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Jin D, Zhang X, Zhang X, Zhou L, Zhu Z, Deogratias UK, Wu Z, Zhang K, Ji X, Ju T, Zhu X, Gao B, Ji L, Zhao R, Ruth G, Wu P. A critical review of comammox and synergistic nitrogen removal coupling anammox: Mechanisms and regulatory strategies. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 948:174855. [PMID: 39034010 DOI: 10.1016/j.scitotenv.2024.174855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 05/13/2024] [Accepted: 07/16/2024] [Indexed: 07/23/2024]
Abstract
Nitrification is highly crucial for both anammox systems and the global nitrogen cycle. The discovery of complete ammonia oxidation (comammox) challenges the inherent concept of nitrification as a two-step process. Its wide distribution, adaptability to low substrate environments, low sludge production, and low greenhouse gas emissions may make it a promising new nitrogen removal treatment process. Meanwhile, anammox technology is considered the most suitable process for future wastewater treatment. The diverse metabolic capabilities and similar ecological niches of comammox bacteria and anammox bacteria are expected to achieve synergistic nitrogen removal within a single system. However, previous studies have overlooked the existence of comammox, and it is necessary to re-evaluate the conclusions drawn. This paper outlined the ecophysiological characteristics of comammox bacteria and summarized the environmental factors affecting their growth. Furthermore, it focused on the enrichment, regulatory strategies, and nitrogen removal mechanisms of comammox and anammox, with a comparative analysis of hydroxylamine, a particular intermediate product. Overall, this is the first critical overview of the conclusions drawn from the last few years of research on comammox-anammox, highlighting possible next steps for research.
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Affiliation(s)
- Da Jin
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, No. 1 Kerui Road, Suzhou 215009, PR China
| | - Xiaonong Zhang
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, No. 1 Kerui Road, Suzhou 215009, PR China
| | - Xingxing Zhang
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Li Zhou
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, No. 1 Kerui Road, Suzhou 215009, PR China
| | - Zixuan Zhu
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, No. 1 Kerui Road, Suzhou 215009, PR China
| | - Ufoymungu Kisa Deogratias
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, No. 1 Kerui Road, Suzhou 215009, PR China
| | - Zhiqiang Wu
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, No. 1 Kerui Road, Suzhou 215009, PR China
| | - Kangyu Zhang
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, No. 1 Kerui Road, Suzhou 215009, PR China
| | - Xu Ji
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, No. 1 Kerui Road, Suzhou 215009, PR China
| | - Ting Ju
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, No. 1 Kerui Road, Suzhou 215009, PR China
| | - Xurui Zhu
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, No. 1 Kerui Road, Suzhou 215009, PR China
| | - Bo Gao
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, No. 1 Kerui Road, Suzhou 215009, PR China
| | - Luomiao Ji
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, No. 1 Kerui Road, Suzhou 215009, PR China
| | - Rui Zhao
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, No. 1 Kerui Road, Suzhou 215009, PR China
| | - Guerra Ruth
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, No. 1 Kerui Road, Suzhou 215009, PR China
| | - Peng Wu
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, No. 1 Kerui Road, Suzhou 215009, PR China; National and Local Joint Engineering Laboratory of Municipal Sewage Resource Utilization Technology, No. 1 Kerui Road, Suzhou 215009, PR China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, No. 1 Kerui Road, Suzhou 215009, PR China.
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2
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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] [Abstract] [Key Words] [MESH Headings] [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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3
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Masuda Y, Mise K, Xu Z, Zhang Z, Shiratori Y, Senoo K, Itoh H. Global soil metagenomics reveals distribution and predominance of Deltaproteobacteria in nitrogen-fixing microbiome. MICROBIOME 2024; 12:95. [PMID: 38790049 PMCID: PMC11127431 DOI: 10.1186/s40168-024-01812-1] [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: 04/28/2023] [Accepted: 04/09/2024] [Indexed: 05/26/2024]
Abstract
BACKGROUND Biological nitrogen fixation is a fundamental process sustaining all life on earth. While distribution and diversity of N2-fixing soil microbes have been investigated by numerous PCR amplicon sequencing of nitrogenase genes, their comprehensive understanding has been hindered by lack of de facto standard protocols for amplicon surveys and possible PCR biases. Here, by fully leveraging the planetary collections of soil shotgun metagenomes along with recently expanded culture collections, we evaluated the global distribution and diversity of terrestrial diazotrophic microbiome. RESULTS After the extensive analysis of 1,451 soil metagenomic samples, we revealed that the Anaeromyxobacteraceae and Geobacteraceae within Deltaproteobacteria are ubiquitous groups of diazotrophic microbiome in the soils with different geographic origins and land usage types, with particular predominance in anaerobic soils (paddy soils and sediments). CONCLUSION Our results indicate that Deltaproteobacteria is a core bacterial taxon in the potential soil nitrogen fixation population, especially in anaerobic environments, which encourages a careful consideration on deltaproteobacterial diazotrophs in understanding terrestrial nitrogen cycling. Video Abstract.
