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Tao R, Ding W, Zhang K, Li Y, Li J, Hu B, Chu G. Response of comammox Nitrospira clades A and B communities to long-term fertilization and rhizosphere effects and their relative contribution to nitrification in a subtropical paddy field of China. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 367:121939. [PMID: 39067343 DOI: 10.1016/j.jenvman.2024.121939] [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: 04/23/2024] [Revised: 06/21/2024] [Accepted: 07/21/2024] [Indexed: 07/30/2024]
Abstract
The recently discovered complete ammonia oxidation (comammox Nitrospira) containing clade A and clade B has further complemented our understanding of nitrification process. Nevertheless, understanding the community feature of comammox Nitrospira clades A and B and their relative contribution to nitrification in paddy rhizosphere are still in its infancy. In this study, we assessed the community diversity and structure of comammox Nitrospira clades A and B in paddy rhizosphere and bulk soils under thirty years of different fertilization strategies, i.e., non-fertilization control (CK), chemical fertilizers application (NPK), and NPK plus swine manure (NPKM), respectively. NPKM significantly increased the a-diversity (Chao1 and Shannon indices) of comammox Nitrospira clade A and altered the community structure (P < 0.05) but had little effect on clade B. A two-way analysis of variance (ANOVA) showed that the effect of long-term fertilization on soil comammox Nitrospira community and nitrification potential rate (PNR) was much greater than that of rhizosphere. Compared with NPK, soil PNR was greatly increased by 51.0% under the NPKM treatment in the rhizosphere (P < 0.05). Phylogenetic analysis showed that NPKM improved the relative abundances of sub-clade A.2.1 and sub-clade A.3.2 of the comammox clade A community, with an average increase of 212.2 and 210.4% in both rhizosphere and bulk soils relative to the NPK treatment. Soil organic matter, NH4+-N, and pH were significant soil drivers of comammox Nitrospira clades A and B community. Furthermore, linear regression and structural equation modeling clearly showed that comammox Nitrospira clade A a-diversity were significantly associated with soil PNR (P < 0.05). Our results suggest (i) that comammox Nitrospira clade A are sensitive to the organic fertilization; and (ii) that comammox Nitrospira clade A contribute more to nitrification than clade B under the long-term organic fertilized paddy soil.
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Affiliation(s)
- Rui Tao
- School of Life and Environmental Science, Shaoxing University, Shaoxing, 312000, PR China.
| | - Wangying Ding
- School of Life and Environmental Science, Shaoxing University, Shaoxing, 312000, PR China
| | - Keyi Zhang
- School of Life and Environmental Science, Shaoxing University, Shaoxing, 312000, PR China
| | - Yanyan Li
- Key Laboratory of Agro-Ecological Processes in Subtropical Regions, Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, PR China
| | - Jun Li
- School of Life and Environmental Science, Shaoxing University, Shaoxing, 312000, PR China
| | - Baowei Hu
- School of Life and Environmental Science, Shaoxing University, Shaoxing, 312000, PR China
| | - Guixin Chu
- School of Life and Environmental Science, Shaoxing University, Shaoxing, 312000, PR China
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Qiang R, Wang M, Li Q, Li Y, Li C, Zhang J, Liu H. The different responses of AOA and AOB communities to irrigation systems in the semi-arid region of Northeast China. Front Microbiol 2024; 15:1374618. [PMID: 38774509 PMCID: PMC11106429 DOI: 10.3389/fmicb.2024.1374618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 04/05/2024] [Indexed: 05/24/2024] Open
Abstract
Ammonia oxidation is the rate-limiting step in nitrification and the key step in the nitrogen (N) cycle. Most soil nutrients and biological indicators are extremely sensitive to irrigation systems, from the perspective of improving soil fertility and soil ecological environment, the evaluation of different irrigation systems and suitability of selection, promote crop production and soil quality, study the influence of the soil microenvironment contribute to accurate evaluation of irrigation farmland soil health. Based on the amoA gene, the abundance and community diversity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) and their responses to soil physicochemical factors and enzyme activities were studied in semi-arid areas of Northeast China. The study consisted of three irrigation systems: flood irrigation (FP), shallow buried drip irrigation (DI), and mulched drip irrigation (MF). The results showed that DI and MF significantly increased the contents of alkaline hydrolyzed nitrogen (AN), nitrate nitrogen (NO3--N), soil moisture, and the activities of ammonia monooxygenase (AMO) and hydroxylamine oxidase (HAO). Compared with FP, DI significantly increased the abundance of soil AOA and AOB, while MF significantly increased the abundance of soil AOB. Irrigation systems significantly affected the community composition of ammonia-oxidizing microorganisms (AOM). Also, AN and soil moisture had the greatest influence on the community composition of AOA and AOB, respectively. The AOB community had better stability and stress resistance. Moreover, the symbiotic network of AOB in the three irrigation systems was more complex than that of AOA. Compared with FP, the AOA community under treatment DI had higher complexity and stability, maintaining the versatility and sustainability of the ecosystem, while the AOB community under treatment MF had higher transfer efficiency in terms of matter and energy. In conclusion, DI and MF were more conducive to the propagation of soil AOM in the semi-arid area of Northeast China, which can provide a scientific basis for rational irrigation and N regulation from the perspective of microbiology.
