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Cheng J, Robles-Lecompte A, McKenna AM, Chang NB. Deciphering linkages between DON and the microbial community for nitrogen removal using two green sorption media in a surface water filtration system. Chemosphere 2024; 357:142042. [PMID: 38621490 DOI: 10.1016/j.chemosphere.2024.142042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 04/17/2024]
Abstract
The presence of dissolved organic nitrogen (DON) in stormwater treatment processes is a continuous challenge because of the intertwined nature of its decomposition, bioavailability, and biodegradability and its unclear molecular characteristics. In this paper, 21 T Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) in combination with quantitative polymerase chain reaction was applied to elucidate the molecular change of DON and microbial population dynamics in a field-scale water filtration system filled with two specialty adsorbents for comparison in South Florida where the dry and wet seasons are distinctive annually. The adsorbents included CPS (clay-perlite and sand sorption media) and ZIPGEM (zero-valent iron and perlite-based green environmental media). Our study revealed that seasonal effects can significantly influence the dynamic characteristics and biodegradability of DON. The microbial population density in the filter beds indicated that three microbial species in the nitrogen cycle were particularly thrived for denitrification, dissimilatory nitrate reduction to ammonium, and anaerobic ammonium oxidation via competition and commensalism relationships during the wet season. Also, there was a decrease in the compositional complexity and molecular weight of the DON groups (CnHmOpN1, CnHmOpN2, CnHmOpN3, and CnHmOpN4), revealed by the 21 T FT-ICR MS bioassay, driven by a microbial population quantified by polymerase chain reaction from the dry to the wet season. These findings indirectly corroborate the assumption that the metabolism of microorganisms is much more vigorous in the wet season. The results affirm that the sustainable materials (CPS and ZIPGEM) can sustain nitrogen removal intermittently by providing a suitable living environment in which the metabolism of microbial species can be cultivated and enhanced to facilitate physico-chemical nitrogen removal across the two types of green sorption media.
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Affiliation(s)
- Jinxiang Cheng
- Department of Civil, Environmental, and Construction Engineering, University of Central Florida, Orlando, FL, USA
| | - Alejandra Robles-Lecompte
- Department of Civil, Environmental, and Construction Engineering, University of Central Florida, Orlando, FL, USA
| | - Amy M McKenna
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, USA; Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Ni-Bin Chang
- Department of Civil, Environmental, and Construction Engineering, University of Central Florida, Orlando, FL, USA.
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2
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Yang X, Shi Y, Ying G, Li M, He Z, Shu L. Cooperation among nitrifying microorganisms promotes the irreversible biotransformation of sulfamonomethoxine. Sci Total Environ 2024; 923:171395. [PMID: 38447730 DOI: 10.1016/j.scitotenv.2024.171395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/08/2024]
Abstract
Ammonia-oxidizing microorganisms, including AOA (ammonia-oxidizing archaea), AOB (ammonia-oxidizing bacteria), and Comammox (complete ammonia oxidization) Nitrospira, have been reported to possess the capability for the biotransformation of sulfonamide antibiotics. However, given that nitrifying microorganisms coexist and operate as communities in the nitrification process, it is surprising that there is a scarcity of studies investigating how their interactions would affect the biotransformation of sulfonamide antibiotics. This study aims to investigate the sulfamonomethoxine (SMM) removal efficiency and mechanisms among pure cultures of phylogenetically distinct nitrifiers and their combinations. Our findings revealed that AOA demonstrated the highest SMM removal efficiency and rate among the pure cultures, followed by Comammox Nitrospira, NOB, and AOB. However, the biotransformation of SMM by AOA N. gargensis is reversible, and the removal efficiency significantly decreased from 63.84 % at 167 h to 26.41 % at 807 h. On the contrary, the co-culture of AOA and NOB demonstrated enhanced and irreversible SMM removal efficiency compared to AOA alone. Furthermore, the presence of NOB altered the SMM biotransformation of AOA by metabolizing TP202 differently, possibly resulting from reduced nitrite accumulation. This study offers novel insights into the potential application of nitrifying communities for the removal of sulfonamide antibiotics (SAs) in engineered ecosystems.
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Affiliation(s)
- Xueqin Yang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Yijing Shi
- SCNU Environmental Research Institute, School of Environment, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China.
| | - Guangguo Ying
- SCNU Environmental Research Institute, School of Environment, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Mengyuan Li
- SCNU Environmental Research Institute, School of Environment, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China.
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Guo Z, Ma XS, Ni SQ. Journey of the swift nitrogen transformation: Unveiling comammox from discovery to deep understanding. Chemosphere 2024; 358:142093. [PMID: 38679176 DOI: 10.1016/j.chemosphere.2024.142093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/02/2024] [Accepted: 04/19/2024] [Indexed: 05/01/2024]
Abstract
COMplete AMMonia OXidizer (comammox) refers to microorganisms that have the function of oxidizing NH4+ to NO3- alone. The discovery of comammox overturned the two-step theory of nitrification in the past century and triggered many important scientific questions about the nitrogen cycle in nature. This comprehensive review delves into the origin and discovery of comammox, providing a detailed account of its detection primers, clades metabolic variations, and environmental factors. An in-depth analysis of the ecological niche differentiation among ammonia oxidizers was also discussed. The intricate role of comammox in anammox systems and the relationship between comammox and nitrogen compound emissions are also discussed. Finally, the relationship between comammox and anammox is displayed, and the future research direction of comammox is prospected. This review reveals the metabolic characteristics and distribution patterns of comammox in ecosystems, providing new perspectives for understanding nitrogen cycling and microbial ecology. Additionally, it offers insights into the potential application value and prospects of comammox.
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Affiliation(s)
- Zheng Guo
- School of Environmental Science and Engineering, Shandong University, Shandong, 266237, China
| | - Xue Song Ma
- School of Environmental Science and Engineering, Shandong University, Shandong, 266237, China
| | - Shou-Qing Ni
- School of Environmental Science and Engineering, Shandong University, Shandong, 266237, China.
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Feng M, Lin Y, He ZY, Hu HW, Jin S, Liu J, Wan S, Cheng Y, He JZ. Higher stochasticity in comammox Nitrospira community assembly in upland soils than the adjacent paddy soils at a regional scale. Sci Total Environ 2024; 921:171227. [PMID: 38402820 DOI: 10.1016/j.scitotenv.2024.171227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/22/2024] [Accepted: 02/21/2024] [Indexed: 02/27/2024]
Abstract
Understanding the assembly mechanisms of microbial communities, particularly comammox Nitrospira, in agroecosystems is crucial for sustainable agriculture. However, the large-scale distribution and assembly processes of comammox Nitrospira in agricultural soils remain largely elusive. We investigated comammox Nitrospira abundance, community structure, and assembly processes in 16 paired upland peanuts and water-logged paddy soils in south China. Higher abundance, richness, and network complexity of comammox Nitrospira were observed in upland soils than in paddy soils, indicating a preference for upland soils over paddy soils among comammox Nitrospira taxa in agricultural environments. Clade A.2.1 and clade A.1 were the predominant comammox Nitrospira taxa in upland and paddy soils, respectively. Soil pH was the most crucial factor shaping comammox Nitrospira community structure. Stochastic processes were found to predominantly drive comammox Nitrospira community assembly in both upland and paddy soils, with deterministic processes playing a more important role in paddy soils than in upland soils. Overall, our findings demonstrate the higher stochasticity of comammox Nitrospira in upland soils than in the adjacent paddy soils, which may have implications for autotrophic nitrification in acidic agricultural soils.
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Affiliation(s)
- Mengmeng Feng
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou 350117, China
| | - Yongxin Lin
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou 350117, China.
| | - Zi-Yang He
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, VIC 3010, Australia
| | - Hang-Wei Hu
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, VIC 3010, Australia
| | - Shengsheng Jin
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou 350117, China
| | - Jia Liu
- Soil and Fertilizer & Resources and Environment Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Song Wan
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou 350117, China
| | - Yuheng Cheng
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou 350117, China
| | - Ji-Zheng He
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou 350117, China; School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, VIC 3010, Australia.
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5
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Zhang J, Zhou M, Shi F, Lei Z, Wang Y, Hu M, Zhao J. The abundance of comammox bacteria was higher than that of ammonia-oxidizing archaea and bacteria in rhizosphere of emergent macrophytes in a typical shallow lake riparian. Int Microbiol 2024; 27:67-79. [PMID: 38062210 DOI: 10.1007/s10123-023-00465-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 06/20/2023] [Accepted: 11/30/2023] [Indexed: 02/01/2024]
Abstract
Complete ammonia oxidation (comammox) bacteria can complete the whole nitrification process independently, which not only challenges the classical two-step nitrification theory but also updates long-held perspective of microbial ecological relationship in nitrification process. Although comammox bacteria have been found in many ecosystems in recent years, there is still a lack of research on the comammox process in rhizosphere of emergent macrophytes in lakeshore zone. Sediment samples were collected in this study from rhizosphere, far-rhizosphere, and non-rhizosphere of emergent macrophytes along the shore of Lake Liangzi, a shallow lake. The diversity of comammox bacteria and amoA gene abundance of comammox bacteria, ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) in these samples were measured. The results showed that comammox bacteria widely existed in the rhizosphere of emergent macrophytes and fell into clade A.1, clade A.2, and clade B, and clade A was the predominant community in all sampling sites. The abundance of comammox amoA gene (6.52 × 106-2.45 × 108 copies g-1 dry sediment) was higher than that of AOB amoA gene (6.58 × 104-3.58 × 106 copies g-1 dry sediment), and four orders of magnitude higher than that of AOA amoA gene (7.24 × 102-6.89 × 103 copies g-1 dry sediment), suggesting that the rhizosphere of emergent macrophytes is more favorable for the growth of comammox bacteria than that of AOB and AOA. Our study indicated that the comammox bacteria may play important roles in ammonia-oxidizing processes in all different rhizosphere regions.
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Affiliation(s)
- Jiahui Zhang
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, Beijing, 100038, China
- Department of Water Ecology and Environment, China Institute of Water Resources and Hydropower Research, Beijing, 100038, China
- Laboratory of Eco-Environmental Engineering Research, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, People's Republic of China
| | - Mingzhi Zhou
- Laboratory of Eco-Environmental Engineering Research, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, People's Republic of China
| | - Fengning Shi
- Yunnan Hydrology and Water Resources Bureau, Kunming, 650100, China
| | - Ziyan Lei
- Laboratory of Eco-Environmental Engineering Research, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, People's Republic of China
| | - Yuchun Wang
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, Beijing, 100038, China
- Department of Water Ecology and Environment, China Institute of Water Resources and Hydropower Research, Beijing, 100038, China
| | - Mingming Hu
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, Beijing, 100038, China.
- Department of Water Ecology and Environment, China Institute of Water Resources and Hydropower Research, Beijing, 100038, China.
| | - Jianwei Zhao
- Laboratory of Eco-Environmental Engineering Research, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, People's Republic of China.
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6
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Yu B, Zeng Q, Li J, Li J, Tan X, Gao X, Mao Z, Huang P, Wu S. Sediment depth-related variations of comammox Nitrospira: Evidence in the Three Gorges Reservoir, China. Sci Total Environ 2023; 905:167055. [PMID: 37709074 DOI: 10.1016/j.scitotenv.2023.167055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 09/04/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
The recent discovery of comammox Nitrospira as complete ammonia-oxidizing microorganism has fundamentally revolutionized our understanding of nitrogen cycling in sediment environments. However, knowledge regarding their abundance, biodiversity, community structure, and interactions is predominantly limited to the upper layers (0-20 cm). To address this gap, we collected sediment samples along profiles ranging from 0 to 300 cm in depth at three locations within the middle segment of the Three Gorges Reservoir (TGR), China. Quantitative real-time PCR (qPCR) analyses suggested that comammox bacteria were not only ubiquitous in deep sediments but also more abundant than ammonia-oxidizing bacteria (AOB). Ammonia monooxygenases subunit A (amoA) gene amplicon sequencing illuminated that comammox bacteria were more sensitive to sedimental depth compared to AOB and ammonia-oxidizing archaea (AOA), as evidenced by a more significant decline in community diversity and similarity over distance along sediment vertical profiles. Notably, we discovered that the amoA gene abundance, alpha- and beta-diversity of comammox bacteria exerted an essential contribution to potential nitrification rates according to random forest model. Phylogenetic analysis indicted that most comammox bacteria within sediment samples belonged to clade A.2. Intriguingly, the average relative abundance of comammox clade A.2 displayed a noteworthy rise with sediment depth, whereas clade A.1 demonstrated a converse pattern, unveiling distinct ecological niche adaptations of these two clades along the sediment profile. Ecological network analysis further revealed closer interactions between comammox bacteria and canonical ammonia oxidizers in the superficial layer (0-40 cm), with the network structure gradually simplifying from superficial to deep sediment (200-300 cm). Overall, these findings broaden the current recognition of the geographic distribution and niche segregation of comammox bacteria at the fine scale of the sediments ecosystems and provide insights into sediment depth-related variations of their coexistence network patterns in large freshwater reservoirs.
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Affiliation(s)
- Baohong Yu
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China; Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, PR China
| | - Quanchao Zeng
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China.
| | - Jinlin Li
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China
| | - Jun Li
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China
| | - Xun Tan
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China
| | - Xin Gao
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China
| | - Ziqiang Mao
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China
| | - Ping Huang
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China
| | - Shengjun Wu
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China.
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Zhao X, Xie Y, Sun B, Liu Y, Zhu S, Li W, Zhao M, Liu D. Unraveling microbial characteristics of simultaneous nitrification, denitrification and phosphorus removal in a membrane-aerated biofilm reactor. Environ Res 2023; 239:117402. [PMID: 37838199 DOI: 10.1016/j.envres.2023.117402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/04/2023] [Accepted: 10/11/2023] [Indexed: 10/16/2023]
Abstract
This study describes the simultaneous removal of carbon, ammonium, and phosphate from domestic wastewater by a membrane-aerated biofilm reactor (MABR) which was operated for 360 days. During the operation, the maximum removal efficiencies of chemical oxygen demand (COD), total nitrogen (TN) and total phosphorus (TP) reached 93.1%, 83.98%, and 96.41%, respectively. Statistical analysis showed that the MABR could potentially treat wastewater with a high ammonium concentration and a relatively low C/N ratio. Dissolved oxygen and multiple pollutants, including ammonium, carbon, phosphate, and sulfate, shaped the structure of the microbial community in the MABR. High throughput sequencing uncovered the crucial microbiome in ammonium transformation in MABR. Phylogenetic analysis of the ammonia monooxygenase (amoA) genes revealed an important role for comammox Nitrospira in the nitrification process. Diverse novel phosphate-accumulating organisms (Thauera, Bacillus, and Pseudomonas) and sulfur-oxidizing bacteria (Thiobacillus, Thiothrix and Sulfurimonas) were potentially involved in denitrification in MABR. The results from this study suggested that MABR could be a feasible system for the simultaneous removal of nitrogen, carbon, phosphorus, and sulfur from sewage water.
