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Shao B, Xie YG, Zhang L, Ruan Y, Liang B, Zhang R, Xu X, Wang W, Lin Z, Pei X, Wang X, Zhao L, Zhou X, Wu X, Xing D, Wang A, Lee DJ, Ren N, Canfield DE, Hedlund BP, Hua ZS, Chen C. Versatile nitrate-respiring heterotrophs are previously concealed contributors to sulfur cycle. Nat Commun 2025; 16:1202. [PMID: 39885140 PMCID: PMC11782648 DOI: 10.1038/s41467-025-56588-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 01/22/2025] [Indexed: 02/01/2025] Open
Abstract
Heterotrophic denitrifiers play crucial roles in global carbon and nitrogen cycling. However, their inability to oxidize sulfide renders them vulnerable to this toxic molecule, which inhibits the key enzymatic reaction responsible for reducing nitrous oxide (N2O), thereby raising greenhouse gas emissions. Here, we applied microcosm incubations, community-isotope-corrected DNA stable-isotope probing, and metagenomics to characterize a cohort of heterotrophic denitrifiers in estuarine sediments that thrive by coupling sulfur oxidation with denitrification through chemolithoheterotrophic metabolism. Remarkably, ecophysiology experiments from enrichments demonstrate that such heterotrophs expedite denitrification with sulfur acting as alternative electron sources and substantially curtail N2O emissions in both organic-rich and organic-limited environments. Their flexible, non-sulfur-dependent physiology may confer competitive advantages over conventional heterotrophic denitrifiers in detoxifying sulfide, adapting to organic matter fluctuations, and mitigating greenhouse gas emissions. Our study provides insights into the ecological role of heterotrophic denitrifiers in microbial communities with implications for sulfur cycling and climate change.
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Affiliation(s)
- Bo Shao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Yuan-Guo Xie
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, PR China
| | - Long Zhang
- College of Life Sciences, Huaibei Normal University, 235000, Huaibei, PR China
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Yang Ruan
- Jangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Bin Liang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, 518055, PR China
| | - Ruochen Zhang
- School of Civil and Transportation, Hebei University of Technology, Tianjin, 300401, PR China
| | - Xijun Xu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Wei Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Zhengda Lin
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Xuanyuan Pei
- School of Environmental Engineering, Wuhan Textile University, Wuhan, 430073, PR China
| | - Xueting Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Lei Zhao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Xu Zhou
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, 518055, PR China
| | - Xiaohui Wu
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan, 430074, PR China
| | - Defeng Xing
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Aijie Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, 518055, PR China
| | - Duu-Jong Lee
- Department of Mechanical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, PR China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Donald E Canfield
- Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, 89154, USA
- Nevada Institute of Personalized Medicine, Las Vegas, NV, 89154, USA
| | - Zheng-Shuang Hua
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, PR China.
| | - Chuan Chen
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China.
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Liu Q, Gao S, Zhou Q, Xu R, Li Z, Hou Y, Huang C. Bio-augmentation of the filler-enhanced denitrifying sulfide removal process in expanded granular sludge bed reactors. ENVIRONMENTAL RESEARCH 2022; 212:113253. [PMID: 35483408 DOI: 10.1016/j.envres.2022.113253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/24/2022] [Accepted: 04/03/2022] [Indexed: 06/14/2023]
Abstract
Sulfur- and nitrogen-containing organic industrial wastewaters, which primarily result from several processes, including pharmaceutical, slaughter, papermaking, and petrochemical processes, are typical examples of refractory wastewaters. To ensure resource utilization, sulfur compounds at high concentrations in such wastewaters can be converted to elemental sulfur through specific methods. Specifically, the denitrifying sulfide removal (DSR) process can be employed to effectively recover elemental sulfur via biological sulfide oxidation, and reportedly, bio-augmentation presents as an effective strategy by which the challenges that limit the application of the DSR process can be overcome. However, the bacterial loss resulting from microorganism activity inhibition owing to toxic effect of high sulfide concentration as well as the complexity of the organic matter (carbon source) in actual wastewater environments reduce the actual elemental sulfur production rate. In this regard, the bio-augmentation effect of adding fillers under complex carbon source conditions was studied. The structure and function of the microbial community on the surface of the fillers were also analysed to reveal the internal factors that contributed to the increased efficiency of elemental sulfur generation. The results obtained showed that relative to the control, elemental sulfur generation increased 1.5- and 2-fold following the addition of fillers and fillers with microbial inoculants, respectively. Further, in the reactor with the added filler, the dominant bacteria in the biofilm on the filler surface were Pseudomonas and Azoarcus, while in reactor with added fillers plus microbial inoculates, the dominant bacteria in the biofilm on the filler surface were Pseudomonas and Arcobacter. These findings indicated that bio-augmentation promoted the expression of sulfur oxidation functional genes. Furthermore, adding Pseudomonas sp. gs1 for bio-augmentation improved the impact load resistance of the biofilm on the surface of the filler, leading to the rapid restoration of the elemental sulfur generation rate after the impact.
