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Ming Y, Abdullah Al M, Zhang D, Zhu W, Liu H, Cai L, Yu X, Wu K, Niu M, Zeng Q, He Z, Yan Q. Insights into the evolutionary and ecological adaption strategies of nirS- and nirK-type denitrifying communities. Mol Ecol 2024:e17507. [PMID: 39158107 DOI: 10.1111/mec.17507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 07/19/2024] [Accepted: 08/07/2024] [Indexed: 08/20/2024]
Abstract
Denitrification is a crucial process in the global nitrogen cycle, in which two functionally equivalent genes, nirS and nirK, catalyse the critical reaction and are usually used as marker genes. The nirK gene can function independently, whereas nirS requires additional genes to encode nitrite reductase and is more sensitive to environmental factors than nirK. However, the ecological differentiation mechanisms of those denitrifying microbial communities and their adaptation strategies to environmental stresses remain unclear. Here, we conducted metagenomic analysis for sediments and bioreactor samples from Lake Donghu, China. We found that nirS-type denitrifying communities had a significantly lower horizontal gene transfer frequency than that of nirK-type denitrifying communities, and nirS gene phylogeny was more congruent with taxonomy than that of nirK gene. Metabolic reconstruction of metagenome-assembled genomes further revealed that nirS-type denitrifying communities have robust metabolic systems for energy conservation, enabling them to survive under environmental stresses. Nevertheless, nirK-type denitrifying communities seemed to adapt to oxygen-limited environments with the ability to utilize various carbon and nitrogen compounds. Thus, this study provides novel insights into the ecological differentiation mechanism of nirS and nirK-type denitrifying communities, as well as the regulation of the global nitrogen cycle and greenhouse gas emissions.
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Affiliation(s)
- Yuzhen Ming
- Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Zhuhai, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Mamun Abdullah Al
- Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Zhuhai, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Dandan Zhang
- Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Zhuhai, China
| | - Wengen Zhu
- Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Zhuhai, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Huanping Liu
- Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Zhuhai, China
| | - Lanlan Cai
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Xiaoli Yu
- Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Zhuhai, China
| | - Kun Wu
- Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Zhuhai, China
| | - Mingyang Niu
- Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Zhuhai, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Qinglu Zeng
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Zhili He
- Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Zhuhai, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
- State Key Laboratory for Biocontrol, Sun Yat-Sen University, Guangzhou, China
| | - Qingyun Yan
- Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Zhuhai, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
- State Key Laboratory for Biocontrol, Sun Yat-Sen University, Guangzhou, China
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Description of five novel thermophilic species of the genus Thermus: Thermus hydrothermalis sp. nov., Thermus neutrinimicus sp. nov., Thermus thalpophilus sp. nov., Thermus albus sp. nov., and Thermus altitudinis sp. nov., isolated from hot spring sediments. Syst Appl Microbiol 2022; 45:126361. [DOI: 10.1016/j.syapm.2022.126361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/27/2022] [Accepted: 09/08/2022] [Indexed: 11/18/2022]
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Incomplete denitrification phenotypes in diverse Thermus species from diverse geothermal spring sediments and adjacent soils in southwest China. Extremophiles 2022; 26:23. [PMID: 35802188 PMCID: PMC9270275 DOI: 10.1007/s00792-022-01272-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 06/06/2022] [Indexed: 01/22/2023]
Abstract
A few members of the bacterial genus Thermus have been shown to be incomplete denitrifiers, terminating with nitrite (NO2−) or nitrous oxide (N2O). However, the denitrification abilities of the genus as a whole remain poorly characterized. Here, we describe diverse denitrification phenotypes and genotypes of a collection of 24 strains representing ten species, all isolated from a variety of geothermal systems in China. Confirmed terminal products of nitrate reduction were nitrite or N2O, while nitric oxide (NO) was inferred as the terminal product in some strains. Most strains produced N2O; complete denitrification was not observed. Denitrification phenotypes were largely consistent with the presence of denitrification genes, and strains of the same species often had the same denitrification phenotypes and largely syntenous denitrification gene clusters. Genes for nirS and nirK coexisted in three Thermus brockianus and three Thermus oshimai genomes, which is a unique hallmark of some denitrifying Thermus strains and may be ecologically important. These results show that incomplete denitrification phenotypes are prominent, but variable, within and between Thermus species. The incomplete denitrification phenotypes described here suggest Thermus species may play important roles in consortial denitrification in high-temperature terrestrial biotopes where sufficient supply of oxidized inorganic nitrogen exists.
