Simultaneous Assessment of Soil Microbial Community Structure and Function through Analysis of the Meta-Transcriptome

By Tim Urich, Anders Lanzén, Ji Qi, Daniel H. Huson, C. Schleper, Stephan C. Schuster. PLoS ONE, 2008

772 citations recorded by the source corpus.

Background Soil ecosystems harbor the most complex prokaryotic and eukaryotic microbial communities on Earth. Experimental approaches studying these systems usually focus on either the soil community's taxonomic structure or its functional characteristics. Many methods target DNA as marker molecule and use PCR for amplification. Methodology/Principal Findings Here we apply an RNA-centered meta-transcriptomic approach to simultaneously obtain information on both structure and function of a soil community. Total community RNA is random reversely transcribed into 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 ∼98 bp length contained 193,219 rRNA-tags with valid taxonomic information, together with 21,133 mRNA-tags. Quantitative information about the relative abundance of organisms from all three domains of life and from different trophic levels was obtained in a single experiment. Less frequent taxa, such as soil Crenarchaeota, were well represented in the data set. These were identified by more than 2,000 rRNA-tags; furthermore, their activity in situ was revealed through the presence of mRNA-tags specific for enzymes involved in ammonia oxidation and CO2 fixation. Conclusions/Significance This approach could be widely applied in microbial ecology by efficiently linking community structure and function in a single experiment while avoiding biases inherent in other methods.

Subfields: Ecology, Soil Science

View Paper: https://www.semanticscholar.org/paper/1e0929930008d239b345194dcf8d221a6fbfd1ec

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Citations in the corpus

The Potential of Metagenomic Approaches for Understanding Soil Microbial Processes (2014, background): “Such differences between genes and transcripts have also been observed when metagenomes and metatranscriptomes from marine or soil environments have been compared (Frias-Lopez et al., 2008; Gilbert et al., 2008; Urich et al., 2008).”
Stimulation of Plant Growth through Interactions of Bacteria and Protozoa: Testing the Auxiliary Microbial Loop Hypothesis (2012, background): “High throughput sequencing methods combined with stable isotope probing allow us for the first time to identify important protozoan players in the plant rhizosphere (Lue ders et al. 2004, 2006; Urich et al. 2008).”
Integrative analysis of environmental sequences using MEGAN4. (2011, background): “2007), soil (Urich et al. 2008), extreme environments (Tringe et al.”
Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions (2010, positive): “To explore an alternative assignment method, a hierarchical tree summarising read assignments into the NCBI taxonomy was constructed using MEGAN (30) on BLAST searches against a previously published 16S rRNA—specific database (31) (with a bit-score threshold of 86, allowing ten hits per read).”
New primers to amplify the fungal ITS2 region--evaluation by 454-sequencing of artificial and natural communities. (2012, background): “A future development towards sequencing of environmental DNA and RNA without prior PCR amplification may be envisaged (Urich et al., 2008), but current analysis of microbial communities depends on reliable PCR primers to target specific genetic markers.”
Gut microbiota in health and disease. (2010, background): “Metatranscriptomics has been successfully used to study complex microbial communities in soil (315) and aquatic environments (78), as well as the host-symbiont interactions in the termite gut (305).”
Culture-independent molecular techniques for soil microbial ecology (2010, background): “High-throughput studies based on RNA to indicate gene activity, “Transcriptomics”, are being developed in parallel with the high-throughput sequencing and microarray methods described above, requiring a preliminary step to convert RNA to DNA (Urich et al., 2008).”
Rhizosphere microbiome assemblage is affected by plant development (2013, background): “…attempted on the rRNA to identify the active members of the microbial community in the rhizosphere of various crop species (Turner et al., 2013); Urich et al. (2008) described the isolation and sequencing of mRNA from a sandy lawn as a means of describing the microbial transcriptome in the soil.”
Metagenomic Analyses: Past and Future Trends (2010, background): “Other metatranscriptomic studies employing direct sequencing of cDNA have targeted the ocean surface waters from the North Pacific subtropical gyre (31), coastal waters of a fjord close to Bergen, Norway (36, 91, 106), a phytoplankton bloom in the Western English Channel (37), and soil samples from ”
Molecular Techniques to Assess Microbial Community Structure, Function, and Dynamics in the Environment (2011, methodology): “More recently, a “double-RNA” method has been devised to analyze the total RNA pool of a community, as it is naturally rich in not only functionally but also taxonomically relevant molecules, i.e., mRNA and rRNA, respectively ( Urich et al. 2008 ).”
Differential Growth Responses of Soil Bacterial Taxa to Carbon Substrates of Varying Chemical Recalcitrance (2011, background): “Rare phyla (Urich et al. 2008) such as Chlorobi, Dictoglomi, SPAM, TM6, and Termite group 1 were also detected (Figure 1 & Table S1).”
Carbon isotopic composition of branched tetraether membrane lipids in soils suggest a rapid turnover and a heterotrophic life style of their source organism(s) (2010, positive): “Evidence for this comes from a study by Urich et al. (2008), who showed the presence of soilCrenarchaeotal gene products diagnostic for a CO2 fixation pathway based on a RNA centered meta-transcriptomic analysis of a nutrient-poor sandy lawn soil from Germany.”