title: Genome sequence of Candidatus Nitrososphaera evergladensis from group I.1b enriched from Everglades soil reveals novel genomic features of the ammonia-oxidizing archaea.
abstract: The activity of ammonia-oxidizing archaea (AOA) leads to the loss of nitrogen from soil, pollution of water sources and elevated emissions of greenhouse gas. To date, eight AOA genomes are available in the public databases, seven are from the group I.1a of the Thaumarchaeota and only one is from the group I.1b, isolated from hot springs. Many soils are dominated by AOA from the group I.1b, but the genomes of soil representatives of this group have not been sequenced and functionally characterized. The lack of knowledge of metabolic pathways of soil AOA presents a critical gap in understanding their role in biogeochemical cycles. Here, we describe the first complete genome of soil archaeon Candidatus Nitrososphaera evergladensis, which has been reconstructed from metagenomic sequencing of a highly enriched culture obtained from an agricultural soil. The AOA enrichment was sequenced with the high throughput next generation sequencing platforms from Pacific Biosciences and Ion Torrent. The de novo assembly of sequences resulted in one 2.95 Mb contig. Annotation of the reconstructed genome revealed many similarities of the basic metabolism with the rest of sequenced AOA. Ca. N. evergladensis belongs to the group I.1b and shares only 40% of whole-genome homology with the closest sequenced relative Ca. N. gargensis. Detailed analysis of the genome revealed coding sequences that were completely absent from the group I.1a. These unique sequences code for proteins involved in control of DNA integrity, transporters, two-component systems and versatile CRISPR defense system. Notably, genomes from the group I.1b have more gene duplications compared to the genomes from the group I.1a. We suggest that the presence of these unique genes and gene duplications may be associated with the environmental versatility of this group.
authors.affiliation: Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, United States of America.
authors.forename: Kateryna V
authors.initials: KV
authors.lastname: Zhalnina
authors.affiliation: Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, United States of America.
authors.forename: Raquel
authors.initials: R
authors.lastname: Dias
authors.affiliation: Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, United States of America.
authors.forename: Michael T
authors.initials: MT
authors.lastname: Leonard
authors.affiliation: Soil Science Department, Federal Unviersity of Rio Grande do Sul, Porto Alegre, RS, Brazil.
authors.forename: Patricia
authors.initials: P
authors.lastname: Dorr de Quadros
authors.affiliation: Soil Science Department, Federal Unviersity of Rio Grande do Sul, Porto Alegre, RS, Brazil.
authors.forename: Flavio A O
authors.initials: FA
authors.lastname: Camargo
authors.affiliation: Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, United States of America.
authors.forename: Jennifer C
authors.initials: JC
authors.lastname: Drew
authors.affiliation: Genome Sequencing Services Laboratory, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, United States of America.
authors.forename: William G
authors.initials: WG
authors.lastname: Farmerie
authors.affiliation: Everglades Research and Education Center, University of Florida, Belle Glade, Florida, United States of America.
authors.forename: Samira H
authors.initials: SH
authors.lastname: Daroub
authors.affiliation: Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, United States of America.
authors.forename: Eric W
authors.initials: EW
authors.lastname: Triplett
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D000641:Ammonia / Q000378:metabolism*; D001105:Archaea / Q000166:cytology / Q000235:genetics* / Q000378:metabolism* / Q000502:physiology; D001692:Biological Transport / Q000235:genetics; D002244:Carbon / Q000378:metabolism; D057486:Carbon Cycle / Q000235:genetics; D002455:Cell Division / Q000235:genetics; D002633:Chemotaxis / Q000235:genetics; D004260:DNA Repair / Q000235:genetics; D004261:DNA Replication / Q000235:genetics; D004734:Energy Metabolism / Q000235:genetics; D023281:Genomics; D019216:Metals, Heavy / Q000633:toxicity; D058977:Molecular Sequence Annotation; D009584:Nitrogen / Q000378:metabolism; D009792:Oceans and Seas; D009997:Osmotic Pressure; D010084:Oxidation-Reduction; D010802:Phylogeny; D012988:Soil Microbiology; D013729:Terpenes / Q000378:metabolism
chemical_list: D019216:Metals, Heavy; D013729:Terpenes; D002244:Carbon; D000641:Ammonia; D009584:Nitrogen