A, Heaphy S (2006) Identification of eukaryotic open reading frames in metagenomic cDNA libraries made from environmental samples. Appl Environ Microbiol 72:135–143. https://doi.org/10.1128/AEM.72.1.135-143.2006

  41. Gruninger RJ, Nguyen TTM, Reid ID, Yanke J, Wang P, Abbott DW, Tsang A, McAllister T (2018) Application of transcriptomics to compare the carbohydrate active enzymes that are expressed by diverse genera of anaerobic fungi to degrade plant cell wall carbohydrates. Front Microbiol 9:1581. https://doi.org/10.3389/fmicb.2018.01581

  42. Gubler U, Hoffman BJ (1983) A simple and very efficient method for generating cDNA libraries. Gene 25:263–269. https://doi.org/10.1016/0378-1119(83)90230-5

  43. Gudynaite-Savitch L, White TC (2016) Fungal biotechnology for industrial enzyme production: focus on (Hemi) cellulase production strategies, advances and challenges. In: Schmoll M, Dattenböck C (eds) Gene expression systems in fungi: advancements and applications. Springer, Cham, pp 395–439. https://doi.org/10.1007/978-3-319-27951-0_19

  44. Guerriero G, Hausman JF, Strauss J, Ertan H, Siddiqui KS (2016) Lignocellulosic biomass: biosynthesis, degradation, and industrial utilization. Eng Life Sci 16:1–16

  45. Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM (1998) Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 5:R245–R249. https://doi.org/10.1016/S1074-5521(98)90108-9

  46. Hesse CN, Mueller RC, Vuyisich M, Gallegos-Graves LV, Gleasner CD, Zak DR, Kuske CR (2015) Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests. Front Microbiol 6:337. https://doi.org/10.3389/fmicb.2015.00337

  47. Hirsch PR, Mauchline TH, Clark IM (2010) Culture-independent molecular techniques for soil microbial ecology. Soil Biol Biochem 42:878–887. https://doi.org/10.1016/j.soilbio.2010.02.019

  48. Hua ZS, Han YJ, Chen LX, Liu J, Hu M, Li SJ, Kuang JL, Chain PS, Huang LN, Shu WS (2015) Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics. ISME J 9:1280. https://doi.org/10.1038/ismej.2014.212

  49. Iost I, Dreyfus M (1995) The stability of Escherichia coli lacZ mRNA depends upon the simultaneity of its synthesis and translation. EMBO J 14:3252

  50. Jarque S, Bittner M, Blaha L, Hilscherova K (2016) Yeast biosensors for detection of environmental pollutants: current state and limitations. Trends Biotechnol 34:408–419. https://doi.org/10.1016/j.tibtech.2016.01.007

  51. Jumpponen A, Johnson LC (2005) Can rDNA analyses of diverse fungal communities in soil and roots detect effects of environmental manipulations—a case study from tallgrass prairie. Mycologia 97:1177–1194. https://doi.org/10.1080/15572536.2006.11832728

  52. Kellner H, Luis P, Portetelle D, Vandenbol M (2011) Screening of a soil metatranscriptomic library by functional complementation of Saccharomyces cerevisiae mutants. Microbiol Res 166:360–368. https://doi.org/10.1016/j.micres.2010.07.006

  53. Khan AG (2005) Role of soil microbes in the rhizospheres of plants growing on trace metal contaminated soils in phytoremediation. J Trace Elem Med Bio 18:355–364. https://doi.org/10.1016/j.jtemb.2005.02.006

  54. Kim J, Kim MS, Koh AY, Xie Y, Zhan X (2016) FMAP: functional mapping and analysis pipeline for metagenomics and metatranscriptomics studies. BMC Bioinform 17:420. https://doi.org/10.1186/s12859-016-1278-0

  55. Knietsch A, Bowien S, Whited G, Gottschalk G, Daniel R (2003) Identification and characterization of coenzyme B12-dependent glycerol dehydratase-and diol dehydratase-encoding genes from metagenomic DNA libraries derived from enrichment cultures. Appl Environ Microbiol 69:3048–3060. https://doi.org/10.1128/AEM.69.6.3048-3060.2003

