ArticlePloS one2014
Genome sequence of Candidatus Nitrososphaera evergladensis from group I.1b enriched from Everglades soil reveals novel genomic features of the ammonia-oxidizing archaea.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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40 citing papers in PubMed, 109 citations in OpenAlex.
- Metabolic potential and contributions of ammonia-oxidizing microorganisms and complete ammonia oxidizers to soil nitrification in upland soils of northern China.ISME communications · 2026Article
- Environmental distribution, physiology and genomic adaptations of arctic ammonia-oxidizing archaea.Frontiers in microbiology · 2026Article
- Genomic profiling of soil nitrifying microorganisms enriched on floating membrane filter.Journal of microbiology (Seoul, Korea) · 2025Article
- Nitrous oxide production via enzymatic nitroxyl from the nitrifying archaeonProceedings of the National Academy of Sciences of the United States of America · 2025Article
- "mSphere · 2024Article
- Plants Restoration Drives the Gobi Soil Microbial Diversity for Improving Soil Quality.Plants (Basel, Switzerland) · 2024Article
- Metabolic potential of Nitrososphaera-associated clades.The ISME journal · 2024Article
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- Draft Metagenome-Assembled Genome Sequences of Three Novel Ammonia-OxidizingMicrobiology resource announcements · 2022Article
- Genome-resolved metagenomics reveals novel archaeal and bacterial genomes from Amazonian forest and pasture soils.Microbial genomics · 2022Article
- Diverse ecophysiological adaptations of subsurface Thaumarchaeota in floodplain sediments revealed through genome-resolved metagenomics.The ISME journal · 2022Article
- Limits to the three domains of life: lessons from community assembly along an Antarctic salinity gradient.Extremophiles : life under extreme conditions · 2022Article
- Comparative Genomics of Thaumarchaeota From Deep-Sea Sponges Reveal Their Niche Adaptation.Frontiers in microbiology · 2022Article
- Improving Nitrogen Use Efficiency in Aerobic Rice Based on Insights Into the Ecophysiology of Archaeal and Bacterial Ammonia Oxidizers.Frontiers in plant science · 2022Review
- Cofactor F420: an expanded view of its distribution, biosynthesis and roles in bacteria and archaea.FEMS microbiology reviews · 2021Article
- Ammonia-oxidizing archaea in biological interactions.Journal of microbiology (Seoul, Korea) · 2021Review
- Expanded Diversity and Phylogeny ofFrontiers in microbiology · 2021Article
- Metagenomics Reveal Correlations Between Microbial Organisms in Soils and the Health ofFrontiers in microbiology · 2020Article
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9 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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