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Affiliation(s)
- Yoko Masuda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
| | - Kazumori Mise
- National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido, 2-17-2-1 Tsukisamu-higashi, Toyohira, Sapporo, Hokkaido, 062-8517, Japan.
| | - Zhenxing Xu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Zhengcheng Zhang
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yutaka Shiratori
- Niigata Agricultural Research Institute, 857 Nagakura-machi, Nagaoka, Niigata, 940-0826, Japan
| | - Keishi Senoo
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Hideomi Itoh
- National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido, 2-17-2-1 Tsukisamu-higashi, Toyohira, Sapporo, Hokkaido, 062-8517, Japan.
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4
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Tang X, Li Y, Liu M, Hou L, Han P. Abundance, diversity and physiological preferences of comammox Nitrospira in urban groundwater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:167333. [PMID: 37748616 DOI: 10.1016/j.scitotenv.2023.167333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 09/01/2023] [Accepted: 09/22/2023] [Indexed: 09/27/2023]
Abstract
Complete ammonia oxidizer (comammox Nitrospira), catalyze complete nitrification process in a single organism, are frequently detected in groundwater ecosystem. However, the ecological niches and environmental driving factors of comammox Nitrospira in urban groundwater are largely unknown. Here we investigated the communities of ammonia oxidizers in urban groundwater located in Shanghai city, China. Quantitative analysis demonstrated the dominance of comammox Nitrospira over classical ammonia oxidizers (ammonia-oxidizing archaea and bacteria, AOA and AOB). Phylogenetic analysis showed clades B and A2 comprise the majority of comammox Nitrospira groups. Temperature was one of the most vital factors affecting comammox Nitrospira community. Furthermore, clade A comammox Nitrospira can be enriched by urea substrate, which was in line with the ability of utilizing urea by the pure clade A comammox culture Nitrospira inopinata. In addition, we observed that relatively low temperature (<20 °C) and high copper levels (>0.04 mg L-1) can stimulate the growth of comammox Nitrospira. Overall, this study revealed the presence, diversity and physiological preferences of comammox Nitrospira in urban groundwater nitrification, shedding insights on the ecological roles of comammox Nitrospira in subsurface environment.
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Affiliation(s)
- Xiufeng Tang
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Ye Li
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Lijun Hou
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Ping Han
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Institute of Eco-Chongming, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China.
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5
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Su Z, Liu T, Guo J, Zheng M. Nitrite Oxidation in Wastewater Treatment: Microbial Adaptation and Suppression Challenges. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:12557-12570. [PMID: 37589598 PMCID: PMC10470456 DOI: 10.1021/acs.est.3c00636] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/18/2023]
Abstract
Microbial nitrite oxidation is the primary pathway that generates nitrate in wastewater treatment systems and can be performed by a variety of microbes: namely, nitrite-oxidizing bacteria (NOB). Since NOB were first isolated 130 years ago, the understanding of the phylogenetical and physiological diversities of NOB has been gradually deepened. In recent endeavors of advanced biological nitrogen removal, NOB have been more considered as a troublesome disruptor, and strategies on NOB suppression often fail in practice after long-term operation due to the growth of specific NOB that are able to adapt to even harsh conditions. In line with a review of the history of currently known NOB genera, a phylogenetic tree is constructed to exhibit a wide range of NOB in different phyla. In addition, the growth behavior and metabolic performance of different NOB strains are summarized. These specific features of various NOB (e.g., high oxygen affinity of Nitrospira, tolerance to chemical inhibitors of Nitrobacter and Candidatus Nitrotoga, and preference to high temperature of Nitrolancea) highlight the differentiation of the NOB ecological niche in biological nitrogen processes and potentially support their adaptation to different suppression strategies (e.g., low dissolved oxygen, chemical treatment, and high temperature). This review implicates the acquired physiological characteristics of NOB to their emergence from a genomic and ecological perspective and emphasizes the importance of understanding physiological characterization and genomic information in future wastewater treatment studies.
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Affiliation(s)
- Zicheng Su
- Australian Centre for Water
and Environmental Biotechnology, The University
of Queensland, St. Lucia, Queensland 4072, Australia
| | - Tao Liu
- Australian Centre for Water
and Environmental Biotechnology, The University
of Queensland, St. Lucia, Queensland 4072, Australia
| | - Jianhua Guo
- Australian Centre for Water
and Environmental Biotechnology, The University
of Queensland, St. Lucia, Queensland 4072, Australia
| | - Min Zheng
- Australian Centre for Water
and Environmental Biotechnology, The University
of Queensland, St. Lucia, Queensland 4072, Australia
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6
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Zheng M, Tian Z, Chai Z, Zhang A, Gu A, Mu G, Wu D, Guo J. Ubiquitous occurrence and functional dominance of comammox Nitrospira in full-scale wastewater treatment plants. WATER RESEARCH 2023; 236:119931. [PMID: 37045640 DOI: 10.1016/j.watres.2023.119931] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/04/2023] [Accepted: 03/28/2023] [Indexed: 06/19/2023]
Abstract
The recent discovery of complete ammonia oxidation (comammox) bacteria has fundamentally upended the traditional two-step nitrification conception, but their functional importance in wastewater treatment plants (WWTPs) is still poorly understood. This study investigated distributions of comammox Nitrospira, ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in activated sludge samples collected from 25 full-scale WWTPs. Using quantitative PCR (qPCR) and 16S rRNA gene amplicon sequencing, our results revealed that comammox Nitrospira ubiquitously occurred in all of 25 WWTPs and even outnumbered AOB and AOA with an average abundance of 1∼183 orders of magnitude higher in 19 WWTPs. Moreover, DNA-based stable isotope probing (DNA-SIP) assays validated that comammox Nitrospira actively participated in ammonia oxidation in the three microcosms seeding with activated sludge from three typical WWTPs, in which the ratios of comammox amoA to AOB amoA were at the range of 1∼10, 10∼100 and >100, respectively. Phylogenetic analysis in heavy fractions further indicated that Nitrospira nitrosa (N. nitrosa) was the dominant and active species. We quantified the contribution of ammonia oxidizers based on the currently available kinetic parameters of the representative species and found that comammox made major contributions to ammonia oxidation than other nitrifiers (5 ∼ 106 times that of AOB). The findings not only demonstrate the ubiquitous occurrence of comammox, but also highlight their functional dominance in ammonia oxidation in WWTPs.
