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. 2017 Sep 12;2(5):e00059-17.
doi: 10.1128/mSystems.00059-17. eCollection Sep-Oct 2017.

Genome-Enabled Insights Into the Ecophysiology of the Comammox Bacterium " Candidatus Nitrospira Nitrosa"

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Free PMC article

Genome-Enabled Insights Into the Ecophysiology of the Comammox Bacterium " Candidatus Nitrospira Nitrosa"

Pamela Y Camejo et al. mSystems. .
Free PMC article

Abstract

The recently discovered comammox bacteria have the potential to completely oxidize ammonia to nitrate. These microorganisms are part of the Nitrospira genus and are present in a variety of environments, including biological nutrient removal (BNR) systems. However, the physiological traits within and between comammox and nitrite-oxidizing bacterium (NOB)-like Nitrospira species have not been analyzed in these ecosystems. In this study, we identified Nitrospira strains dominating the nitrifying community of a sequencing batch reactor (SBR) performing BNR under microaerobic conditions. We recovered metagenome-derived draft genomes from two Nitrospira strains: (i) Nitrospira sp. strain UW-LDO-01, a comammox-like organism classified as "Candidatus Nitrospira nitrosa," and (ii) Nitrospira sp. strain UW-LDO-02, a nitrite-oxidizing strain belonging to the Nitrospira defluvii species. A comparative genomic analysis of these strains with other Nitrospira-like genomes identified genomic differences in "Ca. Nitrospira nitrosa" mainly attributed to each strain's niche adaptation. Traits associated with energy metabolism also differentiate comammox from NOB-like genomes. We also identified several transcriptionally regulated adaptive traits, including stress tolerance, biofilm formation, and microaerobic metabolism, which might explain survival of Nitrospira under multiple environmental conditions. Overall, our analysis expanded our understanding of the genetic functional features of "Ca. Nitrospira nitrosa" and identified genomic traits that further illuminate the phylogenetic diversity and metabolic plasticity of the Nitrospira genus. IMPORTANCENitrospira-like bacteria are among the most diverse and widespread nitrifiers in natural ecosystems and the dominant nitrite oxidizers in wastewater treatment plants (WWTPs). The recent discovery of comammox-like Nitrospira strains, capable of complete oxidation of ammonia to nitrate, raises new questions about specific traits responsible for the functional versatility and adaptation of this genus to a variety of environments. The availability of new Nitrospira genome sequences from both nitrite-oxidizing and comammox bacteria offers a way to analyze traits in different Nitrospira functional groups. Our comparative genomics analysis provided new insights into the adaptation of Nitrospira strains to specific lifestyles and environmental niches.

Keywords: NOB; Nitrospira; comammox; metagenomics; “Ca. Nitrospira nitrosa”.

Figures

FIG 1
FIG 1
Nutrient profiles of nitrogenous compounds (A), phosphorus and acetate (B), and oxygen concentration (C) in a regular cycle of the lab-scale SBR during stage 1. Dotted lines separate operational conditions within cycle. ANO, anoxic; AER, microaerobic; SET, settling.
FIG 2
FIG 2
Comparison of the genome-wide average nucleotide identities and alignment percentages of Nitrospira-like genomes. The heat map shows the average nucleotide identity (red upper section of matrix) and the percentage of the two genomes that aligned (yellow lower section).
FIG 3
FIG 3
RAxML phylogenetic tree of a concatenated alignment of 37 marker genes (nucleotide sequence) from a data set with the root placed on the branch leading to Nitrobacter winogradskyi. The numbers at the nodes of both trees show support values derived from 100 RAxML bootstrap replicates.
FIG 4
FIG 4
(A) Normalized frequency of metagenomic reads mapping to the genome of comammox organisms, AOA, AOB, NOB, and anammox-related organisms in samples from stages 1 and 2 of the lab-scale SBR. (B) Relative abundance of reads mapping to genomes of Nitrospira-related bacteria in stage 1 sample, including the draft genomes retrieved in this study.
FIG 5
FIG 5
Genomic differences between Nitrospira sp. UW-LDO-01 and “Ca. Nitrospira nitrosa.” (A) Venn diagram of ortholog clusters shared between the two draft genomes; (B) distribution of SEED functional categories in the fraction of orthologs shared by the two genomes; (C) distribution of SEED functional categories in ortholog clusters found in only one of the genomes (genome-specific fraction).

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