  56. Koringa PG, Thakkar JR, Pandit RJ, Hinsu AT, Parekh MJ, Shah RK, Jakhesara SJ, Joshi CG (2019) Metagenomic characterisation of ruminal bacterial diversity in buffaloes from birth to adulthood using 16S rRNA gene amplicon sequencing. Funct Integr Genomics 19:237–247. https://doi.org/10.1007/s10142-018-0640-x

  57. Kozdrój J, van Elsas JD (2000) Response of the bacterial community to root exudates in soil polluted with heavy metals assessed by molecular and cultural approaches. Soil Biol Biochem 32:1405–1417. https://doi.org/10.1016/S0038-0717(00)00058-4

  58. Lara E, Berney C, Harms H, Chatzinotas A (2007) Cultivation-independent analysis reveals a shift in ciliate 18S rRNA gene diversity in a polycyclic aromatic hydrocarbon-polluted soil. FEMS Microbiol Ecol 62:365–373. https://doi.org/10.1111/j.1574-6941.2007.00387.x

  59. Lavelle P, Decaëns T, Aubert M, Barot S, Blouin M, Bureau F, Margerie P, Mora P, Rossi JP (2006) Soil invertebrates and ecosystem services. Eur J Soil Biol 42:S3–S15. https://doi.org/10.1016/j.ejsobi.2006.10.002

  60. Lehembre F, Doillon D, David E, Perrotto S, Baude J, Foulon J, Harfouche L, Vallon L, Poulain J, Da Silva C, Wincker P (2013) Soil metatranscriptomics for mining eukaryotic heavy metal resistance genes. Environ Microbiol 15:2829–2840. https://doi.org/10.1111/1462-2920.12143

  61. Lehmann M, Riedel K, Adler K, Kunze G (2000) Amperometric measurement of copper ions with a deputy substrate using a novel Saccharomyces cerevisiae sensor. Biosens Bioelectron 15:211–219. https://doi.org/10.1016/S0956-5663(00)00060-9

  62. Leimena MM, Ramiro-Garcia J, Davids M, van den Bogert B, Smidt H, Smid EJ, Boekhorst J, Zoetendal EG, Schaap PJ, Kleerebezem M (2013) A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets. BMC Genom 14:530. https://doi.org/10.1186/1471-2164-14-530

  63. Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, Prosser JI, Schuster SC, Schleper C (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442:806–809. https://doi.org/10.1038/nature04983

  64. Liles MR, Manske BF, Bintrim SB, Handelsman J, Goodman RM (2003) A census of rRNA genes and linked genomic sequences within a soil metagenomic library. Appl Environ Microbiol 69:2684–2691. https://doi.org/10.1128/AEM.69.5.2684-2691.2003

  65. Liu W, Stahl D (2007) Molecular approaches for the measurement of density, diversity, and phylogeny. In: Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (eds) Manual of environmental microbiology, 3rd edn. ASM Press, Washington DC, pp 139–156. https://dx.doi.org/10.1128/9781555815882.ch12

  66. Liu WT, Marsh TL, Cheng H, Forney LJ (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 63:4516–4522

  67. Luis P, Kellner H, Martin F, Buscot F (2005) A molecular method to evaluate basidiomycete laccase gene expression in forest soils. Geoderma 128:18–27. https://doi.org/10.1016/j.geoderma.2004.12.023

  68. Ma A, Sun M, McDermaid A, Liu B, Ma Q (2019) MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome. Bioinformatics 35:4474–4477. https://doi.org/10.1093/bioinformatics/btz414

  69. Mantere T, Kersten S, Hoischen A (2019) Long-read sequencing emerging in medical genetics. Front Genet 10:426. https://doi.org/10.3389/fgene.2019.00426

  70. Marmeisse R, Kellner H, Fraissinet-Tachet L, Luis P (2017) Discovering protein-coding genes from the environment: time for the eukaryotes? Trends Biotechnol 35:824–835. https://doi.org/10.1016/j.tibtech.2017.02.003

  71. Marsh TL (1999) Terminal restriction fragment length polymorphism (T-RFLP): an emerging method for characterizing diversity among homologous populations of amplification products. Curr Opin Microbiol 2:323–327. https://doi.org/10.1016/S1369-5274(99)80056-3

  72. Martinez X, Pozuelo M, Pascal V, Campos D, Gut I, Gut M, Azpiroz F, Guarner F, Manichanh C (2016) MetaTrans: an open-source pipeline for metatranscriptomics. Sci Rep 6:26447. https://doi.org/10.1038/srep26447

