Genomic profiling ofNitrospiraspecies reveals ecological success of comammoxNitrospira

Palomo, Alejandro; Dechesne, Arnaud; Smets, Barth F.

doi:10.1101/612226

Cited by 27 publications

(45 citation statements)

References 83 publications

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“…These authors contributed equally: Emilie Spasov, Jackson M. Tsuji Compared with AOA and AOB, very little is known about the abundance and diversity of comammox Nitrospira in engineered aquatic environments. Consistent with a low ammonium niche, comammox Nitrospira have been detected in drinking water systems [7][8][9][10][11][12][13][14]. First identified from water treatment system metagenome sequences [5,6], most wastewater-associated comammox Nitrospira belong to clade A [5,7,12,[14][15][16][17][18], albeit with abundances generally lower than those reported for AOA and AOB [7,[18][19][20][21].…”

Section: Introductionmentioning

confidence: 83%

High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant

et al. 2020

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Nitrification, the oxidation of ammonia to nitrate via nitrite, is an important process in municipal wastewater treatment plants (WWTPs). Members of the Nitrospira genus that contribute to complete ammonia oxidation (comammox) have only recently been discovered and their relevance to engineered water treatment systems is poorly understood. This study investigated distributions of Nitrospira, ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) in biofilm samples collected from tertiary rotating biological contactors (RBCs) of a municipal WWTP in Guelph, Ontario, Canada. Using quantitative PCR (qPCR), 16S rRNA gene sequencing, and metagenomics, our results demonstrate that Nitrospira species strongly dominate RBC biofilm samples and that comammox Nitrospira outnumber all other nitrifiers. Genome bins recovered from assembled metagenomes reveal multiple populations of comammox Nitrospira with distinct spatial and temporal distributions, including several taxa that are distinct from previously characterized Nitrospira members. Diverse functional profiles imply a high level of niche heterogeneity among comammox Nitrospira, in contrast to the sole detected AOA representative that was previously cultivated and characterized from the same RBC biofilm. Our metagenome bins also reveal two cyanase-encoding populations of comammox Nitrospira, suggesting an ability to degrade cyanate, which has only been shown previously for several Nitrospira representatives that are strict nitrite oxidizers. This study demonstrates the importance of RBCs as model systems for continued investigation of environmental factors that control the distributions and activities of AOB, AOA, comammox Nitrospira, and other nitrite oxidizers.

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Section: Introductionmentioning

confidence: 83%

High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant

et al. 2020

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“…Nitrous oxide mixing ratios were converted into units of mass per volume using the ideal gas law and values of pressure and air temperature recorded by the weather station. Individual N 2 O fluxes were calculated in R (version 3.2.5, R Core Team, 2016) using the package HMR (Pedersen et al, 2010). This program analyses non-linear concentrationtime series with a regression-based extension of the model of Hutchinson and Mosier (1981) and linear concentration-time series by linear regression (Pedersen et al, 2010).…”

Section: Data Processing and Statistical Analysesmentioning

confidence: 99%

“…Individual N 2 O fluxes were calculated in R (version 3.2.5, R Core Team, 2016) using the package HMR (Pedersen et al, 2010). This program analyses non-linear concentrationtime series with a regression-based extension of the model of Hutchinson and Mosier (1981) and linear concentration-time series by linear regression (Pedersen et al, 2010). Statistical data (p value, 95 % confidence limits) are provided by HMR for both categories of fluxes.…”