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Affiliation(s)
- Ruowen Qiang
- Key Laboratory of Soil Resource Sustainable Utilization for Jilin Province Commodity Grain Bases, College of Resource and Environmental Science, Jilin Agricultural University, Changchun, China
| | - Meng Wang
- Institute of Agricultural Environment and Resources Research, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Qian Li
- Institute of Agricultural Environment and Resources Research, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Yingjie Li
- Key Laboratory of Soil Resource Sustainable Utilization for Jilin Province Commodity Grain Bases, College of Resource and Environmental Science, Jilin Agricultural University, Changchun, China
| | - Cuilan Li
- Key Laboratory of Soil Resource Sustainable Utilization for Jilin Province Commodity Grain Bases, College of Resource and Environmental Science, Jilin Agricultural University, Changchun, China
| | - Jinjing Zhang
- Key Laboratory of Soil Resource Sustainable Utilization for Jilin Province Commodity Grain Bases, College of Resource and Environmental Science, Jilin Agricultural University, Changchun, China
| | - Hang Liu
- Key Laboratory of Soil Resource Sustainable Utilization for Jilin Province Commodity Grain Bases, College of Resource and Environmental Science, Jilin Agricultural University, Changchun, China
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Feng M, Lin Y, He ZY, Hu HW, Jin S, Liu J, Wan S, Cheng Y, He JZ. Higher stochasticity in comammox Nitrospira community assembly in upland soils than the adjacent paddy soils at a regional scale. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 921:171227. [PMID: 38402820 DOI: 10.1016/j.scitotenv.2024.171227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/22/2024] [Accepted: 02/21/2024] [Indexed: 02/27/2024]
Abstract
Understanding the assembly mechanisms of microbial communities, particularly comammox Nitrospira, in agroecosystems is crucial for sustainable agriculture. However, the large-scale distribution and assembly processes of comammox Nitrospira in agricultural soils remain largely elusive. We investigated comammox Nitrospira abundance, community structure, and assembly processes in 16 paired upland peanuts and water-logged paddy soils in south China. Higher abundance, richness, and network complexity of comammox Nitrospira were observed in upland soils than in paddy soils, indicating a preference for upland soils over paddy soils among comammox Nitrospira taxa in agricultural environments. Clade A.2.1 and clade A.1 were the predominant comammox Nitrospira taxa in upland and paddy soils, respectively. Soil pH was the most crucial factor shaping comammox Nitrospira community structure. Stochastic processes were found to predominantly drive comammox Nitrospira community assembly in both upland and paddy soils, with deterministic processes playing a more important role in paddy soils than in upland soils. Overall, our findings demonstrate the higher stochasticity of comammox Nitrospira in upland soils than in the adjacent paddy soils, which may have implications for autotrophic nitrification in acidic agricultural soils.
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Affiliation(s)
- Mengmeng Feng
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou 350117, China
| | - Yongxin Lin
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou 350117, China.
| | - Zi-Yang He
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, VIC 3010, Australia
| | - Hang-Wei Hu
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, VIC 3010, Australia
| | - Shengsheng Jin
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou 350117, China
| | - Jia Liu
- Soil and Fertilizer & Resources and Environment Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Song Wan
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou 350117, China
| | - Yuheng Cheng
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou 350117, China
| | - Ji-Zheng He
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment, Fujian Normal University, Fuzhou 350117, China; School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, VIC 3010, Australia.
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4
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Wei C, Liang J, Wang R, Chi L, Wang W, Tan J, Shi H, Song X, Cui Z, Xie Q, Cheng D, Wang X. Response of bacterial community metabolites to bacterial wilt caused by Ralstonia solanacearum: a multi-omics analysis. FRONTIERS IN PLANT SCIENCE 2024; 14:1339478. [PMID: 38317834 PMCID: PMC10839043 DOI: 10.3389/fpls.2023.1339478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 12/28/2023] [Indexed: 02/07/2024]
Abstract
The soil microbial community plays a critical role in promoting robust plant growth and serves as an effective defence mechanism against root pathogens. Current research has focused on unravelling the compositions and functions of diverse microbial taxa in plant rhizospheres invaded by Ralstonia solanacearum, however, the specific mechanisms by which key microbial groups with distinct functions exert their effects remain unclear. In this study, we employed a combination of amplicon sequencing and metabolomics analysis to investigate the principal metabolic mechanisms of key microbial taxa in plant rhizosphere soil. Compared to the healthy tobacco rhizosphere samples, the bacterial diversity and co-occurrence network of the diseased tobacco rhizosphere soil were significantly reduced. Notably, certain genera, including Gaiella, Rhodoplanes, and MND1 (Nitrosomonadaceae), were found to be significantly more abundant in the rhizosphere of healthy plants than in that of diseased plants. Eight environmental factors, including exchangeable magnesium, available phosphorus, and pH, were found to be crucial factors influencing the composition of the microbial community. Ralstonia displayed negative correlations with pH, exchangeable magnesium, and cation exchange flux, but showed a positive correlation with available iron. Furthermore, metabolomic analysis revealed that the metabolic pathways related to the synthesis of various antibacterial compounds were significantly enriched in the healthy group. The correlation analysis results indicate that the bacterial genera Polycyclovorans, Lysobacter, Pseudomonas, and Nitrosospira may participate in the synthesis of antibacterial compounds. Collectively, our findings contribute to a more in-depth understanding of disease resistance mechanisms within healthy microbial communities and provide a theoretical foundation for the development of targeted strategies using beneficial microorganisms to suppress disease occurrence.