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Jiao J, Lian Z, Li M, Salam N, Zhou E, Liu L, Ming H, Nie G, Shu W, Zhao G, Hedlund BP, Li W. Comparative genomic analysis of Thermus provides insights into the evolutionary history of an incomplete denitrification pathway. MLIFE 2022; 1:198-209. [PMID: 38817678 PMCID: PMC10989939 DOI: 10.1002/mlf2.12009] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/25/2021] [Accepted: 01/08/2022] [Indexed: 06/01/2024]
Abstract
Biological denitrification is a crucial process in the nitrogen biogeochemical cycle, and Thermus has been reported to be a significant heterotrophic denitrifier in terrestrial geothermal environments. However, neither the denitrification potential nor the evolutionary history of denitrification genes in the genus Thermus or phylum Deinococcota is well understood. Here, we performed a comparative analysis of 23 Thermus genomes and identified denitrification genes in 15 Thermus strains. We confirmed that Thermus harbors an incomplete denitrification pathway as none of the strains contain the nosZ gene. Ancestral character state reconstructions and phylogenetic analyses showed that narG, nirS, and norB genes were acquired by the last common ancestor of Thermales and were inherited vertically. In contrast, nirK of Thermales was acquired via two distinct horizontal gene transfers from Proteobacteria to the genus Caldithermus and from an unknown donor to the common ancestor of all known Thermus species except Thermus filiformis. This study expands our understanding of the genomic potential for incomplete denitrification in Thermus, revealing a largely vertical evolutionary history of the denitrification pathway in the Thermaceae, and supporting the important role for Thermus as an important heterotrophic denitrifier in geothermal environments.
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Affiliation(s)
- Jian‐Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Zheng‐Han Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Meng‐Meng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Nimaichand Salam
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - En‐Min Zhou
- International Joint Research Center for Karstology, School of Earth SciencesYunnan UniversityKunmingChina
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Hong Ming
- Synthetic Biology Engineering Laboratory of Henan Province, College of Life Sciences and TechnologyXinxiang Medical UniversityXinxiangChina
| | - Guoxing Nie
- College of FisheriesHenan Normal UniversityXinxiangChina
| | - Wensheng Shu
- Institute of Ecological Science, School of Life ScienceSouth China Normal UniversityGuangzhouChina
| | - Guoping Zhao
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhenChina
| | - Brian P. Hedlund
- School of Life SciencesUniversity of NevadaLas VegasNevadaUSA
- Nevada Institute of Personalized MedicineUniversity of NevadaLas VegasNevadaUSA
| | - Wen‐Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
- State Key Laboratory of Desert and Oasis EcologyXinjiang Institute of Ecology and Geography, Chinese Academy of SciencesUrumqiChina.
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Liu X, Zhu H. Treatment of Low C/N Ratio Wastewater by a Carbon Cloth Bipolar Plate Multicompartment Electroenhanced Bioreactor (CBM-EEB). ACS OMEGA 2020; 5:27823-27832. [PMID: 33163765 PMCID: PMC7643109 DOI: 10.1021/acsomega.0c02828] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 09/25/2020] [Indexed: 05/04/2023]
Abstract
The traditional biological denitrification process has the problems of low removal rates and lack of a carbon source when treating wastewater with high ammonia nitrogen concentration and a low carbon-nitrogen ratio. Based on a bio-electrochemical system (BES), a novel carbon cloth bipolar plate multicompartment electroenhanced bioreactor (CBM-EEB) system was constructed. In this study, nitrogen removal efficiency and enrichment of functional bacteria using CBM-EEB under different voltage conditions were investigated. The results from next-generation sequencing indicated that the CBM-EEB included heterotrophic nitrification and aerobic denitrification (HNAD) and was dominated by heterotrophic nitrification aerobic denitrifying bacteria (HNADB). The applied voltage was confirmed as having the ability to regulate the microbial community structure and abundance of functional genes, thereby further enhancing the nitrogen removal efficiency of the system. The total nitrogen removal efficiency was 77.70 ± 1.14, 87.10 ± 0.56, 86.40 ± 0.59, and 89.30 ± 0.53% under applied voltages of 0.4, 0.7, 1.0, and 1.3 V, respectively. All values were significantly higher than the control group (62.86 ± 2.06%). HNADB had the highest abundance among the 17 detected genera related to nitrogen metabolism. Facultative denitrifying bacteria, Pseudoxanthomonas, along with key bacteria of HNADB, such as Flavobacterium, constructed a shortcut simultaneous nitrification-denitrification (SND) process. Poisson analysis and redundancy analysis (RDA) showed that the applied voltage improved the denitrification efficiency by changing the microbial community structure, reducing the abundance of heterotrophic bacteria, and increasing the unit abundance of key functional genes so that less organics were required for the denitrification process. The increased nitrogen removal efficiency in the experimental group was mainly related to simultaneous nitrification-denitrification process and cooperation of microbial communities in the anode and the cathode. This study highlighted the feasibility of CBM-EEB to enhance the HNAD reaction and the response of wastewater with a low C/N ratio to enhance the abundance of microbial bacteria and their functional gene abundance.
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Affiliation(s)
- Xueyu Liu
- Biomass Energy Research Center, Tongji University, Shanghai 201804, P. R. China
| | - Hongguang Zhu
- Biomass Energy Research Center, Tongji University, Shanghai 201804, P. R. China
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