title: A metagenomic-based survey of microbial (de)halogenation potential in a German forest soil.
abstract: In soils halogens (fluorine, chlorine, bromine, iodine) are cycled through the transformation of inorganic halides into organohalogen compounds and vice versa. There is evidence that these reactions are microbially driven but the key enzymes and groups of microorganisms involved are largely unknown. Our aim was to uncover the diversity, abundance and distribution of genes encoding for halogenating and dehalogenating enzymes in a German forest soil by shotgun metagenomic sequencing. Metagenomic libraries of three soil horizons revealed the presence of genera known to be involved in halogenation and dehalogenation processes such as Bradyrhizobium or Pseudomonas. We detected a so far unknown diversity of genes encoding for (de)halogenating enzymes in the soil metagenome including specific and unspecific halogenases as well as metabolic and cometabolic dehalogenases. Genes for non-heme, no-metal chloroperoxidases and haloalkane dehalogenases were the most abundant halogenase and dehalogenase genes, respectively. The high diversity and abundance of (de)halogenating enzymes suggests a strong microbial contribution to natural halogen cycling. This was also confirmed in microcosm experiments in which we quantified the biotic formation of chloroform and bromoform. Knowledge on microorganisms and genes that catalyze (de)halogenation reactions is critical because they are highly relevant to industrial biotechnologies and bioremediation applications.
authors.affiliation: Geomicrobiology, Center for Applied Geosciences, University of Tuebingen, Germany.
authors.forename: Pascal
authors.initials: P
authors.lastname: Weigold
authors.affiliation: Algorithms in Bioinformatics, Center for Bioinformatics, University of Tuebingen, Germany.
authors.forename: Mohamed
authors.initials: M
authors.lastname: El-Hadidi
authors.affiliation: Geomicrobiology, Center for Applied Geosciences, University of Tuebingen, Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Ruecker
authors.affiliation: Algorithms in Bioinformatics, Center for Bioinformatics, University of Tuebingen, Germany.
authors.forename: Daniel H
authors.initials: DH
authors.lastname: Huson
authors.affiliation: Soil Science and Geomorphology, Geography, University of Tuebingen, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Scholten
authors.affiliation: Instrumental Analytical Chemistry, Faculty of Chemistry, University of Duisburg-Essen, Germany.
authors.forename: Maik
authors.initials: M
authors.lastname: Jochmann
authors.affiliation: Geomicrobiology, Center for Applied Geosciences, University of Tuebingen, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Kappler
authors.affiliation: Department of Civil, Environmental, and Geo- Engineering, University of Minnesota, MN, USA.|BioTechnology Institute, University of Minnesota, MN, USA.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Behrens
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000201:enzymology / Q000235:genetics; D001426:Bacterial Proteins / Q000235:genetics*; D005858:Germany; D006219:Halogens / Q000378:metabolism*; D053858:Metabolic Networks and Pathways; D056186:Metagenomics / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods; D012987:Soil / Q000737:chemistry; D012988:Soil Microbiology
chemical_list: D001426:Bacterial Proteins; D006219:Halogens; D012987:Soil