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Affiliation(s)
- Chengjian Wei
- College of Agriculture, Guangxi University, Nanning, China
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Jinchang Liang
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Rui Wang
- Enshi Tobacco Science and Technology Center, Enshi, China
| | - Luping Chi
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Wenjing Wang
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Jun Tan
- Enshi Tobacco Science and Technology Center, Enshi, China
| | - Heli Shi
- Enshi Tobacco Science and Technology Center, Enshi, China
| | - Xueru Song
- Engineering Center for Biological Control of Diseases and Pests in Tobacco Industry, Yuxi, China
| | - Zhenzhen Cui
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Qiang Xie
- Sichuan Tobacco Science and Technology Center, Chengdu, China
| | - Dejie Cheng
- College of Agriculture, Guangxi University, Nanning, China
| | - Xiaoqiang Wang
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
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Ding F, He T, Qi X, Zhang H, An L, Xu S, Zhang X. Comammox Nitrospira dominates the nitrification in artificial coniferous forest soils of the Qilian Mountains. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167653. [PMID: 37806577 DOI: 10.1016/j.scitotenv.2023.167653] [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: 08/03/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 10/10/2023]
Abstract
Complete ammonia oxidizers (Comammox, CMX) are a newly discovered and important component of the nitrogen cycle. While CMX Nitrospira has been detected in various ecosystems, few studies so far have focused on the relative contribution and co-occurrence network of ammonia oxidizing archaea (AOA), bacteria (AOB), and CMX Nitrospira in artificial forest ecosystems (tree plantations). We evaluated the dynamics of composition, co-occurrence patterns and contribution of soil microbial nitrifiers to nitrification in soil of various tree species with different ages in the Qilian Mountains employing the space for time substitution approach, quantitative PCR and high-throughput sequencing technology. Generally, plantation development significantly reduced soil potential nitrification rates. Inhibition experiments and modular analysis showed that AOA played leading roles in nitrification of abandoned farmland and 17-year-old Hippophae rhamnoides, whereas CMX Nitrospira dominated in 36-year-old Picea crassifolia, 36-year-old Picea crassifolia and Larix gmelinii mixed plantation, and 50-year-old Picea crassifolia. The dominant AOA and CMX Nitrospira lineages in all samples were Group I.1b and Clade B, respectively. The assembly of nitrifier community was governed by stochastic processes, in which dispersal limitation made a significant contribution. The nitrifiers coexist in a mutualistic manner, albeit with possible functional redundancy, while the modular analysis revealed the aggregation pattern of the four modules in different artificial forests' soil. The Mantel test showed that modular formation is mainly affected by NH4+ and SOM. These results broaden our current understanding of the relation between CMX Nitrospira and canonical ammonia oxidizers in terrestrial ecosystems, and provide empirical evidence for not only niche differentiation, but also the relative contribution and co-occurrence patterns of nitrifying communities in an artificial forest ecosystem.
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Affiliation(s)
- Fan Ding
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Tianjiao He
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Xing'e Qi
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Hui Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Lizhe An
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, China; The College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Shijian Xu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Xinfang Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, China.
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6
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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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7
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Dong Z, Ma Y, Yu M, Cai Y, Chen Y, Wu J, Ma F, Hu B. Affinity difference determines the assembly and interaction mode of anammox community reconstructed by siderophores. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 899:165278. [PMID: 37414172 DOI: 10.1016/j.scitotenv.2023.165278] [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: 04/21/2023] [Revised: 06/16/2023] [Accepted: 07/01/2023] [Indexed: 07/08/2023]
Abstract
Anammox community is the core of anammox process. The constancy of the anammox community determines the stability of the anammox process and the ability of withstand environmental impact. Community stability is influenced by the assembly and interaction mode of the community. This study aimed to explore the assembly, interaction mode, and stability of anammox community influenced by two siderophores (enterobactin and putrebactin) specific for Ca. Brocadia and Ca. Kuenenia as produced in our previous research. Siderophores improved the stability of the anammox community, among which vulnerability dropped by 30.02 % and 72.53 % respectively. Enterobactin and putrebactin altered the succession speed and assembly pattern of communities, with a respective increase of 9.77 % and 80.87 % in the deterministic process of anammox community assembly, respectively. Enterobactin and putrebactin reduced the dependence of Ca. Brocadia and Ca. Kuenenia on companion bacteria by 60 items and 27 items respectively. The affinity of different siderophore-Fe with bacterial membrane receptors caused variations in community reconstruction, with Ca. Brocadia and Ca. Kuenenia exhibiting the highest affinity with enterobactin-Fe (-11.4 kcal/mol) and putrebactin-Fe (-9.0 kcal/mol), respectively. This study demonstrated how siderophores can enhance the stability of anammox process by regulating assembly and interaction mode of anammox community, while also revealing the underlying molecular mechanisms.
