Nature Communications
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2026
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IF 18.1
Song Kang,Wang Yuren,Li Lu,Deng Min,Wu Fengchang,Xia Zhiwei,Zhao Xiaoli,Greening Chris,Lücker Sebastian,Guo Jianhua
Complete ammonia-oxidizing (comammox) Nitrospira are recognized as key players in the nitrogen cycle, yet their ecological roles in extreme environments remain poorly understood. Here, we show that comammox Nitrospira occupy distinct ecological niches in Tibetan Plateau thermokarst lakes (pH 7.5–10.2) using stable isotope probing, metagenomics, and metatranscriptomics. While gross nitrification rates are significantly higher in subalkaline lakes due to the active presence of ammonia-oxidizing archaea (AOA) and bacteria (AOB), these canonical nitrifiers are inhibited under elevated pH. In contrast, comammox Nitrospira activity is significantly higher in alkaline than in subalkaline lakes, becoming the predominant nitrifiers with activities exceeding those of AOA and AOB by over 6- and 15-fold, respectively. This niche transition, coupled with the inherently low N 2 O yield of comammox, results in significantly attenuated nitrous oxide (N 2 O) production in alkaline lakes. Under saline-alkaline stress, these bacteria maintained high expression of carbon fixation and sulfur metabolism genes while upregulating compatible solute biosynthesis, cation transporters, and protein chaperones. Altogether, these findings identify comammox bacteria as key mediators of nitrogen cycling in permafrost-affected thermokarst lakes, expanding their known physiological range and providing mechanistic insights into their adaptations to extreme environments.
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DOI
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SOIL BIOLOGY & BIOCHEMISTRY
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2021
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IF 7.609
Haiyang Liu,Hangwei Hu,Xing Huang,Tida Ge,Yongfu Li,Zhenke Zhu,Xingmei Liu,Wenfeng Tan,Zhongjun Jia,Hongjie Di,Jianming Xu,Yong Li
Chemoautotrophic canonical ammonia-oxidizers and complete ammonia oxidizers (comammox) are responsible for ammonia oxidation, which is the rate-limiting step of nitrification in terrestrial ecosystems. However, the relative importance of autotrophic nitrification and the related active nitrifiers during mineralization of organic substances with different C/N ratios have not been fully elucidated to date. In this study, 15 N tracing and 13 CO 2 -DNA-based stable isotope probing (DNA-SIP) techniques were employed to investigate the responses of soil nitrification processes and the active nitrifying phylotypes in acidic and neutral paddy soils with amendment of glutamine (Gln) or rice straw with low C/N (LS) or high C/N (HS). Acetylene (C 2 H 2 ) was utilized to differentiate autotrophic and heterotrophic nitrification. The results indicated that C 2 H 2 completely blocked the production of 15 NO 3 − in Gln and LS treatments, implying the predominance of autotrophic nitrification with the N derived from the mineralization of Gln and LS. Neither 15 NH 4 + nor 15 NO 3 − was detected in the HS-amended soils, suggesting that NH 4 + derived from organic N mineralization was immobilized immediately by microorganisms. In the DNA-SIP microcosms, the abundance of ammonia-oxidizing bacteria (AOB) in the unamended control (CK), Gln and LS treatments of acidic paddy soil increased by 22.1-, 71.9- and 27.6-fold, respectively. A significantly larger proportion of Nitrosospira -like AOB, rather than ammonia-oxidizing archaea (AOA) and comammox Nitrospira , was labelled by 13 CO 2 , indicating that AOB made a stronger contribution to autotrophic nitrification in acidic paddy soil. The active nitrification of neutral paddy soil was predominated by AOA affiliated with the Nitrososphaera viennensis lineage in the CK and LS microcosms but by Nitrosospira -like AOB in the Gln microcosm. These results suggest the significance of autotrophic nitrification catalysed by canonical ammonia oxidizers, rather than comammox, during the mineralization of organic substances with low C/N in paddy soils.
研究领域:
微生物学
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土壤学
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生态学
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CHEMOSPHERE
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2022
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IF 8.943
Xiaoqi Dong,Zidan Huang,Xingxing Peng,Xiaoshan Jia
A novel coupled yeast-sludge system (CYSS) was constructed by the yeast Candida sp. PNY integrated with activated sludge to treat non-sterile mainstream wastewater. After 240-day cultivation, compared with single activated sludge , simultaneous removal efficiency of total organic carbon (TOC), nitrogen and phosphorus increased by 19.5% (176.34 mg TOC g −1 d −1 ), 21.3% (11.25 mg TN g −1 d −1 ) and 15.0% (6.95 mg TP g −1 d −1 ), respectively, while the amount of sludge reduced by 50%. Amplicon sequencing analysis showed that the abundance of Nitrosomonas , Nitrospira , Zoogloea , Dechloromonas , and Candidatus Accumulibacter significantly decreased to 0% on Day 200. Abundance of nirS and nirK for denitrification significantly decreased in CYSS by quantitative PCR (qPCR), and the copies of nirS and nirK were 3.37-fold and 1.71-fold decrease from Day 0 to Day 240, respectively. The results of Fluorescence in situ hybridization and co-occurrence network showed that Candida sp. PNY predominated its distribution in CYSS, and strongly connected with environmental variables based on network analysis. Furthermore, this study reconstructed the carbon, nitrogen and phosphorus metabolic pathways of the CYSS based on metagenomics .
研究领域:
环境工程
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微生物学
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废水处理
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生物技术
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产品关联
DOI
PubMed
高影响因子
BIORESOURCE TECHNOLOGY
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2021
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IF 9.642
Yu-Xi Gao,Xing Li,Jun-Ru Zhao,Zhong-Xing Zhang,Xiao-Yan Fan
The responses of microbial communities and antibiotic resistance genes (ARGs) to azithromycin and copper combined pollution under gradient increasing (from 0.5 to 10 mg/L) and decreasing exposure (from 10 to 0.5 mg/L) modes were investigated. Nitrification was inhibited more obviously under gradient increasing exposure mode. Responses of archaeal community and function structure were more obvious than bacteria under both exposure modes. The dominant bacterial and archaeal compositions ( Hyphomicrobium , Euryarchaeota , etc.) were affected by two exposure modes, except some rare archaea ( Methanoregula and Methanosarcina ). There were more positive correlations between bacteria and archaea, and Nitrospira was keystone genus. Ammonia-oxidizing archaea (0.37–3.06%) and complete ammonia oxidizers ( Nitrospira_ENR4 ) were enriched, and Nitrososphaera_viennensis was closely related to denitrifying genes ( napA/B , nosZ , etc.). 50 ARG subtypes were detected and specific ARG subtypes ( aac , ImrA , etc.) proliferated in two exposure modes. Bacteria and archaea were common hosts for 24 ARGs and contributed to their shifts.
研究领域:
环境科学
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微生物学
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废水处理
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生态毒理学
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产品关联
DOI
PubMed
高影响因子
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