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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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Prekrasna-Kviatkovska Y, Parnikoza I, Yerkhova A, Stelmakh O, Pavlovska M, Dzyndra M, Yarovyi O, Dykyi E. From acidophilic to ornithogenic: microbial community dynamics in moss banks altered by gentoo penguins. Front Microbiol 2024; 15:1362975. [PMID: 38525081 PMCID: PMC10959021 DOI: 10.3389/fmicb.2024.1362975] [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: 12/29/2023] [Accepted: 02/21/2024] [Indexed: 03/26/2024] Open
Abstract
Introduction The study explores the indirect impact of climate change driven by gentoo's penguin colonization pressure on the microbial communities of moss banks formed by Tall moss turf subformation in central maritime Antarctica. Methods Microbial communities and chemical composition of the differently affected moss banks (Unaffected, Impacted and Desolated) located on Galindez Island and Сape Tuxen on the mainland of Kyiv Peninsula were analyzed. Results The native microbiota of the moss banks' peat was analyzed for the first time, revealing a predominant presence of Acidobacteria (32.2 ± 14.4%), followed by Actinobacteria (15.1 ± 4.0%) and Alphaproteobacteria (9.7 ± 4.1%). Penguin colonization and subsequent desolation of moss banks resulted in an increase in peat pH (from 4.7 ± 0.05 to 7.2 ± 0.6) and elevated concentrations of soluble nitrogen (from 1.8 ± 0.4 to 46.9 ± 2.1 DIN, mg/kg) and soluble phosphorus compounds (from 3.6 ± 2.6 to 20.0 ± 1.8 DIP, mg/kg). The contrasting composition of peat and penguin feces led to the elimination of the initial peat microbiota, with an increase in Betaproteobacteria (from 1.3 ± 0.8% to 30.5 ± 23%) and Bacteroidota (from 5.5 ± 3.7% to 19.0 ± 3.7%) proportional to the intensity of penguins' impact, accompanied by a decrease in community diversity. Microbial taxa associated with birds' guts, such as Gottschalkia and Tissierella, emerged in Impacted and Desolated moss banks, along with bacteria likely benefiting from eutrophication. The changes in the functional capacity of the penguin-affected peat microbial communities were also detected. The nitrogen-cycling genes that regulate the conversion of urea into ammonia, nitrite oxide, and nitrate oxide (ureC, amoA, nirS, nosZ, nxrB) had elevated copy numbers in the affected peat. Desolated peat samples exhibit the highest nitrogen-cycle gene numbers, significantly differing from Unaffected peat (p < 0.05). Discussion The expansion of gentoo penguins induced by climate change led to the replacement of acidophilic microbiomes associated with moss banks, shaping a new microbial community influenced by penguin guano's chemical and microbial composition.