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Affiliation(s)
- Ziyang Dong
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Yuxin Ma
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Mengwen Yu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Yufei Cai
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Yingluo Chen
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Junwei Wu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Fang Ma
- State Key Lab of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China; Key Laboratory of Environment Remediation and Ecological Health (Zhejiang University), Ministry of Education, Hangzhou 310058, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, 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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Li W, Xiao Y. Microplastics increase soil microbial network complexity and trigger diversity-driven community assembly. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 333:122095. [PMID: 37385357 DOI: 10.1016/j.envpol.2023.122095] [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: 04/03/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/01/2023]
Abstract
The widespread existence of microplastics (MPs) in soil has been extensively demonstrated, and their presence would ineluctably change soil physicochemical properties and microbial community composition. However, there is limited understanding of how MPs affect soil microbial assembly. In this study, three different polymer types of MPs, i.e., high-density polyethylene (HDPE), polystyrene (PS), and polylactic acid (PLA), with the same particle size (100 μm) and dose (2%) were applied under the planted and unplanted condition, Pennisetum alopecuroides was chosen as a model species. Plant growth parameters, soil physicochemical properties, and microbial communities (including bacteria and eukaryotes) were determined. The assembly and the co-occurrence network of microbial communities were analyzed. Results revealed that the effect of MPs on soil physicochemical properties was type-dependent and could influenced by the presence of P . alopecuroides. MPs could enrich bacterial genera related to nitrogen cycle and some pathogens of eukaryotes. The presence of MPs changed bacterial and eukaryotic community assembly, in which diversity drove the deterministic/stochastic assembly processes. MPs addition increased the complexity of bacterial network, while had a minor effect on eukaryotic network. The inhibition of MPs on P . alopecuroides growth decayed over time, HDPE MPs was more harmful to P . alopecuroides growth than PS and PLA MPs. Our findings enormously improved our comprehensions of MPs-induced ecological impacts and interactions of soil bacterial and eukaryotic communities .
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Affiliation(s)
- Wanlin Li
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Yan Xiao
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, 210095, PR China.
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Dong Z, Yu M, Cai Y, Ma Y, Chen Y, Hu B. Directed regulation of anammox communities based on exogenous siderophores for highly efficient nitrogen removal. WATER RESEARCH 2023; 243:120394. [PMID: 37494745 DOI: 10.1016/j.watres.2023.120394] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 07/28/2023]
Abstract
It is expected that the quicker domestication of anaerobic ammonia oxidation (anammox) communities and the enhancement of their nitrogen transformation capability can be achieved through targeted regulation of anammox communities. Iron cast a vital role in the growth and metabolism of anammox bacteria. Specific siderophores offer promising prospects for the targeted regulation of anammox communities by facilitating the efficient utilization of iron. Two siderophores-enterobactin and putrebactin-exclusively for Ca. Brocadia and Ca. Kuenenia were developed to specifically regulate anammox communities towards different directions, respectively. Anammox communities in the reactors evoluted targetedly towards Ca. Brocadia-dominated communities and Ca. Kuenenia-dominated communities, respectively, leading to a maximum increase in community nitrogen removal capacity by 84.64±0.55% and 210.26±0.57%, respectively, under different nitrogen concentrations. It was indicated that siderophores could regulate anammox communities by redistributing iron resources in a targeted manner based on the analyses of transcriptome and proteome. This study provides novel insights into the rational selection and utilization of exogenous siderophores as an effective implement to manipulate anammox communities and create communities with high nitrogen removal ability fleetly.
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Affiliation(s)
- Ziyang Dong
- Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Mengwen Yu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yufei Cai
- Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuxin Ma
- Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yingluo Chen
- Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China; Key Laboratory of Water Pollution Control and Environmental Safety, Zhejiang, China; Key Laboratory of Environment Remediation and Ecological Health (Zhejiang University), Ministry of Education, Hangzhou 310058, China.
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11
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Wentzien NM, Fernández-González AJ, Villadas PJ, Valverde-Corredor A, Mercado-Blanco J, Fernández-López M. Thriving beneath olive trees: The influence of organic farming on microbial communities. Comput Struct Biotechnol J 2023; 21:3575-3589. [PMID: 37520283 PMCID: PMC10372477 DOI: 10.1016/j.csbj.2023.07.015] [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] [Received: 03/09/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 08/01/2023] Open
Abstract
Soil health and root-associated microbiome are interconnected factors involved in plant health. The use of manure amendment on agricultural fields exerts a direct benefit on soil nutrient content and water retention, among others. However, little is known about the impact of manure amendment on the root-associated microbiome, particularly in woody species. In this study, we aimed to evaluate the effects of ovine manure on the microbial communities of the olive rhizosphere and root endosphere. Two adjacent orchards subjected to conventional (CM) and organic (OM) management were selected. We used metabarcoding sequencing to assess the bacterial and fungal communities. Our results point out a clear effect of manure amendment on the microbial community. Fungal richness and diversity were increased in the rhizosphere. The fungal biomass in the rhizosphere was more than doubled, ranging from 1.72 × 106 ± 1.62 × 105 (CM) to 4.54 × 106 ± 8.07 × 105 (OM) copies of the 18 S rRNA gene g-1 soil. Soil nutrient content was also enhanced in the OM orchard. Specifically, oxidable organic matter, total nitrogen, nitrate, phosphorous, potassium and sulfate concentrations were significantly increased in the OM orchard. Moreover, we predicted a higher abundance of bacteria in OM with metabolic functions involved in pollutant degradation and defence against pathogens. Lastly, microbial co-occurrence network showed more positive interactions, complexity and shorter geodesic distance in the OM orchard. According to our results, manure amendment on olive orchards represents a promising tool for positively modulating the microbial community in direct contact with the plant.