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Affiliation(s)
- Qian Liu
- Research Center for Eco-environmental Engineering, Dongguan University of Technology, Dongguan, 523808, China
| | - Shuang Gao
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin, 150090, China
| | - Qi Zhou
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Ran Xu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Zhiling Li
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin, 150090, China
| | - Yanan Hou
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Cong Huang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
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Gao S, Li Z, Hou Y, Nan J, Wang A, Liu Q, Huang C. Rapid start of high-concentration denitrification and desulfurization reactors by heterotrophic denitrification sulphur-oxidising bacteria. ENVIRONMENTAL RESEARCH 2022; 204:111826. [PMID: 34375658 DOI: 10.1016/j.envres.2021.111826] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
High sulphide concentrations can be toxic to denitrifying and desulphurising microorganisms. In this study, bioaugmentation was used to solve this problem. Pseudomonas sp. gs1 can tolerate 400 mg/L sulphide and converts most of the sulphide into elemental sulphur after 4 h. A solid inoculum of Pseudomonas sp. h1 was prepared. Two reactors, that is, one with and one without inoculum, were simultaneously run for 60 days. Bioreactor II to which bacterial inoculum was added reached a good treatment performance on day 3. The elemental sulphur concentration of the effluent was 342.6 mg/L. It was maintained at 245.3-333.8 mg/L during the subsequent operation. In contrast, reactor I without inoculants achieved the same performance on day 50. High-throughput sequencing shows that Pseudomonas and Azoarcus are the dominant genera. The abundance of the genus Pseudomonas and related denitrifying sulphur-oxidising bacteria in reactor I increases with the operation time. This phenomenon was confirmed by testing the sqr and gltA genes. The quantitative fluorescence PCR test also proves that the addition of bacteria leads to a rapid increase in the sulphur oxidation and carbon metabolism of the activated sludge in the reactor.
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Affiliation(s)
- Shuang Gao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Zhiling Li
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Yanan Hou
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Jun Nan
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Aijie Wang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Qian Liu
- Research Center for Eco-environmental Engineering, Dongguan University of Technology, Dongguan, 523808, China
| | - Cong Huang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
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Ma Q, Qu H, Meng N, Li S, Wang J, Liu S, Qu Y, Sun Y. Biodegradation of skatole by Burkholderia sp. IDO3 and its successful bioaugmentation in activated sludge systems. ENVIRONMENTAL RESEARCH 2020; 182:109123. [PMID: 32069749 DOI: 10.1016/j.envres.2020.109123] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/03/2020] [Accepted: 01/06/2020] [Indexed: 06/10/2023]
Abstract
Skatole is the key malodorous compound in livestock and poultry waste and wastewater with a low odor threshold. It not only causes serious nuisance to residents and workers, but also poses threat to the environment and human health due to its biotoxicity and recalcitrant nature. Biological treatment is an eco-friendly and cost-effective approach for skatole removal, while the bacterial resources are scarce. Herein, the Burkholderia strain was reported to efficiently degrade skatole for the first time. Results showed that strain IDO3 maintained high skatole-degrading performance under the conditions of pH 4.0-9.0, rotate speed 0-250 rpm, and temperature 30-35 °C. RNA-seq analysis indicated that skatole activated the oxidative phosphorylation and ATP production levels in strain IDO3. The oxidoreductase activity item which contained 373 differently expressed genes was significantly impacted by Gene Ontology analysis. Furthermore, the bioaugmentation experiment demonstrated that strain IDO3 could notably increase the removal of skatole in activated sludge systems. High-throughput 16S rRNA gene sequencing data indicated that the alpha-diversity and bacterial community tended to be stable in the bioaugmented group after 8 days operation. PICRUSt analysis indicated that xenobiotics biodegradation and metabolism, and membrane transport categories significantly increased, consistent with the improved skatole removal performance in the bioaugmented group. Burkholderia was survived and colonized to be the predominant population during the whole operation process (34.19-64.00%), confirming the feasibility of Burkholderia sp. IDO3 as the bioaugmentation agent in complex systems.