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Affiliation(s)
| | - Ivan Parnikoza
- Biology and Ecology Department, State Institution National Antarctic Scientific Center, Kyiv, Ukraine
- Department of Cell Population Genetics, Institute of Molecular Biology and Genetics, Kyiv, Ukraine
- Faculty of Natural Science, National University of “Kyiv-Mohyla Academy”, Kyiv, Ukraine
| | - Anna Yerkhova
- Biomedical Institute, Open International University of Human Development Ukraine, Kyiv, Ukraine
| | - Olesia Stelmakh
- Faculty of Molecular Biology and Biotechnology, Kyiv Academic University, Kyiv, Ukraine
| | - Mariia Pavlovska
- Biology and Ecology Department, State Institution National Antarctic Scientific Center, Kyiv, Ukraine
- Faculty of Plant Protection, Biotechnology and Ecology, National University of Life and Environmental Sciences of Ukraine, Kyiv, Ukraine
| | - Marta Dzyndra
- Biology and Ecology Department, State Institution National Antarctic Scientific Center, Kyiv, Ukraine
| | - Oleksandr Yarovyi
- Biology and Ecology Department, State Institution National Antarctic Scientific Center, Kyiv, Ukraine
| | - Evgen Dykyi
- Biology and Ecology Department, State Institution National Antarctic Scientific Center, Kyiv, Ukraine
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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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Manasa RL, Mehta A. Study of bacterial population dynamics in seed culture developed for ammonia reduction from synthetic wastewater. World J Microbiol Biotechnol 2024; 40:75. [PMID: 38246888 DOI: 10.1007/s11274-023-03858-z] [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: 06/17/2023] [Accepted: 11/26/2023] [Indexed: 01/23/2024]
Abstract
The waterbodies have been polluted by various natural and anthropogenic activities. The aquatic waste includes ammonia as one of the most toxic pollutants. Several biological treatment systems involving anoxic and semi anoxic bacteria have been proposed for reducing nitrogen loads from wastewater and increasing the efficiency and cost effectiveness. These bacteria play a vital role in the processes involved in the nitrogen cycle in nature. However, the enrichment, sustainability and identification of bacterial communities for wastewater treatment is an important aspect. Most of the chemolithotrophs are unculturable hence their identification and measurement of abundance remains a challenging task. In this study the different bacteria involved in total nitrogen removal from the wastewater are enriched for 700 days under anoxic condition. The synthetic wastewater containing 0.382 g/L of ammonium chloride was used. Molecular identification of the bacteria involved in various steps of the nitrogen cycle was carried out based on amplification of functional genes and 16S rRNA gene Polymerase chain reaction followed by DNA sequencing. Change in the abundance of chemolithotrophs was studied using qPCR. The mutual growth of various nitrifiers along with anaerobic bacteria were identified by molecular characterisation of DNA at various time intervals with the different genes involved in the nitrogen cycle. Nitrosomonas species like Nitrosomonas europaea were identified throughout the batch scale studies possessing the genes associated with ammonia oxidizing bacteria and nitrite oxidizing bacteria which act as a complete ammonia oxidizer. The uncultured species of Nitrospira and anammox bacteria were also observed which predicts the coexistence of the anammox and comammox bacteria in a batch scale study. The coexistence of the semi anoxic and anoxic bacteria helped in the growth of these bacteria for a longer duration of time. The nitrite produced by the comammox during nitrification can be utilized by anammox as an electron carrier. The other species of denitrifiers like Pseudomonas denitrificans and Aminobacter aminovorans were also observed. It is concluded that the enrichment of semi anoxic and anoxic bacteria was faster with the increase in growth of the bacteria involved in nitrification, comammox, anammox and partial denitrification process. The bacterial growth is enhanced and the efficiency is increased which can be further used in the development of small pilot scale bioreactor for total nitrogen removal.
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Affiliation(s)
- Raghupatruni Lakshmi Manasa
- Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Alka Mehta
- Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
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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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6
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Yuan D, Fu C, Zheng L, Tan Q, Wang X, Xing Y, Wu H, Tian Q. Abundance, community and driving factor of nitrifiers in western China plateau. Environ Res 2023; 234:116565. [PMID: 37419201 DOI: 10.1016/j.envres.2023.116565] [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: 05/19/2023] [Revised: 06/24/2023] [Accepted: 07/04/2023] [Indexed: 07/09/2023]
Abstract
Complete ammonia oxidation (comammox) is one of the most important biogeochemical processes, with recent studies showing that comammox process dominates nitrification in many ecosystems. However, the abundance, community and driving factor of comammox bacteria and other nitrifying microorganisms in plateau wetland is still unclear. Here, the abundances and community features of comammox bacteria, ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the wetland sediments of western China plateaus were examined using qPCR and high-throughput sequencing. The results indicate that comammox bacteria were more abundant than AOA and AOB, and dominated the nitrification process. Compared with low-elevation samples (below 3000 m: samples 6-10, 12, 13, 15, 16), the abundance of comammox bacteria was much higher at high-elevation samples (above 3000 m: samples 1-5, 11, 14, 17, 18). The key species of AOA, AOB, and comammox bacteria were Nitrososphaera viennensis, Nitrosomonas europaea, and Nitrospira nitrificans, respectively. The key factor affecting comammox bacteria community was elevation. Elevation could increase the interaction links of key species Nitrospira nitrificans, resulting in high comammox bacterial abundance. The results of this study advance our knowledge of comammox bacteria in natural ecosystems.
