Metatranscriptomic analyses of chlorophototrophs of a hot-spring microbial mat.

The phototrophic microbial mat community of Mushroom Spring, an alkaline siliceous hot spring inYellowstone National Park, was studied by metatranscriptomic methods. RNA was extracted frommat specimens collected at four timepoints during light-to-dark and dark-to-light transitions in onediel cycle, and these RNA samples were analyzed by both pyrosequencing and SOLiD technologies.Pyrosequencing was used to assess the community composition, which showed that B84% of therRNA was derived from members of four kingdoms Cyanobacteria, Chloroflexi, Chlorobi andAcidobacteria. Transcription of photosynthesis-related genes conclusively demonstrated thephototrophic nature of two newly discovered populations; these organisms, which were discoveredthrough metagenomics, are currently uncultured and previously undescribed members ofChloroflexi and Chlorobi. Data sets produced by SOLiD sequencing of complementary DNAprovided 4100-fold greater sequence coverage. The much greater sequencing depth allowedtranscripts to be detected from B15000 genes and could be used to demonstrate statisticallysignificant differential transcription of thousands of genes. Temporal differences for in situtranscription patterns of photosynthesis-related genes suggested that the six types of chloro-phototrophs in the mats may use different strategies for maximizing their solar-energy capture,usage and growth. On the basis of both temporal pattern and transcript abundance, intra-guild geneexpression differences were also detected for two populations of the oxygenic photosynthesisguild. This study showed that, when community-relevant genomes and metagenomes are available,SOLiD sequencing technology can be used for metatranscriptomic analyses, and the resultssuggested that this method can potentially reveal new insights into the ecophysiology of this modelmicrobial community.The ISME Journal (2011) 5, 1279–1290; doi:10.1038/ismej.2011.37; published online 23 June 2011Subject Category: integrated genomics and post-genomics approaches in microbial ecologyKeywords: metatranscriptome; photosynthesis; phototrophy; cyanobacteria; chlorophyll; reaction centers