  73. Matsuura H, Yamamoto Y, Muraoka M, Akaishi K, Hori Y, Uemura K, Tsuji N, Harada K, Hirata K, Bamba T, Miyasaka H (2013) Development of surface-engineered yeast cells displaying phytochelatin synthase and their application to cadmium biosensors by the combined use of pyrene-excimer fluorescence. Biotechnol Prog 29:1197–1202. https://doi.org/10.1002/btpr.1789

  74. Medini D, Serruto D, Parkhill J, Relman DA, Donati C, Moxon R, Falkow S, Rappuoli R (2008) Microbiology in the post-genomic era. Nat Rev Microbiol 6:419–430. https://doi.org/10.1038/nrmicro1901

  75. Mehra RK, Winge DR (1991) Metal ion resistance in fungi: molecular mechanisms and their regulated expression. J Cell Biochem 45:30–40. https://doi.org/10.1002/jcb.240450109

  76. Miller DN, Bryant JE, Madsen EL, Ghiorse WC (1999) Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Appl Environ Microbiol 65:4715–4724

  77. Minet M, Dufour ME, Lacroute F (1992) Complementation of Saccharomyces cerevisiae auxotrophic mutants by Arabidopsis thaliana cDNAs. Plant J 2:417–422. https://doi.org/10.1046/j.1365-313X.1992.t01-38-00999.x

  78. Mitchell E, Frisbie S, Sarkar B (2011) Exposure to multiple metals from groundwater—a global crisis: geology, climate change, health effects, testing, and mitigation. Metallomics 3:874–908. https://doi.org/10.1039/C1MT00052G

  79. Moran MA (2009) Metatranscriptomics: eavesdropping on complex microbial communities-large-scale sequencing of mRNAs retrieved from natural communities provides insights into microbial activities and how they are regulated. Microbe 4:329. https://doi.org/10.1128/microbe.4.329.1

  80. Mukherjee A, Yadav R, Marmeisse R, Fraissinet-Tachet L, Reddy MS (2019a) Heavy metal hypertolerant eukaryotic aldehyde dehydrogenase isolated from metal contaminated soil by metatranscriptomics approach. Biochimie 160:183–192. https://doi.org/10.1016/j.biochi.2019.03.010

  81. Mukherjee A, Yadav R, Marmeisse R, Fraissinet-Tachet L, Reddy MS (2019b) Detoxification of toxic heavy metals by serine protease inhibitor isolated from polluted soil. Int Biodeterior Biodegrad 143:104718. https://doi.org/10.1016/j.ibiod.2019.104718

  82. Muyzer G, Smalla K (1998) Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Van Leeuwenhoek 73:127–141. https://doi.org/10.1023/A:1000669317571

  83. Nannipieri P, Ascher J, Ceccherini M, Landi L, Pietramellara G, Renella G (2003) Microbial diversity and soil functions. Eur J Soil Sci 54:655–670. https://doi.org/10.1046/j.1351-0754.2003.0556.x

  84. Narayanasamy S, Jarosz Y, Muller EE, Heintz-Buschart A, Herold M, Kaysen A, Laczny CC, Pinel N, May P, Wilmes P (2016) IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses. Genome Biol 17:260. https://doi.org/10.1186/s13059-016-1116-8

  85. Ni Y, Li J, Panagiotou G (2016) COMAN: a web server for comprehensive metatranscriptomics analysis. BMC Genom 17:622. https://doi.org/10.1186/s12864-016-2964-z

  86. Niehaus F, Gabor E, Wieland S, Siegert P, Maurer KH, Eck J (2011) Enzymes for the laundry industries: tapping the vast metagenomic pool of alkaline proteases. Microb Biotechnol 4:767–776. https://doi.org/10.1111/j.1751-7915.2011.00279.x

  87. Nüsslein K, Tiedje JM (1998) Characterization of the dominant and rare members of a young Hawaiian soil bacterial community with small-subunit ribosomal DNA amplified from DNA fractionated on the basis of its guanine and cytosine composition. Appl Environ Microbiol 64:1283–1289

  88. O'Brien HE, Parrent JL, Jackson JA, Moncalvo JM, Vilgalys R (2005) Fungal community analysis by large-scale sequencing of environmental samples. Appl Environ Microbiol 71:5544–5550. https://doi.org/10.1128/AEM.71.9.5544-5550.2005