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Affiliation(s)
- Qiao Ma
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026, China.
| | - Hui Qu
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026, China
| | - Nan Meng
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026, China
| | - Shuzhen Li
- School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Jingwei Wang
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026, China
| | - Shengwei Liu
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026, China
| | - Yuanyuan Qu
- School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Yeqing Sun
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026, China.
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Hong X, Zhao Y, Zhuang R, Liu J, Guo G, Chen J, Yao Y. Bioremediation of tetracycline antibiotics-contaminated soil by bioaugmentation. RSC Adv 2020; 10:33086-33102. [PMID: 35694106 PMCID: PMC9122622 DOI: 10.1039/d0ra04705h] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/16/2020] [Indexed: 12/03/2022] Open
Abstract
Bioaugmentation using specific microbial strains or consortia was deemed to be a useful bioremediation technology for increasing bioremediation efficiency. The present study confirmed the effectiveness and feasibility of bioaugmentation capability of the bacterium BC immobilized on sugarcane bagasse (SCB) for degradation of tetracycline antibiotics (TCAs) in soil. It was found that an inoculation dose of 15% (v/w), 28–43 °C, slightly acidic pH (4.5–6.5), and the addition of oxytetracycline (OTC, from 80 mg kg−1 to 160 mg kg−1) favored the bioaugmentation capability of the bacterium BC, indicating its strong tolerance to high temperature, pH, and high substrate concentrations. Moreover, SCB-immobilized bacterium BC system exhibited strong tolerance to heavy metal ions, such as Pb2+ and Cd2+, and could fit into the simulated soil environment very well. In addition, the bioaugmentation and metabolism of the co-culture with various microbes was a complicated process, and was closely related to various species of bacteria. Finally, in the dual-substrate co-biodegradation system, the presence of TC at low concentrations contributed to substantial biomass growth but simultaneously led to a decline in OTC biodegradation efficiency by the SCB-immobilized bacterium BC. As the total antibiotic concentration was increased, the OTC degradation efficiency decreased gradually, while the TC degradation efficiency still exhibited a slow rise tendency. Moreover, the TC was preferentially consumed and degraded by continuous introduction of OTC into the system during the bioremediation treatment. Therefore, we propose that the SCB-immobilized bacterium BC exhibits great potential in the bioremediation of TCAs-contaminated environments. Bioaugmentation using specific microbial strains or consortia was deemed to be a useful bioremediation technology for increasing bioremediation efficiency.![]()
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Affiliation(s)
- Xiaxiao Hong
- College of Materials and Energy
- South China Agricultural University
- Guangzhou
- PR China
| | - Yuechun Zhao
- College of Materials and Energy
- South China Agricultural University
- Guangzhou
- PR China
| | - Rudong Zhuang
- College of Materials and Energy
- South China Agricultural University
- Guangzhou
- PR China
| | - Jiaying Liu
- College of Materials and Energy
- South China Agricultural University
- Guangzhou
- PR China
| | - Guantian Guo
- College of Materials and Energy
- South China Agricultural University
- Guangzhou
- PR China
| | - Jinman Chen
- College of Materials and Energy
- South China Agricultural University
- Guangzhou
- PR China
| | - Yingming Yao
- College of Materials and Energy
- South China Agricultural University
- Guangzhou
- PR China
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