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Affiliation(s)
- Maosheng Zheng
- Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China.
| | - Zhichao Tian
- Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Zimin Chai
- Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Anqi Zhang
- Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Ailu Gu
- Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Guangli Mu
- Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Dedong Wu
- Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD, Australia.
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7
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Meng S, Liang X, Peng T, Liu Y, Wang H, Huang T, Gu JD, Hu Z. Ecological distribution and function of comammox Nitrospira in the environment. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12557-6. [PMID: 37195422 DOI: 10.1007/s00253-023-12557-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/18/2023]
Abstract
Complete ammonia oxidizers (Comammox) are of great significance for studying nitrification and expanding the understanding of the nitrogen cycle. Moreover, Comammox bacteria are also crucial in natural and engineered environments due to their role in wastewater treatment and maintaining the flux of greenhouse gases to the atmosphere. However, only few studies are there regarding the Comammox bacteria and their role in ammonia and nitrite oxidation in the environment. This review mainly focuses on summarizing the genomes of Nitrospira in the NCBI database. Ecological distribution of Nitrospira was also reviewed and the influence of environmental parameters on genus Nitrospira in different environments has been summarized. Furthermore, the role of Nitrospira in carbon cycle, nitrogen cycle, and sulfur cycle were discussed, especially the comammox Nitrospira. In addition, the overviews of current research and development regarding comammox Nitrospira, were summarized along with the scope of future research. KEY POINTS: • Most of Comammox Nitrospira are widely distributed in both aquatic and terrestrial ecosystems, but it has been studied less frequently in the extreme environments. • Comammox Nitrospira can be involved in different nitrogen transformation process, but rarely involved in nitrogen fixation. • The stable isotope and transcriptome techniques are important methods to study the metabolic function of comammox Nitrospira.
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Affiliation(s)
- Shanshan Meng
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, P.R. China
| | - Xueji Liang
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, P.R. China
| | - Tao Peng
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, P.R. China
| | - Yongjin Liu
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, P.R. China
| | - Hui Wang
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, P.R. China
| | - Tongwang Huang
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, P.R. China
| | - Ji-Dong Gu
- Environmental Science and Engineering Research Group, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, 515063, Guangdong, China
- Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, 515063, Guangdong, China
| | - Zhong Hu
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, P.R. China.
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8
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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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Ma B, LaPara TM, Kim T, Hozalski RM. Multi-scale Investigation of Ammonia-Oxidizing Microorganisms in Biofilters Used for Drinking Water Treatment. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:3833-3842. [PMID: 36811531 DOI: 10.1021/acs.est.2c06858] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Ammonia-oxidizing microorganisms (AOMs) include ammonia-oxidizing bacteria (AOB), archaea (AOA), and Nitrospira spp. sublineage II capable of complete ammonia oxidation (comammox). These organisms can affect water quality not only by oxidizing ammonia to nitrite (or nitrate) but also by cometabolically degrading trace organic contaminants. In this study, the abundance and composition of AOM communities were investigated in full-scale biofilters at 14 facilities across North America and in pilot-scale biofilters operated for 18 months at a full-scale water treatment plant. In general, the relative abundance of AOM in most full-scale biofilters and in the pilot-scale biofilters was as follows: AOB > comammox Nitrospira > AOA. The abundance of AOB in the pilot-scale biofilters increased with increasing influent ammonia concentration and decreasing temperature, whereas AOA and comammox Nitrospira exhibited no correlations with these parameters. The biofilters affected AOM abundance in the water passing through the filters via collecting and shedding but exhibited a minor influence on the composition of AOB and Nitrospira sublineage II communities in the filtrate. Overall, this study highlights the relative importance of AOB and comammox Nitrospira compared to AOA in biofilters and the influence of filter influent water quality on AOM in biofilters and their release into the filtrate.