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Affiliation(s)
- Xin Zhao
- Key Laboratory of Equipment and Informatization in Environment Controlled Agriculture from Ministry of Agriculture and Rural Affairs of China, Key Laboratory of Intelligent Equipment and Robotics for Agriculture of Zhejiang Province, Institute of Agri-biological Environment Engineering, Zhejiang University, Hangzhou, 310058, China; National & Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China
| | - Yinglong Xie
- Key Laboratory of Equipment and Informatization in Environment Controlled Agriculture from Ministry of Agriculture and Rural Affairs of China, Key Laboratory of Intelligent Equipment and Robotics for Agriculture of Zhejiang Province, Institute of Agri-biological Environment Engineering, Zhejiang University, Hangzhou, 310058, China; College of Environment, Zhejiang University of Technology, 310014 Hangzhou, China
| | - Bo Sun
- National & Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China
| | - Ying Liu
- Key Laboratory of Equipment and Informatization in Environment Controlled Agriculture from Ministry of Agriculture and Rural Affairs of China, Key Laboratory of Intelligent Equipment and Robotics for Agriculture of Zhejiang Province, Institute of Agri-biological Environment Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Songming Zhu
- Key Laboratory of Equipment and Informatization in Environment Controlled Agriculture from Ministry of Agriculture and Rural Affairs of China, Key Laboratory of Intelligent Equipment and Robotics for Agriculture of Zhejiang Province, Institute of Agri-biological Environment Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Wei Li
- Research Center for Eco-environmental Engineering, Dongguan University of Technology, Dongguan, 523808, China
| | - Min Zhao
- National & Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China.
| | - Dezhao Liu
- Key Laboratory of Equipment and Informatization in Environment Controlled Agriculture from Ministry of Agriculture and Rural Affairs of China, Key Laboratory of Intelligent Equipment and Robotics for Agriculture of Zhejiang Province, Institute of Agri-biological Environment Engineering, Zhejiang University, Hangzhou, 310058, China.
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Tang X, Li Y, Liu M, Hou L, Han P. Abundance, diversity and physiological preferences of comammox Nitrospira in urban groundwater. Sci Total Environ 2023; 904:167333. [PMID: 37748616 DOI: 10.1016/j.scitotenv.2023.167333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 09/01/2023] [Accepted: 09/22/2023] [Indexed: 09/27/2023]
Abstract
Complete ammonia oxidizer (comammox Nitrospira), catalyze complete nitrification process in a single organism, are frequently detected in groundwater ecosystem. However, the ecological niches and environmental driving factors of comammox Nitrospira in urban groundwater are largely unknown. Here we investigated the communities of ammonia oxidizers in urban groundwater located in Shanghai city, China. Quantitative analysis demonstrated the dominance of comammox Nitrospira over classical ammonia oxidizers (ammonia-oxidizing archaea and bacteria, AOA and AOB). Phylogenetic analysis showed clades B and A2 comprise the majority of comammox Nitrospira groups. Temperature was one of the most vital factors affecting comammox Nitrospira community. Furthermore, clade A comammox Nitrospira can be enriched by urea substrate, which was in line with the ability of utilizing urea by the pure clade A comammox culture Nitrospira inopinata. In addition, we observed that relatively low temperature (<20 °C) and high copper levels (>0.04 mg L-1) can stimulate the growth of comammox Nitrospira. Overall, this study revealed the presence, diversity and physiological preferences of comammox Nitrospira in urban groundwater nitrification, shedding insights on the ecological roles of comammox Nitrospira in subsurface environment.
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Affiliation(s)
- Xiufeng Tang
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Ye Li
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Lijun Hou
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Ping Han
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Institute of Eco-Chongming, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China.
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9
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Fudjoe SK, Li L, Anwar S, Shi S, Xie J, Yeboah FK, Wang L. The impact of fertilization on ammonia-oxidizing bacteria and comammox Nitrospira communities and the subsequent effect on N 2O emission and maize yield in a semi-arid region. Front Microbiol 2023; 14:1249668. [PMID: 37840719 PMCID: PMC10570556 DOI: 10.3389/fmicb.2023.1249668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/06/2023] [Indexed: 10/17/2023] Open
Abstract
The control of nitrous oxide (N2O) emissions through nitrification and the optimization of maize yield are important in agricultural systems. However, within the semi-arid region, the impact of fertilization on the function of nitrification communities and its connection with N2O emissions in the rhizosphere soil is still unclear. Our study investigates the influence of fertilization treatments on the communities of ammonia-oxidizing bacteria (AOB) and the complete ammonia oxidizers of the Nitrospira known as comammox (CAOB) in a maize agroecosystem. Nitrous oxide production, potential nitrification activity (PNA), maize yield, and nitrogen use efficiency (NUE) were determined for the same samples. The fertilizer treatments included a control group without fertilization (NA), inorganic fertilizer (CF), organic fertilizer (SM), combined inorganic and organic fertilizer (SC), and maize straw (MS). The SC treatment indicated a lower cumulative N2O emission than the CF treatment in the 2020 and 2021 cropping seasons. The AOB community under the CF, MS, and SM treatments was predominantly composed of Nitrosospira cluster 3b, while the SC treatment was associated with the comammox Nitrospira clade A.1 lineage, related to key species such as Ca. Nitrospira inopinata and Ca. Nitrospira nitrificans. Network analysis demonstrated a positive potential for competitive interaction between hub taxonomy and distinct keystone taxa among AOB and comammox Nitrospira nitrifiers. The structural equation model further revealed a significant positive association between AOB nitrifiers and N2O emission, PNA, soil pH, SOC, NO 3 - -N, and DON under organic fertilization. The keystone taxa in the comammox Nitrospira nitrifier and network Module II exhibited a positive correlation with maize productivity and NUE, likely due to their functional activities stimulated by the SC treatment. It is noteworthy that the AOB community played a more significant role in driving nitrification compared to the composition of comammox Nitrospira. Collectively, combined inorganic and organic fertilizer (SC) treatment exhibits high potential for reducing N2O emissions, enhancing maize productivity, increasing NUE, and increasing the sustainability of the nitrogen dynamics of maize agroecosystems in the semi-arid Loess Plateau.
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Affiliation(s)
- Setor Kwami Fudjoe
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Lingling Li
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Sumera Anwar
- Department of Botany, Government College Women University Faisalabad, Faisalabad, Pakistan
| | - Shangli Shi
- College of Grassland Science, Gansu Agricultural University, Lanzhou, China
| | - Junhong Xie
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Frederick Kwame Yeboah
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Beijing Normal University, Beijing, China
| | - Linlin Wang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
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10
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Lin Y, Tang KW, Ye G, Yang P, Hu HW, Tong C, Zheng Y, Feng M, Deng M, He ZY, He JZ. Community assembly of comammox Nitrospira in coastal wetlands across southeastern China. Appl Environ Microbiol 2023; 89:e0080723. [PMID: 37671870 PMCID: PMC10537594 DOI: 10.1128/aem.00807-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/17/2023] [Indexed: 09/07/2023] Open
Abstract
Complete ammonia oxidizers (comammox Nitrospira) are ubiquitous in coastal wetland sediments and play an important role in nitrification. Our study examined the impact of habitat modifications on comammox Nitrospira communities in coastal wetland sediments across tropical and subtropical regions of southeastern China. Samples were collected from 21 coastal wetlands in five provinces where native mudflats were invaded by Spartina alterniflora and subsequently converted to aquaculture ponds. The results showed that comammox Nitrospira abundances were mainly influenced by sediment grain size rather than by habitat modifications. Compared to S. alterniflora marshes and native mudflats, aquaculture pond sediments had lower comammox Nitrospira diversity, lower clade A.1 abundance, and higher clade A.2 abundance. Sulfate concentration was the most important factor controlling the diversity of comammox Nitrospira. The response of comammox Nitrospira community to habitat change varied significantly by location, and environmental variables accounted for only 11.2% of the variations in community structure across all sites. In all three habitat types, dispersal limitation largely controlled the comammox Nitrospira community assembly process, indicating the stochastic nature of these sediment communities in coastal wetlands. IMPORTANCE Comammox Nitrospira have recently gained attention for their potential role in nitrification and nitrous oxide (N2O) emissions in soil and sediment. However, their distribution and assembly in impacted coastal wetland are poorly understood, particularly on a large spatial scale. Our study provides novel evidence that the effects of habitat modification on comammox Nitrospira communities are dependent on the location of the wetland. We also found that the assembly of comammox Nitrospira communities in coastal wetlands was mainly governed by stochastic processes. Nevertheless, sediment grain size and sulfate concentration were identified as key variables affecting comammox Nitrospira abundance and diversity in coastal sediments. These findings are significant as they advance our understanding of the environmental adaptation of comammox Nitrospira and how future landscape modifications may impact their abundance and diversity in coastal wetlands.
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Affiliation(s)
- Yongxin Lin
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou, Fujian, China
| | - Kam W. Tang
- Department of Biosciences, Swansea University, Swansea, United Kingdom
| | - Guiping Ye
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, Fujian, China
- Technology Innovation Center for Monitoring and Restoration Engineering of Ecological Fragile Zone in Southeast China, Ministry of Natural Resources, Fuzhou, Fujian, China
| | - Ping Yang
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou, Fujian, China
- Research Centre of Wetlands in Subtropical Region, Fujian Normal University, Fuzhou, Fujian, China
| | - Hang-Wei Hu
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Melbourne, Victoria, Australia
| | - Chuan Tong
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou, Fujian, China
- Research Centre of Wetlands in Subtropical Region, Fujian Normal University, Fuzhou, Fujian, China
| | - Yong Zheng
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou, Fujian, China
| | - Mengmeng Feng
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou, Fujian, China
| | - Milin Deng
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou, Fujian, China
| | - Zi-Yang He
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou, Fujian, China
| | - Ji-Zheng He
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou, Fujian, China
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Melbourne, Victoria, Australia
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11
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Ishizaki Y, Kurisu F, Furumai H, Kasuga I. Autotrophic growth activity of complete ammonia oxidizers in an upflow biological contact filter for drinking water treatment. Lett Appl Microbiol 2023; 76:ovad105. [PMID: 37679291 DOI: 10.1093/lambio/ovad105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 08/24/2023] [Accepted: 09/05/2023] [Indexed: 09/09/2023]
Abstract
Biological filters effectively remove ammonium from drinking water via nitrification. In a pilot-scale upflow biological contact filter (U-BCF), complete ammonia oxidizers (comammox), which are capable of oxidizing ammonia to nitrate in one cell, were more abundant than ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). However, little information is available on the contribution of comammox to nitrification. In this study, we evaluated the autotrophic growth activity of comammox associated with biological activated carbon (BAC) in a U-BCF by DNA-stable isotope probing (DNA-SIP). BAC samples collected from the U-BCF were continuously fed mineral medium containing 0.14 mg N L-1 ammonium and 12C- or 13C-labeled bicarbonate for 20 days. DNA-SIP analysis revealed that comammox (clades A and B) as well as AOA assimilated bicarbonate after 10 days of incubation, proving that dominant comammox could contribute to nitrification. Contrarily, AOB remained inactive throughout the observation period. Amplicon sequencing of the 13C-labeled DNA fractions of comammox revealed that specific genotypes other than the most dominant genotype in the original sample were more enriched under the incubation condition for the DNA-SIP experiment. Thus, dominant genotypes of comammox in a U-BCF might utilize organic nitrogen to fuel nitrification in ammonia-limited environments.
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Affiliation(s)
- Yuta Ishizaki
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, Bunkyo, Tokyo 113-8656, Japan
| | - Futoshi Kurisu
- Research Center for Water Environment Technology, Graduate School of Engineering, The University of Tokyo, Bunkyo, Tokyo 113-8656, Japan
| | - Hiroaki Furumai
- Research and Development Initiative, Chuo University, Bunkyo, Tokyo 112-8551, Japan
| | - Ikuro Kasuga
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, Bunkyo, Tokyo 113-8656, Japan
- Research Center for Advanced Science and Technology, The University of Tokyo, Meguro, Tokyo 153-8904, Japan
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12
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Tan Q, Zhang G, Ding A, Bian Z, Wang X, Xing Y, Zheng L. Anthropogenic land-use activities within watersheds reduce comammox activity and diversity in rivers. J Environ Manage 2023; 338:117841. [PMID: 37003226 DOI: 10.1016/j.jenvman.2023.117841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/12/2023] [Accepted: 03/27/2023] [Indexed: 06/19/2023]
Abstract
Nitrogen cycling plays a key role in maintaining river ecological functions which are threatened by anthropogenic activities. The newly discovered complete ammonia oxidation, comammox, provides novel insights into the ecological effects of nitrogen on that it oxidizes ammonia directly to nitrate without releasing nitrite as canonical ammonia oxidization conducted by AOA or AOB which is believed to play an important role in greenhouse gas generation. Theoretically, contribution of commamox, AOA and AOB to ammonia oxidization in rivers might be impacted by anthropogenic land-use activities through alterations in flow regime and nutrient input. While how land use pattern affects comammox and other canonical ammonia oxidizers remains elusive. In this study, we examined the ecological effects of land use practices on the activity and contribution of three distinctive groups of ammonia oxidizers (AOA, AOB, comammox) as well as the composition of comammox bacterial communities from 15 subbasins covering an area of 6166 km2 in North China. The results showed that comammox dominated nitrification (55.71%-81.21%) in less disturbed basins characterized by extensive forests and grassland, while AOB became the major player (53.83%-76.43%) in highly developed basins with drastic urban and agricultural development. In addition, increasing anthropogenic land use activities within the watershed lowered the alpha diversity of comammox communities and simplified the comammox network. Additionally, the alterations of NH4+-N, pH and C/N induced by land use change were found to be crucial drivers in determining the distribution and activity of AOB and comammox. Together, our findings cast a new light on aquatic-terrestrial linkages from the view of microorganism-mediated nitrogen cycling and can further be applied to target watershed land use management.
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Affiliation(s)
- Qiuyang Tan
- College of Water Science, Beijing Normal University, Beijing, 100875, China
| | - Guoyu Zhang
- Department of Environmental Engineering, School of Marine Science and Technology, Harbin Institute of Technology, Weihai, 264209, China
| | - Aizhong Ding
- College of Water Science, Beijing Normal University, Beijing, 100875, China
| | - Zhaoyong Bian
- College of Water Science, Beijing Normal University, Beijing, 100875, China
| | - Xue Wang
- College of Water Science, Beijing Normal University, Beijing, 100875, China
| | - Yuzi Xing
- College of Water Science, Beijing Normal University, Beijing, 100875, China
| | - Lei Zheng
- College of Water Science, Beijing Normal University, Beijing, 100875, China.
