Simultaneous Assessment of Soil Microbial Community Structure and Function through Analysis of the Meta-Transcriptome 英文参考文献.docVIP

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Simultaneous Assessment of Soil Microbial Community Structure and Function through Analysis of the Meta-Transcriptome 英文参考文献.doc

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Simultaneous Assessment of Soil Microbial Community Structure and Function through Analysis of the Meta-Transcriptome 英文参考文献

SimultaneousAssessmentofSoilMicrobialCommunity StructureandFunctionthroughAnalysisoftheMeta- Transcriptome TimUrich1,2,AndersLanze′n3,JiQi4,DanielH.Huson5,ChristaSchleper1,2*,StephanC.Schuster4* 1CentreofGeobiology,DepartmentofBiology,UniversityofBergen,Bergen,Norway,2DepartmentofGeneticsinEcology,ViennaEcologyCenter,UniversityofVienna, Vienna,Austria,3ComputationalBiologyUnit,BergenCenterforComputationalScience,UniversityofBergen,Bergen,Norway,4CenterforComparativeGenomicsand Bioinformatics,PennsylvaniaStateUniversity,StateCollege,Pennsylvania,UnitedStatesofAmerica,5CenterforBioinformatics,Tu¨bingenUniversity,Tu¨bingen,Germany Abstract Background: Soil ecosystems harbor the most complex prokaryotic and eukaryotic microbial communities on Earth. Experimentalapproachesstudyingthesesystemsusuallyfocusoneitherthesoilcommunity’staxonomicstructureorits functionalcharacteristics.ManymethodstargetDNAasmarkermoleculeandusePCRforamplification. Methodology/PrincipalFindings:HereweapplyanRNA-centeredmeta-transcriptomicapproachtosimultaneouslyobtain informationonbothstructureandfunctionofasoilcommunity.TotalcommunityRNAisrandomreverselytranscribedinto cDNA without any PCR or cloning step. Direct pyrosequencing produces large numbers of cDNA rRNA-tags; these are taxonomically profiled in a binning approach using the MEGAN software and two specifically compiled rRNA reference databases containing small and large subunit rRNA sequences. The pyrosequencing also produces mRNA-tags; these provide a sequence-based transcriptome of the community. One soil dataset of 258,411 RNA-tags of ,98bp length contained193,219rRNA-tagswithvalidtaxonomicinformation,togetherwith21,133mRNA-tags.Quantitativeinformation abouttherelativeabundanceoforganismsfromallthreedomainsoflifeandfromdifferenttrophiclevelswasobtainedina single experiment. Less frequent taxa, such as soil Crenarchaeota, were well represented in the data set. These were identifiedbymorethan2,000rRNA-tags;furthermore,theiractivityins