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Tan Q, Wu H, Zheng L, Wang X, Xing Y, Tian Q, Zhang Y. Urban and agricultural land use led to niche differentiation of AOA, AOB and comammox along the Beiyun River continuum. WATER RESEARCH 2024; 255:121480. [PMID: 38518415 DOI: 10.1016/j.watres.2024.121480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/22/2024] [Accepted: 03/15/2024] [Indexed: 03/24/2024]
Abstract
River ecological health has been severely threatened by anthropogenic land-use pressures. Here, by combining remote sensing and molecular biology methods, we evaluated the impact of land-use activities on nitrification, a fundamental ecological process in rivers, which is conducted by ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB), or the newly discovered complete ammonia oxidisers (comammox). We explored the relationships of the abundance, activity, and diversity of AOA, AOB, and comammox in river sediments with land-use pressure by proposing a quantitative land use pattern index (LPI) over a 184 km continuum along the Beiyun River in North China. We found that comammox dominated nitrification in the forestry upstream (67.07 % in summer, 56.40 % in winter), while AOB became the major player in the urban middle (56.51 % in summer, 53.08 % in winter) and agricultural downstream reaches (62.98 % in summer, 50.74 % in winter). In addition, urban and agricultural land use lowered the α diversity of AOA and comammox, as well as simplified their co-occurrence networks, but promoted AOB diversity and complicated their networks. The structural equation model illustrated that the key drivers affecting the key taxa and activities were ammonia, and C/N for AOB, and total organic matter, and pH for comammox. We thus conclude that watershed urban and agricultural land use drive the niche differentiation of AOA, AOB, and comammox, specifically leading to a robust AOB community but weakened AOA and comammox communities. Our study connects the macro and micro worlds and provides a new paradigm for studying the variation in microbial communities as well as the potential ecological consequences under the increased anthropogenic land-use pressures in the Anthropocene.
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Affiliation(s)
- Qiuyang Tan
- College of Water Science, Beijing Normal University, Beijing 100875, PR China
| | - Haoming Wu
- College of Water Science, Beijing Normal University, Beijing 100875, PR China
| | - Lei Zheng
- College of Water Science, Beijing Normal University, Beijing 100875, PR China.
| | - Xue Wang
- College of Water Science, Beijing Normal University, Beijing 100875, PR China
| | - Yuzi Xing
- College of Water Science, Beijing Normal University, Beijing 100875, PR China
| | - Qi Tian
- College of Water Science, Beijing Normal University, Beijing 100875, PR China
| | - Yaoxin Zhang
- College of Water Science, Beijing Normal University, Beijing 100875, PR China
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2
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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] [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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Zhu Y, Hou J, Liu J, Huo P, Yang L, Zheng M, Wei W, Ni BJ, Chen X. Model-based development of strategies enabling effective enrichment and application of comammox bacteria in floccular sludge under mainstream conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 895:165051. [PMID: 37391158 DOI: 10.1016/j.scitotenv.2023.165051] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/11/2023] [Accepted: 06/19/2023] [Indexed: 07/02/2023]
Abstract
The discovery of complete ammonium oxidation (comammox) has redefined the perception of the nitrification process which plays a vital part in biological nitrogen removal (BNR) from wastewater. Despite the reported detection or cultivation of comammox bacteria in biofilm or granular sludge reactors, limited attempts have been made to enrich or assess comammox bacteria in floccular sludge reactors with suspended growth of microbes, which are most extensively applied at wastewater treatment plants. Therefore, through making use of a comammox-inclusive bioprocess model reliably evaluated using batch experimental data with joint contributions of different nitrifying guilds, this work probed into the proliferation and functioning of comammox bacteria in two commonly-used floccular sludge reactor configurations, i.e., continuous stirred tank reactor (CSTR) and sequencing batch reactor (SBR), under mainstream conditions. The results indicated that compared with the studied SBR, the CSTR was observed to favor the enrichment of comammox bacteria through maintaining a sufficient sludge retention time (40-100 d) while avoiding an extremely low DO level (e.g., 0.05 g-O2/m3), irrespective of the varied influent NH4+-N of 10-100 g-N/m3. Meanwhile, the inoculum sludge was found to greatly influence the start-up process of the studied CSTR. By inoculating the CSTR with a sufficient amount of sludge, finally enriched floccular sludge with a high abundance of comammox bacteria (up to 70.5 %) could be rapidly obtained. These results not only benefitted further investigation and application of comammox-inclusive sustainable BNR technologies but also explained, to some extent, the discrepancy in the reported presence and abundance of comammox bacteria at wastewater treatment plants adopting floccular sludge-based BNR technologies.
