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.

Proteomics and comparative genomics of Nitrososphaera viennensis reveal the core genome and adaptations of archaeal ammonia oxidizers

“…Nitrososphaera gargensis" (28) and "Ca. Nitrososphaera evergladensis" (29) of the order Nitrososphaerales; Ca. N. maritimus (26), "Ca.…”

“…2, distinguishing the core AOA gene repertoire (genes labeled in gray) from genes with a more limited distribution (orange and blue). Notably, Nitrososphaerales seem to be particularly versatile with respect to interconversions of the key metabolite pyruvate (28,29), as indicated by the presence of a pyruvate/phosphate dikinase, converting pyruvate to phosphoenolpyruvate (PEP), a putative pyruvate dehydrogenase/oxidase converting it to acetate, and an alanine dehydrogenase (Dataset S2). All Thaumarchaeota harbor candidate enzymes for all steps of an oxidative TCA cycle, the functionality of which in vivo is, however, debated.…”

“…The AmoC protein family includes a single homolog in the Ca. Nitrosopumilales genomes but is enlarged in the soil-dwelling Nitrososphaerales and AOB (28,29,50), with N. viennensis encoding six homologs (72-96% amino acid identity). The core AmoC COG includes two copies in Nitrososphaerales (AmoC3 and C6 in N. viennensis).…”

“…Motilityassociated genes are encoded in all investigated genomes of the genus Nitrososphaera as well as in N. devanaterra (17,28,29,31) (Fig. 5).…”

Cloning, expression, purification and preliminary X-ray analysis of EstN2, a novel archaeal α/β-hydrolase fromCandidatusNitrososphaera gargensis

“…AIF85481.1; 91% query coverage, E-value 2 Â 10 À129 , 70% identity). The biochemical properties of this putative enzyme have not been studied to our knowledge (Zhalnina et al, 2014). Furthermore, the BLASTX alignment (date of search: 5 August 2014) resulted in a hypothetical protein from the bacterium JKG1 (NCBI accession No.…”