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Affiliation(s)
- Dongdan Yuan
- College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Chaochen Fu
- School of Water Conservancy and Hydroelectric Power, Hebei University of Engineering, Handan, 056038, 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
| | - Haoming Wu
- College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Qi Tian
- College of Water Sciences, Beijing Normal University, Beijing, 100875, China
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7
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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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8
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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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Mei P, Wang Z, Guo W, Gao Y, A Vanrolleghem P, Li Y. The ASM2d model with two-step nitrification can better simulate biological nutrient removal systems enriched with complete ammonia oxidizing bacteria (comammox Nitrospira). Chemosphere 2023; 335:139169. [PMID: 37295682 DOI: 10.1016/j.chemosphere.2023.139169] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/12/2023]
Abstract
The discovery of comammox Nitrospira, a complete ammonia-oxidizing microorganism belonging to the genus Nitrospira, has brought new insights into the nitrification process in wastewater treatment plants (WWTPs). The applicability of Activated Sludge Model No. 2 d with one-step nitrification (ASM2d-OSN) or two-step nitrification (ASM2d-TSN) for the simulation of the biological nutrient removal (BNR) processes of a full-scale WWTP in the presence of comammox Nitrospira was studied. Microbial analysis and kinetic parameter measurements showed comammox Nitrospira was enriched in the BNR system operated under low dissolved oxygen (DO) and long sludge retention time (SRT). The relative abundance of Nitrospira under the conditions of stage I (DO = 0.5 mg/L, SRT = 60 d) was about twice of that under stage II conditions (DO = 4.0 mg/L, SRT = 26 d), and the copy number of the comammox amoA gene for stage I was 33 times higher than that for stage II. Compared to the ASM2d-OSN model, the ASM2d-TSN model simulated the performance of the WWTP under stage I conditions better, and the Theil inequality coefficient values of all the tested water quality parameters were lower than using ASM2d-OSN. These results indicate that an ASM2d model with two-step nitrification is a better choice for the simulation of WWTPs with the presence of comammox.
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Affiliation(s)
- Peng Mei
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, PR China
| | - Zhiqi Wang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, PR China
| | - Wenjie Guo
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, PR China
| | - Yuan Gao
- Shanghai Urban Construction Design & Research Institute (Group) Co., Ltd, Shanghai, 200001, PR China
| | | | - Yongmei Li
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, PR China.
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10
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Ding H, Zhang J, Wang Y, Hu M, Wen J, Li S, Bao Y, Zhao J. Community composition and abundance of complete ammonia oxidation (comammox) bacteria in the Lancang River cascade reservoir. Ecotoxicol Environ Saf 2023; 256:114907. [PMID: 37059014 DOI: 10.1016/j.ecoenv.2023.114907] [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: 11/10/2022] [Revised: 04/06/2023] [Accepted: 04/09/2023] [Indexed: 06/19/2023]
Abstract
The construction of the reservoir has changed the nitrogen migration and transformation processes in the river, and a large amount of sediment deposition in the reservoir may also lead to the spatial differentiation of complete ammonia oxidation (comammox) bacteria. The study investigated the abundance and diversity of comammox bacteria in the sediments of three cascade reservoirs, namely, Xiaowan, Manwan, and Nuozhadu on the Lancang River in China. In these reservoirs, the average amoA gene abundance of clade A and clade B of comammox bacteria, ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) was 4.16 ± 0.85 × 105, 1.15 ± 0.33 × 105, 7.39 ± 2.31 × 104, and 3.28 ± 0.99 × 105 copies g-1, respectively. The abundance of clade A was higher than that of other ammonia oxidizing microorganisms. The spatial variation of comammox bacteria abundance differed among different reservoirs, but the spatial variation trends of the two clades of comammox bacteria in the same reservoir were similar. At each sampling point, clade A1, clade A2, and clade B coexisted, and clade A2 was usually the dominant species. The connection between comammox bacteria in the pre-dam sediments was looser than that in non-pre-dam sediments, and comammox bacteria in pre-dam sediments exhibited a simpler network structure. The main factor affecting comammox bacteria abundance was NH4+-N, while altitude, temperature, and conductivity of overlying water were the main factors affecting comammox bacteria diversity. Environmental changes caused by differences in the spatial distribution of these cascade reservoirs may be the main driver of the changes of community composition and abundance of comammox bacteria. This study confirms that the construction of cascade reservoirs results in niche spatial differentiation of comammox bacteria.