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Affiliation(s)
- Nuria M. Wentzien
- Soil and Plant Microbiology Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
| | - Antonio J. Fernández-González
- Soil and Plant Microbiology Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
| | - Pablo J. Villadas
- Soil and Plant Microbiology Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
| | | | - Jesús Mercado-Blanco
- Soil and Plant Microbiology Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
- Crop Protection Department, Instituto de Agricultura Sostenible (CSIC), 14004 Córdoba, Spain
| | - Manuel Fernández-López
- Soil and Plant Microbiology Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
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Hu Z, Yang L, Liu Z, Han J, Zhao Y, Jin Y, Sheng Y, Zhu L, Hu B. Excessive disinfection aggravated the environmental prevalence of antimicrobial resistance during COVID-19 pandemic. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 882:163598. [PMID: 37094669 PMCID: PMC10122561 DOI: 10.1016/j.scitotenv.2023.163598] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 04/01/2023] [Accepted: 04/15/2023] [Indexed: 05/03/2023]
Abstract
During COVID-19 pandemic, chemicals from excessive consumption of pharmaceuticals and disinfectants i.e., antibiotics, quaternary ammonium compounds (QACs), and trihalomethanes (THMs), flowed into the urban environment, imposing unprecedented selective pressure to antimicrobial resistance (AMR). To decipher the obscure character pandemic-related chemicals portrayed in altering environmental AMR, 40 environmental samples covering water and soil matrix from surroundings of Wuhan designated hospitals were collected on March 2020 and June 2020. Chemical concentrations and antibiotic resistance gene (ARG) profiles were revealed by ultra-high-performance liquid chromatography-tandem mass spectrometry and metagenomics. Selective pressure from pandemic-related chemicals ascended by 1.4-5.8 times in March 2020 and then declined to normal level of pre-pandemic period in June 2020. Correspondingly, the relative abundance of ARGs under increasing selective pressure was 20.1 times that under normal selective pressure. Moreover, effect from QACs and THMs in aggravating the prevalence of AMR was elaborated by null model, variation partition and co-occurrence network analyses. Pandemic-related chemicals, of which QACs and THMs respectively displayed close interaction with efflux pump genes and mobile genetic elements, contributed >50 % in shaping ARG profile. QACs bolstered the cross resistance effectuated by qacEΔ1 and cmeB to 3.0 times higher while THMs boosted horizon ARG transfer by 7.9 times for initiating microbial response to oxidative stress. Under ascending selective pressure, qepA encoding quinolone efflux pump and oxa-20 encoding β-lactamases were identified as priority ARGs with potential human health risk. Collectively, this research validated the synergistic effect of QACs and THMs in exacerbating environmental AMR, appealing for the rational usage of disinfectants and the attention for environmental microbes in one-health perspective.
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Affiliation(s)
- Zhichao Hu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lihua Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zishu Liu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jian Han
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yuxiang Zhao
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yihao Jin
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yaqi Sheng
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lizhong Zhu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Baolan Hu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou 310058, China.
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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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14
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Li D, Ren Z, Zhou Y, Jiang L, Zheng M, Liu G. Comammox Nitrospira and Ammonia-Oxidizing Archaea Are Dominant Ammonia Oxidizers in Sediments of an Acid Mine Lake Containing High Ammonium Concentrations. Appl Environ Microbiol 2023; 89:e0004723. [PMID: 36912626 PMCID: PMC10056971 DOI: 10.1128/aem.00047-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 01/31/2023] [Indexed: 03/14/2023] Open
Abstract
Exploring nitrifiers in extreme environments is vital to expanding our understanding of nitrogen cycle and microbial diversity. This study presents that complete ammonia oxidation (comammox) Nitrospira, together with acidophilic ammonia-oxidizing archaea (AOA), dominate in the nitrifying guild in sediments of an acid mine lake (AML). The lake water was characterized by acidic pH below 5 with a high ammonium concentration of 175 mg-N/liter, which is rare on the earth. Nitrification was active in sediments with a maximum nitrate production potential of 70.5 μg-N/(g-dry weight [dw] day) for mixed sediments. Quantitative PCR assays determined that in AML sediments, comammox Nitrospira and AOA amoA genes had relative abundances of 52% and 41%, respectively, among the total amoA genes. Further assays with 16S rRNA and amoA gene amplicon sequencing and metagenomics confirmed their dominance and revealed that the comammox Nitrospira found in sediments belonged to comammox Nitrospira clade A.2. Metagenomic binning retrieved a metagenome-assembled genome (MAG) of the comammox Nitrospira from sediments (completeness = 96.76%), and phylogenomic analysis suggested that it was a novel comammox Nitrospira. Comparative genomic investigation revealed that this comammox Nitrospira contained diverse metal resistance genes and an acidophile-affiliated F-type ATPase. Moreover, it had a more diverse genomic characteristic on nitrogen metabolism than the AOA in sediments and canonical AOB did. The results suggest that comammox Nitrospira is a versatile nitrifier that can adapt to acidic environments even with high ammonium concentrations. IMPORTANCE Ammonia-oxidizing archaea (AOA) was previously considered the sole dominant ammonia oxidizer in acidic environments. This study, however, found that complete ammonia oxidation (comammox) Nitrospira was also a dominant ammonia oxidizer in the sediments of an acidic mine lake, which had an acidic pH < 5 and a high ammonium concentration of 175 mg-N/liter. In combination with average nucleotide identity analysis, phylogenomic analysis suggested it is a novel strain of comammox Nitrospira. Moreover, the adaption of comammox Nitrospira to the acidic lake had been comprehensively investigated based on genome-centric metagenomic approaches. The outcomes of this study significantly expand our understanding of the diversity and adaptability of ammonia oxidizers in the acidic environments.