  89. Opel KL, Chung D, McCord BR (2010) A study of PCR inhibition mechanisms using real time PCR. J Forensic Sci 55:25–33. https://doi.org/10.1111/j.1556-4029.2009.01245.x

  90. Pace NR (1997) A molecular view of microbial diversity and the biosphere. Science 276:734–740. https://doi.org/10.1126/science.276.5313.734

  91. Patel DD, Patel AK, Parmar NR, Shah TM, Patel JB, Pandya PR, Joshi CG (2014) Microbial and carbohydrate active enzyme profile of buffalo rumen metagenome and their alteration in response to variation in the diet. Gene 545:88–94. https://doi.org/10.1016/j.gene.2014.05.003

  92. Pointing SB, Belnap J (2012) Microbial colonization and controls in dryland systems. Nat Rev Microbiol 10:551–562. https://doi.org/10.1038/nrmicro2831

  93. Poretsky RS, Bano N, Buchan A, LeCleir G, Kleikemper J, Pickering M, Pate WM, Moran MA, Hollibaugh JT (2005) Analysis of microbial gene transcripts in environmental samples. Appl Environ Microbiol 71:4121–4126. https://doi.org/10.1128/AEM.71.7.4121-4126.2005

  94. Radhika V, Milkevitch M, Audigé V, Proikas-Cezanne T, Dhanasekaran N (2005) Engineered Saccharomyces cerevisiae strain BioS-1, for the detection of water-borne toxic metal contaminants. Biotechnol Bioeng 90:29–35. https://doi.org/10.1002/bit.20344

  95. Ranjard L, Nazaret S, Gourbière F, Thioulouse J, Linet P, Richaume A (2000) A soil microscale study to reveal the heterogeneity of Hg (II) impact on indigenous bacteria by quantification of adapted phenotypes and analysis of community DNA fingerprints. FEMS Microbiol Ecol 31:107–115. https://doi.org/10.1111/j.1574-6941.2000.tb00676.x

  96. Redon E, Loubière P, Cocaign-Bousquet M (2005) Role of mRNA stability during genome-wide adaptation of Lactococcus lactis to carbon starvation. J Biol Chem 280:36380–36385. https://doi.org/10.1074/jbc.M506006200

  97. Roane TM, Pepper IL (1999) Microbial responses to environmentally toxic cadmium. Microb Ecol 38:358–364. https://doi.org/10.1007/s002489901001

  98. Roda A, Roda B, Cevenini L, Michelini E, Mezzanotte L, Reschiglian P, Hakkila K, Virta M (2011) Analytical strategies for improving the robustness and reproducibility of bioluminescent microbial bioreporters. Anal Bioanal Chem 401:201–211. https://doi.org/10.1007/s00216-011-5091-3

  99. Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, Liles MR, Loiacono KA, Lynch BA, MacNeil IA, Minor C, Tiong CL (2000) Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol 66:2541–2547. https://doi.org/10.1128/AEM.66.6.2541-2547.2000

  100. Rossman AY (1998) Protocols for an all taxa biodiversity inventory of fungi in a Costa Rican conservation area. Parkway Publishers, Inc., USA. https://doi.org/10.2307/3761287

  101. Sandaa RA, Torsvik V, Enger Ø, Daae FL, Castberg T, Hahn D (1999) Analysis of bacterial communities in heavy metal-contaminated soils at different levels of resolution. FEMS Microbiol Ecol 30:237–251. https://doi.org/10.1111/j.1574-6941.1999.tb00652.x

  102. Scherens B, Goffeau A (2004) The uses of genome-wide yeast mutant collections. Genome Biol 5:229. https://doi.org/10.1186/gb-2004-5-7-229

  103. Schloss PD, Handelsman J (2003) Biotechnological prospects from metagenomics. Curr Opin Biotechnol 14:303–310. https://doi.org/10.1016/S0958-1669(03)00067-3

  104. Sequeira JC, Rocha M, Alves MM, Salvador AF (2019) MOSCA: an automated pipeline for integrated metagenomics and metatranscriptomics data analysis. Practical Applications of Computational Biology and Bioinformatics, 12th International Conference (Springer International Publishing). https://doi.org/10.1007/978-3-319-98702-6_2