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Affiliation(s)
- Ying Zhu
- Fujian Provincial Engineering Research Center of Rural Waste Recycling Technology, College of Environment and Safety Engineering, Fuzhou University, Fuzhou 350116, China
| | - Jiaying Hou
- Fujian Provincial Engineering Research Center of Rural Waste Recycling Technology, College of Environment and Safety Engineering, Fuzhou University, Fuzhou 350116, China
| | - Jinzhong Liu
- Fujian Provincial Engineering Research Center of Rural Waste Recycling Technology, College of Environment and Safety Engineering, Fuzhou University, Fuzhou 350116, China
| | - Pengfei Huo
- Fujian Provincial Engineering Research Center of Rural Waste Recycling Technology, College of Environment and Safety Engineering, Fuzhou University, Fuzhou 350116, China
| | - Linyan Yang
- School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Min Zheng
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Wei Wei
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Bing-Jie Ni
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Xueming Chen
- Fujian Provincial Engineering Research Center of Rural Waste Recycling Technology, College of Environment and Safety Engineering, Fuzhou University, Fuzhou 350116, China.
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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. ENVIRONMENTAL RESEARCH 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] [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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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. JOURNAL OF ENVIRONMENTAL MANAGEMENT 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] [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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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. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 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] [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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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. THE SCIENCE OF THE TOTAL ENVIRONMENT 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] [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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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 RESEARCH 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] [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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Zhang H, Cheng F, Sun S, Li Z. Diversity distribution and characteristics of comammox in different ecosystems. ENVIRONMENTAL RESEARCH 2022; 214:113900. [PMID: 35839911 DOI: 10.1016/j.envres.2022.113900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/14/2022] [Accepted: 07/10/2022] [Indexed: 06/15/2023]
Abstract
The discovery of complete ammonia oxidizers (comammox), which can oxidize ammonia into nitrate, has recently changed the concept of traditional nitrification. However, comparative studies on the analysis of comammox microbial community in different ecosystems are still scarce. In this study, the distribution and diversity of the comammox microbial community in farmlands, riparian zones, and river sediments in summer and winter were investigated by high-throughput sequencing. And the relative abundance of ammonia-oxidizing microorganisms was measured via their amoA genes of real-time quantitative polymerase chain reaction (qPCR). The relationships between ammonia oxidation microorganisms and the environmental factors were further analyzed. The abundance of comammox clade A was one order of magnitude lower than that of ammonia-oxidizing archaea (AOA) but higher than that of ammonia-oxidizing bacteria (AOB). The abundance of comammox was higher in summer than in winter and higher in farmland soils (1.81 ± 0.95 × 107 copies g-1) than in riparian zones and river sediments. Meanwhile, Candidatus Nitrospira nitrosa were the most widespread comammox in most samples (up to 86.31%), followed by Candidatus Nitrospira nitrificans, with a low abundance of Candidatus Nitrospira inopinata (lower than 0.61%). Furthermore, the abundance of comammox clade A had a significantly negative correlation with pH and NH4+ concentration (P < 0.05). The study revealed the potential advantages of comammox in farmlands and may be conducive to further research on comammox in microbial nitrogen cycling.