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13
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Zheng M, Tian Z, Chai Z, Zhang A, Gu A, Mu G, Wu D, Guo J. Ubiquitous occurrence and functional dominance of comammox Nitrospira in full-scale wastewater treatment plants. Water Res 2023; 236:119931. [PMID: 37045640 DOI: 10.1016/j.watres.2023.119931] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/04/2023] [Accepted: 03/28/2023] [Indexed: 06/19/2023]
Abstract
The recent discovery of complete ammonia oxidation (comammox) bacteria has fundamentally upended the traditional two-step nitrification conception, but their functional importance in wastewater treatment plants (WWTPs) is still poorly understood. This study investigated distributions of comammox Nitrospira, ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in activated sludge samples collected from 25 full-scale WWTPs. Using quantitative PCR (qPCR) and 16S rRNA gene amplicon sequencing, our results revealed that comammox Nitrospira ubiquitously occurred in all of 25 WWTPs and even outnumbered AOB and AOA with an average abundance of 1∼183 orders of magnitude higher in 19 WWTPs. Moreover, DNA-based stable isotope probing (DNA-SIP) assays validated that comammox Nitrospira actively participated in ammonia oxidation in the three microcosms seeding with activated sludge from three typical WWTPs, in which the ratios of comammox amoA to AOB amoA were at the range of 1∼10, 10∼100 and >100, respectively. Phylogenetic analysis in heavy fractions further indicated that Nitrospira nitrosa (N. nitrosa) was the dominant and active species. We quantified the contribution of ammonia oxidizers based on the currently available kinetic parameters of the representative species and found that comammox made major contributions to ammonia oxidation than other nitrifiers (5 ∼ 106 times that of AOB). The findings not only demonstrate the ubiquitous occurrence of comammox, but also highlight their functional dominance in ammonia oxidation in WWTPs.
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Affiliation(s)
- Maosheng Zheng
- Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China.
| | - Zhichao Tian
- Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Zimin Chai
- Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Anqi Zhang
- Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Ailu Gu
- Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Guangli Mu
- Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Dedong Wu
- Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD, Australia.
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14
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Daebeler A, Güell‐Bujons Q, Mooshammer M, Zechmeister T, Herbold CW, Richter A, Wagner M, Daims H. Rapid nitrification involving comammox and canonical Nitrospira at extreme pH in saline-alkaline lakes. Environ Microbiol 2023; 25:1055-1067. [PMID: 36651641 PMCID: PMC10947350 DOI: 10.1111/1462-2920.16337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 01/10/2023] [Indexed: 01/19/2023]
Abstract
Nitrite-oxidizing bacteria (NOB) catalyse the second nitrification step and are the main biological source of nitrate. The most diverse and widespread NOB genus is Nitrospira, which also contains complete ammonia oxidizers (comammox) that oxidize ammonia to nitrate. To date, little is known about the occurrence and biology of comammox and canonical nitrite oxidizing Nitrospira in extremely alkaline environments. Here, we studied the seasonal distribution and diversity, and the effect of short-term pH changes on comammox and canonical Nitrospira in sediments of two saline, highly alkaline lakes. We identified diverse canonical and comammox Nitrospira clade A-like phylotypes as the only detectable NOB during more than a year, suggesting their major importance for nitrification in these habitats. Gross nitrification rates measured in microcosm incubations were highest at pH 10 and considerably faster than reported for other natural, aquatic environments. Nitrification could be attributed to canonical and comammox Nitrospira and to Nitrososphaerales ammonia-oxidizing archaea. Furthermore, our data suggested that comammox Nitrospira contributed to ammonia oxidation at an extremely alkaline pH of 11. These results identify saline, highly alkaline lake sediments as environments of uniquely strong nitrification with novel comammox Nitrospira as key microbial players.
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Affiliation(s)
- Anne Daebeler
- University of ViennaCentre for Microbiology and Environmental Systems Science, Division of Microbial EcologyViennaAustria
- Biology Centre CAS, BudweisInstitute of Soil Biology and BiogeochemistryCzechia
| | - Queralt Güell‐Bujons
- University of ViennaCentre for Microbiology and Environmental Systems Science, Division of Microbial EcologyViennaAustria
- Institut de Ciències del Mar (ICM‐CSIC), Passeig Marítim de la Barceloneta 37‐49BarcelonaCataloniaSpain
| | - Maria Mooshammer
- Centre for Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem ResearchUniversity of ViennaViennaAustria
| | | | - Craig W. Herbold
- University of ViennaCentre for Microbiology and Environmental Systems Science, Division of Microbial EcologyViennaAustria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem ResearchUniversity of ViennaViennaAustria
| | - Michael Wagner
- University of ViennaCentre for Microbiology and Environmental Systems Science, Division of Microbial EcologyViennaAustria
- The Comammox Research PlatformUniversity of ViennaViennaAustria
- Center for Microbial Communities, Department of Chemistry and BioscienceAalborg UniversityAalborgDenmark
| | - Holger Daims
- University of ViennaCentre for Microbiology and Environmental Systems Science, Division of Microbial EcologyViennaAustria
- The Comammox Research PlatformUniversity of ViennaViennaAustria
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15
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Li D, Ren Z, Zhou Y, Jiang L, Zheng M, Liu G. Comammox Nitrospira and Ammonia-Oxidizing Archaea Are Dominant Ammonia Oxidizers in Sediments of an Acid Mine Lake Containing High Ammonium Concentrations. Appl Environ Microbiol 2023; 89:e0004723. [PMID: 36912626 PMCID: PMC10056971 DOI: 10.1128/aem.00047-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 01/31/2023] [Indexed: 03/14/2023] Open
Abstract
Exploring nitrifiers in extreme environments is vital to expanding our understanding of nitrogen cycle and microbial diversity. This study presents that complete ammonia oxidation (comammox) Nitrospira, together with acidophilic ammonia-oxidizing archaea (AOA), dominate in the nitrifying guild in sediments of an acid mine lake (AML). The lake water was characterized by acidic pH below 5 with a high ammonium concentration of 175 mg-N/liter, which is rare on the earth. Nitrification was active in sediments with a maximum nitrate production potential of 70.5 μg-N/(g-dry weight [dw] day) for mixed sediments. Quantitative PCR assays determined that in AML sediments, comammox Nitrospira and AOA amoA genes had relative abundances of 52% and 41%, respectively, among the total amoA genes. Further assays with 16S rRNA and amoA gene amplicon sequencing and metagenomics confirmed their dominance and revealed that the comammox Nitrospira found in sediments belonged to comammox Nitrospira clade A.2. Metagenomic binning retrieved a metagenome-assembled genome (MAG) of the comammox Nitrospira from sediments (completeness = 96.76%), and phylogenomic analysis suggested that it was a novel comammox Nitrospira. Comparative genomic investigation revealed that this comammox Nitrospira contained diverse metal resistance genes and an acidophile-affiliated F-type ATPase. Moreover, it had a more diverse genomic characteristic on nitrogen metabolism than the AOA in sediments and canonical AOB did. The results suggest that comammox Nitrospira is a versatile nitrifier that can adapt to acidic environments even with high ammonium concentrations. IMPORTANCE Ammonia-oxidizing archaea (AOA) was previously considered the sole dominant ammonia oxidizer in acidic environments. This study, however, found that complete ammonia oxidation (comammox) Nitrospira was also a dominant ammonia oxidizer in the sediments of an acidic mine lake, which had an acidic pH < 5 and a high ammonium concentration of 175 mg-N/liter. In combination with average nucleotide identity analysis, phylogenomic analysis suggested it is a novel strain of comammox Nitrospira. Moreover, the adaption of comammox Nitrospira to the acidic lake had been comprehensively investigated based on genome-centric metagenomic approaches. The outcomes of this study significantly expand our understanding of the diversity and adaptability of ammonia oxidizers in the acidic environments.
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Affiliation(s)
- Deyong Li
- Center for Environmental Microplastics Studies, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, and School of Environment, Jinan University, Guangzhou, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Zhichang Ren
- Center for Environmental Microplastics Studies, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, and School of Environment, Jinan University, Guangzhou, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Yangqi Zhou
- Center for Environmental Microplastics Studies, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, and School of Environment, Jinan University, Guangzhou, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Lugao Jiang
- Center for Environmental Microplastics Studies, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, and School of Environment, Jinan University, Guangzhou, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Min Zheng
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), University of Queensland, St. Lucia, Brisbane, Queensland, Australia
| | - Guoqiang Liu
- Center for Environmental Microplastics Studies, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, and School of Environment, Jinan University, Guangzhou, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
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16
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Zhao W, Bi X, Bai M, Wang Y. Research advances of ammonia oxidation microorganisms in wastewater: metabolic characteristics, microbial community, influencing factors and process applications. Bioprocess Biosyst Eng 2023; 46:621-633. [PMID: 36988685 DOI: 10.1007/s00449-023-02866-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 03/21/2023] [Indexed: 03/30/2023]
Abstract
Ammonia oxidation carried out by ammonia-oxidizing microorganisms (AOMs) is a central step in the global nitrogen cycle. Aerobic AOMs comprise conventional ammonia-oxidizing bacteria (AOB), novel ammonia-oxidizing archaea (AOA), which could exist in complex and extreme conditions, and complete ammonia oxidizers (comammox), which directly oxidize ammonia to nitrate within a single cell. Anaerobic AOMs mainly comprise anaerobic ammonia-oxidizing bacteria (AnAOB), which can transform NH4+-N and NO2--N into N2 under anaerobic conditions. In this review, the unique metabolic characteristics, microbial community of AOMs and the influencing factors are discussed. Process applications of nitrification/denitrification, nitritation/denitrification, nitritation/anammox and partial denitrification/anammox in wastewater treatment systems are emphasized. The future development of nitrogen removal processes using AOMs is expected, enrichment of comammox facilitates the complete nitrification performance, inhibiting the activity of comammox and NOB could achieve stable nitritation, and additionally, AnAOB conducting the anammox process in municipal wastewater is a promising development direction.
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Affiliation(s)
- Weihua Zhao
- State and Local Joint Engineering Research Center of Municipal Wastewater Treatment and Resource Recycling, Qingdao University of Technology, Qingdao, 266033, People's Republic of China.
- School of Marine Science and Technology, Harbin Institute of Technology, Weihai, 264209, People's Republic of China.
- Qingdao University of Technology, Huangdao District, Qingdao, 266525, People's Republic of China.
| | - Xuejun Bi
- State and Local Joint Engineering Research Center of Municipal Wastewater Treatment and Resource Recycling, Qingdao University of Technology, Qingdao, 266033, People's Republic of China
| | - Meng Bai
- State and Local Joint Engineering Research Center of Municipal Wastewater Treatment and Resource Recycling, Qingdao University of Technology, Qingdao, 266033, People's Republic of China
| | - Yanyan Wang
- State and Local Joint Engineering Research Center of Municipal Wastewater Treatment and Resource Recycling, Qingdao University of Technology, Qingdao, 266033, People's Republic of China
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17
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Vilardi K, Cotto I, Bachmann M, Parsons M, Klaus S, Wilson C, Bott CB, Pieper KJ, Pinto AJ. Co-Occurrence and Cooperation between Comammox and Anammox Bacteria in a Full-Scale Attached Growth Municipal Wastewater Treatment Process. Environ Sci Technol 2023; 57:5013-5023. [PMID: 36913533 PMCID: PMC10061930 DOI: 10.1021/acs.est.2c09223] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/02/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
Cooperation between comammox and anammox bacteria for nitrogen removal has been recently reported in laboratory-scale systems, including synthetic community constructs; however, there are no reports of full-scale municipal wastewater treatment systems with such cooperation. Here, we report intrinsic and extant kinetics as well as genome-resolved community characterization of a full-scale integrated fixed film activated sludge (IFAS) system where comammox and anammox bacteria co-occur and appear to drive nitrogen loss. Intrinsic batch kinetic assays indicated that majority of the aerobic ammonia oxidation was driven by comammox bacteria (1.75 ± 0.08 mg-N/g TS-h) in the attached growth phase, with minimal contribution by ammonia-oxidizing bacteria. Interestingly, a portion of total inorganic nitrogen (∼8%) was consistently lost during these aerobic assays. Aerobic nitrite oxidation assays eliminated the possibility of denitrification as a cause of nitrogen loss, while anaerobic ammonia oxidation assays resulted in rates consistent with anammox stoichiometry. Full-scale experiments at different dissolved oxygen (DO = 2 - 6 mg/L) setpoints indicated persistent nitrogen loss that was partly sensitive to DO concentrations. Genome-resolved metagenomics confirmed the high abundance (relative abundance 6.53 ± 0.34%) of two Brocadia-like anammox populations, while comammox bacteria within the Ca. Nitrospira nitrosa cluster were lower in abundance (0.37 ± 0.03%) and Nitrosomonas-like ammonia oxidizers were even lower (0.12 ± 0.02%). Collectively, our study reports for the first time the co-occurrence and cooperation of comammox and anammox bacteria in a full-scale municipal wastewater treatment system.
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Affiliation(s)
- Katherine Vilardi
- Department
of Civil and Environmental Engineering, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Irmarie Cotto
- School
of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, Georgia 30318, United States
| | - Megan Bachmann
- Hampton
Roads Sanitation District, 1434 Air Rail Avenue, Virginia
Beach, Virginia 23455, United States
| | - Mike Parsons
- Hampton
Roads Sanitation District, 1434 Air Rail Avenue, Virginia
Beach, Virginia 23455, United States
| | - Stephanie Klaus
- Hampton
Roads Sanitation District, 1434 Air Rail Avenue, Virginia
Beach, Virginia 23455, United States
| | - Christopher Wilson
- Hampton
Roads Sanitation District, 1434 Air Rail Avenue, Virginia
Beach, Virginia 23455, United States
| | - Charles B. Bott
- Hampton
Roads Sanitation District, 1434 Air Rail Avenue, Virginia
Beach, Virginia 23455, United States
| | - Kelsey J. Pieper
- Department
of Civil and Environmental Engineering, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Ameet J. Pinto
- School
of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, Georgia 30318, United States
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18
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Wang Y, Zhang S, Jin H, Chen J, Zhou K, Chen J, Chen J, Zhu G. Effects of dam building on the occurrence and activity of comammox bacteria in river sediments and their contribution to nitrification. Sci Total Environ 2023; 864:161167. [PMID: 36572300 DOI: 10.1016/j.scitotenv.2022.161167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/26/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
The recent discovery of complete ammonia oxidizers (comammox) has fundamentally changed our understanding of nitrification. However, studies on the occurrence and activity of comammox bacteria and their contribution to nitrification remain unclear. Here, we investigated the abundance, activity, and diversity of comammox bacteria and their contribution to nitrification in sediments from dammed rivers in winter and summer. Our results indicated that comammox clade A was ubiquitous in all sediment samples and the community structure in comammox varied between the upper and lower reaches, but not on the time scale (winter and summer). Comammox activity in the dammed river sediments in summer was prominently higher than in winter (summer: 1.08 ± 0.52; winter: 0.197 ± 0.148 mg N kg-1 day-1). Furthermore, the activity of comammox bacteria in summer appeared higher in the vicinity of the dammed river and in the Sanjiang estuary, which is located downstream of the dammed river. The activity of ammonia-oxidizing bacteria (AOB) (0.77 ± 0.478 mg N kg-1 day-1) was higher compared to comammox (0.639 ± 0.588 mg N kg-1 day-1) and ammonia-oxidizing archaea (AOA) (0.026 ± 0.022 mg N kg-1 day-1) in both winter and summer. In terms of contribution to the nitrification process, AOB (winter: 67.13 ± 12.21 %; summer: 50.57 ± 16.14 %) outperformed comammox (winter: 28.59 ± 12.51 %; summer: 48.38 ± 16.62 %) and AOA (winter: <7.39 %; summer: <2.09 %). These findings indicated that the nitrification process in dammed river sediments was mainly dominated by AOB. Additionally, comammox activity was significantly affected by temperature and NH4+, suggesting that these variables were key determinants of the niche partitioning of comammox. Collectively, our findings provide novel perspectives into the widespread distribution and contribution of comammox to nitrification in dammed river ecosystems, thus broadening our understanding of the nitrification processes.