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Affiliation(s)
- Hang Ding
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, Beijing 10038, China; Department of Water Ecology and Environment, China Institute of Water Resources and Hydropower Research, Beijing 100038, China; Laboratory of Eco-Environmental Engineering Research, State Environmental Protection Key Laboratory of Soil Health and Green Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiahui Zhang
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, Beijing 10038, China; Department of Water Ecology and Environment, China Institute of Water Resources and Hydropower Research, Beijing 100038, China; Laboratory of Eco-Environmental Engineering Research, State Environmental Protection Key Laboratory of Soil Health and Green Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuchun Wang
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, Beijing 10038, 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 10038, China; Department of Water Ecology and Environment, China Institute of Water Resources and Hydropower Research, Beijing 100038, China.
| | - Jie Wen
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, Beijing 10038, China; Department of Water Ecology and Environment, China Institute of Water Resources and Hydropower Research, Beijing 100038, China
| | - Shanze Li
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, Beijing 10038, China; Department of Water Ecology and Environment, China Institute of Water Resources and Hydropower Research, Beijing 100038, China
| | - Yufei Bao
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, Beijing 10038, 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, State Environmental Protection Key Laboratory of Soil Health and Green Remediation, Huazhong Agricultural University, Wuhan 430070, China.
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11
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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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12
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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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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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14
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Chu X, Bai N, Zheng X, Wang Q, Pan X, Li S, Zhang J, Zhang H, He W, Zhong F, Lv W, Zhang H. Effects of straw returning combined with earthworm addition on nitrification and ammonia oxidizers in paddy soil. Front Microbiol 2022; 13:1069554. [PMID: 36590424 PMCID: PMC9800607 DOI: 10.3389/fmicb.2022.1069554] [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: 10/14/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022] Open
Abstract
Introduction Soil ammonia oxidation, which acts as the first and rate-limiting step of nitrification, is driven by ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) and complete ammonia oxidizer (comammox, amoA gene of clade-A and clade-B). Straw returning, widely used ecological technology in China, is an effective measure for promoting straw decomposition and soil nutrient cycling when combined with earthworm addition. However, the effects of straw returning combined with earthworm addition on soil ammonia oxidizers remain poorly understood. Methods A 2-year plot experiment was conducted with 5 treatments: no fertilizer (CK); regular fertilization (RT); straw returning (SR); earthworm addition (W); straw returning + earthworm addition (SRW). The AOA, AOB, comammox clade-A and clade-B community microbial diversities and structures were investigated by high-throughput sequencing. Results The results showed that (1) compared to RT treatment, W, SR, and SRW treatments all significantly increased the richness of AOA and comammox clade-A and clade-B (p < 0.05), and the richness of AOB was only significantly promoted by SRW treatment (p < 0.05). However, only SRW had a higher comammox clade-B diversity index than RT. (2) The ammonia oxidizer community structures were altered by both straw returning and earthworm addition. Soil NH4 +-N was the critical environmental driver for altering the ammonia oxidizer community structure. (3) Compared with RT treatment, the soil potential nitrification rate (PNR) of W and SRW treatments increased by 1.19 and 1.20 times, respectively. The PNR was significantly positively correlated with AOB abundance (path coefficient = 0.712, p < 0.05) and negatively correlated with clade-B abundance (path coefficient = -0.106, p < 0.05). Discussion This study provides scientific support for the application of straw returning combined with earthworm addition to improve soil nitrification with respect to soil ammonia-oxidizing microorganisms.
