Evaluation of hydroxylamine oxidoreductase as a functional and phylogenetic marker to differentiate <i>Nitrosomonas</i> spp.

Keluskar, Radhika; Desai, Anjana J.

doi:10.1002/jobm.201200378

Cited by 5 publications

(4 citation statements)

References 24 publications

(33 reference statements)

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“…The amoA and hao genes are functional genes involved in redox nitrogen transformations and are also considered phylogenetic markers to study the diversity of ammonia oxidizing microorganisms (AOM). 30–33 The phylogenetic tree topologies based on these genes (Fig. S1) further confirm the classification of UW-LDO-01 as related to Ca.…”

Section: Resultssupporting

confidence: 65%

Genome-enabled insights into the ecophysiology of the comammox bacteriumCandidatusNitrospira nitrosa

Camejo

Domingo²,

McMahon

et al. 2017

Preprint

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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 bacteria (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 micro-aerobic conditions. We recovered metagenomes-derived draft genomes from two Nitrospira strains: (1) Nitrospira sp. UW-LDO-01, a comammox-like organism classified as Candidatus Nitrospira nitrosa, and (2) Nitrospira sp. 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 strains’ 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 micro-aerobic 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.

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Section: Resultssupporting

confidence: 65%

Genome-enabled insights into the ecophysiology of the comammox bacteriumCandidatusNitrospira nitrosa

Camejo

Domingo²,

McMahon

et al. 2017

Preprint

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“…The amoA and hao genes are functional genes involved in redox nitrogen transformations and are also considered phylogenetic markers to study the diversity of ammonia-oxidizing microorganisms (AOM) ( 12 – 15 ). The phylogenetic tree topologies based on these genes ( Fig.…”

Section: Resultsmentioning

confidence: 99%

Genome-Enabled Insights into the Ecophysiology of the Comammox Bacterium “ Candidatus Nitrospira nitrosa”

et al. 2017

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Nitrospira-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.

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“…The use of hao as a molecular marker for identifying AOB was suggested by Shinozaki and Fukui [20], and subsequently Schmid et al [21] used it to detect AOB from environmental samples. More recently, grouping of AOB through hao gene SSCP analysis has been shown to follow the same pattern as 16S rRNA and amoA gene based analysis [22]. hao, like amoA, is unique to this group of organisms and hence its sequence based analysis as a phylogenetic marker in comparison with amoA and 16S rRNA needs detailed investigation.…”

Section: Introductionmentioning

confidence: 93%

“…Sequences of 16S rRNA, amoA and hao genes of 21 AOB (9 AOB strains belonging to β and γsubclass of proteobacteria and 12 uncultured AOB such that all the three genes sequences were available) were examined in this study (Table 1). Sequences for the AOB strains were obtained from GenBank, amongst which 12 uncultured AOB sequences were obtained indigenously by the authors in previous studies [22]. The size of hao, amoA and 16S rRNA genes ranged from 654bp -850bp, 453bp -883bp and 1207bp -1529bp respectively.…”

Section: Sequence Datamentioning

confidence: 99%

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2018

RJLBPCS

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In aerobic autotrophic ammonia oxidizing bacteria (AOB), an octaheme enzyme, hydroxylamine oxidoreductase (hao) catalyzes the conversion of hydroxylamine to nitrite. For hao to be considered as a functional and phylogenetic marker, sequence based analysis was carried out.Sequence diversity in hao gene fragment was assessed and compared with 16S rRNA and ammonia monooxygenase (amoA) gene fragments from 21 AOB. Phylogenetic analysis of AOB based on 16S rRNA, hao, and amoA gene fragments showed similar tree topologies. The diversity of the studied AOB was found to be similar in both richness and evenness for the three genes and the minor differences observed in the Shannon's diversity index were not found to be significant according to t-test and p-values. Co-evolution of hao and amoA genes was established based on the congruence observed amongst amoA and hao gene fragments phylogenetic trees, similarities in the rates of synonymous and non-synonymous mutations, correlation plots of amoA and hao gene fragments (r 2 -0.9) and their percentage sequence similarity. These evidences suggest high potential of hao gene fragment to be used as a functional and phylogenetic marker for the evolutionary evaluation of AOB.

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Evaluation of hydroxylamine oxidoreductase as a functional and phylogenetic marker to differentiate Nitrosomonas spp.

Cited by 5 publications

References 24 publications

Genome-enabled insights into the ecophysiology of the comammox bacteriumCandidatusNitrospira nitrosa

Genome-enabled insights into the ecophysiology of the comammox bacteriumCandidatusNitrospira nitrosa

Genome-Enabled Insights into the Ecophysiology of the Comammox Bacterium “ Candidatus Nitrospira nitrosa”

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