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Affiliation(s)
- Yuantao Wang
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Science, Beijing 100049, China; CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315100, China
| | - Shenghua Zhang
- College of Harbour and Coastal Engineering, Jimei University, Xiamen 361021, China.
| | - Huixia Jin
- NingboTech University, Ningbo 315100, China
| | - Jiwei Chen
- Ningbo River Management Center, Ningbo 315100, China
| | - Ketao Zhou
- Ningbo River Management Center, Ningbo 315100, China
| | - Jinxi Chen
- NingboTech University, Ningbo 315100, China
| | - Jinfang Chen
- College of Harbour and Coastal Engineering, Jimei University, Xiamen 361021, China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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Ghimire-Kafle S, Weaver ME Jr, Bollmann A. Ecophysiological and Genomic Characterization of the Freshwater Complete Ammonia Oxidizer Nitrospira sp. Strain BO4. Appl Environ Microbiol 2023; 89:e0196522. [PMID: 36719237 DOI: 10.1128/aem.01965-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Complete ammonia oxidizers (comammox) are a group of ubiquitous chemolithoautotrophic bacteria capable of deriving energy from the oxidation of ammonia to nitrate via nitrite. Here, we present a study characterizing the comammox strain Nitrospira sp. BO4 using a combination of cultivation-dependent and molecular methods. The enrichment culture BO4 was obtained from the sediment of Lake Burr Oak, a mesotrophic lake in eastern Ohio. The metagenome of the enrichment culture was sequenced, and a metagenome-assembled genome (MAG) was constructed for Nitrospira sp. BO4. The closest characterized relative of Nitrospira sp. BO4 was "Candidatus Nitrospira kreftii." All genes for ammonia and nitrite oxidation, reductive tricarboxylic acid (TCA) cycle, and other pathways of the central metabolism were detected. Nitrospira sp. BO4 used ammonia and oxidized it to nitrate with nitrite as the intermediate. The culture grew on initial ammonium concentrations between 0.01 and 3 mM with the highest rates observed at the lowest ammonium concentrations. Blue light completely inhibited the growth of Nitrospira sp. BO4, while white light reduced the growth and red light had no effect on the growth. Nitrospira sp. BO4 did not grow on nitrite as its sole substrate. When supplied with ammonium and nitrite, the culture utilized nitrite after most of the ammonium was consumed. In summary, the genomic information of Nitrospira sp. BO4 coupled with the growth experiments shows that Nitrospira sp. BO4 is a freshwater comammox species. Future research will focus on further characterization of the niches of comammox in freshwater environments. IMPORTANCE Nitrification is a key process in the global nitrogen cycle. Complete ammonia oxidizers (comammox) were discovered recently, and only three enrichment cultures and one pure culture have been characterized with respect to activity and growth under different conditions. The cultivated comammox strains were obtained from engineered systems such as a recirculating aquaculture system and hot water pipes. Here, we present the first study characterizing a comammox strain obtained from a mesotrophic freshwater lake. In freshwater environments, comammox coexist with ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Our results will help elucidate physiological characteristics of comammox and the distribution and niche differentiation of different ammonia oxidizers in freshwater environments.
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Chisholm C, Di HJ, Cameron K, Podolyan A, Shah A, Hsu L, Shen J. Soil moisture is a primary driver of comammox Nitrospira abundance in New Zealand soils. Sci Total Environ 2023; 858:159961. [PMID: 36343813 DOI: 10.1016/j.scitotenv.2022.159961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 10/31/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
The objectives of this study were to investigate the abundance and community composition of comammox Nitrospira under: (i) pasture-based dairy farms from different regions, and (ii) different land uses from the same region and soil type. The results clearly showed that comammox Nitrospira were most abundant (3.0 × 106 copies) under the west coast dairy farm conditions, where they were also significantly more abundant than canonical ammonia oxidisers. This was also true in the Canterbury dairy farm. The six land uses investigated were pine monoculture, a long term no input ecological trial, sheep + beef and Dairy, both irrigated and non-irrigated. It was concluded that comammox Nitrospira was most abundant under the irrigated dairy farm (2.7 × 106 copies). Contrary to the current industry opinion, the relatively high abundance of comammox Nitrospira under fertile irrigated dairy land suggests that comammox Nitrospira found in terrestrial ecosystems may be copiotrophic. it was also determined that comammox Nitrospira was more abundant under irrigated land use than their non-irrigated counterparts, suggesting that soil moisture is a key environmental parameter influencing comammox abundance. Comammox abundance was also positively correlated with annual rainfall, further supporting this theory. Phylogenetic analysis of the comammox Nitrospira detected determined that 17 % of the comammox community belonged to a newly distinguished subclade, clade B.2. The remaining 83 % belonged to clade B.1. No sequences from clade A were found.
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Affiliation(s)
- Chris Chisholm
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, 7647, Christchurch, New Zealand
| | - Hong J Di
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, 7647, Christchurch, New Zealand.
| | - Keith Cameron
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, 7647, Christchurch, New Zealand
| | - Andriy Podolyan
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, 7647, Christchurch, New Zealand
| | - Anish Shah
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, 7647, Christchurch, New Zealand
| | - Lisa Hsu
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, 7647, Christchurch, New Zealand
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21
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Wang Y, Zeng X, Ma Q, Zhang Y, Yu W, Zheng Z, Zhang N, Xu L. Differential responses of canonical nitrifiers and comammox Nitrospira to long-term fertilization in an Alfisol of Northeast China. Front Microbiol 2023; 14:1095937. [PMID: 36819044 PMCID: PMC9929954 DOI: 10.3389/fmicb.2023.1095937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/12/2023] [Indexed: 02/04/2023] Open
Abstract
The newly identified complete ammonia oxidizer (comammox) that converts ammonia directly into nitrate has redefined the long-held paradigm of two-step nitrification mediated by two distinct groups of nitrifiers. However, exploration of the niche differentiation of canonical nitrifiers and comammox Nitrospira and their ecological importance in agroecosystems is still limited. Here, we adopted quantitative PCR (qPCR) and Illumina MiSeq sequencing to investigate the effects of five long-term fertilization regimes in the variations of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), nitrite-oxidizing bacteria (NOB), and comammox Nitrospira abundances and comammox community composition in two soil layers (0-20 cm, topsoil; 20-40 cm, subsoil) in an Alfisol in Northeast China. The fertilization treatments included no fertilizer (CK); chemical nitrogen (N) fertilizer; chemical N; phosphorus (P) and potassium (K) fertilizers (NPK); recycled organic manure (M) and chemical N, P, K plus recycled manure (MNPK). Compared with CK, manure and/or chemical fertilizer significantly increased the AOB amoA gene abundance. Long-term recycled manure increased soil organic matter (SOM) contents and maintained the soil pH, but decreased the NH4 +-N concentrations, which markedly promoted the nxrA and nxrB gene abundances of NOB and the amoA gene abundances of comammox Nitrospira clade A and AOA. Although the comammox Nitrospira clade B abundance tended to decrease after fertilization, the structural equation modeling analysis showed that comammox clade B had direct positive impacts on soil potential ammonia oxidation (PAO; λ = 0.59, p < 0.001). The long-term fertilization regime altered the community composition of comammox Nitrospira. Additionally, comammox Nitrospira clades A and B had individual response patterns to the soil layer. The relative abundance of clade A was predominant in the topsoil in the N (86.5%) and MNPK (76.4%) treatments, while clade B appeared to be dominant in the subsoil (from 78.7 to 88.1%) with lower ammonium contents, implying niche separation between these clades. Soil pH, NH4 +-N and SOM content were crucial factors shaping the soil nitrifying microbial abundances and the comammox Nitrospira community. Together, these findings expand the current understanding of the niche specialization and the important role of comammox Nitrospira in terrestrial ecosystems.
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Affiliation(s)
- Yanan Wang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xibai Zeng
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China,*Correspondence: Xibai Zeng, ✉
| | - Qiang Ma
- Insitute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Yang Zhang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wantai Yu
- Insitute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Zhong Zheng
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Nan Zhang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liyang Xu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
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22
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Cotto I, Vilardi KJ, Huo L, Fogarty EC, Khunjar W, Wilson C, De Clippeleir H, Gilmore K, Bailey E, Lücker S, Pinto AJ. Low diversity and microdiversity of comammox bacteria in wastewater systems suggest specific adaptations within the Ca. Nitrospira nitrosa cluster. Water Res 2023; 229:119497. [PMID: 36563511 DOI: 10.1016/j.watres.2022.119497] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
Studies have found Ca. Nitrospira nitrosa-like bacteria to be the principal or sole comammox bacteria in nitrogen removal systems for wastewater treatment. In contrast, multiple populations of strict ammonia and nitrite oxidizers co-exist in similar systems. This apparent lack of diversity is surprising and could impact the feasibility of leveraging comammox bacteria for nitrogen removal. We used full-length 16S rRNA gene sequencing and genome-resolved metagenomics to compare the species-level diversity of comammox bacteria with that of strict nitrifiers in full-scale wastewater treatment systems and assess whether this comparison is consistent or diverged at the strain-level. Full-length 16S rRNA gene sequencing indicated that Nitrosomonas-like bacteria exhibited higher species-level diversity in comparison with other nitrifying bacteria, while the strain-level diversity (also called microdiversity) of most Nitrospira-like bacteria were higher than Nitrosomonas-like bacteria with few exceptions (one Nitrospira lineage II population). Comammox bacterial metagenome assembled genomes (MAGs) were associated with Ca. Nitrospira nitrosa. The average amino acid identity between principal comammox bacterial MAGs (93% ± 3) across systems was significantly higher than that of the Nitrosomonas-like ammonia oxidizers (73% ± 8), the Nitrospira_A-like nitrite oxidizer (85% ± 4), and the Nitrospira_D-like nitrite oxidizer (83% ± 1). This demonstrated the low species-level diversity of comammox bacteria compared with strict nitrifiers and further suggests that the same comammox population was detected in all systems. Comammox bacteria (Nitrospira lineage II), Nitrosomonas and, Nitrospira_D (Nitrospira lineage II) MAGs were significantly less microdiverse than the Nitrospira_A (lineage I) MAGs. Interestingly, strain-resolved analysis also indicates that different nitrogen removal systems harbor different comammox bacterial strains within the Ca. Nitrospira nitrosa cluster. These results suggest that comammox bacteria associated with Ca. Nitrospira nitrosa have low species- and strain-level diversity in nitrogen removal systems and may thus harbor specific adaptations to the wastewater ecosystem.
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Affiliation(s)
- Irmarie Cotto
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, United States
| | - Katherine J Vilardi
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, United States
| | - Linxuan Huo
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Emily C Fogarty
- Committee on Microbiology, The University of Chicago, Chicago, IL, United States
| | | | | | | | - Kevin Gilmore
- Department of Civil and Environmental Engineering, Bucknell University, Lewisburg, PA, United States
| | - Erika Bailey
- City of Raleigh Public Utilities, Raleigh, NC, United States
| | - Sebastian Lücker
- Department of Microbiology, RIBES, Radboud University, Nijmegen, the Netherlands
| | - Ameet J Pinto
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States.
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23
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Ohbayashi T, Wang Y, Aoyagi LN, Hara S, Tago K, Hayatsu M. Diversity of the Hydroxylamine Oxidoreductase (HAO) Gene and Its Enzyme Active Site in Agricultural Field Soils. Microbes Environ 2023; 38:ME23068. [PMID: 38092410 PMCID: PMC10728637 DOI: 10.1264/jsme2.me23068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/06/2023] [Indexed: 12/18/2023] Open
Abstract
Nitrification is a key process in the biogeochemical nitrogen cycle and a major emission source of the greenhouse gas nitrous oxide (N2O). The periplasmic enzyme hydroxylamine oxidoreductase (HAO) is involved in the oxidation of hydroxylamine to nitric oxide in the second step of nitrification, producing N2O as a byproduct. Its three-dimensional structure demonstrates that slight differences in HAO active site residues have inhibitor effects. Therefore, a more detailed understanding of the diversity of HAO active site residues in soil microorganisms is important for the development of novel nitrification inhibitors using structure-guided drug design. However, this has not yet been examined. In the present study, we investigated hao gene diversity in beta-proteobacterial ammonia-oxidizing bacteria (β-AOB) and complete ammonia-oxidizing (comammox; Nitrospira spp.) bacteria in agricultural fields using a clone library ana-lysis. A total of 1,949 hao gene sequences revealed that hao gene diversity in β-AOB and comammox bacteria was affected by the fertilizer treatment and field type, respectively. Moreover, hao sequences showed the almost complete conservation of the six HAO active site residues in both β-AOB and comammox bacteria. The diversity of nitrifying bacteria showed similarity between hao and amoA genes. The nxrB amplicon sequence revealed the dominance of Nitrospira cluster II in tea field soils. The present study is the first to reveal hao gene diversity in agricultural soils, which will accelerate the efficient screening of HAO inhibitors and evaluations of their suppressive effects on nitrification in agricultural soils.
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Affiliation(s)
- Tsubasa Ohbayashi
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 305–8604, Tsukuba, Japan
| | - Yong Wang
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 305–8604, Tsukuba, Japan
| | - Luciano Nobuhiro Aoyagi
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 305–8604, Tsukuba, Japan
| | - Shintaro Hara
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 305–8604, Tsukuba, Japan
| | - Kanako Tago
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 305–8604, Tsukuba, Japan
| | - Masahito Hayatsu
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 305–8604, Tsukuba, Japan
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24
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Lin Y, Ye G, Hu HW, Yang P, Wan S, Feng M, He ZY, He JZ. Plant Species-Driven Distribution of Individual Clades of Comammox Nitrospira in a Subtropical Estuarine Wetland. Microb Ecol 2023; 85:209-220. [PMID: 35034141 DOI: 10.1007/s00248-021-01940-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 12/07/2021] [Indexed: 06/14/2023]
Abstract
Plant species play a crucial role in mediating the activity and community structure of soil microbiomes through differential inputs of litter and rhizosphere exudates, but we have a poor understanding of how plant species influence comammox Nitrospira, a newly discovered ammonia oxidizer with pivotal functionality. Here, we investigate the abundance, diversity, and community structure of comammox Nitrospira underneath five plant species and a bare tidal flat at three soil depths in a subtropical estuarine wetland. Plant species played a critical role in driving the distribution of individual clades of comammox Nitrospira, explaining 59.3% of the variation of community structure. Clade A.1 was widely detected in all samples, while clades A.2.1, A.2.2, A.3 and B showed plant species-dependent distribution patterns. Compared with the native species Cyperus malaccensis, the invasion of Spartina alterniflora increased the network complexity and changed the community structure of comammox Nitrospira, while the invasive effects from Kandelia obovata and Phragmites australis were relatively weak. Soil depths significantly influenced the community structure of comammox Nitrospira, but the effect was much weaker than that from plant species. Altogether, our results highlight the previously unrecognized critical role of plant species in driving the distribution of comammox Nitrospira in a subtropical estuarine wetland.