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Affiliation(s)
- Deyong Li
- Center for Environmental Microplastics Studies, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, and School of Environment, Jinan University, Guangzhou, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Zhichang Ren
- Center for Environmental Microplastics Studies, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, and School of Environment, Jinan University, Guangzhou, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Yangqi Zhou
- Center for Environmental Microplastics Studies, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, and School of Environment, Jinan University, Guangzhou, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Lugao Jiang
- Center for Environmental Microplastics Studies, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, and School of Environment, Jinan University, Guangzhou, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Min Zheng
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), University of Queensland, St. Lucia, Brisbane, Queensland, Australia
| | - Guoqiang Liu
- Center for Environmental Microplastics Studies, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, and School of Environment, Jinan University, Guangzhou, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
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15
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Ecophysiological and Genomic Characterization of the Freshwater Complete Ammonia Oxidizer Nitrospira sp. Strain BO4. Appl Environ Microbiol 2023; 89:e0196522. [PMID: 36719237 PMCID: PMC9973019 DOI: 10.1128/aem.01965-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Complete ammonia oxidizers (comammox) are a group of ubiquitous chemolithoautotrophic bacteria capable of deriving energy from the oxidation of ammonia to nitrate via nitrite. Here, we present a study characterizing the comammox strain Nitrospira sp. BO4 using a combination of cultivation-dependent and molecular methods. The enrichment culture BO4 was obtained from the sediment of Lake Burr Oak, a mesotrophic lake in eastern Ohio. The metagenome of the enrichment culture was sequenced, and a metagenome-assembled genome (MAG) was constructed for Nitrospira sp. BO4. The closest characterized relative of Nitrospira sp. BO4 was "Candidatus Nitrospira kreftii." All genes for ammonia and nitrite oxidation, reductive tricarboxylic acid (TCA) cycle, and other pathways of the central metabolism were detected. Nitrospira sp. BO4 used ammonia and oxidized it to nitrate with nitrite as the intermediate. The culture grew on initial ammonium concentrations between 0.01 and 3 mM with the highest rates observed at the lowest ammonium concentrations. Blue light completely inhibited the growth of Nitrospira sp. BO4, while white light reduced the growth and red light had no effect on the growth. Nitrospira sp. BO4 did not grow on nitrite as its sole substrate. When supplied with ammonium and nitrite, the culture utilized nitrite after most of the ammonium was consumed. In summary, the genomic information of Nitrospira sp. BO4 coupled with the growth experiments shows that Nitrospira sp. BO4 is a freshwater comammox species. Future research will focus on further characterization of the niches of comammox in freshwater environments. IMPORTANCE Nitrification is a key process in the global nitrogen cycle. Complete ammonia oxidizers (comammox) were discovered recently, and only three enrichment cultures and one pure culture have been characterized with respect to activity and growth under different conditions. The cultivated comammox strains were obtained from engineered systems such as a recirculating aquaculture system and hot water pipes. Here, we present the first study characterizing a comammox strain obtained from a mesotrophic freshwater lake. In freshwater environments, comammox coexist with ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Our results will help elucidate physiological characteristics of comammox and the distribution and niche differentiation of different ammonia oxidizers in freshwater environments.
