Summary:
Metatranscriptomics is a state-of-the-art technique to elucidate the functional activities of microbial communities, but its application is still limited to marine microbial assemblages. In my PhD project, we established the complete approach of soil metatranscriptomics, involving RNA extraction, cDNA library preparation by random priming, 454-pyrosequencing, and bioinformatic data analysis. The approach was tested on microbial communities in the oxic surface layer and the anoxic bulk soil of flooded rice paddy soil microcosms.
Total RNA was recovered in high integrity and purity by low-pH phenol extraction (pH 5.0) followed by Q-Sepharose column chromatography. We were able to enrich mRNA sequences up to 50-70% in the metatranscriptome libraries using Ribo-Zero™ rRNA removal kit (Meta-Bacteria). All the 454 reads obtained were preprocessed prior to data analysis to minimize sequence ambiguities. A total of 10,000 SSU-ribotags (total RNA) were analyzed to elucidate community composition in the oxic and anoxic zones at three different incubation time points (25, 45 and 90 days after transplantation of rice seedlings). Additionally, about 45,000 and 12,000 mRNA-tags (enriched mRNA) were obtained for the analysis of functional activities in, respectively, the oxic and anoxic zone of 90-day-old rice microcosms.
SSU-ribotag data analysis revealed no major temporal changes in community composition except for Geobacter, Clostridia and methanogens in the anoxic bulk soil. However, the taxonomic composition of microbial communities was clearly distinct between the oxic and anoxic zones, with cyanobacteria being the dominant group in the surface layer. Although mRNA-tags related to basic cellular functions were most abundant in both mRNA datasets, the expression of specific functions in response to different oxygen conditions was observed such as, for example, methane oxidation in the oxic zone and methanogenesis in the anoxic zone.
Our metatranscriptomic approach provides a means to analyze the composition and functional gene expression of complex soil microbial communities while avoiding the limitations of PCR-based approaches.
Bibliographie / References
- Roslev P & King GM (1995) Aerobic and Anaerobic Starvation Metabolism in Methanotrophic Bacteria. Applied and Environmental Microbiology 61: 1563-1570
- 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. Applied and Environmental Microbiology 71: 4121-4126
- Revsbech NP, Pedersen O, Reichardt W & Briones A (1999) Microsensor analysis of oxygen and pH in the rice rhizosphere under field and laboratory conditions. Biology and Fertility of Soils 29: 379-385
- Meyer H, Kaiser C, Biasi C, Hämmerle R, Rusalimova O, Lashchinsky N, Baranyi C, Daims H, Barsukov P & Richter A (2006) Soil carbon and nitrogen dynamics along a latitudinal transect in Western Siberia, Russia. Biogeochemistry 81: 239- 252
- Phelan VV, Liu W-T, Pogliano K & Dorrestein PC (2011) Microbial metabolic exchange—the chemotype-to-phenotype link. Nature Chemical Biology 8: 26-35
- McInerney MJ, Rohlin L, Mouttaki H, Kim U, Krupp RS, Rios-Hernandez L, Sieber J, Struchtemeyer CG, Bhattacharyya A, Campbell JW & Gunsalus RP (2007) The genome of Syntrophus aciditrophicus: life at the thermodynamic limit of microbial growth. Proceedings of the National Academy of Sciences of the United States of America 104: 7600-7605
- McCarren J, Becker JW, Repeta DJ, Shi Y, Young CR, Malmstrom RR, Chisholm SW & DeLong EF (2010) Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea. Proceedings of the National Academy of Sciences of the United States of America 107: 16420-16427
- Pratscher J, Dumont MG & Conrad R (2011) Ammonia oxidation coupled to CO2 fixation by archaea and bacteria in an agricultural soil. Proceedings of the National Academy of Sciences of the United States of America 108: 4170-5
- Parks DH & Beiko RG (2010) Identifying biologically relevant differences between metagenomic communities. Bioinformatics 26: 715-721
- Schmieder R & Edwards R (2011) Quality control and preprocessing of metagenomic datasets. Bioinformatics 27: 863-864
- Zhang W, Li F & Nie L (2010) Integrating multiple " omics " analysis for microbial biology: application and methodologies. Microbiology 156: 287-301 Curriculum Vitae Yongkyu Kim Education 2008 – present Ph.D. study at the International Max Planck Research School for Environmental, Cellular and Molecular Microbiology,Marburg, Germany. Supervisor: Dr. Werner Liesack 2005 – 2007
- Shrestha M, Abraham W-R, Shrestha PM, Noll M & Conrad R (2008) Activity and composition of methanotrophic bacterial communities in planted rice soil studied by flux measurements, analyses of pmoA gene and stable isotope probing of phospholipid fatty acids. Environmental Microbiology 10: 400-412
- Shrestha PM, Kube M, Reinhardt R & Liesack W (2009) Transcriptional activity of paddy soil bacterial communities. Environmental Microbiology 11: 960-970
- Stewart FJ, Ulloa O & Delong EF (2011) Microbial metatranscriptomics in a permanent marine oxygen minimum zone. Environmental Microbiology 2: 23-40
- Mou X, Vila-Costa M, Sun S, Zhao W, Sharma S & Moran MA (2011) Metatranscriptomic signature of exogenous polyamine utilization by coastal bacterioplankton. Environmental Microbiology Reports 3: 798-806
- Steglich C, Lindell D, Futschik M, Rector T, Steen R & Chisholm SW (2010) Short RNA half-lives in the slow-growing marine cyanobacterium Prochlorococcus.