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Affiliation(s)
- Yongxin Lin
- State Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, China
| | - Guiping Ye
- Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Hang-Wei Hu
- State Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, China
| | - Ping Yang
- State Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, China
| | - Song Wan
- State Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, China
| | - Mengmeng Feng
- State Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, China
| | - Zi-Yang He
- State Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, China
| | - Ji-Zheng He
- State Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, China.
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25
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Gottshall EY, Godfrey B, Li B, Abrahamson B, Qin W, Winkler M. Photoinhibition of comammox reaction in Nitrospira inopinata in a dose- and wavelength-dependent manner. Front Microbiol 2022; 13:1022899. [PMID: 36590435 PMCID: PMC9797979 DOI: 10.3389/fmicb.2022.1022899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 11/22/2022] [Indexed: 12/23/2022] Open
Abstract
Apparent contribution of complete ammonia-oxidizing organisms (comammox) to the global nitrogen cycle highlights the necessity for understanding niche differentiation of comammox bacteria among other ammonia oxidizers. While the high affinity for ammonia of the comammox species Nitrospira inopinata suggests their niche partitioning is expected to be centered in oligotrophic environments, their absence in nutrient-depleted environments (such as the oceans) suggests that other (abiotic) factors might control their distribution and spatial localization within microbial communities. Many ammonia- and nitrite-oxidizing organisms are sensitive to light; however, the photosensitivity of comammox has not been explored. Since comammox bacteria encode enzymatic machinery homologous to canonical ammonia-and nitrite-oxidizers, we hypothesized that comammox N. inopinata, the only available pure culture of this group of microorganisms, may be inhibited by illumination in a similar manner. We evaluated the impact of light intensity, wavelength, and duration on the degree of photoinhibition for cultures of the comammox species N. inopinata and the soil ammonia-oxidizing archaea Nitrososphaera viennensis. Both species were highly sensitive to light. Interestingly, mimicking diurnal light exposure caused an uncoupling of ammonia and nitrite oxidation in N. inopinata, indicating nitrite oxidation might be more sensitive to light exposure than ammonia oxidation. It is likely that light influences comammox spatial distribution in natural environments such as surface fresh waters according to diurnal cycles, light attenuation coefficients, and the light penetration depths. Our findings therefore provide ecophysiological insights for further studies on comammox both in field and laboratory settings.
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Affiliation(s)
- Ekaterina Y. Gottshall
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States,*Correspondence: Ekaterina Y. Gottshall,
| | - Bruce Godfrey
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
| | - Bo Li
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
| | - Britt Abrahamson
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
| | - Wei Qin
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
| | - Mari Winkler
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
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Hsu PC(L, Di HJ, Cameron K, Podolyan A, Chau H, Luo J, Miller B, Carrick S, Johnstone P, Ferguson S, Wei W, Shen J, Zhang L, Liu H, Zhao T, Wei W, Ding W, Pan H, Liu Y, Li B. Comammox Nitrospira Clade B is the most abundant complete ammonia oxidizer in a dairy pasture soil and inhibited by dicyandiamide and high ammonium concentrations. Front Microbiol 2022; 13:1048735. [PMID: 36578577 PMCID: PMC9791190 DOI: 10.3389/fmicb.2022.1048735] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/07/2022] [Indexed: 12/14/2022] Open
Abstract
The recent discovery of comammox Nitrospira, a complete ammonia oxidizer, capable of completing the nitrification on their own has presented tremendous challenges to our understanding of the nitrification process. There are two divergent clades of comammox Nitrospira, Clade A and B. However, their population abundance, community structure and role in ammonia and nitrite oxidation are poorly understood. We conducted a 94-day microcosm study using a grazed dairy pasture soil amended with urea fertilizers, synthetic cow urine, and the nitrification inhibitor, dicyandiamide (DCD), to investigate the growth and community structure of comammox Nitrospira spp. We discovered that comammox Nitrospira Clade B was two orders of magnitude more abundant than Clade A in this fertile dairy pasture soil and the most abundant subcluster was a distinctive phylogenetic uncultured subcluster Clade B2. We found that comammox Nitrospira Clade B might not play a major role in nitrite oxidation compared to the role of canonical Nitrospira nitrite-oxidizers, however, comammox Nitrospira Clade B is active in nitrification and the growth of comammox Nitrospira Clade B was inhibited by a high ammonium concentration (700 kg synthetic urine-N ha-1) and the nitrification inhibitor DCD. We concluded that comammox Nitrospira Clade B: (1) was the most abundant comammox in the dairy pasture soil; (2) had a low tolerance to ammonium and can be inhibited by DCD; and (3) was not the dominant nitrite-oxidizer in the soil. This is the first study discovering a new subcluster of comammox Nitrospira Clade B2 from an agricultural soil.
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Affiliation(s)
- Pei-Chun (Lisa) Hsu
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, New Zealand
| | - Hong J. Di
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, New Zealand,*Correspondence: Hong J. Di,
| | - Keith Cameron
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, New Zealand
| | - Andriy Podolyan
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, New Zealand
| | - Henry Chau
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, New Zealand
| | | | - Blair Miller
- Lincoln Agritech Ltd, Lincoln University, Lincoln, New Zealand
| | - Sam Carrick
- Manaaki Whenua – Landcare Research, Lincoln, New Zealand
| | - Paul Johnstone
- The New Zealand Institute for Plant and Food Research, Havelock North, New Zealand
| | - Scott Ferguson
- Department of Microbiology, University of Otago, Dunedin, New Zealand
| | - Wenhua Wei
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | | | - Limei Zhang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Hongbin Liu
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tongke Zhao
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Wenxue Wei
- Institute of Subtropical Agricultural Ecology, Chinese Academy of Sciences, Changsha, China
| | - Weixin Ding
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Hong Pan
- College of Natural Resources and Environment, Shandong Agricultural University, Taian, China
| | - Yimeng Liu
- Centre for Innovation and Development, Beijing Normal University, Zhuhai, China
| | - Bowen Li
- College of Natural Resources and Environment, Hebei Agricultural University, Baoding, China
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Palomo A, Dechesne A, Pedersen AG, Smets BF. Genomic profiling of Nitrospira species reveals ecological success of comammox Nitrospira. Microbiome 2022; 10:204. [PMID: 36451244 PMCID: PMC9714041 DOI: 10.1186/s40168-022-01411-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/03/2022] [Indexed: 05/19/2023]
Abstract
BACKGROUND The discovery of microorganisms capable of complete ammonia oxidation to nitrate (comammox) has prompted a paradigm shift in our understanding of nitrification, an essential process in N cycling, hitherto considered to require both ammonia oxidizing and nitrite oxidizing microorganisms. This intriguing metabolism is unique to the genus Nitrospira, a diverse taxon previously known to only contain canonical nitrite oxidizers. Comammox Nitrospira have been detected in diverse environments; however, a global view of the distribution, abundance, and diversity of Nitrospira species is still incomplete. RESULTS In this study, we retrieved 55 metagenome-assembled Nitrospira genomes (MAGs) from newly obtained and publicly available metagenomes. Combined with publicly available MAGs, this constitutes the largest Nitrospira genome database to date with 205 MAGs, representing 132 putative species, most without cultivated representatives. Mapping of metagenomic sequencing reads from various environments against this database enabled an analysis of the distribution and habitat preferences of Nitrospira species. Comammox Nitrospira's ecological success is evident as they outnumber and present higher species-level richness than canonical Nitrospira in all environments examined, except for marine and wastewaters samples. The type of environment governs Nitrospira species distribution, without large-scale biogeographical signal. We found that closely related Nitrospira species tend to occupy the same habitats, and that this phylogenetic signal in habitat preference is stronger for canonical Nitrospira species. Comammox Nitrospira eco-evolutionary history is more complex, with subclades achieving rapid niche divergence via horizontal transfer of genes, including the gene encoding hydroxylamine oxidoreductase, a key enzyme in nitrification. CONCLUSIONS Our study expands the genomic inventory of the Nitrospira genus, exposes the ecological success of complete ammonia oxidizers within a wide range of habitats, identifies the habitat preferences of (sub)lineages of canonical and comammox Nitrospira species, and proposes that horizontal transfer of genes involved in nitrification is linked to niche separation within a sublineage of comammox Nitrospira. Video Abstract.
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Affiliation(s)
- Alejandro Palomo
- Department of Environmental and Resource Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Arnaud Dechesne
- Department of Environmental and Resource Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Anders G. Pedersen
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Copenhagen, Denmark
| | - Barth F. Smets
- Department of Environmental and Resource Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
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Yang X, Yu X, He Q, Deng T, Guan X, Lian Y, Xu K, Shu L, Wang C, Yan Q, Yang Y, Wu B, He Z. Niche differentiation among comammox (Nitrospira inopinata) and other metabolically distinct nitrifiers. Front Microbiol 2022; 13:956860. [PMID: 36187961 PMCID: PMC9515657 DOI: 10.3389/fmicb.2022.956860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
Due to global change, increasing nutrient input to ecosystems dramatically affects the nitrogen cycle, especially the nitrification process. Nitrifiers including ammonia-oxidizing archaea (AOAs), ammonia-oxidizing bacteria (AOBs), nitrite-oxidizing bacteria (NOBs), and recently discovered complete ammonia oxidizers (comammoxs) perform nitrification individually or in a community. However, much remains to be learned about their niche differentiation, coexistence, and interactions among those metabolically distinct nitrifiers. Here, we used synthetic microbial ecology approaches to construct synthetic nitrifying communities (SNCs) with different combinations of Nitrospira inopinata as comammox, Nitrososphaera gargensis as AOA, Nitrosomonas communis as AOB, and Nitrospira moscoviensis as NOB. Our results showed that niche differentiation and potential interactions among those metabolically distinct nitrifiers were determined by their kinetic characteristics. The dominant species shifted from N. inopinata to N. communis in the N4 community (with all four types of nitrifiers) as ammonium concentrations increased, which could be well explained by the kinetic difference in ammonia affinity, specific growth rate, and substrate tolerance of nitrifiers in the SNCs. In addition, a conceptual model was developed to infer niche differentiation and possible interactions among the four types of nitrifiers. This study advances our understanding of niche differentiation and provides new strategies to further study their interactions among the four types of nitrifiers.
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Affiliation(s)
- Xueqin Yang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Xiaoli Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Qiang He
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, TN, United States
| | - Ting Deng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Xiaotong Guan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Yingli Lian
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Kui Xu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Yuchun Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
| | - Bo Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
- *Correspondence: Bo Wu
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
- College of Agronomy, Hunan Agricultural University, Changsha, China
- Zhili He
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Huang T, Xia J, Liu T, Su Z, Guan Y, Guo J, Wang C, Zheng M. Comammox Nitrospira Bacteria Are Dominant Ammonia Oxidizers in Mainstream Nitrification Bioreactors Emended with Sponge Carriers. Environ Sci Technol 2022; 56:12584-12591. [PMID: 35973026 DOI: 10.1021/acs.est.2c03641] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Complete ammonia oxidation (i.e., comammox) is a newly discovered microbial process performed by a subset of the Nitrospira genus, and this unique microbial process has been ubiquitously detected in various wastewater treatment units. However, the operational conditions favoring comammox prevalence remain unclear. In this study, the dominance of comammox Nitrospira in four sponge biofilm reactors fed with low-strength ammonium (NH4+ = 23 ± 3 mg N/L) wastewater was proved by coupling 16S rRNA gene amplicon sequencing, quantitative polymerase chain reaction (qPCR), and metagenomic sequencing. The results showed that comammox Nitrospira dominated in the nitrifying guild over canonical ammonia-oxidizing bacteria (AOB) constantly, despite the significant variation in the residual ammonium concentration (0.01-15 mg N/L) under different sets of operating conditions. This result indicates that sponge biofilms greatly favor retaining comammox Nitrospira in wastewater treatment and highlights an essential role of biomass retention in the comammox prevalence. Moreover, analyses of the assembled metagenomic sequences revealed that the retrieved amoA gene sequences affiliated with comammox Nitrospira (53.9-66.0% read counts of total amoA gene reads) were always higher than those (28.4-43.4%) related to β-proteobacterial AOB taxa. The comammox Nitrospira bacteria detected in the present biofilm systems were close to clade A Candidatus Nitrospira nitrosa.
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Affiliation(s)
- Tuo Huang
- School of Environment, Tsinghua University, Beijing 100084, China
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Jun Xia
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Tao Liu
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Zicheng Su
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Yuntao Guan
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Chengwen Wang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Min Zheng
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
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Wang W, Ding B, Hu Y, Zhang H, He Y, She Y, Li Z. Evidence for the occurrence of Feammox coupled with nitrate-dependent Fe(II) oxidation in natural enrichment cultures. Chemosphere 2022; 303:134903. [PMID: 35551943 DOI: 10.1016/j.chemosphere.2022.134903] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 06/15/2023]
Abstract
Feammox is a newly discovered process of anaerobic ammonium oxidation driven by Fe(III) reduction. Nitrate-dependent Fe(II) oxidation (NDFO) is the coupling of Fe(II) oxidation and nitrate reduction to produce N2 under anaerobic conditions. It has not been reported whether the coupling of the two reactions exists in natural enrichment. In this study, enrichment culture experiments were carrired out to prove the occurrence of Feammox with NDFO. The results indicated that the nitrogen and iron cycle were formed during natural enrichment cultures, including Fe(III) reduction and NH4+-N was oxidation to NO3--N, NO2--N and N2, Fe(III) and Fe(II) were cyclically formed, and Fe(II) was oxidized with NO3--N reduced to N2. The removal efficiencies of ammonium nitrogen and total nitrogen in the incubation were about 92.9% and 20% respectively. Organic carbon experiments indicate that sodium acetate can promote the initial NO3--N removal and a low concentration of organic carbon limited the NDFO process because iron-oxidizing bacteria are mixotrophic microorganisms. The added 9,10-anthraquinone-2,6-disulfonate (AQDS) in the later stage can promote NDFO to remove nitrate, thereby increasing the TN removal efficiency to 50%. 15N-isotope tracer incubations provided direct evidence for the occurrence of Feammox coupled to NDFO, with rates producing 30N2 of Feammox (0.024-0.0288 mg N·L-1·d-1) and NDFO (0.0465-0.0833 mg N·L-1·d-1) in three groups (Wetland/Wheat soil/Sediment). 16S rRNA sequencing further demonstrated that Pseudomonas, Rhodanobacter, Acinetobacter and Thermomonas were the dominant generas among the enrichment cultures, and these bacteria belonged to FeOB and FeRB, which may further promote Feammox coupled to NDFO in the cultivation system.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Pollution Control and Resource Reuse, Nanjing University, Nanjing, 210023, China; School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Bangjing Ding
- State Key Laboratory of Pollution Control and Resource Reuse, Nanjing University, Nanjing, 210023, China; School of the Environment, Nanjing University, Nanjing, 210023, China; Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Youyou Hu
- State Key Laboratory of Pollution Control and Resource Reuse, Nanjing University, Nanjing, 210023, China; School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Hui Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, Nanjing University, Nanjing, 210023, China; School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Yanqing He
- State Key Laboratory of Pollution Control and Resource Reuse, Nanjing University, Nanjing, 210023, China; School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Yuecheng She
- State Key Laboratory of Pollution Control and Resource Reuse, Nanjing University, Nanjing, 210023, China; School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Zhengkui Li
- State Key Laboratory of Pollution Control and Resource Reuse, Nanjing University, Nanjing, 210023, China; School of the Environment, Nanjing University, Nanjing, 210023, China.