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Affiliation(s)
- 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
| | - Fan Cheng
- State Key Laboratory of Pollution Control and Resource Reuse, Nanjing University, Nanjing, 210023, China; School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Siyu Sun
- 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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10
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Deterministic Factors Determine the Comammox Community Composition in the Pearl River Estuary Ecosystem. Microbiol Spectr 2022; 10:e0101622. [PMID: 35913204 PMCID: PMC9431512 DOI: 10.1128/spectrum.01016-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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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11
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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] [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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12
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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] [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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13
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Hu J, Ke X, Wang B, Mei Y, Xiao N, Wan X, Liu G, Hu M, Zhao J. SSThe coexistence and diversity of Candidatus methylomirabilis oxyfera-like and anammox bacteria in sediments of an urban eutrophic lake. Int Microbiol 2022; 25:457-469. [DOI: 10.1007/s10123-021-00230-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 12/03/2021] [Accepted: 12/17/2021] [Indexed: 11/28/2022]
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14
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Zhao Y, Hu J, Yang W, Wang J, Jia Z, Zheng P, Hu B. The long-term effects of using nitrite and urea on the enrichment of comammox bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 755:142580. [PMID: 33059137 DOI: 10.1016/j.scitotenv.2020.142580] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/25/2020] [Accepted: 09/23/2020] [Indexed: 06/11/2023]
Abstract
The discovery of complete ammonia oxidizer (comammox) was a breakthrough in the study of nitrification. However, slow growth of comammox bacteria makes it challenging to distinguish them from traditional ammonia oxidizing microorganisms. Genomic data indicated that comammox bacteria encoded genes that can metabolize urea and had higher nitrite tolerance, which could only be found in several ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). This implies that using nitrite and urea as nitrogen sources may accelerate comammox bacteria's enrichment efficiency. In this study, two reactors using nitrite and urea as substrates, respectively, were operated for 390 days. At the end of cultivation, the reactor fed with urea exhibited higher nitrification potential than the reactor fed with nitrite. Comammox bacteria outcompeted AOA and AOB, regardless of whether they were cultured with nitrite or urea. Using nitrite can improve the proportion of comammox amoA to total amoA of 92%, while using urea may increase the proportion of comammox bacteria among total bacteria to 14.2%. Metagenomic results implied that nitrite was converted to ammonia by nitrate reduction and absorbed by comammox bacteria. On the other hand, urea may be directly utilized as substrate. These results demonstrated that using different nitrogen sources caused niche differentiation of comammox bacteria, AOA, and AOB. Using nitrite can increase the relative abundance of comammox amoA to total amoA, while using urea can increase the quantity of comammox amoA. Comammox bacteria were dominant among ammonia oxidizing microorganisms for both nitrite and urea cultures.
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Affiliation(s)
- Yuxiang Zhao
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Jiajie Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Weiling Yang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China.
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15
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Primer evaluation and development of a droplet digital PCR protocol targeting amoA genes for the quantification of Comammox in lakes. Sci Rep 2021; 11:2982. [PMID: 33536606 PMCID: PMC7858572 DOI: 10.1038/s41598-021-82613-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/22/2021] [Indexed: 01/30/2023] Open
Abstract
To date, little is known about the ecological significance of Comammox (COMplete AMMonia OXidizers) Nitrospira in the water column of freshwater lakes. Water samples collected along depth profiles were used to investigate the distribution of Comammox in 13 lakes characterized by a wide range of physicochemical properties. Several published primers, which target the α-subunit of the ammonia monooxygenase, generated non-specific PCR products or did not amplify target genes from lake water and other habitats. Therefore, a new primer set has been designed for specific detection of Comammox in lakes. The high specificity of the PCR assay was confirmed by sequencing analysis. Quantification of Comammox amoA genes in lake water samples based on droplet digital PCR (ddPCR) revealed very low abundances (not exceeding 85 amoA copies ml-1), which suggest that Comammox is of minor importance for the nitrification process in the water column of the study sites. Surprisingly, samples taken from the sediment/water-interface along an oxygen gradient in dimictic Piburger See showed Comammox abundances three to four magnitudes higher than in the pelagic realm of the lake, which indicates a preference of Comammox to a particle-attached lifestyle.