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Affiliation(s)
- Xiangqian Chu
- Shanghai Academy of Agricultural Sciences, Eco-environmental Protection Institute, Shanghai, China
- Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Naling Bai
- Shanghai Academy of Agricultural Sciences, Eco-environmental Protection Institute, Shanghai, China
- Shanghai Agricultural Academy of Sciences, Key Laboratory of Integrated Rice-Fish Farming Ecosystem, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Xianqing Zheng
- Shanghai Academy of Agricultural Sciences, Eco-environmental Protection Institute, Shanghai, China
- Shanghai Agricultural Academy of Sciences, Key Laboratory of Integrated Rice-Fish Farming Ecosystem, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Quanhua Wang
- Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Xi Pan
- Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Shuangxi Li
- Shanghai Academy of Agricultural Sciences, Eco-environmental Protection Institute, Shanghai, China
- Shanghai Agricultural Academy of Sciences, Key Laboratory of Integrated Rice-Fish Farming Ecosystem, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Juanqin Zhang
- Shanghai Academy of Agricultural Sciences, Eco-environmental Protection Institute, Shanghai, China
- Shanghai Agricultural Academy of Sciences, Key Laboratory of Integrated Rice-Fish Farming Ecosystem, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Haiyun Zhang
- Shanghai Academy of Agricultural Sciences, Eco-environmental Protection Institute, Shanghai, China
- Shanghai Agricultural Academy of Sciences, Key Laboratory of Integrated Rice-Fish Farming Ecosystem, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Wenjie He
- Faculty of Resources and Environmental Science, Hubei University, Wuhan, China
| | - Feng Zhong
- Faculty of Resources and Environmental Science, Hubei University, Wuhan, China
| | - Weiguang Lv
- Shanghai Academy of Agricultural Sciences, Eco-environmental Protection Institute, Shanghai, China
- Shanghai Agricultural Academy of Sciences, Key Laboratory of Integrated Rice-Fish Farming Ecosystem, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Hanlin Zhang
- Shanghai Academy of Agricultural Sciences, Eco-environmental Protection Institute, Shanghai, China
- Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
- Agricultural Environment and Farmland Conservation Experiment Station of Ministry Agriculture, Shanghai, China
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15
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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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16
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Zhang M, Peng Y, Yan P, Huang JC, He S, Sun S, Bai X, Tian Y. Molecular analysis of microbial nitrogen transformation and removal potential in the plant rhizosphere of artificial tidal wetlands across salinity gradients. Environ Res 2022; 215:114235. [PMID: 36055394 DOI: 10.1016/j.envres.2022.114235] [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: 07/13/2022] [Revised: 08/23/2022] [Accepted: 08/26/2022] [Indexed: 06/15/2023]
Abstract
This study explored the microbial nitrogen transformation and removal potential in the plant rhizosphere of seven artificial tidal wetlands under different salinity gradients (0-30‰). Molecular biological and stable isotopic analyses revealed the existence of simultaneous anammox (anaerobic ammonium oxidation), nitrification, DNRA (dissimilatory nitrate reduction to ammonium) and denitrification processes, contributing to nitrogen loss in rhizosphere soil. The microbial abundances were 2.87 × 103-9.12 × 108 (nitrogen functional genes) and 1.24 × 108-8.43 × 109 copies/g (16S rRNA gene), and the relative abundances of dissimilatory nitrate reduction and nitrification genera ranged from 6.75% to 24.41% and from 0.77% to 1.81%, respectively. The bacterial 16S rRNA high-throughput sequencing indicated that Bacillus, Zobellella and Paracoccus had obvious effects on nitrogen removal by heterotrophic nitrifying/aerobic denitrifying process (HN-AD), and autotrophic nitrification (Nitrosomonas, Nitrospira and Nitrospina), conventional denitrification (Bradyrhizobium, Burkholderia and Flavobacterium), anammox (Candidatus Brocadia and Candidatus Scalindua) and DNRA (Clostridium, Desulfovibrio and Photobacterium) organisms co-existed with HN-AD bacteria. The potential activities of DNRA, nitrification, anammox and denitrification were 1.23-9.23, 400.03-755.91, 3.12-35.24 and 30.51-300.04 nmolN2·g-1·d-1, respectively. The denitrification process contributed to 73.59-88.65% of NOx- reduction, compared to 0.71-13.20% and 8.20-15.42% via DNRA and anammox, as 83.83-90.74% of N2 production was conducted by denitrification, with the rest through anammox. Meanwhile, the nitrification pathway accounted for 95.28-99.23% of NH4+ oxidation, with the rest completed by anammox bacteria. Collectively, these findings improved our understanding on global nitrogen cycles, and provided a new idea for the removal of contaminants in saline water treatment.
