Genome sequence of Candidatus Nitrososphaera evergladensis from group I.1b enriched from Everglades soil reveals novel genomic features of the ammonia-oxidizing archaea

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...

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Published in:	PloS one Vol. 9; no. 7; p. e101648
Main Authors:	Zhalnina, Kateryna V, Dias, Raquel, Leonard, Michael T, Dorr de Quadros, Patricia, Camargo, Flavio A O, Drew, Jennifer C, Farmerie, William G, Daroub, Samira H, Triplett, Eric W
Format:	Journal Article
Language:	English
Published:	United States Public Library of Science 07-07-2014 Public Library of Science (PLoS)
Subjects:	Acids Adaptation, Physiological - genetics Agricultural land Air pollution Ammonia Ammonia - metabolism Ammonia-oxidizing bacteria Analysis Annotations Archaea Archaea - cytology Archaea - genetics Archaea - metabolism Archaea - physiology Biogeochemical cycles Bioinformatics Biological Transport - genetics Biology and Life Sciences Candidatus Nitrososphaera evergladensis Carbon - metabolism Carbon Cycle - genetics Cell Division - genetics Chemotaxis - genetics CRISPR Deoxyribonucleic acid DNA DNA Repair - genetics DNA Replication - genetics Ecology and Environmental Sciences Energy Metabolism - genetics Enrichment Food Gene sequencing Genes Genetic aspects Genomes Genomics Greenhouse effect Greenhouse gases Homology Hot springs Metabolic pathways Metabolism Metals, Heavy - toxicity Molecular Sequence Annotation Nitrogen Nitrogen - metabolism Nitrous oxide Nucleotide sequence Oceans and Seas Osmotic Pressure Oxidation Oxidation-Reduction Phylogeny Pollution sources Proteins Reproduction (copying) Science Sediments Soil erosion Soil loss Soil Microbiology Soil pollution Soil sciences Soil water Soils Terpenes - metabolism Thaumarchaeota Water pollution Water sources Water springs Brazil Rio Grande do Sul Brazil Everglades Florida United States > US
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Summary:	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.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Conceived and designed the experiments: KVZ RD MTL PDDQ SHD EWT. Performed the experiments: KVZ RD MTL PDDQ. Analyzed the data: KVZ RD MTL PDDQ WGF. Contributed reagents/materials/analysis tools: FAOC WGF SHD EWT. Wrote the paper: KVZ RD MTL JCD EWT. Competing Interests: The authors have declared that no competing interests exist.
ISSN:	1932-6203 1932-6203
DOI:	10.1371/journal.pone.0101648