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Affiliation(s)
- Ben Ma
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, 500 Pillsbury Dr. SE, Minneapolis, Minnesota 55455, United States
| | - Timothy M LaPara
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, 500 Pillsbury Dr. SE, Minneapolis, Minnesota 55455, United States
- Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
| | - Taegyu Kim
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, 500 Pillsbury Dr. SE, Minneapolis, Minnesota 55455, United States
| | - Raymond M Hozalski
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, 500 Pillsbury Dr. SE, Minneapolis, Minnesota 55455, United States
- Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
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Genome-Resolved Metaproteomics Decodes the Microbial and Viral Contributions to Coupled Carbon and Nitrogen Cycling in River Sediments. mSystems 2022; 7:e0051622. [PMID: 35861508 PMCID: PMC9426555 DOI: 10.1128/msystems.00516-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Rivers have a significant role in global carbon and nitrogen cycles, serving as a nexus for nutrient transport between terrestrial and marine ecosystems. Although rivers have a small global surface area, they contribute substantially to worldwide greenhouse gas emissions through microbially mediated processes within the river hyporheic zone. Despite this importance, research linking microbial and viral communities to specific biogeochemical reactions is still nascent in these sediment environments. To survey the metabolic potential and gene expression underpinning carbon and nitrogen biogeochemical cycling in river sediments, we collected an integrated data set of 33 metagenomes, metaproteomes, and paired metabolomes. We reconstructed over 500 microbial metagenome-assembled genomes (MAGs), which we dereplicated into 55 unique, nearly complete medium- and high-quality MAGs spanning 12 bacterial and archaeal phyla. We also reconstructed 2,482 viral genomic contigs, which were dereplicated into 111 viral MAGs (vMAGs) of >10 kb in size. As a result of integrating gene expression data with geochemical and metabolite data, we created a conceptual model that uncovered new roles for microorganisms in organic matter decomposition, carbon sequestration, nitrogen mineralization, nitrification, and denitrification. We show how these metabolic pathways, integrated through shared resource pools of ammonium, carbon dioxide, and inorganic nitrogen, could ultimately contribute to carbon dioxide and nitrous oxide fluxes from hyporheic sediments. Further, by linking viral MAGs to these active microbial hosts, we provide some of the first insights into viral modulation of river sediment carbon and nitrogen cycling. IMPORTANCE Here we created HUM-V (hyporheic uncultured microbial and viral), an annotated microbial and viral MAG catalog that captures strain and functional diversity encoded in these Columbia River sediment samples. Demonstrating its utility, this genomic inventory encompasses multiple representatives of dominant microbial and archaeal phyla reported in other river sediments and provides novel viral MAGs that can putatively infect these. Furthermore, we used HUM-V to recruit gene expression data to decipher the functional activities of these MAGs and reconstruct their active roles in Columbia River sediment biogeochemical cycling. Ultimately, we show the power of MAG-resolved multi-omics to uncover interactions and chemical handoffs in river sediments that shape an intertwined carbon and nitrogen metabolic network. The accessible microbial and viral MAGs in HUM-V will serve as a community resource to further advance more untargeted, activity-based measurements in these, and related, freshwater terrestrial-aquatic ecosystems.
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11
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Lai KP, Tsang CF, Li L, Yu RMK, Kong RYC. Microplastics act as a carrier for wastewater-borne pathogenic bacteria in sewage. CHEMOSPHERE 2022; 301:134692. [PMID: 35504476 DOI: 10.1016/j.chemosphere.2022.134692] [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: 03/01/2022] [Revised: 04/06/2022] [Accepted: 04/20/2022] [Indexed: 06/14/2023]
Abstract
Microplastic pollution, a pressing global environmental problem, has a severe impact on both aquatic ecosystems and public health worldwide. Due to the small size of microplastics, they are able to pass through the filtration systems of municipal wastewater treatment works (WWTWs). In recent years, studies have focused on the environmental abundance and ecotoxicological effects of microplastics, but there are limited studies investigating the colonization of microplastics by bacteria, especially those pathogenic ones. In this study, we examined the colonization and composition of the bacterial communities on polyethylene microbeads after incubation in raw sewage collected from three municipal WWTWs in Hong Kong (Sha Tin Sewage Treatment Works, Stonecutters Island Sewage Treatment Works, and Shek Wu Hui Sewage Treatment Works). Scanning electron microscopy (SEM) results indicate that bacterial cells were colonized on the surfaces of the microbeads and formed biofilms after sewage incubation. Metagenomic sequencing data demonstrated an increase in bacterial diversity after 21 days of sewage incubation when compared to shorter incubation periods of 6, 11 and 16 days. Importantly, human and fish pathogens such as Arcobacter cryaerophilus, Aeromonas salmonicida, Vibrio areninigrae and Vibrio navarrensis were found in the resident bacterial communities. Taken together, our results demonstrate that microplastics could act as a carrier for wastewater-borne pathogenic bacteria in municipal sewage.
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Affiliation(s)
- Keng Po Lai
- Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Guilin, PR China; Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China; State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China.
| | - Chau Fong Tsang
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
| | - Lei Li
- Guangdong Provincial Key Laboratory of Brain Connectome and Behavior, CAS Key Laboratory of Brain Connectome and Manipulation, The Brain Cognition and Brain Disease Institute (BCBDI), Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, 518055, China
| | - Richard Man Kit Yu
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales, Australia.
| | - Richard Yuen Chong Kong
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China; State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China.