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Wang Y, Zeng X, Ma Q, Zhang Y, Yu W, Zheng Z, Zhang N, Xu L. Differential responses of canonical nitrifiers and comammox Nitrospira to long-term fertilization in an Alfisol of Northeast China. Front Microbiol 2023; 14:1095937. [PMID: 36819044 PMCID: PMC9929954 DOI: 10.3389/fmicb.2023.1095937] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/12/2023] [Indexed: 02/04/2023] Open
Abstract
The newly identified complete ammonia oxidizer (comammox) that converts ammonia directly into nitrate has redefined the long-held paradigm of two-step nitrification mediated by two distinct groups of nitrifiers. However, exploration of the niche differentiation of canonical nitrifiers and comammox Nitrospira and their ecological importance in agroecosystems is still limited. Here, we adopted quantitative PCR (qPCR) and Illumina MiSeq sequencing to investigate the effects of five long-term fertilization regimes in the variations of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), nitrite-oxidizing bacteria (NOB), and comammox Nitrospira abundances and comammox community composition in two soil layers (0-20 cm, topsoil; 20-40 cm, subsoil) in an Alfisol in Northeast China. The fertilization treatments included no fertilizer (CK); chemical nitrogen (N) fertilizer; chemical N; phosphorus (P) and potassium (K) fertilizers (NPK); recycled organic manure (M) and chemical N, P, K plus recycled manure (MNPK). Compared with CK, manure and/or chemical fertilizer significantly increased the AOB amoA gene abundance. Long-term recycled manure increased soil organic matter (SOM) contents and maintained the soil pH, but decreased the NH4 +-N concentrations, which markedly promoted the nxrA and nxrB gene abundances of NOB and the amoA gene abundances of comammox Nitrospira clade A and AOA. Although the comammox Nitrospira clade B abundance tended to decrease after fertilization, the structural equation modeling analysis showed that comammox clade B had direct positive impacts on soil potential ammonia oxidation (PAO; λ = 0.59, p < 0.001). The long-term fertilization regime altered the community composition of comammox Nitrospira. Additionally, comammox Nitrospira clades A and B had individual response patterns to the soil layer. The relative abundance of clade A was predominant in the topsoil in the N (86.5%) and MNPK (76.4%) treatments, while clade B appeared to be dominant in the subsoil (from 78.7 to 88.1%) with lower ammonium contents, implying niche separation between these clades. Soil pH, NH4 +-N and SOM content were crucial factors shaping the soil nitrifying microbial abundances and the comammox Nitrospira community. Together, these findings expand the current understanding of the niche specialization and the important role of comammox Nitrospira in terrestrial ecosystems.
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Affiliation(s)
- Yanan Wang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xibai Zeng
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China,*Correspondence: Xibai Zeng, ✉
| | - Qiang Ma
- Insitute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Yang Zhang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wantai Yu
- Insitute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Zhong Zheng
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Nan Zhang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liyang Xu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
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Liu Z, Zhao Y, Zhang B, Wang J, Zhu L, Hu B. Deterministic Effect of pH on Shaping Soil Resistome Revealed by Metagenomic Analysis. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:985-996. [PMID: 36603127 DOI: 10.1021/acs.est.2c06684] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Soil is recognized as the major reservoir of antibiotic resistance genes (ARGs), harboring the most diverse naturally evolved ARGs on the planet. Multidrug resistance genes are a class of ARGs, and their high prevalence in natural soil ecosystems has recently raised concerns. Since most of these genes express proton motive force (PMF) driven efflux pumps, studying whether soil pH is a determinant for the selection of multidrug efflux pump genes and thus shaping the soil resistome are of great interest. In this study, we collected 108 soils with pH values ranging from 4.37 to 9.69 from multiple ecosystems and profiled the composition of ARGs for metagenomes and metagenome-assembled genomes. We observed the multidrug efflux pump genes enriched in the acidic soil resistome, and their abundances have significant soil pH dependence. This reflects the benefits of high soil proton activity on the multidrug efflux pump genes, especially for the PMF-driven inner membrane transferase. In addition, we preliminary indicate the putative microbial participants in pH shaping the soil resistome by applying ecological analyzing tools such as stepwise regression and random forest model fitting. The decisive influence of proton activity on shaping the resistome is more impactful than any other examined factors, and as the consequence, we revisited the influence of edaphic factors on the soil resistome; i.e., the deterministic selection of resistance mechanisms by edaphic factors could lead to the bottom-up shaping of the ARG composition. Such natural developing mechanisms of the resistome are herein suggested to be considered in assessing human-driven ARG transmissions.
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Affiliation(s)
- Zishu Liu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuxiang Zhao
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Baofeng Zhang
- Hangzhou Ecological and Environmental Monitoring Center, Hangzhou 310007, China
| | - Jiaqi Wang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lizhong Zhu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Baolan Hu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, Hangzhou 310058, China
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18
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Sun X, Tao R, Xu D, Qu M, Zheng M, Zhang M, Mei Y. Role of polyamide microplastic in altering microbial consortium and carbon and nitrogen cycles in a simulated agricultural soil microcosm. CHEMOSPHERE 2023; 312:137155. [PMID: 36372334 DOI: 10.1016/j.chemosphere.2022.137155] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 11/02/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
Microplastics (MPs) are persistent organic pollutants globally, with a continuous increase in MP wastes near and away from the regions of human activities. Studies to date aimed to explore the impact of MPs on ecosystems, but the area of research could not go beyond environmental pollution caused by MPs. To address the menace of MPs, scientists need to pay enough attention to the biogeochemical cycles, microbial communities, and functional microorganisms. Hence, this study aimed to evaluate the impact of adding 0.3% (mass ratio) [low-concentration (LC) group] and 1% [high-concentration (HC) group] of polyamide (PA) MP to the soil microenvironment with regard to the aforementioned parameters. PA MP decreased the soil microbial diversity (Shannon and Simpson indices, P < 0.05). At the phylum level, PA MP increased the abundance of Acidobacteria, Firmicutes, and Crenarchaeota (P < 0.05); at the genus level, it enhanced that of Geobacter, Thiobacillus, Pseudomonas, and Bradyrhizobium (P < 0.01) while decreased that of Bacillus, Flavisolibacter, Geothrix, and Pseudarthrobacter (P < 0.05). PA MP affected the carbon (C) cycle. PA MP accelerated the soil C fixation by enhancing the abundance of the genes accA and pccA. The LC PA MP accelerated organic C degradation and methane metabolism by changing the abundance of mnp, chiA, mcrA, pmoA, and mmoX genes, while the HC PA MP inhibited them with increasing the experimental time. Regarding the effects of PA on the nitrogen (N) cycle, the PA MP promoted N assimilation and ammonification by increasing the abundance of the genes gdh and ureC, the impact of PA MP on N fixation and denitrification depended on its concentration and treating time. This study showed that PA MP impacted the microbial consortium, it also affected the C and N cycles and its effect depended on its concentration and the treating time.
