Abstract
Ammonia-oxidizing archaea (AOA) are thought to be among the most abundant microorganisms on Earth and may significantly impact the global nitrogen and carbon cycles. We sequenced the genome of AOA in an enrichment culture from low-salinity sediments in San Francisco Bay using single-cell and metagenomic genome sequence data. Five single cells were isolated inside an integrated microfluidic device using laser tweezers, the cells' genomic DNA was amplified by multiple displacement amplification (MDA) in 50 nL volumes and then sequenced by high-throughput DNA pyrosequencing. This microscopy-based approach to single-cell genomics minimizes contamination and allows correlation of high-resolution cell images with genomic sequences. Statistical properties of coverage across the five single cells, in combination with the contrasting properties of the metagenomic dataset allowed the assembly of a high-quality draft genome. The genome of this AOA, which we designate Candidatus Nitrosoarchaeum limnia SFB1, is ∼1.77 Mb with >2100 genes and a G+C content of 32%. Across the entire genome, the average nucleotide identity to Nitrosopumilus maritimus, the only AOA in pure culture, is ∼70%, suggesting this AOA represents a new genus of Crenarchaeota. Phylogenetically, the 16S rRNA and ammonia monooxygenase subunit A (amoA) genes of this AOA are most closely related to sequences reported from a wide variety of freshwater ecosystems. Like N. maritimus, the low-salinity AOA genome appears to have an ammonia oxidation pathway distinct from ammonia oxidizing bacteria (AOB). In contrast to other described AOA, these low-salinity AOA appear to be motile, based on the presence of numerous motility- and chemotaxis-associated genes in the genome. This genome data will be used to inform targeted physiological and metabolic studies of this novel group of AOA, which may ultimately advance our understanding of AOA metabolism and their impacts on the global carbon and nitrogen cycles.
Highlights
Mesophilic Crenarchaea are among the most abundant microorganisms on the planet [1,2]
An ammonia-oxidizing enrichment culture initiated from sediments in the low-salinity region of San Francisco Bay was dominated by Ammonia-oxidizing archaea (AOA); CARD-fluorescent in situ hybridization (FISH) showed that Archaea (Arch915 probe) accounted for approximately 84% of cells in the enrichment and the remaining 16% were Bacteria (Eub338 I–III probes)
Archaeal ammonia monooxygenase (amoA) and 16S rRNA gene sequences from the AOA enrichment culture were phylogenetically distinct from N. martimus [Figure 1], and were instead most closely related to environmental clones derived from freshwater ecosystems
Summary
Mesophilic Crenarchaea (first discovered by Fuhrman et al [1] and DeLong [2]) are among the most abundant microorganisms on the planet [1,2]. Crenarchaea generally comprise 1–5% of the total prokaryotic community [7,8,9], but can reach upwards to 38% in some systems (e.g., temperate acidic forest soils) [10]. It appears that the vast majority of Crenarchaea in soils and the open ocean possess ammonia monooxygenase (amoA) genes and may be capable of oxidizing ammonia to nitrite, based on quantitative PCR estimates of 16S rRNA and amoA genes, fluorescent in situ hybridization, and metagenomic analyses [11,12,13,14,15,16,17,18]. Recent phylogenetic and genomic analyses suggest that these mesophilic Crenarchaea should be recognized as a third archaeal phylum, the Thaumarchaeota [19,20]
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