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12
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Millimeter-scale vertical partitioning of nitrogen cycling in hypersaline mats reveals prominence of genes encoding multi-heme and prismane proteins. THE ISME JOURNAL 2022; 16:1119-1129. [PMID: 34862473 PMCID: PMC8940962 DOI: 10.1038/s41396-021-01161-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 11/09/2021] [Accepted: 11/18/2021] [Indexed: 12/01/2022]
Abstract
Microbial mats are modern analogues of the first ecosystems on the Earth. As extant representatives of microbial communities where free oxygen may have first been available on a changing planet, they offer an ecosystem within which to study the evolution of biogeochemical cycles requiring and inhibited by oxygen. Here, we report the distribution of genes involved in nitrogen metabolism across a vertical oxygen gradient at 1 mm resolution in a microbial mat using quantitative PCR (qPCR), retro-transcribed qPCR (RT-qPCR) and metagenome sequencing. Vertical patterns in the presence and expression of nitrogen cycling genes, corresponding to oxygen requiring and non-oxygen requiring nitrogen metabolism, could be seen across gradients of dissolved oxygen and ammonium. Metagenome analysis revealed that genes annotated as hydroxylamine dehydrogenase (proper enzyme designation EC 1.7.2.6, hao) and hydroxylamine reductase (hcp) were the most abundant nitrogen metabolism genes in the mat. The recovered hao genes encode hydroxylamine dehydrogenase EC 1.7.2.6 (HAO) proteins lacking the tyrosine residue present in aerobic ammonia oxidizing bacteria (AOB). Phylogenetic analysis confirmed that those proteins were more closely related to ɛHao protein present in Campylobacterota lineages (previously known as Epsilonproteobacteria) rather than oxidative HAO of AOB. The presence of hao sequences related with ɛHao protein, as well as numerous hcp genes encoding a prismane protein, suggest the presence of a nitrogen cycling pathway previously described in Nautilia profundicola as ancestral to the most commonly studied present day nitrogen cycling pathways.
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13
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RedCorn R, Lamb JR, Gottshall E, Stahl DA, Winkler MK. Light-weight oxygen supply for portable biological nitrogen removal from urine and sweat. CHEMICAL ENGINEERING JOURNAL ADVANCES 2022. [DOI: 10.1016/j.ceja.2021.100235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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14
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Higgins E, Parr TB, Vaughn CC. Mussels and Local Conditions Interact to Influence Microbial Communities in Mussel Beds. Front Microbiol 2022; 12:790554. [PMID: 35095802 PMCID: PMC8793333 DOI: 10.3389/fmicb.2021.790554] [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: 10/06/2021] [Accepted: 11/24/2021] [Indexed: 11/13/2022] Open
Abstract
Microbiomes are increasingly recognized as widespread regulators of function from individual organism to ecosystem scales. However, the manner in which animals influence the structure and function of environmental microbiomes has received considerably less attention. Using a comparative field study, we investigated the relationship between freshwater mussel microbiomes and environmental microbiomes. We used two focal species of unionid mussels, Amblema plicata and Actinonaias ligamentina, with distinct behavioral and physiological characteristics. Mussel microbiomes, those of the shell and biodeposits, were less diverse than both surface and subsurface sediment microbiomes. Mussel abundance was a significant predictor of sediment microbial community composition, but mussel species richness was not. Our data suggest that local habitat conditions which change dynamically along streams, such as discharge, water turnover, and canopy cover, work in tandem to influence environmental microbial community assemblages at discreet rather than landscape scales. Further, mussel burrowing activity and mussel shells may provide habitat for microbial communities critical to nutrient cycling in these systems.
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Affiliation(s)
- Edward Higgins
- Oklahoma Biological Survey and Department of Biology, University of Oklahoma, Norman, OK, United States
- *Correspondence: Edward Higgins,
| | - Thomas B. Parr
- Oklahoma Biological Survey and Department of Biology, University of Oklahoma, Norman, OK, United States
- National Park Service, Great Lakes Inventory and Monitoring Network, Ashland, WI, United States
| | - Caryn C. Vaughn
- Oklahoma Biological Survey and Department of Biology, University of Oklahoma, Norman, OK, United States
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15
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Yang W, Yao J, He Y, Huang Y, Liu H, Zhi Y, Qian S, Yan X, Jian S, Li W. Nitrogen removal enhanced by benthic bioturbation coupled with biofilm formation: A new strategy to alleviate freshwater eutrophication. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 292:112814. [PMID: 34030016 DOI: 10.1016/j.jenvman.2021.112814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 05/07/2021] [Accepted: 05/15/2021] [Indexed: 06/12/2023]
Abstract
Excessive nitrogen input into the water caused eutrophication thereby reducing biodiversity and degrades freshwater function. Nitrogen pollution in sediments is one key reason that makes eutrophication difficult to control. The physicochemical technologies such as dredging and coverage for sediment pollution easily destroyed and homogenized aquatic habitats. To alleviate freshwater eutrophication in ecological way, this work combined the functions of bioturbation and biofilm to test their effect on the removal of nitrogen from sediment and water. The total nitrogen removal by employing the coupled function (bioturbation + biofilm, SCB) was greater than that of the single function (bioturbation or biofilm). The mean efficiency of total nitrogen removal in SCB treatment was 3.19 times that of the control without chironomids nor biofilm medium. Chironomid bioturbation promoted nitrogen release from sediments to the overlying water. Biofilm enhanced the conversion and removal of nitrogen stirred up by chironomids, resulting the lowest concentration of total nitrogen in overlying water of SCB treatment. The enhancement of nitrogen removal may be due to the coupled function increased the abundance of denitrifying and anammox functional bacteria in sediment and biofilm. Therefore, the method of combining benthic animals with biofilm medium is not only a viable solution for reducing sedimentary nitrogen loading in freshwater ecosystems, but also a solution to mitigate eutrophication in the overlying water. The restoration and management for aquatic ecosystems should consider protecting habitat for benthic organisms while maintaining heterogeneity for biofilm.