Section: Data Processing and Statistical Analysesmentioning

confidence: 99%

See 1 more Smart Citation

Regulation of N2O emissions from acid organic soil drained for agriculture

Taghizadeh‐Toosi¹,

Elsgaard²,

Clough³

et al. 2019

Biogeosciences

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Abstract. Organic soils drained for crop production or grazing land are agroecosystems with potentially high but variable emissions of nitrous oxide (N2O). The present study investigated the regulation of N2O emissions in a raised bog area drained for agriculture, which is classified as potentially acid sulfate soil. We hypothesised that pyrite (FeS2) oxidation was a potential driver of N2O emissions through microbially mediated reduction of nitrate (NO3-). Two sites with rotational grass, and two sites with a potato crop, were equipped for monitoring of N2O emissions and soil N2O concentrations at the 5, 10, 20, 50 and 100 cm depth during weekly field campaigns in spring and autumn 2015. Further data acquisition included temperature, precipitation, soil moisture, water table (WT) depth, and soil NO3- and ammonium (NH4+) concentrations. At all sites, the soil was acidic, with pH ranging from 4.7 to 5.4. Spring and autumn monitoring periods together represented between 152 and 174 d, with cumulative emissions of 4–5 kg N2O-N ha−1 at sites with rotational grass and 20–50 kg N2O-N ha−1 at sites with a potato crop. Equivalent soil gas-phase concentrations of N2O at grassland sites varied between 0 and 25 µL L−1 except for a sampling after slurry application at one of the sites in spring, with a maximum of 560 µL L−1 at the 1 m depth. At the two potato sites the levels of below-ground N2O concentrations ranged from 0.4 to 2270 µL L−1 and from 0.1 to 470 µL L−1, in accordance with the higher soil mineral N availability at arable sites. Statistical analyses using graphical models showed that soil N2O concentration in the capillary fringe (i.e. the soil volume above the water table influenced by tension saturation) was the strongest predictor of N2O emissions in spring and, for grassland sites, also in the autumn. For potato sites in autumn, there was evidence that NO3- availability in the topsoil and temperature were the main controls on N2O emissions. Chemical analyses of intact soil cores from the 0 to 1 m depth, collected at adjacent grassland and potato sites, showed that the total reduction capacity of the peat soil (assessed by cerium(IV) reduction) was much higher than that represented by FeS2, and the concentrations of total reactive iron (TRFe) were higher than those of FeS2. Based on the statistical graphical models and the tentative estimates of reduction capacities, FeS2 oxidation was unlikely to be important for N2O emissions. Instead, archaeal ammonia oxidation and either chemodenitrification or nitrifier denitrification were considered to be plausible pathways of N2O production in spring, whereas in the autumn heterotrophic denitrification may have been more important at arable sites.

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“…50All comammox Nitrospira reported to date belong to lineage II of the genus Nitrospira.Although two major clades of comammox Nitrospira have been described (i.e., clades A and B) based on ammonia monooxygenase (amoA) gene phylogeny, all enriched and cultivated species of comammox Nitrospira belong to clade A [5,6].Compared to AOB and AOA, very little is known about the abundance and diversity of 55 comammox Nitrospira in engineered aquatic environments. Consistent with a low ammonium niche, comammox Nitrospira have been detected in drinking water systems [7][8][9][10][11][12][13][14]. First identified from water treatment system metagenome sequences [5,6], most wastewaterassociated comammox Nitrospira belong to clade A [5, 7,12,[14][15][16][17][18], albeit with abundances generally lower than those reported for AOA and AOB [7,[18][19][20][21].…”

mentioning

confidence: 97%

High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant

Spasov

Tsuji

Hug

et al. 2019

Preprint

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AbstractNitrification, the oxidation of ammonia to nitrate via nitrite, is an important process in municipal wastewater treatment plants (WWTPs). Members of the Nitrospira genus that contribute to complete ammonia oxidation (comammox) have only recently been discovered and their relevance to engineered water treatment systems is poorly understood. This study investigated distributions of Nitrospira, ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) in biofilm samples collected from tertiary rotating biological contactors (RBCs) of a municipal WWTP in Guelph, Ontario, Canada. Using quantitative PCR (qPCR), 16S rRNA gene sequencing, and metagenomics, our results demonstrate that Nitrospira species strongly dominate RBC biofilm samples and that comammox Nitrospira outnumber all other nitrifiers. Genome bins recovered from assembled metagenomes reveal multiple populations of comammox Nitrospira with distinct spatial and temporal distributions, including several taxa that are distinct from previously characterized Nitrospira members. Diverse functional profiles imply a high level of niche heterogeneity among comammox Nitrospira, in contrast to the sole detected AOA representative that was previously cultivated and characterized from the same RBC biofilm. Our metagenome bins also reveal two cyanase-encoding populations of comammox Nitrospira, suggesting an ability to degrade cyanate, which has not been shown previously for Nitrospira that are not strict nitrite oxidizers. This study demonstrates the importance of RBCs as model systems for continued investigation of environmental factors that control the distributions and activities of AOB, AOA, comammox Nitrospira, and other nitrite oxidizers.

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Genomic profiling ofNitrospiraspecies reveals ecological success of comammoxNitrospira

Cited by 27 publications

References 83 publications

High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant

High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant

Regulation of N<sub>2</sub>O emissions from acid organic soil drained for agriculture

High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant

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Genomic profiling ofNitrospiraspecies reveals ecological success of comammoxNitrospira

Cited by 27 publications

References 83 publications

High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant

High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant

Regulation of N&lt;sub&gt;2&lt;/sub&gt;O emissions from acid organic soil drained for agriculture

High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant

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Regulation of N<sub>2</sub>O emissions from acid organic soil drained for agriculture