title: Unraveling the stratification of an iron-oxidizing microbial mat by metatranscriptomics.
abstract: A metatranscriptomic approach was used to study community gene expression in a naturally occurring iron-rich microbial mat. Total microbial community RNA was reversely transcribed and sequenced by pyrosequencing. Characterization of expressed gene sequences provided accurate and detailed information of the composition of the transcriptionally active community and revealed phylogenetic and functional stratifications within the mat. Comparison of 16S rRNA reads and delineation of OTUs showed significantly lower values of metatranscriptomic-based richness and diversity in the upper parts of the mat than in the deeper regions. Taxonomic affiliation of rRNA sequences and mRNA genome recruitments indicated that iron-oxidizing bacteria affiliated to the genus Leptothrix, dominated the community in the upper layers of the mat. Surprisingly, type I methanotrophs contributed to the majority of the sequences in the deep layers of the mat. Analysis of mRNA expression patterns showed that genes encoding the three subunits of the particulate methane monooxygenase (pmoCAB) were the most highly expressed in our dataset. These results provide strong hints that iron-oxidation and methane-oxidation occur simultaneously in microbial mats and that both groups of microorganisms are major players in the functioning of this ecosystem.
authors.affiliation: Université de Rennes 1, CNRS UMR6553 EcoBio, Rennes, France.
authors.forename: Achim
authors.initials: A
authors.lastname: Quaiser
authors.affiliation: Université de Rennes 1, CNRS UMR6553 EcoBio, Rennes, France.
authors.forename: Xavier
authors.initials: X
authors.lastname: Bodi
authors.affiliation: Université de Rennes 1, CNRS UMR6553 EcoBio, Rennes, France.
authors.forename: Alexis
authors.initials: A
authors.lastname: Dufresne
authors.affiliation: CNRS FRC3115 Centre de Recherches de Gif-sur-Yvette, Gif sur Yvette, France.
authors.forename: Delphine
authors.initials: D
authors.lastname: Naquin
authors.affiliation: Université de Rennes 1, CNRS UMR6553 EcoBio, Rennes, France.
authors.forename: André-Jean
authors.initials: AJ
authors.lastname: Francez
authors.affiliation: Université de Rennes 1, CNRS UMS3343 OSUR, Plateforme génomique environnementale et fonctionnelle, Rennes, France.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Dheilly
authors.affiliation: Université de Rennes 1, CNRS UMS3343 OSUR, Plateforme génomique environnementale et fonctionnelle, Rennes, France.
authors.forename: Sophie
authors.initials: S
authors.lastname: Coudouel
authors.affiliation: Université de Rennes 1, CNRS UMR6118 Géosciences, Rennes, France.
authors.forename: Mathieu
authors.initials: M
authors.lastname: Pedrot
authors.affiliation: Université de Rennes 1, CNRS UMR6553 EcoBio, Rennes, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Vandenkoornhuyse
mesh_terms: D001105:Archaea / Q000235:genetics*; D001483:Base Sequence; D044822:Biodiversity; D017753:Ecosystem; D020869:Gene Expression Profiling; D007501:Iron / Q000378:metabolism*; D042743:Leptothrix / Q000235:genetics*; D008697:Methane / Q000378:metabolism*; D059013:Microbial Consortia / Q000235:genetics; D010084:Oxidation-Reduction; D010105:Oxygenases / Q000235:genetics*; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017423:Sequence Analysis, RNA
chemical_list: D012336:RNA, Ribosomal, 16S; D007501:Iron; D010105:Oxygenases; C021555:methane monooxygenase; D008697:Methane