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Affiliation(s)
- Wei Yang
- Department of Ecological Sciences and Engineering, Chongqing University, Chongqing, 400045, PR China
| | - Jingmei Yao
- Department of Ecological Sciences and Engineering, Chongqing University, Chongqing, 400045, PR China; Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, PR China
| | - Yan He
- Department of Ecological Sciences and Engineering, Chongqing University, Chongqing, 400045, PR China
| | - Yuyue Huang
- Department of Ecological Sciences and Engineering, Chongqing University, Chongqing, 400045, PR China
| | - Huazu Liu
- Department of Ecological Sciences and Engineering, Chongqing University, Chongqing, 400045, PR China
| | - Yue Zhi
- Department of Ecological Sciences and Engineering, Chongqing University, Chongqing, 400045, PR China; Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, PR China; Department of Civil, Construction, and Environmental Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Shenhua Qian
- Department of Ecological Sciences and Engineering, Chongqing University, Chongqing, 400045, PR China; Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, PR China
| | - Xiaoman Yan
- Department of Ecological Sciences and Engineering, Chongqing University, Chongqing, 400045, PR China
| | - Shuai Jian
- Department of Ecological Sciences and Engineering, Chongqing University, Chongqing, 400045, PR China
| | - Wei Li
- Department of Ecological Sciences and Engineering, Chongqing University, Chongqing, 400045, PR China; Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, PR China.
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16
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Liu S, Cai H, Wang J, Wang H, Zheng T, Chen Q, Ni J. In-situ expressions of comammox Nitrospira along the Yangtze River. WATER RESEARCH 2021; 200:117241. [PMID: 34051458 DOI: 10.1016/j.watres.2021.117241] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/07/2021] [Accepted: 05/09/2021] [Indexed: 06/12/2023]
Abstract
The recent discovery of comammox Nitrospira as complete nitrifiers has significantly enriched our understanding on the nitrogen cycle, yet little is known about their metabolic transcripts in natural aquatic ecosystems. Using the genome-centric metatranscriptomics, we provided the first in-situ expression patterns of comammox Nitrospira along the Yangtze River. Our study confirmed widespread expressions of comammox Nitrospira, with the highest transcription accounting for 33.3% and 63.8% of amoA and nxrAB genes expressed in ammonia-oxidizing prokaryotes (AOPs) and Nitrospira sublineages I/II, respectively. Moreover, comammox two clades differed in nitrification, with clade A acting as the dominator to ammonia oxidation in comammox, and clade B contributing more transcripts to nitrite oxidation than to ammonia oxidation. Compared to canonical Nitrospira, comammox community had lower expressions of ammonia/nitrite transporters and nitrogen assimilatory genes, but far higher expressions in urea transport and hydrolysis, facilitating to derivation of ammonia and energy mainly through intracellular ureolytic metabolism. This suggests no need for "reciprocal-feeding" between canonical Nitrospira and AOPs in a natural river. Aerobic mixotrophy of comammox bacteria was suggested by expressions of genes coding for respiratory complexes I-V, oxidative/reductive TCA cycle, oxygen stress defenses, and transport/catabolism of simple carbohydrates and low-biosynthetic-cost amino acids. Intriguingly, significant positive correlations among expressions of ammonia monooxygenases, hydroxylamine dehydrogenase and copper-dependent nitrite reductase indicated that comammox Nitrospira had the potential of converting nitrite to nitric oxide accompanied by ammonia oxidation under low-C/N and aerobic conditions, while gene expressions in this pathway were significantly and positively associated with pH. Overall, this study illustrated novel transcriptional characteristics of comammox Nitrospira, and highlighted the necessity of reassessing their contributions to biogeochemical carbon and nitrogen cycling with perspective of in-situ meta-omics as well as culture experiments.
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Affiliation(s)
- Shufeng Liu
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Peking University, Beijing 100871, China
| | - Hetong Cai
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Peking University, Beijing 100871, China
| | - Jiawen Wang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Peking University, Beijing 100871, China
| | - Haiying Wang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Tong Zheng
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Peking University, Beijing 100871, China; South China Institute of Environmental Sciences, Ministry of Environmental Protection (MEP), Guangzhou 510655, China
| | - Qian Chen
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Peking University, Beijing 100871, China; State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Jinren Ni
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Peking University, Beijing 100871, China; State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China.