  105. Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D (2018) Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nat Biotechnol 36:359. https://doi.org/10.1038/nbt.4110

  106. Shakya M, Lo CC, Chain PS (2019) Advances and challenges in metatranscriptomic analysis. Front Genet 10:904. https://doi.org/10.3389/fgene.2019.00904

  107. Sharma R, Sharma PK (2018) Metatranscriptome sequencing and analysis of agriculture soil provided significant insights about the microbial community structure and function. Ecol Genet Genomics 6:9–15. https://doi.org/10.1016/j.egg.2017.10.001

  108. Shetty RS, Deo SK, Liu Y, Daunert S (2004) Fluorescence-based sensing system for copper using genetically engineered living yeast cells. Biotechnol Bioeng 88:664–670. https://doi.org/10.1002/bit.20331

  109. Singh DP, Prabha R, Gupta VK, Verma MK (2018) Metatranscriptome analysis deciphers multifunctional genes and enzymes linked with the degradation of aromatic compounds and pesticides in the wheat rhizosphere. Front Microbiol 9:1331. https://doi.org/10.3389/fmicb.2018.01331

  110. Sjostrom SL, Bai Y, Huang M, Liu Z, Nielsen J, Joensson HN, Svahn HA (2014) High-throughput screening for industrial enzyme production hosts by droplet microfluidics. Lab Chip 14:806–813. https://doi.org/10.1039/c3lc51202a

  111. Smit E, Leeflang P, Wernars K (1997) Detection of shifts in microbial community structure and diversity in soil caused by copper contamination using amplified ribosomal DNA restriction analysis. FEMS Microbiol Ecol 23:249–261. https://doi.org/10.1111/j.1574-6941.1997.tb00407.x

  112. Söllinger A, Tveit AT, Poulsen M, Noel SJ, Bengtsso M, Bernhardt J, Hellwing ALF, Lund P, Riedel K, Schleper C, Højberg O (2018) Holistic assessment of rumen microbiome dynamics through quantitative metatranscriptomics reveals multifunctional redundancy during key steps of anaerobic feed degradation. MSystems 3:e00038–e118. https://doi.org/10.1128/mSystems.00038-18

  113. Štursová M, Žifčáková L, Leigh MB, Burgess R, Baldrian P (2012) Cellulose utilization in forest litter and soil: identification of bacterial and fungal decomposers. FEMS Microbiol Ecol 80:735–746. https://doi.org/10.1111/j.1574-6941.2012.01343.x

  114. Takasaki K, Miura T, Kanno M, Tamaki H, Hanada S, Kamagata Y, Kimura N (2013) Discovery of glycoside hydrolase enzymes in an avicel-adapted forest soil fungal community by a metatranscriptomic approach. PLoS ONE 8:e55485. https://doi.org/10.1371/journal.pone.0055485

  115. Tamames J, Puente-Sanchez F (2019) SqueezeM, a highly portable, fully automatic metagenomic analysis pipeline. Front Microbiol 9:3349. https://doi.org/10.3389/fmicb.2018.03349

  116. Terry SA, Badhan A, Wang Y, Chaves AV, McAllister TA (2019) Fibre digestion by rumen microbiota—a review of recent metagenomic and metatranscriptomic studies. Can J Anim Sci 99:678–692. https://doi.org/10.1139/cjas-2019-0024

  117. Thakur B, Yadav R, Fraissinet-Tachet L, Marmeisse R, Reddy MS (2018) Isolation of multi-metal tolerant ubiquitin fusion protein from metal polluted soil by metatranscriptomic approach. J Microbiol Methods 152:119–125. https://doi.org/10.1016/j.mimet.2018.08.001

  118. Thakur B, Yadav R, Vallon L, Marmeisse R, Fraissinet-Tachet L, Reddy MS (2019) Multi-metal tolerance of von Willebrand factor type D domain isolated from metal contaminated site by metatranscriptomics approach. Sci Total Environ 661:432–440. https://doi.org/10.1016/j.scitotenv.2019.01.201

  119. Torsvik V, Sørheim R, Goksøyr J (1996) Total bacterial diversity in soil and sediment communities—a review. J Ind Microbiol Biotechnol 17:170–178. https://doi.org/10.1007/BF01574690