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16
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Wang X, Lu L, Zhou X, Tang X, Kuang L, Chen J, Shan J, Lu H, Qin H, Adams J, Wang B. Niche Differentiation of Comammox Nitrospira in the Mudflat and Reclaimed Agricultural Soils Along the North Branch of Yangtze River Estuary. Front Microbiol 2021; 11:618287. [PMID: 33584582 PMCID: PMC7873905 DOI: 10.3389/fmicb.2020.618287] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/15/2020] [Indexed: 01/13/2023] Open
Abstract
The discovery of complete ammonia oxidation (comammox), oxidizing ammonia to nitrate via nitrite in a single organism, has redefined the traditional recognition of the two-step nitrification driven by two functional groups (ammonia-oxidizing and nitrite-oxidizing microorganisms). However, the understanding of the distribution and niche differentiation of comammox Nitrospira in the estuarine mudflats and their reclaimed agricultural soils is still limited. Here, we investigated the abundance, diversity and community structures of comammox Nitrospira in the mudflats and the reclaimed agricultural soils in the northern Yangtze River estuary. Quantitative PCR showed the abundances of amoA genes of comammox were lower than that of ammonia-oxidizing bacteria (AOB) in nearly all samples. Amplicon sequencing of amoA genes revealed that the community structures of comammox Nitrospira were significantly (P < 0.001) different between the original mudflats and the reclaimed agricultural soils, indicating niche differentiation among comammox Nitrospira clades (clade A.1, clade A.2, and clade B). The clade A.1 was the dominant group of comammox Nitrospira in the mudflats, while clade B predominated in the agricultural soils. However, the members of clade A.2 could be clearly divided into two groups, the mudflat-preferred and agricultural soil-preferred groups, suggesting more complicated ecological preferences within this sub-clade. Furthermore, it was demonstrated that salinity, organic matter (OM) and NO3–-N had a significantly influence on the distribution of comammox Nitrospira in the estuarine environment. Clade A.1 and nearly half members of clade A.2 were positively correlated with salinity, and negatively correlated with the concentrations of OM and NO3–-N. In contrast, the clade B and the other half members of clade A.2 showed the exact opposite pattern: a negative correlation with salinity and positive correlation with OM and NO3–-N. The co-occurrence network demonstrated that the operational taxonomic units (OTUs) within the same (sub-)clade were mostly positively correlated, indicating the similar niche preferences among the members from the same (sub-)clade of comammox Nitrospira. Taken together, our results revealed the niche differentiation of comammox Nitrospira in estuarine ecosystems where salinity and OM were the primary factors responsible for the distinct ecological distribution patterns.
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Affiliation(s)
- Xinxin Wang
- College of Environmental Science and Engineering, China West Normal University, Nanchong, China.,Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China.,State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Lu Lu
- College of Environmental Science and Engineering, China West Normal University, Nanchong, China
| | - Xue Zhou
- College of Agricultural Engineering, Hohai University, Nanjing, China
| | - Xiufeng Tang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Lu Kuang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Junhui Chen
- Key State Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Jun Shan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Huijie Lu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China
| | - Hua Qin
- Key State Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Jonathan Adams
- School of Geography and Ocean Science, Nanjing University, Nanjing, China
| | - Baozhan Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
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17
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Vijayan A, Vattiringal Jayadradhan RK, Pillai D, Prasannan Geetha P, Joseph V, Isaac Sarojini BS. Nitrospira as versatile nitrifiers: Taxonomy, ecophysiology, genome characteristics, growth, and metabolic diversity. J Basic Microbiol 2021; 61:88-109. [PMID: 33448079 DOI: 10.1002/jobm.202000485] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/30/2020] [Accepted: 12/28/2020] [Indexed: 12/14/2022]
Abstract
The global nitrogen cycle is of paramount significance as it affects important processes like primary productivity and decomposition. Nitrification, the oxidation of ammonia to nitrate via nitrite, is a key process in the nitrogen cycle. The knowledge about nitrification has been challenged during the last few decades with inventions like anaerobic ammonia oxidation, ammonia-oxidizing archaea, and recently the complete ammonia oxidation (comammox). The discovery of comammox Nitrospira has made a paradigm shift in nitrification, before which it was considered as a two-step process, mediated by chemolithoautotrophic ammonia oxidizers and nitrite oxidizers. The genome of comammox Nitrospira equipped with molecular machineries for both ammonia and nitrite oxidation. The genus Nitrospira is ubiquitous, comes under phylum Nitrospirae, which comprises six sublineages consisting of canonical nitrite oxidizers and comammox. The single-step nitrification is energetically more feasible; furthermore, the existence of diverse metabolic pathways in Nitrospira is critical for its establishment in various habitats. The present review discusses the taxonomy, ecophysiology, isolation, identification, growth, and metabolic diversity of the genus Nitrospira; compares the genomes of canonical nitrite-oxidizing Nitrospira and comammox Nitrospira, and analyses the differences of Nitrospira with other nitrifying bacteria.
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Affiliation(s)
- Ardhra Vijayan
- Department of Aquatic Animal Health Management, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
| | - Rejish Kumar Vattiringal Jayadradhan
- Department of Aquatic Animal Health Management, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India.,Department of Aquaculture, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
| | - Devika Pillai
- Department of Aquatic Animal Health Management, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
| | - Preena Prasannan Geetha
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Kochi, Kerala, India
| | - Valsamma Joseph
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Kochi, Kerala, India
| | - Bright Singh Isaac Sarojini
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Kochi, Kerala, India
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