title: Metagenomic analysis of rapid gravity sand filter microbial communities suggests novel physiology of Nitrospira spp.
abstract: Rapid gravity sand filtration is a drinking water production technology widely used around the world. Microbially catalyzed processes dominate the oxidative transformation of ammonia, reduced manganese and iron, methane and hydrogen sulfide, which may all be present at millimolar concentrations when groundwater is the source water. In this study, six metagenomes from various locations within a groundwater-fed rapid sand filter (RSF) were analyzed. The community gene catalog contained most genes of the nitrogen cycle, with particular abundance in genes of the nitrification pathway. Genes involved in different carbon fixation pathways were also abundant, with the reverse tricarboxylic acid cycle pathway most abundant, consistent with an observed Nitrospira dominance. From the metagenomic data set, 14 near-complete genomes were reconstructed and functionally characterized. On the basis of their genetic content, a metabolic and geochemical model was proposed. The organisms represented by draft genomes had the capability to oxidize ammonium, nitrite, hydrogen sulfide, methane, potentially iron and manganese as well as to assimilate organic compounds. A composite Nitrospira genome was recovered, and amo-containing Nitrospira genome contigs were identified. This finding, together with the high Nitrospira abundance, and the abundance of atypical amo and hao genes, suggests the potential for complete ammonium oxidation by Nitrospira, and a major role of Nitrospira in the investigated RSFs and potentially other nitrifying environments.
authors.affiliation: Department of Environmental Engineering, Technical University of Denmark, Kongens Lyngby, Denmark.|Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark.
authors.forename: Alejandro
authors.identifier: 0000-0003-4940-0059
authors.initials: A
authors.lastname: Palomo
authors.affiliation: Department of Environmental Engineering, Technical University of Denmark, Kongens Lyngby, Denmark.
authors.forename: S
authors.initials: S
authors.lastname: Jane Fowler
authors.affiliation: Department of Environmental Engineering, Technical University of Denmark, Kongens Lyngby, Denmark.
authors.forename: Arda
authors.initials: A
authors.lastname: Gülay
authors.affiliation: Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark.
authors.forename: Simon
authors.initials: S
authors.lastname: Rasmussen
authors.affiliation: Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark.
authors.forename: Thomas
authors.initials: T
authors.lastname: Sicheritz-Ponten
authors.affiliation: Department of Environmental Engineering, Technical University of Denmark, Kongens Lyngby, Denmark.
authors.forename: Barth F
authors.identifier: 0000-0003-4119-6292
authors.initials: BF
authors.lastname: Smets
mesh_terms: D000641:Ammonia / Q000378:metabolism; D064751:Ammonium Compounds / Q000378:metabolism; D001419:Bacteria / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification* / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D005374:Filtration; D006112:Gravitation; D060587:Groundwater / Q000737:chemistry / Q000382:microbiology*; D007501:Iron / Q000378:metabolism; D008345:Manganese / Q000378:metabolism; D056186:Metagenomics; D008697:Methane / Q000378:metabolism; D009573:Nitrites / Q000378:metabolism; D010084:Oxidation-Reduction; D012822:Silicon Dioxide / Q000737:chemistry
chemical_list: D064751:Ammonium Compounds; D001426:Bacterial Proteins; D009573:Nitrites; D008345:Manganese; D012822:Silicon Dioxide; D000641:Ammonia; D007501:Iron; D008697:Methane