eprintid: 114892 rev_number: 21 eprint_status: archive userid: 28768 dir: disk0/00/11/48/92 datestamp: 2016-01-22 16:48:56 lastmod: 2016-08-25 14:19:30 status_changed: 2016-01-22 16:48:56 type: article metadata_visibility: show creators_name: Pinto, Ameet J. creators_name: Marcus, Daniel N. creators_name: Ijaz, Umer Zeeshan creators_name: Bautista-de lose Santos, Quyen Melina creators_name: Dick, Gregory J. creators_name: Raskin, Lutgarde creators_id: Ameet.Pinto@glasgow.ac.uk creators_id: Umer.Ijaz@glasgow.ac.uk title: Metagenomic evidence for the Presence of Comammox Nitrospira-Like Bacteria in a Drinking Water System ispublished: pub divisions: 30301000 full_text_status: public abstract: We report metagenomic evidence for the presence of a Nitrospira-like organism with the metabolic potential to perform the complete oxidation of ammonia to nitrate (i.e., it is a complete ammonia oxidizer [comammox]) in a drinking water system. This metagenome bin was discovered through shotgun DNA sequencing of samples from biologically active filters at the drinking water treatment plant in Ann Arbor, MI. Ribosomal proteins, 16S rRNA, and nxrA gene analyses confirmed that this genome is related to Nitrospira-like nitrite-oxidizing bacteria. The presence of the full suite of ammonia oxidation genes, including ammonia monooxygenase and hydroxylamine dehydrogenase, on a single ungapped scaffold within this metagenome bin suggests the presence of recently discovered comammox potential. Evaluations based on coverage and k-mer frequency distribution, use of two different genome-binning approaches, and nucleic acid and protein similarity analyses support the presence of this scaffold within the Nitrospira metagenome bin. The amoA gene found in this metagenome bin is divergent from those of canonical ammonia and methane oxidizers and clusters closely with the unusual amoA gene of comammox Nitrospira. This finding suggests that previously reported imbalances in abundances of nitrite- and ammonia-oxidizing bacteria/archaea may likely be explained by the capacity of Nitrospira-like organisms to completely oxidize ammonia. This finding might have significant implications for our understanding of microbially mediated nitrogen transformations in engineered and natural systems. date: 2015-12-30 date_type: published publication: mSphere volume: 1 number: 1 publisher: American Society for Microbiology id_number: 10.1128/mSphere.00054-15 refereed: TRUE issn: 2379-5042 copyright_holders: Copyright © 2015 Pinto et al. prior: First published in mSphere 1(1):e00054-15 repro: Reproduced under a Creative Commons License uniqueid: glaseprints:2015-114892 creators_browse_id: 29132 creators_browse_id: 28768 staff_edit: Item viewed, online version. 22.01.16 LA published_online: 2015-12-30 issn_online: 2379-5042 funding_project_code: 66580 funding_award_no: 1 funding_project_name: Healthy drinking water funding_investigator_name: Ameet Pinto funding_funder_name: Engineering & Physical Sciences Research Council (EPSRC) funding_funder_code: EP/M016811/1 funding_investigator_dept: ENG - ENGINEERING INFRASTRUCTURE & ENVIR metadata_qc: full article_number: e00054-15 fp7_project: no fp7_type: info:eu-repo/semantics/article access_rights: info:eu-repo/semantics/restrictedAccess dates_date: 2015-12-30 dates_date: 2015-12-08 dates_date_type: published dates_date_type: accepted hoa_compliant: 511 hoa_date_acc: 2015-12-08 hoa_date_pub: 2015-12-30 hoa_date_fcd: 2016-01-22 hoa_date_foa: 2016-01-22 hoa_version_fcd: VoR oa_date_of_comp_deposit: 2016-01-22 oa_est_cost: 2000 oa_notes: 10.12.15 AS Sent to A&A 10.12.15 LA Metadata made live. Added to Dec 2015 shelf for tracking. 22.01.16 LA Publisher PDF added with CC BY. oa_type: Gold oa_charge: 883.20 oa_vat: 176.64 oa_total_cost: pre_april_2016 oa_apc_fund: RCUK oa_transaction_number: 2002452515 oa_transaction_number: 2147483647 oa_period: 201606 oa_funder_ack: Yes oa_research_materials_ack: Yes oa_cost_recovery: FALSE oa_sent_to_aa: FALSE rioxx2_license_ref_input_license_ref: http://creativecommons.org/licenses/by/4.0/ rioxx2_license_ref_input_start_date: 2015-12-30 citation: Pinto, A. J. , Marcus, D. N., Ijaz, U. Z. , Bautista-de lose Santos, Q. M., Dick, G. J. and Raskin, L. (2015) Metagenomic evidence for the Presence of Comammox Nitrospira-Like Bacteria in a Drinking Water System. mSphere , 1(1), e00054-15. (doi:10.1128/mSphere.00054-15 ) document_url: http://eprints.gla.ac.uk/114892/1/114892.pdf