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Meng S, Peng T, Wang H, Huang T, Gu JD, Hu Z. Evaluation of PCR primers for detecting the distribution of nitrifiers in mangrove sediments. Appl Microbiol Biotechnol 2022; 106:5811-5822. [PMID: 35941255 DOI: 10.1007/s00253-022-12104-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 11/28/2022]
Abstract
Ammonia-oxidizing archaea and ammonia-oxidizing bacteria (AOA and AOB), complete ammonia oxidizers (Comammox), and nitrite-oxidizing bacteria (NOB) play a crucial role in the nitrification process during the nitrogen cycle. However, their occurrence and diversity in mangrove ecosystems are still not fully understood. Here, a total of 11 pairs of PCR primers were evaluated to study the distribution and abundances of these nitrifiers in rhizosphere and non-rhizosphere sediments of a mangrove ecosystem. The amplification efficiency of these 11 pairs of primers was first evaluated and their performances were found to vary considerably. The CamoA-19F/CamoA-616R primer pair was suitable for the amplification of AOA in mangrove sediments, especially on the surface of rhizosphere sediments. Primer pair amoA1F/amoA2R was better for the characterization of novel AOB in the bacterial community of non-rhizosphere sediments of mangroves. In contrast, primer nxrB169F/nxrB638R showed a low abundance of NOB in mangrove sediments (except for R1). Comammox bacteria were abundant and diverse in mangrove sediments, as indicated by both the amoB gene for Comammox clade A and the amoA gene for Comammox Nitrospira clade B. However, the amoA gene for Comammox Nitrospira clade A was not successful in detecting them in the mangrove sediments. Furthermore, 568 operational taxonomic units (OTUs) were obtained by generating a clone library and a high abundance of OTUs was correlated with ammonium, pH, NO2-, and NO3-. Comammox and Comammox Nitrospira were identified by phylogenetic tree analysis, indicating that mangrove sediments harbor newly discovered nitrifiers. Additionally, many AOA and NOB were mainly distributed in the surface layer of the rhizosphere, whereas AOB and Comammox Nitrospira were in the subsurface of non-rhizosphere, as determined by qPCR analysis. Collectively, our findings highlight the limitations of some primers for the identification of specific nitrifying bacteria. Therefore, primers must be carefully selected to gain accurate insights into the ecological distribution of nitrifiers in mangroves. KEY POINTS: • Several sets of PCR primers perform well for the detection of nitrifiers in mangroves. • Mangroves are an important source of newly discovered nitrifiers. • Ammonium, pH, NO2-, and NO3- are important shapers of nitrifier communities in mangroves.
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Affiliation(s)
- Shanshan Meng
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, People's Republic of China
| | - Tao Peng
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, People's Republic of China
| | - Hui Wang
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, People's Republic of China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangdong, 511458, Guangzhou, People's Republic of China
| | - Tongwang Huang
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, People's Republic of China
| | - Ji-Dong Gu
- Environmental Science and Engineering Research Group, Guangdong Technion-Israel Institute of Technology, 241 Daxue Road, Shantou, 515063, Guangdong, China.,Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, Guangdong Technion-Israel Institute of Technology, 241 Daxue Road, Shantou, 515063, Guangdong, China
| | - Zhong Hu
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, People's Republic of China. .,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangdong, 511458, Guangzhou, People's Republic of China.
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Mosley OE, Gios E, Close M, Weaver L, Daughney C, Handley KM. Nitrogen cycling and microbial cooperation in the terrestrial subsurface. ISME J 2022; 16:2561-2573. [PMID: 35941171 PMCID: PMC9562985 DOI: 10.1038/s41396-022-01300-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 07/19/2022] [Accepted: 07/22/2022] [Indexed: 11/25/2022]
Abstract
The nitrogen cycle plays a major role in aquatic nitrogen transformations, including in the terrestrial subsurface. However, the variety of transformations remains understudied. To determine how nitrogen cycling microorganisms respond to different aquifer chemistries, we sampled groundwater with varying nutrient and oxygen contents. Genes and transcripts involved in major nitrogen-cycling pathways were quantified from 55 and 26 sites, respectively, and metagenomes and metatranscriptomes were analyzed from a subset of oxic and dysoxic sites (0.3-1.1 mg/L bulk dissolved oxygen). Nitrogen-cycling mechanisms (e.g. ammonia oxidation, denitrification, dissimilatory nitrate reduction to ammonium) were prevalent and highly redundant, regardless of site-specific physicochemistry or nitrate availability, and present in 40% of reconstructed genomes, suggesting that nitrogen cycling is a core function of aquifer communities. Transcriptional activity for nitrification, denitrification, nitrite-dependent anaerobic methane oxidation and anaerobic ammonia oxidation (anammox) occurred simultaneously in oxic and dysoxic groundwater, indicating the availability of oxic-anoxic interfaces. Concurrent activity by these microorganisms indicates potential synergisms through metabolite exchange across these interfaces (e.g. nitrite and oxygen). Fragmented denitrification pathway encoding and transcription was widespread among groundwater bacteria, although a considerable proportion of associated transcriptional activity was driven by complete denitrifiers, especially under dysoxic conditions. Despite large differences in transcription, the capacity for the final steps of denitrification was largely invariant to aquifer conditions, and most genes and transcripts encoding N2O reductases were the atypical Sec-dependant type, suggesting energy-efficiency prioritization. Results provide insights into the capacity for cooperative relationships in groundwater communities, and the richness and complexity of metabolic mechanisms leading to the loss of fixed nitrogen.
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Liu Z, Wei Q, Zou D, Zhang S, Zhang C, Quan Z, Li M. Deterministic Factors Determine the Comammox Community Composition in the Pearl River Estuary Ecosystem. Microbiol Spectr 2022;:e0101622. [PMID: 35913204 DOI: 10.1128/spectrum.01016-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Complete ammonia oxidizers (comammox) have been widely detected in riverine and estuarine ecosystems. However, knowledge about the process of comammox community assembly from freshwater to marine environments is still limited. Here, based on deep sequencing, we investigated the community composition of comammox along a salinity gradient in the Pearl River Estuary (PRE), South China. Our results showed that comammox microorganisms in the PRE sediments were extremely diverse and displayed distinct distributional patterns between upstream and downstream habitats. Quantitative PCR demonstrated that comammox was the dominant ammonia-oxidizing microorganism (AOM) in the PRE upstream sediments, and ammonia-oxidizing archaea (AOA) dominated the PRE downstream sediments, while ammonia-oxidizing bacteria (AOB) were not dominant in any section of the PRE. Neutral modeling revealed that stochastic processes explained a limited part of the variation in the comammox community. The majority of beta nearest-taxon index values were higher than 2, indicating that comammox community assembly in the PRE sediments was better explained through a deterministic process than through a stochastic process. Salinity and total nitrogen were the most important contributing factors that shaped the comammox community. This study expanded the current knowledge of the diversity and niche preference of comammox in the estuarine ecosystem, and further enhances our understanding of the assembly of comammox community from freshwater to marine environments. IMPORTANCE Microbial communities are shaped by stochastic (emigration, immigration, birth, death, and genetic drift of species) and deterministic (e.g., environmental factors) processes. However, it remains unknown as to which type of process is more important in influencing the comammox community assembly from freshwater to marine environments. In this study, we compared the relative importance of stochastic and deterministic processes in shaping the assembly of the comammox community, which demonstrated that the deterministic process was more important in determining the community assembly patterns in the PRE ecosystem.
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Bai X, Hu X, Liu J, Gu H, Jin J, Liu X, Wang G. Evaluation of four primer sets for analysis of comammox communities in black soils. Front Microbiol 2022; 13:944373. [PMID: 35958136 PMCID: PMC9362984 DOI: 10.3389/fmicb.2022.944373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/29/2022] [Indexed: 11/13/2022] Open
Abstract
Comammox, as a newly discovered ammonia oxidizer, urgently needs highly efficient and specific primers to detect its community structure and diversity. In this study, the performance of widely used primer set Ntsp-amoA 162F/359R and newly designed primer sets comamoA F/R, CA377f/C576r, and CB377f/C576r were evaluated, for high-throughput sequencing of comammox amoA genes in natural and arable soils sampled from two locations in the black soil region of northeast China. Results showed that, compared with the primer set comamoA F/R, primers Ntsp-amoA 162F/359R had more advantages in detecting comammox operational taxonomic unit (OTU) numbers, diversity, and community structure. The primer sets CA377f/C576r and CB377f/C576r had an advantage in detecting comammox sequences with low relative abundance. In addition, the results of the phylogenetic tree and the relative abundance of dominant OTUs showed that the comammox in the black soils of northeast China was dominated by Nitrospira Clade B. Furthermore, our study found that long-term land use reduced the alpha diversity of the comammox community, but lead to the convergent evolution of community structure. The Mantel test and canonical correspondence analysis indicated that soil NO3–-N content was the most important factor affecting the community structure of comammox. Our study provided experience accumulation for the selection of comammox primers for high-throughput sequencing in the black soil of northeast China.
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Affiliation(s)
- Xin Bai
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaojing Hu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Junjie Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Haidong Gu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jian Jin
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Xiaobing Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Guanghua Wang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- *Correspondence: Guanghua Wang,
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Lei J, Fan Q, Yu J, Ma Y, Yin J, Liu R. A meta-analysis to examine whether nitrification inhibitors work through selectively inhibiting ammonia-oxidizing bacteria. Front Microbiol 2022; 13:962146. [PMID: 35928162 PMCID: PMC9343776 DOI: 10.3389/fmicb.2022.962146] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 06/29/2022] [Indexed: 11/18/2022] Open
Abstract
Nitrification inhibitor (NI) is often claimed to be efficient in mitigating nitrogen (N) losses from agricultural production systems by slowing down nitrification. Increasing evidence suggests that ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) have the genetic potential to produce nitrous oxide (N2O) and perform the first step of nitrification, but their contribution to N2O and nitrification remains unclear. Furthermore, both AOA and AOB are probably targets for NIs, but a quantitative synthesis is lacking to identify the “indicator microbe” as the best predictor of NI efficiency under different environmental conditions. In this present study, a meta-analysis to assess the response characteristics of AOB and AOA to NI application was conducted and the relationship between NI efficiency and the AOA and AOB amoA genes response under different conditions was evaluated. The dataset consisted of 48 papers (214 observations). This study showed that NIs on average reduced 58.1% of N2O emissions and increased 71.4% of soil NH4+ concentrations, respectively. When 3, 4-dimethylpyrazole phosphate (DMPP) was applied with both organic and inorganic fertilizers in alkaline medium soils, it had higher efficacy of decreasing N2O emissions than in acidic soils. The abundance of AOB amoA genes was dramatically reduced by about 50% with NI application in most soil types. Decrease in N2O emissions with NI addition was significantly correlated with AOB changes (R2 = 0.135, n = 110, P < 0.01) rather than changes in AOA, and there was an obvious correlation between the changes in NH4+ concentration and AOB amoA gene abundance after NI application (R2 = 0.037, n = 136, P = 0.014). The results indicated the principal role of AOB in nitrification, furthermore, AOB would be the best predictor of NI efficiency.
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Zhu G, Wang X, Wang S, Yu L, Armanbek G, Yu J, Jiang L, Yuan D, Guo Z, Zhang H, Zheng L, Schwark L, Jetten MSM, Yadav AK, Zhu YG. Towards a more labor-saving way in microbial ammonium oxidation: A review on complete ammonia oxidization (comammox). Sci Total Environ 2022; 829:154590. [PMID: 35306060 DOI: 10.1016/j.scitotenv.2022.154590] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
In the Anthropocene, nitrogen pollution is becoming an increasing challenge for both mankind and the Earth system. Microbial nitrogen cycling begins with aerobic nitrification, which is also the key rate-limiting step. For over a century, it has been accepted that nitrification occurs sequentially involving ammonia oxidation, which produces nitrite followed by nitrite oxidation, generating nitrate. This perception was changed by the discovery of comammox Nitrospira bacteria and their metabolic pathway. In addition, this also provided us with new knowledge concerning the complex nitrogen cycle network. In the comammox process, ammonia can be completely oxidized to nitrate in one cell via the subsequent activity of the enzyme complexes, ammonia monooxygenase, hydroxylamine dehydrogenase, and nitrite oxidodreductase. Over the past five years, research on comammox made great progress. However, there still exist a lot of questions, including how much does comammox contribute to nitrification? How large is the diversity and are there new strains to be discovered? Do comammox bacteria produce the greenhouse gas N2O, and how or to which extent may they contribute to global climate change? The above four aspects are of great significance on the farmland nitrogen management, aquatic environment restoration, and mitigation of global climate change. As large number of comammox bacteria and pathways have been detected in various terrestrial and aquatic ecosystems, indicating that the comammox process may exert an important role in the global nitrogen cycle.
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Affiliation(s)
- Guibing Zhu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xiaomin Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shanyun Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Longbin Yu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gawhar Armanbek
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jie Yu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Liping Jiang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongdan Yuan
- College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Zhongrui Guo
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Hanrui Zhang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Lei Zheng
- College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Lorenz Schwark
- Institute for Geosciences, University of Kiel, 24118 Kiel, Germany
| | - Mike S M Jetten
- Department of Microbiology, Radboud University Nijmegen, 36525 AJ Nijmegen, the Netherlands
| | - Asheesh Kumar Yadav
- Department of Environment and Sustainability, CSIR-Institute of Minerals and Materials Technology, Bhubaneswar 751013, India
| | - Yong-Guan Zhu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
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Zhang SN, Wang JG, Wang DQ, Jiang QY, Quan ZX. Abundance and Niche Differentiation of Comammox in the Sludges of Wastewater Treatment Plants That Use the Anaerobic-Anoxic-Aerobic Process. Life (Basel) 2022; 12:life12070954. [PMID: 35888046 PMCID: PMC9322089 DOI: 10.3390/life12070954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 11/27/2022] Open
Abstract
Complete ammonia oxidizers (comammox), which directly oxidize ammonia to nitrate, were recently identified and found to be ubiquitous in artificial systems. Research on the abundance and niche differentiation of comammox in the sludges of wastewater treatment plants (WWTPs) would be useful for improving the nitrogen removal efficiency of WWTPs. Here, we investigated the relative abundance and diversity of comammox in fifteen sludges of five WWTPs that use the anaerobic−anoxic−aerobic process in Jinan, China, via quantitative polymerase chain reaction and high-throughput sequencing of the 16S rRNA gene and ammonia monooxygenase gene. In the activated sludges in the WWTPs, comammox clade A.1 was widely distributed and mostly comprised Candidatus Nitrospira nitrosa-like comammox (>98% of all comammox). The proportion of this clade was negatively correlated (p < 0.01) with the dissolved oxygen (DO) level (1.7−8 mg/L), and slight pH changes (7.20−7.70) affected the structure of the comammox populations. Nitrospira lineage I frequently coexisted with Nitrosomonas, which generally had a significant positive correlation (p < 0.05) with the DO level. Our study provided an insight into the structure of comammox and other nitrifier populations in WWTPs that use the anaerobic−anoxic−aerobic process, broadening the knowledge about the effects of DO on comammox and other nitrifiers.