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17
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Huang Y, Li W, Gao J, Wang F, Yang W, Han L, Lin D, Min B, Zhi Y, Grieger K, Yao J. Effect of microplastics on ecosystem functioning: Microbial nitrogen removal mediated by benthic invertebrates. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 754:142133. [PMID: 32916494 DOI: 10.1016/j.scitotenv.2020.142133] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/28/2020] [Accepted: 08/31/2020] [Indexed: 06/11/2023]
Abstract
While ecotoxicological impacts of microplastics on aquatic organisms have started to be investigated recently, impacts on ecosystem functions mediated by benthic biota remain largely unknown. We investigated the effect of microplastics on nitrogen removal in freshwater sediments where microorganisms and benthic invertebrates (i.e., chironomid larvae) co-existed. Using microcosm experiments, sediments with and without invertebrate chironomid larvae were exposed to microplastics (polyethylene) at concentrations of 0, 0.1, and 1 wt%. After 28 days of exposure, the addition of microplastics or chironomid larvae promoted the growth of denitrifying and anammox bacteria, leading to increased total nitrogen removal, in both cases. However, in microcosms with chironomid larvae and microplastics co-existing, nitrogen removal was less than the sum of their individual effects, especially at microplastics concentration of 1 wt%, indicating an adverse effect on microbial nitrogen removal mediated by macroinvertebrates. This study reveals that the increasing concentration of microplastics entangled the nitrogen cycling mediated by benthic invertebrates in freshwater ecosystems. These findings highlight the pursuit of a comprehensive understanding of the impacts of microplastics on the functioning in freshwater ecosystems.
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Affiliation(s)
- Yuyue Huang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400045, PR China
| | - Wei Li
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400045, PR China
| | - Jie Gao
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400045, PR China
| | - Fang Wang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400045, PR China
| | - Wei Yang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400045, PR China
| | - Le Han
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400045, PR China
| | - Dunmei Lin
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400045, PR China
| | - Bolin Min
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400045, PR China
| | - Yue Zhi
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400045, PR China; Department of Civil, Construction, and Environmental Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Khara Grieger
- Department of Applied Ecology, North Carolina State University, Raleigh, NC 27695, USA
| | - Jingmei Yao
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400045, PR China.
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18
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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: 19] [Impact Index Per Article: 6.3] [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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19
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Liu S, Wang H, Chen L, Wang J, Zheng M, Liu S, Chen Q, Ni J. Comammox Nitrospira within the Yangtze River continuum: community, biogeography, and ecological drivers. THE ISME JOURNAL 2020; 14:2488-2504. [PMID: 32555502 PMCID: PMC7490378 DOI: 10.1038/s41396-020-0701-8] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 06/02/2020] [Accepted: 06/09/2020] [Indexed: 12/14/2022]
Abstract
The recent discovery of comammox Nitrospira as complete nitrifiers has fundamentally renewed perceptions of nitrogen cycling in natural and engineered systems, yet little is known about the environmental controls on these newly recognized bacteria. Based on improved phylogenetic resolution through successful assembly of ten novel genomes (71-96% completeness), we provided the first biogeographic patterns for planktonic and benthic comammox Nitrospira in the Yangtze River over a 6030 km continuum. Our study revealed the widespread distributions and relative abundance of comammox Nitrospira in this large freshwater system, constituting 30 and 46% of ammonia-oxidizing prokaryotes (AOPs) and displaying 30.4- and 17.9-fold greater abundances than canonical Nitrospira representatives in water and sediments, respectively. Comammox Nitrospira contributed more to nitrifier abundances (34-87% of AOPs) in typical oligotrophic environments with a higher pH and lower temperature, particularly in the plateau (clade B), mountain and foothill (clade A) areas of the upper reach. The dominant position of planktonic comammox Nitrospira was replaced by canonical Nitrospira sublineages I/II and ammonia-oxidizing bacteria from the plateau to downstream plain due to environmental selection, while the dissimilarity of benthic comammox Nitrospira was moderately associated with geographic distance. A substantial decrease (83%) in benthic comammox Nitrospira abundance occurred immediately downstream of the Three Gorges Dam, consistent with a similarly considerable decrease in overall sediment bacterial taxa. Together, this study highlights the previously unrecognized dominance of comammox Nitrospira in major river systems and underlines the importance of revisiting the distributions of and controls on nitrification processes within global freshwater environments.
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Affiliation(s)
- Shufeng Liu
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, 100871, Beijing, China
- Beijing Innovation Center for Engineering Science and Advanced Technology, Peking University, 100871, Beijing, China
| | - Haiying Wang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, 100871, Beijing, China
| | - Liming Chen
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, 100871, Beijing, China
| | - Jiawen Wang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, 100871, Beijing, China
| | - Maosheng Zheng
- Key Laboratory of Regional Energy Systems Optimization, Resources and Environmental Research Academy, North China Electric Power University, 102206, Beijing, China
| | - Sitong Liu
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, 100871, Beijing, China
| | - Qian Chen
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, 100871, Beijing, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, 810016, Xining, China
| | - Jinren Ni
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, 100871, Beijing, China.