  120. Tringe SG, Rubin EM (2005) Metagenomics: DNA sequencing of environmental samples. Nat Rev Genet 6:805–814. https://doi.org/10.1038/nrg1709

  121. Urich T, Lanzén A, Qi J, Huson DH, Schleper C, Schuster SC (2008) Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS ONE 3:e2527. https://doi.org/10.1371/journal.pone.0002527

  122. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66–74. https://doi.org/10.1126/science.1093857

  123. Vopálenská I, Váchová L, Palková Z (2015) New biosensor for detection of copper ions in water based on immobilized genetically modified yeast cells. Biosens Bioelectron 72:160–167. https://doi.org/10.1016/j.bios.2015.05.006

  124. Warnecke F, Hess M (2009) A perspective: metatranscriptomics as a tool for the discovery of novel biocatalysts. J Biotech 142:91–95. https://doi.org/10.1016/j.jbiotec.2009.03.022

  125. Warnecke F, Luginbühl P, Ivanova N, Ghassemian M, Richardson TH, Stege JT, Cayouette M, McHardy AC, Djordjevic G, Aboushadi N, Sorek R (2007) Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450:560–565. https://doi.org/10.1038/nature06269

  126. Wasserman GA, Liu X, Factor-Litvak P, Gardner JM, Graziano JH (2008) Developmental impacts of heavy metals and undernutrition. Basic Clin Pharmacol Toxicol 102:212–217. https://doi.org/10.1111/j.1742-7843.2007.00187.x

  127. Weidner S, Arnold W, Puhler A (1996) Diversity of uncultured microorganisms associated with the seagrass Halophila stipulacea estimated by restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA genes. Appl Environ Microbiol 62:766–771

  128. Westreich ST, Kor I, Mills DA, Lemay DG (2016) SAMSA: a comprehensive metatranscriptome analysis pipeline. BMC Bioinform 17:399. https://doi.org/10.1186/s12859-016-1270-8

  129. Wood V, Gwilliam R, Rajandream MA, Lyne M, Lyne R, Stewart A, Sgouros J, Peat N, Hayles J, Baker S, Basham D (2002) The genome sequence of Schizosaccharomyces pombe. Nature 415:871–880. https://doi.org/10.1038/nature724

  130. Yadav RK, Barbi F, Ziller A, Luis P, Marmeisse R, Reddy MS, Fraissinet-Tachet L (2014) Construction of sized eukaryotic cDNA libraries using low input of total environmental metatranscriptomic RNA. BMC Biotechnol 14:80. https://doi.org/10.1186/1472-6750-14-80

  131. Zhang Y, Zhang X, Zhang H, He Q, Zhou Q, Su Z, Zhang C (2009) Responses of soil bacteria to long-term and short-term cadmium stress as revealed by microbial community analysis. Bull Environ Contam Toxicol 82:367–372. https://doi.org/10.1007/s00128-008-9613-4

  132. Zhu YY, Machleder EM, Chenchik A, Li R, Siebert PD (2001) Reverse transcriptase template switching: A SMART™ approach for full-length cDNA library construction. Biotechniques 30:892–897. https://doi.org/10.2144/01304pf02

  133. Ziller A, Yadav RK, Capdevila M, Reddy MS, Vallon L, Marmeisse R, Atrian S, Palacios Ò, Fraissinet-Tachet L (2017) Metagenomics analysis reveals a new metallothionein family: sequence and metal-binding features of new environmental cysteine-rich proteins. J Inorg Biochem 167:1–11. https://doi.org/10.1016/j.jinorgbio.2016.11.017

Download references

Acknowledgements

Authors are thankful to Council of Scientific and Industrial Research, Govt. of India for sponsoring a research project on “Novel gene pool from copper polluted soil ecosystem using metatranscriptomic approach” under file No. 38(1425)/16/EMR-II.

Author information

Correspondence to M. Sudhakara Reddy.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Mukherjee, A., Reddy, M.S. Metatranscriptomics: an approach for retrieving novel eukaryotic genes from polluted and related environments. 3 Biotech 10, 71 (2020). https://doi.org/10.1007/s13205-020-2057-1

Download citation

Keywords

  • Metatranscriptomics
  • Eukaryotic genes
  • Toxic metal tolerance
  • Functional diversity
  • Microbiomes
  • Metagenomes