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Affiliation(s)
| | | | | | - Qiu-Yue Jiang
- Correspondence: (Q.-Y.J.); (Z.-X.Q.); Tel.: +86-21-3124-0665 (Z.-X.Q.)
| | - Zhe-Xue Quan
- Correspondence: (Q.-Y.J.); (Z.-X.Q.); Tel.: +86-21-3124-0665 (Z.-X.Q.)
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Oshiki M, Netsu H, Kuroda K, Narihiro T, Fujii N, Kindaichi T, Suzuki Y, Watari T, Hatamoto M, Yamaguchi T, Araki N, Okabe S. Growth of nitrite-oxidizing Nitrospira and ammonia-oxidizing Nitrosomonas in marine recirculating trickling biofilter reactors. Environ Microbiol 2022; 24:3735-3750. [PMID: 35672869 DOI: 10.1111/1462-2920.16085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/25/2022] [Indexed: 11/27/2022]
Abstract
Aerobic ammonia and nitrite oxidation reactions are fundamental biogeochemical reactions contributing to the global nitrogen cycle. Although aerobic nitrite oxidation yields 4.8-folds less Gibbs free energy (∆Gr ) than aerobic ammonia oxidation in the NH4 + -feeding marine recirculating trickling biofilter reactors operated in the present study, nitrite-oxidizing and not ammonia-oxidizing Nitrospira (sublineage IV) outnumbered ammonia-oxidizing Nitrosomonas (relative abundance; 53.8% and 7.59% respectively). CO2 assimilation efficiencies during ammonia or nitrite oxidation were 0.077 μmol-14 CO2 /μmol-NH3 and 0.053-0.054 μmol-14 CO2 /μmol-NO2 - respectively, and the difference between ammonia and nitrite oxidation was much smaller than the difference of ∆Gr . Free-energy efficiency of nitrite oxidation was higher than ammonia oxidation (31%-32% and 13% respectively), and high CO2 assimilation and free-energy efficiencies were a determinant for the dominance of Nitrospira over Nitrosomonas. Washout of Nitrospira and Nitrosomonas from the trickling biofilter reactors was also examined by quantitative PCR assay. Normalized copy numbers of Nitrosomonas amoA were 1.5- to 1.7-folds greater than Nitrospira nxrB and 16S rRNA gene in the reactor effluents. Nitrosomonas was more susceptible for washout than Nitrospira in the trickling biofilter reactors, which was another determinant for the dominance of Nitrospira in the trickling biofilter reactors.
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Affiliation(s)
- Mamoru Oshiki
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan.,Department of Civil Engineering, National Institute of Technology, Nagaoka College, 888 Nishikatakaimachi, Nagaoka, Niigata, 940-8532, Japan
| | - Hirotoshi Netsu
- Department of Civil Engineering, National Institute of Technology, Nagaoka College, 888 Nishikatakaimachi, Nagaoka, Niigata, 940-8532, Japan.,Department of Civil and Environmental Engineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Kyohei Kuroda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido, 062-8517, Japan
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido, 062-8517, Japan
| | - Naoki Fujii
- Department of Civil and Environmental Engineering, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashihiroshima, Hiroshima, 739-8527, Japan
| | - Tomonori Kindaichi
- Department of Civil and Environmental Engineering, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashihiroshima, Hiroshima, 739-8527, Japan
| | - Yoshiyuki Suzuki
- Department of Civil Engineering, National Institute of Technology, Nagaoka College, 888 Nishikatakaimachi, Nagaoka, Niigata, 940-8532, Japan
| | - Takahiro Watari
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Masashi Hatamoto
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Takashi Yamaguchi
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Nobuo Araki
- Department of Civil Engineering, National Institute of Technology, Nagaoka College, 888 Nishikatakaimachi, Nagaoka, Niigata, 940-8532, Japan
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
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Al-Ajeel S, Spasov E, Sauder LA, McKnight MM, Neufeld JD. Ammonia-oxidizing archaea and complete ammonia-oxidizing Nitrospira in water treatment systems. Water Res X 2022; 15:100131. [PMID: 35402889 PMCID: PMC8990171 DOI: 10.1016/j.wroa.2022.100131] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/07/2022] [Accepted: 03/11/2022] [Indexed: 05/27/2023]
Abstract
Nitrification, the oxidation of ammonia to nitrate via nitrite, is important for many engineered water treatment systems. The sequential steps of this respiratory process are carried out by distinct microbial guilds, including ammonia-oxidizing bacteria (AOB) and archaea (AOA), nitrite-oxidizing bacteria (NOB), and newly discovered members of the genus Nitrospira that conduct complete ammonia oxidation (comammox). Even though all of these nitrifiers have been identified within water treatment systems, their relative contributions to nitrogen cycling are poorly understood. Although AOA contribute to nitrification in many wastewater treatment plants, they are generally outnumbered by AOB. In contrast, AOA and comammox Nitrospira typically dominate relatively low ammonia environments such as drinking water treatment, tertiary wastewater treatment systems, and aquaculture/aquarium filtration. Studies that focus on the abundance of ammonia oxidizers may misconstrue the actual role that distinct nitrifying guilds play in a system. Understanding which ammonia oxidizers are active is useful for further optimization of engineered systems that rely on nitrifiers for ammonia removal. This review highlights known distributions of AOA and comammox Nitrospira in engineered water treatment systems and suggests future research directions that will help assess their contributions to nitrification and identify factors that influence their distributions and activity.
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Zhang J, Hu M, Wang Y, Zhao J, Li S, Bao Y, Wen J, Hu J, Zhou M. Niche differentiation of comammox Nitrospira in sediments of the Three Gorges Reservoir typical tributaries, China. Sci Rep 2022; 12:6820. [PMID: 35474096 PMCID: PMC9042867 DOI: 10.1038/s41598-022-10948-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/15/2022] [Indexed: 11/09/2022] Open
Abstract
Complete ammonia oxidizer (Comammox) can complete the whole nitrification process independently, whose niche differentiation is important guarantee for its survival and ecological function. This study investigated the niche differentiation of comammox Nitrospira in the sediments of three typical tributaries of the Three Gorges Reservoir (TGR). Clade A and clade B of comammox Nitrospira coexisted in all sampling sites simultaneously. The amoA gene abundance of clade A and B was gradually increased or decreased along the flow path of the three tributaries with obvious spatial differentiation. The amoA gene abundance of comammox Nitrospira clade A (6.36 × 103 - 5.06 × 104 copies g-1 dry sediment) was higher than that of clade B (6.26 × 102 - 6.27 × 103 copies g-1 dry sediment), and the clade A amoA gene abundance was one order of magnitude higher than that of AOA (7.24 × 102 - 6.89 × 103 copies g-1 dry sediment) and AOB (1.44 × 102 - 1.46 × 103 copies g-1 dry sediment). A significant positive correlation was observed between comammox Nitrospira clade A amoA gene abundance and flow distance (P < 0.05). The number of operational taxonomic units (OTUs) in two sub-clades of clade A accounted for the majority in different tributaries, indicating that clade A also had population differentiation among different tributaries. This study revealed that comammox Nitrospira in the sediments of TGR tributaries have niche differentiation and clade A.2 played a more crucial role in comammox Nitrospira community.
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Affiliation(s)
- Jiahui Zhang
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, Beijing, 10038, People's Republic of China.,Department of Water Ecology and Environment, China Institute of Water Resources and Hydropower Research, Beijing, 100038, People's Republic of China.,Laboratory of Eco-Environmental Engineering Research, State Environmental Protection Key Laboratory of Soil Health and Green Remediation, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Mingming Hu
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, Beijing, 10038, People's Republic of China. .,Department of Water Ecology and Environment, China Institute of Water Resources and Hydropower Research, Beijing, 100038, People's Republic of China.
| | - Yuchun Wang
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, Beijing, 10038, People's Republic of China.,Department of Water Ecology and Environment, China Institute of Water Resources and Hydropower Research, Beijing, 100038, People's Republic of China
| | - Jianwei Zhao
- Laboratory of Eco-Environmental Engineering Research, State Environmental Protection Key Laboratory of Soil Health and Green Remediation, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China.
| | - Shanze Li
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, Beijing, 10038, People's Republic of China.,Department of Water Ecology and Environment, China Institute of Water Resources and Hydropower Research, Beijing, 100038, People's Republic of China
| | - Yufei Bao
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, Beijing, 10038, People's Republic of China.,Department of Water Ecology and Environment, China Institute of Water Resources and Hydropower Research, Beijing, 100038, People's Republic of China
| | - Jie Wen
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, Beijing, 10038, People's Republic of China.,Department of Water Ecology and Environment, China Institute of Water Resources and Hydropower Research, Beijing, 100038, People's Republic of China
| | - Jinlong Hu
- Laboratory of Eco-Environmental Engineering Research, State Environmental Protection Key Laboratory of Soil Health and Green Remediation, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Mingzhi Zhou
- Laboratory of Eco-Environmental Engineering Research, State Environmental Protection Key Laboratory of Soil Health and Green Remediation, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
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Ramond JB, Jordaan K, Díez B, Heinzelmann SM, Cowan DA. Microbial Biogeochemical Cycling of Nitrogen in Arid Ecosystems. Microbiol Mol Biol Rev 2022;:e0010921. [PMID: 35389249 DOI: 10.1128/mmbr.00109-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Arid ecosystems cover ∼40% of the Earth's terrestrial surface and store a high proportion of the global nitrogen (N) pool. They are low-productivity, low-biomass, and polyextreme ecosystems, i.e., with (hyper)arid and (hyper)oligotrophic conditions and high surface UV irradiation and evapotranspiration. These polyextreme conditions severely limit the presence of macrofauna and -flora and, particularly, the growth and productivity of plant species. Therefore, it is generally recognized that much of the primary production (including N-input processes) and nutrient biogeochemical cycling (particularly N cycling) in these ecosystems are microbially mediated. Consequently, we present a comprehensive survey of the current state of knowledge of biotic and abiotic N-cycling processes of edaphic (i.e., open soil, biological soil crust, or plant-associated rhizosphere and rhizosheath) and hypo/endolithic refuge niches from drylands in general, including hot, cold, and polar desert ecosystems. We particularly focused on the microbially mediated biological nitrogen fixation, N mineralization, assimilatory and dissimilatory nitrate reduction, and nitrification N-input processes and the denitrification and anaerobic ammonium oxidation (anammox) N-loss processes. We note that the application of modern meta-omics and related methods has generated comprehensive data sets on the abundance, diversity, and ecology of the different N-cycling microbial guilds. However, it is worth mentioning that microbial N-cycling data from important deserts (e.g., Sahara) and quantitative rate data on N transformation processes from various desert niches are lacking or sparse. Filling this knowledge gap is particularly important, as climate change models often lack data on microbial activity and environmental microbial N-cycling communities can be key actors of climate change by producing or consuming nitrous oxide (N2O), a potent greenhouse gas.
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Sakoula D, Smith GJ, Frank J, Mesman RJ, Kop LFM, Blom P, Jetten MSM, van Kessel MAHJ, Lücker S. Universal activity-based labeling method for ammonia- and alkane-oxidizing bacteria. ISME J 2022; 16:958-71. [PMID: 34743174 DOI: 10.1038/s41396-021-01144-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 10/13/2021] [Accepted: 10/15/2021] [Indexed: 12/13/2022]
Abstract
The advance of metagenomics in combination with intricate cultivation approaches has facilitated the discovery of novel ammonia-, methane-, and other short-chain alkane-oxidizing microorganisms, indicating that our understanding of the microbial biodiversity within the biogeochemical nitrogen and carbon cycles still is incomplete. The in situ detection and phylogenetic identification of novel ammonia- and alkane-oxidizing bacteria remain challenging due to their naturally low abundances and difficulties in obtaining new isolates from complex samples. Here, we describe an activity-based protein profiling protocol allowing cultivation-independent unveiling of ammonia- and alkane-oxidizing bacteria. In this protocol, 1,7-octadiyne is used as a bifunctional enzyme probe that, in combination with a highly specific alkyne-azide cycloaddition reaction, enables the fluorescent or biotin labeling of cells harboring active ammonia and alkane monooxygenases. Biotinylation of these enzymes in combination with immunogold labeling revealed the subcellular localization of the tagged proteins, which corroborated expected enzyme targets in model strains. In addition, fluorescent labeling of cells harboring active ammonia or alkane monooxygenases provided a direct link of these functional lifestyles to phylogenetic identification when combined with fluorescence in situ hybridization. Furthermore, we show that this activity-based labeling protocol can be successfully coupled with fluorescence-activated cell sorting for the enrichment of nitrifiers and alkane-oxidizing bacteria from complex environmental samples, enabling the recovery of high-quality metagenome-assembled genomes. In conclusion, this study demonstrates a novel, functional tagging technique for the reliable detection, identification, and enrichment of ammonia- and alkane-oxidizing bacteria present in complex microbial communities.
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Oshiki M, Nagai K, Ishii S, Suzuki Y, Saito N, Yamaguchi T, Araki N, Okabe S. Determination of 15N/ 14N of Ammonium, Nitrite, Nitrate, Hydroxylamine, and Hydrazine Using Colorimetric Reagents and Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS). Appl Environ Microbiol 2022;:e0241621. [PMID: 35285242 DOI: 10.1128/aem.02416-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the nitrogen (N) cycle, nitrogenous compounds are chemically and biologically converted to various aqueous and gaseous N species. The 15N-labeling approach is a powerful culture-dependent technique to obtain insights into the complex nitrogen transformation reactions that occur in cultures. In the 15N-labeling approach, the fates of supplemented 15N- and/or unlabeled gaseous and aqueous compounds are tracked by mass spectrometry (MS) analysis, whereas MS analysis of aqueous N species requires laborious sample preparation steps and is performed using isotope-ratio mass spectrometry, which requires an expensive mass spectrometer. We developed a simple and high-throughput MS method for determining the 15N atoms percent of NH4+, NO2-, NO3-, NH2OH, and N2H4, where liquid samples (<0.5 mL) were mixed with colorimetric reagents (naphthylethylenediamine for NO2-, indophenol for NH4+, and p-aminobenzaldehyde for N2H4), and the mass spectra of the formed N complex dyes were obtained by matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) MS. NH2OH and NO3- were chemically converted to NO2- by iodine oxidation and copper/hydrazine reduction reaction, respectively, prior to the above colorimetric reaction. The intensity of the isotope peak (M + 1 or M + 2) increased when the N complex dye was formed by coupling with a 15N-labeled compound, and a linear relationship was found between the determined 15N/14N peak ratio and 15N atom% for the tested N species. The developed method was applied to bacterial cultures to examine their N-transformation reactions, enabling us to observe the occurrence of NO2- oxidation and NO3- reduction in a hypoxic Nitrobacter winogradskyi culture. IMPORTANCE 15N/14N analysis for aqueous N species is a powerful tool for obtaining insights into the global N cycle, but the procedure is cumbersome and laborious. The combined use of colorimetric reagents and MALDI-TOF MS, designated color MALDI-TOF MS, enabled us to determine the 15N atom% of common aqueous N species without laborious sample preparation and chromatographic separation steps; for instance, the 15N atom% of NO2- can be determined from >1,000 liquid samples daily at <$1 (U.S.) per 384 samples for routine analysis. This convenient MS method is a powerful tool that will advance our ability to explore the N-transformation reactions that occur in various environments and biological samples.