- Beijing Innovation Center for Engineering Science and Advanced Technology, Peking University, 100871, Beijing, China.
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, 810016, Xining, China.
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20
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Wang L, Lim CK, Klotz MG. High Synteny and Sequence Identity between Genomes of Nitrosococcus oceani Strains Isolated from Different Oceanic Gyres Reveals Genome Economization and Autochthonous Clonal Evolution. Microorganisms 2020; 8:E693. [PMID: 32397339 PMCID: PMC7285500 DOI: 10.3390/microorganisms8050693] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/18/2020] [Accepted: 05/04/2020] [Indexed: 12/31/2022] Open
Abstract
The ammonia-oxidizing obligate aerobic chemolithoautotrophic gammaproteobacterium, Nitrosococcus oceani, is omnipresent in the world's oceans and as such important to the global nitrogen cycle. We generated and compared high quality draft genome sequences of N. oceani strains isolated from the Northeast (AFC27) and Southeast (AFC132) Pacific Ocean and the coastal waters near Barbados at the interface between the Caribbean Sea and the North Atlantic Ocean (C-27) with the recently published Draft Genome Sequence of N. oceani Strain NS58 (West Pacific Ocean) and the complete genome sequence of N. oceani C-107, the type strain (ATCC 19707) isolated from the open North Atlantic, with the goal to identify indicators for the evolutionary origin of the species. The genomes of strains C-107, NS58, C-27, and AFC27 were highly conserved in content and synteny, and these four genomes contained one nearly sequence-identical plasmid. The genome of strain AFC132 revealed the presence of genetic inventory unknown from other marine ammonia-oxidizing bacteria such as genes encoding NiFe-hydrogenase and a non-ribosomal peptide synthetase (NRPS)-like siderophore biosynthesis module. Comparative genome analysis in context with the literature suggests that AFC132 represents a metabolically more diverse ancestral lineage to the other strains with C-107 and NS58 potentially being the youngest. The results suggest that the N. oceani species evolved by genome economization characterized by the loss of genes encoding catabolic diversity while acquiring a higher redundancy in inventory dedicated to nitrogen catabolism, both of which could have been facilitated by their rich complements of CRISPR/Cas and Restriction Modification systems.
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Affiliation(s)
- Lin Wang
- Department of Biological Sciences, University of North Carolina, 9201 University City Boulevard, Charlotte, NC 28223, USA; (L.W.); (C.K.L.)
| | - Chee Kent Lim
- Department of Biological Sciences, University of North Carolina, 9201 University City Boulevard, Charlotte, NC 28223, USA; (L.W.); (C.K.L.)
| | - Martin G. Klotz
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, 2710 Crimson Way, Richland, WA 99354, USA
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21
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Lu S, Sun Y, Lu B, Zheng D, Xu S. Change of abundance and correlation of Nitrospira inopinata-like comammox and populations in nitrogen cycle during different seasons. CHEMOSPHERE 2020; 241:125098. [PMID: 31877618 DOI: 10.1016/j.chemosphere.2019.125098] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 07/25/2019] [Accepted: 10/09/2019] [Indexed: 06/10/2023]
Abstract
Complete-nitrifying bacteria (comammox) play important roles in nitrogen-overloading aquatic systems. However, the understanding of the environmental relevance is still limited. Here, we studied the responses of comammox bacteria (Nitrospira inopinata) in a tributary of the Yellow River, with the water and sediment, microbial, seasonal, and chemical variations considered. Illumina sequencing indicated that the predominant phyla in the river sediment were Proterobacteria, Bacteroidetes, Actinobacteria, and Chloroflex. Quantitative PCR revealed that N. inopinata-like comammox were approximately twice as abundant in the water during the wet season and in the sediment during the dry season than that of other conditions. Significant correlations were found between the abundance of N. inopinata-like comammox and pH (r = 0.58), temperature (r = 0.63), and dissolved oxygen (r = - 0.77). The abundance of N. inopinata-like comammox was higher than that of ammonia oxidizing archaea (AOA), and lower than that of ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB). Furthermore, a significant correlation was discovered between N. inopinata-like comammox and NOB (r = 0.60), and so was anammox bacteria (r = 0.358). Interestingly, N. inopinata-like comammox also showed positive relationships with denitrifying microbes (r = 0.559).
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Affiliation(s)
- Sidan Lu
- College of Water Sciences, Beijing Normal University, Beijing, China
| | - Yujiao Sun
- College of Water Sciences, Beijing Normal University, Beijing, China; Beijing Key Laboratory of Urban Hydrological Cycle and Sponge City Technology, Beijing, China.
| | - Baiyun Lu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Heilongjiang, Harbin, 150090 China
| | - Danyang Zheng
- College of Water Sciences, Beijing Normal University, Beijing, China
| | - Shangwei Xu
- College of Water Sciences, Beijing Normal University, Beijing, China
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