- Selenska-Pobell S & Evguenieva-Hackenberg E (1995) Fragmentations of the large-subunit rRNA in the family Rhizobiaceae. Journal Of Bacteriology 177: 6993-6998
- Schmid M, Schmitz-Esser S, Jetten M & Wagner M (2001) 16S-23S rDNA intergenic spacer and 23S rDNA of anaerobic ammonium-oxidizing bacteria: implications for phylogeny and in situ detection. Environmental Microbiology 3: 450-459
- Pace NR (1997) A Molecular View of Microbial Diversity and the Biosphere. Science 276: 734-740
- Mutter GL, Zahrieh D, Liu C, Neuberg D, Finkelstein D, Baker HE & Warrington JA (2004) Comparison of frozen and RNALater solid tissue storage methods for use in RNA expression microarrays. BMC Genomics 5: 88
- Sharma S, Aneja MK, Mayer J, Munch JC & Schloter M (2005) Diversity of Transcripts of Nitrite Reductase Genes (nirK and nirS) in Rhizospheres of Grain Legumes. Applied and Environmental Microbiology 71: 2001-2007
- Mettel C, Kim Y, Shrestha PM & Liesack W (2010) Extraction of mRNA from Soil. Applied and Environmental Microbiology 76: 5995-6000
- Newman DK & Banfield JF (2002) Geomicrobiology: how molecular-scale interactions underpin biogeochemical systems. Science 296: 1071-1077
- Schloss PD & Handelsman J (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Applied and Environmental Microbiology 71: 1501-1506
- Ratering S & Schnell S (2000) Localization of iron-reducing activity in paddy soil by profile studies. Biogeochemistry 48: 341-365
- Mackelprang R, Waldrop MP, DeAngelis KM, David MM, Chavarria KL, Blazewicz SJ, Rubin EM & Jansson JK (2011) Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature 05: 368-371
- Shi Y, Tyson GW & DeLong EF (2009) Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column. Nature 459: 266-269
- Prosser JI (2007) Microorganisms Cycling Soil Nutrients and Their Diversity. In Modern Soil Microbiology, Van Elsas JD Jansson JK, & Trevors JT (eds) pp 237- 261. CRC Press
- Surette MG, Miller MB & Bassler BL (1999) Quorum sensing in Escherichia coli, Salmonella typhimurium, and Vibrio harveyi: A new family of genes responsible for autoinducer production. Proceeding of the National Academy of Sciences of the United States of America 96: 1639-1644
- Pruesse E, Quast C, Yilmaz P, Ludwig W, Peplies J & Glöckner FO (2011) SILVA: comprehensive databases for quality checked and aligned ribosomal RNA sequence data compatible with ARB. In Handbook of Molecular Microbial Ecology I Metagenomics and Complementary Approaches, De Bruijn FJ (ed) pp 393-398. John Wiley & Sons Raamsdonk LM, Teusink B, Broadhurst D, Zhang N, Hayes A, Walsh MC, Berden JA, Brindle KM, Kell DB, Rowland JJ, Westerhoff HV, Van Dam K & Oliver SG (2001) A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations. Nature Biotechnology 19: 45-50
- Schink B (2000) Syntrophism among prokaryotes. The Prokaryotes 1: 276-299 74
- McInerney MJ, Sieber JR & Gunsalus RP (2009) Syntrophy in anaerobic global carbon cycles. Current Opinion in Biotechnology 20: 623-632
- The Brain Korea 21 BT-IT integration program scholarship by Korean Research Foundation 2001-2004
- Rondon MR, Goodman RM & Handelsman J (1999) The Earth's bounty: assessing and accessing soil microbial diversity. Trends in biotechnology 17: 403-409
- Mount BDW (2001) The first step toward a definitive bioinformatics textbook Bioinformatics: Sequence and Genome Analysis. Bioinformatics 28: 2001-2001
- Shi Y, McCarren J & DeLong EF (2011) Transcriptional responses of surface water marine microbial assemblages to deep-sea water amendment. Environmental Microbiology 14: 191-206
- Poretsky RS, Sun S, Mou X & Moran MA (2010) Transporter genes expressed by coastal bacterioplankton in response to dissolved organic carbon. Environmental Microbiology 12: 616-627