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Sun N, Wang Y, Chen J, Wang P, Song W, Ma P, Duan Y, Jiao Z, Li Y. Colonization and Interaction of Bacteria Associated With Chinese Chives Affected by Ecological Compartments and Growth Conditions. Front Microbiol 2022; 13:775002. [PMID: 35237245 PMCID: PMC8883035 DOI: 10.3389/fmicb.2022.775002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 01/14/2022] [Indexed: 11/13/2022] Open
Abstract
Chinese chive has a long history of planting in China. At present, there are many studies on endophytic bacteria and rhizosphere microorganisms of Chinese chive, but the effects of ecological compartment and growth conditions on bacterial communities in Chinese chives are unclear. Here, we aimed to elucidate the differences in bacterial a-diversity, β-diversity, community structure, core species differences, interaction networks and predicted metabolic functions among bacterial communities in different ecological compartments (the phylloplane, leaf endosphere, stem endosphere, root endosphere, and rhizosphere) in Chinese chives in an open field, a solar greenhouse, an arched shed, and a hydroponic system. Sixty samples were collected from these five ecological compartments under four growth conditions, and we compared the bacterial profiles of these groups using 16S rRNA sequencing. We evaluated the differences in diversity and composition among bacterial communities in these ecological compartments, analyzed the bacterial interaction patterns under the different growth conditions, and predicted the bacterial metabolic pathways in these ecological compartments and growth conditions. The results showed that the effects of ecological compartments on bacterial diversity, community composition, interaction network pattern, and functional expression of Chinese chives were greater than those of growth condition. Ecological compartments (R2 = 0.5292) could better explain bacterial community division than growth conditions (R2 = 0.1056). The microbial interaction networks and indicator bacteria in different ecological compartments showed that most of the bacteria that played the role of key nodes (OTUs) in each ecological compartment were bacteria with high relative abundance in the compartment. However, the bacteria that played the role of key nodes (OTUs) in bulbs were not Proteobacteria with the highest relative abundance in the compartment, but Actinobacteria that were significantly enriched in the root endosphere and rhizosphere ecological compartments. In addition, interactions among bacteria were interrupted in the hydroponic system, and specific bacterial communities and interaction patterns in Chinese chives varied among growth conditions. Prediction of metabolic functions indicated that plant metabolic activity related to stress responses and induction of system resistance was greater in belowground ecological compartments.
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Affiliation(s)
- Nan Sun
- College of Water Resources and Civil Engineering, China Agricultural University, Beijing, China
| | - Yuxin Wang
- College of Water Resources and Civil Engineering, China Agricultural University, Beijing, China
- *Correspondence: Yuxin Wang
| | - Jianhua Chen
- Pingdingshan Academy of Agricultural Sciences, Pingdingshan, China
| | - Pingzhi Wang
- College of Water Resources and Civil Engineering, China Agricultural University, Beijing, China
| | - Weitang Song
- College of Water Resources and Civil Engineering, China Agricultural University, Beijing, China
| | - Peifang Ma
- Pingdingshan Academy of Agricultural Sciences, Pingdingshan, China
| | - Yabin Duan
- Pingdingshan Academy of Agricultural Sciences, Pingdingshan, China
| | - Ziyuan Jiao
- Pingdingshan Academy of Agricultural Sciences, Pingdingshan, China
| | - Yixiao Li
- Pingdingshan Academy of Agricultural Sciences, Pingdingshan, China
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Abstract
The ocean is home to a diverse and metabolically versatile microbial community that performs the complex biochemical transformations that drive the nitrogen cycle, including nitrogen fixation, assimilation, nitrification and nitrogen loss processes. In this Review, we discuss the wealth of new ocean nitrogen cycle research in disciplines from metaproteomics to global biogeochemical modelling and in environments from productive estuaries to the abyssal deep sea. Influential recent discoveries include new microbial functional groups, novel metabolic pathways, original conceptual perspectives and ground-breaking analytical capabilities. These emerging research directions are already contributing to urgent efforts to address the primary challenge facing marine microbiologists today: the unprecedented onslaught of anthropogenic environmental change on marine ecosystems. Ocean warming, acidification, nutrient enrichment and seawater stratification have major effects on the microbial nitrogen cycle, but widespread ocean deoxygenation is perhaps the most consequential for the microorganisms involved in both aerobic and anaerobic nitrogen transformation pathways. In turn, these changes feed back to the global cycles of greenhouse gases such as carbon dioxide and nitrous oxide. At a time when our species casts a lengthening shadow across all marine ecosystems, timely new advances offer us unique opportunities to understand and better predict human impacts on nitrogen biogeochemistry in the changing ocean of the Anthropocene.
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Xi H, Zhou X, Arslan M, Luo Z, Wei J, Wu Z, Gamal El-Din M. Heterotrophic nitrification and aerobic denitrification process: Promising but a long way to go in the wastewater treatment. Sci Total Environ 2022; 805:150212. [PMID: 34536867 DOI: 10.1016/j.scitotenv.2021.150212] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 09/03/2021] [Accepted: 09/03/2021] [Indexed: 05/27/2023]
Abstract
The traditional biological nitrogen removal (BNR) follows the conventional scheme of sequential nitrification and denitrification. In recent years, novel processes such as anaerobic ammonia oxidation (anammox), complete oxidation of ammonia to nitrate in one organism (comammox), heterotrophic nitrification and aerobic denitrification (HN-AD), and dissimilatory nitrate reduction to ammonium (DNRA) are gaining tremendous attention after the discovery of metabolically versatile bacteria. Among them, HN-AD offers several advantages because individual bacteria could achieve one-stage nitrogen removal under aerobic conditions in the presence of organic carbon. In this review, besides classical BNR processes, we summarized the existing literature on HN-AD bacteria which have been isolated from diverse habitats. A particular focus was given on the diversity and physiology of HN-AD bacteria, influences of physiological and biochemical factors on their growth, nitrogen removal performances, as well as limitations and strategies in unraveling HN-AD metabolic pathways. We also presented case studies of HN-AD application in wastewater treatment facilities, pointed out forthcoming challenges of HN-AD in these systems, and presented modulation strategies for HN-AD application in engineering. This review may help improve the existing design of wastewater treatment plants by harnessing HN-AD bacteria for effective nitrogen removal.
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Affiliation(s)
- Haipeng Xi
- Institute of Environmental Health and Ecological Safety, Jiangsu University, Zhenjiang 212013, China
| | - Xiangtong Zhou
- Institute of Environmental Health and Ecological Safety, Jiangsu University, Zhenjiang 212013, China.
| | - Muhammad Arslan
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Zhijun Luo
- Institute of Environmental Health and Ecological Safety, Jiangsu University, Zhenjiang 212013, China
| | - Jing Wei
- Institute of Environmental Health and Ecological Safety, Jiangsu University, Zhenjiang 212013, China
| | - Zhiren Wu
- Institute of Environmental Health and Ecological Safety, Jiangsu University, Zhenjiang 212013, China
| | - Mohamed Gamal El-Din
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
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Zajac O, Zubrowska-sudol M, Ciesielski S, Godzieba M. Effect of the Aeration Strategy on NOB Suppression in Activated Sludge and Biofilm in a Hybrid Reactor with Nitrification/Denitrification. Water 2022; 14:72. [DOI: 10.3390/w14010072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The purpose of the study was to analyse the impact of aeration strategies defined by the changes in the duration of aerated sub-phases, the ratio between non-aerated and aerated sub-phase times (R), and dissolved oxygen concentrations (DO) on the suppression of nitrite-oxidizing bacteria (NOB) in activated sludge and biofilm developing in a hybrid reactor with nitrification/denitrification. The primary factor causing NOB suppression both in biofilm and in activated sludge was an increase in the R-value (from 0 to 1/4 and from 1/4 to 1/3). After reducing the DO from 3 to 2 mg O2/L, there were no changes in the frequency of NOB occurrence, and no reduction in the nitrite oxidation rate was recorded. The abundance of Comammox bacteria was considerably affected by the change from continuous to intermittent aeration. Activated sludge showed a substantial increase in the quantity of clade A and B, whereas the quantity considerably decreased in biofilm.
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Zhao M, Tang X, Sun D, Hou L, Liu M, Zhao Q, Klümper U, Quan Z, Gu JD, Han P. Salinity gradients shape the nitrifier community composition in Nanliu River Estuary sediments and the ecophysiology of comammox Nitrospira inopinata. Sci Total Environ 2021; 795:148768. [PMID: 34247082 DOI: 10.1016/j.scitotenv.2021.148768] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/24/2021] [Accepted: 06/27/2021] [Indexed: 06/13/2023]
Abstract
The recent discovery of complete ammonia oxidizers (comammox), which convert ammonia to nitrate in a single organism, revolutionized the conventional understanding that two types of nitrifying microorganisms have to be involved in the nitrification process for more than 100 years. However, how different types of nitrifiers in response to salinity change remains largely unclear. This study not only investigated nitrifier community (including ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), comammox and nitrite-oxidizing Nitrospira) in the Nanliu estuary to find the ecological relationship between salinity and functional communities and also studied the physiology of a typical comammox Nitrospira inopinata in response to a salinity gradient. Based on sequences retrieved with four sets of functional gene primes, comammox Nitrospira was in general, mainly composed of clade A, with a clear separation of clade A1 subgroup in all samples and clade A2 subgroup in low salinity ones. As expected, group I.1b and group I.1a AOA dominated the AOA community in low- and high-salinity samples, respectively. Nitrosomonas-AOB were detected in all samples while Nitrosospira-AOB were mainly found in relatively high-salinity samples. Regarding general Nitrospira, lineages II and IV were the major groups in most of the samples, while lineage I Nitrospira was only detected in low-salinity samples. Furthermore, the comammox pure culture of N. inopinata showed an optimal salinity at 0.5‰ and ceased to grow at 12.8‰ for ammonia oxidation, but remained active for nitrite oxidation. These results show new evidence regarding niche specificity of different nitrifying microorganisms modulated mainly by salinity, and also a clear response by comammox N. inopinata to a wide range of simulated salinity levels.
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Affiliation(s)
- Mengyue Zhao
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xiufeng Tang
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Dongyao Sun
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Institute of Eco-Chongming, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China
| | - Qiang Zhao
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Uli Klümper
- Institute for Hydrobiology, Technische Universität Dresden, 01062 Dresden, Germany
| | - Zhexue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ji-Dong Gu
- Environmental Engineering, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, China
| | - Ping Han
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Institute of Eco-Chongming, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China.
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Xia F, Jiang QY, Zhu T, Zou B, Liu H, Quan ZX. Ammonium promoting methane oxidation by stimulating the Type Ia methane-oxidizing bacteria in tidal flat sediments of the Yangtze River estuary. Sci Total Environ 2021; 793:148470. [PMID: 34166901 DOI: 10.1016/j.scitotenv.2021.148470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 06/13/2023]
Abstract
Estuary and coastal environments have essential ecosystem functions in greenhouse gas sinks and removal of nitrogen pollution. Methane-oxidizing bacteria (MOB) and ammonia-oxidizing bacteria (AOB) communities play critical functions in the estuary's tidal flat sediments. Therefore, the effects of ammonium on MOB communities and methane on AOB communities need to be further explained. In this study, microcosm incubations with different contents of ammonium or methane were conducted for a relatively short (24 h) or long (28 days) period with tidal flat sediments from the Yangtze River estuary. Subsequently, the tagged highly degenerate primer PCR and DNA-based stable isotope probing method were employed to demonstrate the effects on MOB and AOB populations. The results indicated that the methane consumption was enhanced with ammonium supplements within 24 h of incubation. Supplement of 2 μmol/g d.w.s (μmol per gram dry weight soil) NH4+ increased the amount of MOB and its proportion to the total bacteria (p < 0.05) for 28 days incubation. The ammonium supplement increased the proportion of Methylomonas and Methylobacter based on the 16S rRNA gene. According to the functional gene analysis, the MOB primarily engaged in methane oxidation include Methylomonas, Methylobacter, Methylomicrobium, and Methylosarcina, which were associated with Type Ia MOB. It suggested that ammonium supplement may promote methane oxidation by stimulating the Type Ia MOB in tidal flat sediments of the Yangtze River estuary. The current research helps understand the effect of ammonium on methane consumption in the estuary and coastal environments.
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Affiliation(s)
- Fei Xia
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China; Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Qiu-Yue Jiang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Ting Zhu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Bin Zou
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Huan Liu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China.
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Yuan D, Zheng L, Tan Q, Wang X, Xing Y, Wang H, Wang S, Zhu G. Comammox activity dominates nitrification process in the sediments of plateau wetland. Water Res 2021; 206:117774. [PMID: 34757282 DOI: 10.1016/j.watres.2021.117774] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 10/10/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Abstract
The recent discovery of complete ammonia oxidation (comammox) has increased our understanding of nitrification. Although comammox has been shown to play an important role in plain wetland ecosystems, studies of comammox contribution are still limited in plateau wetland ecosystems. Here, we analyzed the abundance, activity, community and biogeochemical mechanisms of the comammox bacteria in Yunnan-kweichow and Qinghai-Tibet plateau wetlands from elevations of 1000-5000 m. Comammox bacteria were widely distributed in all 16 sediment samples with abundances higher than 0.96 ± 0.26 × 107 copies g-1 (n = 16). Comammox showed high activity (1.18 ± 0.17 to 1.98 ± 0.08 mg N kg-1 d-1) at high-elevation (3000-5000 m) and dominated the nitrification process (activity contribution: 37.20 - 60.62%). The activity contribution of ammonia-oxidizing bacteria (1.07 ± 0.08 to 2.79 ± 0.35 mg N kg-1 d-1) dominated the nitrification process (44.55 - 64.15%) in low-elevation (1000-3000 m) samples. All detected comammox Nitrospira belonged to clade A, while clade B was not detected. Elevation always had a strongest effect on key comammox species. Thus, we infer that elevation may drive the high relative abundance of the species Candidatus Nitrospira nitrificans (avg. 12.40%) and the low relative abundance of the species Nitrospira sp. SG-bin2 (avg. 4.75%) in high-elevation samples that showed a high comammox activity (avg. 1.62 mg N kg-1 d-1) and high contribution (avg. 46.08%) to the nitrification process. These results indicate that comammox may be an important and currently underestimated microbial nitrification process in plateau wetland ecosystems.
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Affiliation(s)
- Dongdan Yuan
- College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Lei Zheng
- College of Water Sciences, Beijing Normal University, Beijing 100875, China.
| | - Qiuyang Tan
- College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Xue Wang
- College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Yuzi Xing
- College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Huipeng Wang
- College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Shanyun Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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