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Affiliation(s)
- Manping Zhang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, PR China; School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Yuanyuan Peng
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Pan Yan
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Jung-Chen Huang
- Department of Environmental Engineering, National Cheng Kung University, Tainan City 701, Taiwan
| | - Shengbing He
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, PR China.
| | - Shanshan Sun
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, PR China.
| | - Xiaohui Bai
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, PR China
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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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18
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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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19
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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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20
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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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21
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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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22
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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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23
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Wang DQ, Zhou CH, Nie M, Gu JD, Quan ZX. Abundance and niche specificity of different types of complete ammonia oxidizers (comammox) in salt marshes covered by different plants. Sci Total Environ 2021; 768:144993. [PMID: 33736320 DOI: 10.1016/j.scitotenv.2021.144993] [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: 09/17/2020] [Revised: 12/24/2020] [Accepted: 12/31/2020] [Indexed: 06/12/2023]
Abstract
The recently discovered complete ammonia oxidizers (comammox), which are ubiquitous in various natural and artificial ecosystems, have led to a paradigm shift in our understanding of aerobic nitrification. The coastal salt marsh covered by various plant species is an important ecosystem to link nitrogen cycles of terrestrial and marine environments; however, the distribution and structure of comammox in such ecosystems have not been clearly investigated. Here, we applied quantitative PCR and partial nested-PCR to investigate the abundance and community composition of comammox in salt marsh sediment samples covered by three plant types along the southern coastline of China. Our results showed a predominance of comammox clade A in majority of the samples, suggesting their ubiquity and the important role they play in nitrification in salt marsh ecosystems. However, variations by the sites were found when comparing the abundance of subclades of comammox clade A. Redundancy analysis demonstrated a coexistence pattern by comammox clade A.1 with ammonia-oxidizing archaea and comammox clade A.2 with canonical ammonia-oxidizing bacteria, indicating their differences in potential niche preference. However, the abundance of comammox clade B was lower than that of comammox clade A and other ammonia oxidizers in most samples. Moreover, pH and salinity were found to be the most significant factors affecting comammox community structures, suggesting their roles in driving niche partitioning of comammox, whereas plant types did not show a significant effect on the comammox community structure. Our study provided insights into the abundance, community diversity, and niche partitions of comammox, broadening the current understanding of the relationship of comammox with other ammonia oxidizers in salt marsh ecosystems.
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Affiliation(s)
- Dan-Qi Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China
| | - Chen-Hao Zhou
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China
| | - Ming Nie
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China
| | - Ji-Dong Gu
- Environmental Engineering, Guangdong Technion Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, People's Republic of China
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China.
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