Main environmental drivers of abundance, diversity and community structure of comammox Nitrospira in paddy soils

Gao, Fuyun; LI, Yaying; Fan, Haoxin; XUE, Jiantao; YAO, Huaiying

doi:10.1016/j.pedsph.2022.06.061

Cited by 12 publications

(4 citation statements)

References 50 publications

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“…maritimus, and AOB Nitrosospira (Figures and ). This is consistent with earlier studies demonstrating that geographic distance, climatic conditions, and water quality play important roles in driving the differentiation of microbial river communities. , Previous studies reported that latitude can account for 24.1 and 11.8% of the variations in comammox Nitrospira clade B abundance and composition in paddy soils, respectively . Our RDA results also revealed that Nitrospira sp .…”

Section: Discussionsupporting

confidence: 93%

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Discrepancy in Response of Complete Ammonia Oxidizers and Ammonia-Oxidizing Bacteria and Archaea in the Lhasa River to High-Elevation Conditions

Ma,

Pan,

Wang

et al. 2023

ACS EST Water

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Nitrogen cycle in rivers is significantly influenced by ammonia oxidation, which is driven by ammonia-oxidizing archaea/bacteria (AOA/AOB) and complete ammonia oxidizers (comammox). However, the performance of different ammonia oxidizers in high-elevation rivers is poorly documented. Activity, abundance, diversity, and community composition of ammonia oxidizers in the Lhasa River were investigated. Unamended nitrification rates (UNRs) greatly changed and showed remarkable seasonality and were significantly correlated with solar radiation, dissolved oxygen (DO), and ammonium nitrogen (NH4 +-N). AOB abundance and solar radiation had the strongest direct and indirect effects on UNR. Comammox amoA gene abundance exceeded that of AOA and AOB in 96% of the samples. Most comammox sequences were grouped into clade B, and dominant comammox species were strongly affected by latitude, water NH4 +-N, and total organic carbon. Temperature and total suspended solids were key factors explaining the dominance of the AOA species. Nitrosospira and Nitrosovibrio clusters were found in large proportions in the AOB communities. The co-occurrence pattern of ammonia oxidizers in the Lhasa River was mainly attributed to interspecific symbiosis, even though more modules were found in AOB communities. This provides a comprehensive understanding of the adaptation mechanisms of ammonia oxidizers and their roles in the nitrogen cycle of plateau rivers under global climate warming.

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Section: Discussionsupporting

confidence: 93%

“…41,42 Previous studies reported that latitude can account for 24.1 and 11.8% of the variations in comammox Nitrospira clade B abundance and composition in paddy soils, respectively. 43 Our RDA results also revealed that Nitrospira sp. CG24A (OTU 27) and Nitrospira sp.…”

Section: ■ Discussionsupporting

confidence: 55%

Discrepancy in Response of Complete Ammonia Oxidizers and Ammonia-Oxidizing Bacteria and Archaea in the Lhasa River to High-Elevation Conditions

Ma,

Pan,

Wang

et al. 2023

ACS EST Water

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“…Under high ammonium availability, the ability of ComA to absorb urea may lead to a change in competitiveness, which may be weaker compared to AOA and/or AOB (Liu et al 2021 ), also having a K m (NH 3 ) in comammox Nitrospira of only 63 nM (Kits et al 2017 ). In the neutral soil, the ComA was observed with 15 N-urea labeling (Gao et al 2022 ), and this study supports evidence from previous observations that it grew autotrophically (Li et al 2019 ; Zhao et al 2020 ; Liu et al 2021 ). All current comammox Nitrospira strains were isolated from aquatic systems, and comammox Nitrospira grows preferentially in neutral to slightly alkaline conditions (Daims et al 2015 ; van Kessel et al 2015 ; Li et al 2019 ).…”

Section: Discussionsupporting

confidence: 90%

“…However, in another experiment with acidic forest soil, ComA incorporated 13 CO 2 (Li et al 2019 , 2020 ). Recent studies have revealed that the ComA is highly similar to the Rh-type transporters which were found in almost all β-AOB (Palomo et al 2018 ; Gao et al 2022 ). The Rh-type ammonia transporter can exhibit affinity for ammonium with high absorption capacity within the range of millimole (Palomo et al 2018 ), which may favor the autotrophic growth of ComA at high ammonium concentrations.…”

Section: Discussionmentioning

confidence: 99%

15N-DNA stable isotope probing reveals niche differentiation of ammonia oxidizers in paddy soils

Gao,

Li,

Fan

et al. 2024

Appl Microbiol Biotechnol

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Chemoautotrophic canonical ammonia oxidizers (ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB)) and complete ammonia oxidizers (comammox Nitrospira) are accountable for ammonia oxidation, which is a fundamental process of nitrification in terrestrial ecosystems. However, the relationship between autotrophic nitrification and the active nitrifying populations during 15N-urea incubation has not been totally clarified. The 15N-labeled DNA stable isotope probing (DNA-SIP) technique was utilized in order to study the response from the soil nitrification process and the active nitrifying populations, in both acidic and neutral paddy soils, to the application of urea. The presence of C2H2 almost completely inhibited NO3−-N production, indicating that autotrophic ammonia oxidation was dominant in both paddy soils. 15N-DNA-SIP technology could effectively distinguish active nitrifying populations in both soils. The active ammonia oxidation groups in both soils were significantly different, AOA (NS (Nitrososphaerales)-Alpha, NS-Gamma, NS-Beta, NS-Delta, NS-Zeta and NT (Ca. Nitrosotaleales)-Alpha), and AOB (Nitrosospira) were functionally active in the acidic paddy soil, whereas comammox Nitrospira clade A and Nitrosospira AOB were functionally active in the neutral paddy soil. This study highlights the effective discriminative effect of 15N-DNA-SIP and niche differentiation of nitrifying populations in these paddy soils. Key points • 15N-DNA-SIP technology could effectively distinguish active ammonia oxidizers. • Comammox Nitrospira clade A plays a lesser role than canonical ammonia oxidizers. • The active groups in the acidic and neutral paddy soils were significantly different. Graphical Abstract

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Environmental driving factors of diazotrophic community diversity and activity in Chinese paddy soils

Gao,

Fang,

et al. 2024

J Soils Sediments

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Main environmental drivers of abundance, diversity and community structure of comammox Nitrospira in paddy soils

Cited by 12 publications

References 50 publications

Discrepancy in Response of Complete Ammonia Oxidizers and Ammonia-Oxidizing Bacteria and Archaea in the Lhasa River to High-Elevation Conditions

Discrepancy in Response of Complete Ammonia Oxidizers and Ammonia-Oxidizing Bacteria and Archaea in the Lhasa River to High-Elevation Conditions

15N-DNA stable isotope probing reveals niche differentiation of ammonia oxidizers in paddy soils

Environmental driving factors of diazotrophic community diversity and activity in Chinese paddy soils

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