title: Metagenomic evidence for the presence of phototrophic Gemmatimonadetes bacteria in diverse environments.
abstract: Gemmatimonadetes represents a poorly understood bacterial phylum with only a handful of cultured species. Recently, one of its few representatives, Gemmatimonas phototrophica, was found to contain purple bacterial photosynthetic reaction centres. However, almost nothing is known about the environmental distribution of phototrophic Gemmatimonadetes bacteria. To fill this gap, we took advantage of fast-growing public metagenomic databases and performed an extensive survey of metagenomes deposited into the NCBI's WGS database, the JGI's IMG webserver and the MG-RAST webserver. By employing Mg protoporphyrin IX monomethyl ester oxidative cyclase (AcsF) as a marker gene, we identified 291 AcsF fragments (24-361 amino acids long) that are closely related to G. phototrophica from 161 metagenomes originating from various habitats, including air, river waters/sediment, estuarine waters, lake waters, biofilms, plant surfaces, intertidal sediment, soils, springs and wastewater treatment plants, but none from marine waters or sediment. Based on AcsF hit counts, phototrophic Gemmatimonadetes bacteria make up 0.4-11.9% of whole phototrophic microbial communities in these habitats. Unexpectedly, an almost complete 37.9 kb long photosynthesis gene cluster with identical gene composition and arrangement to those in G. phototrophica was reconstructed from the Odense wastewater metagenome, only differing in a 7.2 kb long non-photosynthesis-gene insert. These data suggest that phototrophic Gemmatimonadetes bacteria are much more widely distributed in the environment and exhibit a higher genetic diversity than previously thought.
authors.affiliation: Nordic Center for Earth Evolution (NordCEE) & Institute of Biology, University of Southern Denmark, Odense, 5230, Denmark.|Center Algatech, Institute of Microbiology CAS, Třeboň, 37981, Czech Republic.
authors.forename: Yonghui
authors.initials: Y
authors.lastname: Zeng
authors.affiliation: Department of Mathematics and Computer Science, University of Southern Denmark, Odense, 5230, Denmark.
authors.forename: Jan
authors.initials: J
authors.lastname: Baumbach
authors.affiliation: Department of Mathematics and Computer Science, University of Southern Denmark, Odense, 5230, Denmark.|Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Brazil.
authors.forename: Eudes Guilherme Vieira
authors.initials: EG
authors.lastname: Barbosa
authors.affiliation: Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Brazil.
authors.forename: Vasco
authors.initials: V
authors.lastname: Azevedo
authors.affiliation: State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China.
authors.forename: Chuanlun
authors.initials: C
authors.lastname: Zhang
authors.affiliation: Center Algatech, Institute of Microbiology CAS, Třeboň, 37981, Czech Republic.
authors.forename: Michal
authors.initials: M
authors.lastname: Koblížek
mesh_terms: D001419:Bacteria / Q000235:genetics* / Q000378:metabolism*; D019295:Computational Biology; D004783:Environmental Microbiology; D053858:Metabolic Networks and Pathways; D056186:Metagenomics; D005810:Multigene Family; D052817:Phototrophic Processes