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Affiliation(s)
- Xia Sun
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Ruidong Tao
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Daoqing Xu
- Cotton Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Mengjie Qu
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Mingming Zheng
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Meng Zhang
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Yunjun Mei
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, 430023, China.
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Jiang X, Guo Y, Li H, Li X, Liu J. Ecological evolution during the three-year restoration using rhizosphere soil cover method at a Lead-Zinc tailing pond in Karst areas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 853:158291. [PMID: 36030848 DOI: 10.1016/j.scitotenv.2022.158291] [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: 04/18/2022] [Revised: 08/21/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
A major challenge for the restoration of the Lead-Zinc tailing pond in Karst areas lies in how to establish vegetation with less soil and restore the ecological functions of the substrate. In this study, a novel method, rhizosphere soil cover method (RSC), was applied to recover the vegetation at a Pb-Zn tailing pond in Karst areas. Two local tolerate plants, Miscanthus sinensis and Pueraria phaseoloides, were planted as pioneer species. Although 68 % of the tailing pond was not covered with soil, the vegetation coverage has reached over 90 % after restoration for three years. Compared with the natural revegetation process (vegetation coverage was <5 % after 20 years of natural succession), the revegetation in the tailing pond was accelerated by RSC and planting pioneer species. Both the plant's diversity and richness have significantly increased in the tailings pond during the restoration (p < 0.05). The important value indicators of M. sinensis and P. phaseoloides were the highest in the plant community, indicating the dominant role of these two plants in revegetation. Moreover, the total organic carbon, total nitrogen, total phosphorus, and total potassium in the tailings increased annually (p < 0.05), which demonstrated that the revegetation has improved the chemical properties in the substrate. In addition, the Shannon diversity index of bacteria in the tailings increased significantly from 4.11 to 5.51. The relative abundance of microbial genes related to carbon fixation and nitrogen fixation in the tailings increased by 17 % and 43 %, respectively. Meanwhile, the physicochemical properties, microbial community structure, and nutrient cycling function in the tailings without topsoil were improved more obviously than those in soils. It is thereby concluded that RSC is an efficient means for ecological restoration of the tailing ponds in Karst areas to improve the ecosystem structure and function of Pb-Zn tailings.
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Affiliation(s)
- Xusheng Jiang
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin 541004, China
| | - Yu Guo
- Technical Innovation Center of Mine Geological Environmental Restoration Engineering in Southern Karst Area, MNR, Guilin 541004, China
| | - Haixiang Li
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin 541004, China
| | - Xiangmin Li
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin 541004, China
| | - Jie Liu
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin 541004, China; Technical Innovation Center of Mine Geological Environmental Restoration Engineering in Southern Karst Area, MNR, Guilin 541004, China.
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Chu X, Bai N, Zheng X, Wang Q, Pan X, Li S, Zhang J, Zhang H, He W, Zhong F, Lv W, Zhang H. Effects of straw returning combined with earthworm addition on nitrification and ammonia oxidizers in paddy soil. Front Microbiol 2022; 13:1069554. [PMID: 36590424 PMCID: PMC9800607 DOI: 10.3389/fmicb.2022.1069554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022] Open
Abstract
Introduction Soil ammonia oxidation, which acts as the first and rate-limiting step of nitrification, is driven by ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) and complete ammonia oxidizer (comammox, amoA gene of clade-A and clade-B). Straw returning, widely used ecological technology in China, is an effective measure for promoting straw decomposition and soil nutrient cycling when combined with earthworm addition. However, the effects of straw returning combined with earthworm addition on soil ammonia oxidizers remain poorly understood. Methods A 2-year plot experiment was conducted with 5 treatments: no fertilizer (CK); regular fertilization (RT); straw returning (SR); earthworm addition (W); straw returning + earthworm addition (SRW). The AOA, AOB, comammox clade-A and clade-B community microbial diversities and structures were investigated by high-throughput sequencing. Results The results showed that (1) compared to RT treatment, W, SR, and SRW treatments all significantly increased the richness of AOA and comammox clade-A and clade-B (p < 0.05), and the richness of AOB was only significantly promoted by SRW treatment (p < 0.05). However, only SRW had a higher comammox clade-B diversity index than RT. (2) The ammonia oxidizer community structures were altered by both straw returning and earthworm addition. Soil NH4 +-N was the critical environmental driver for altering the ammonia oxidizer community structure. (3) Compared with RT treatment, the soil potential nitrification rate (PNR) of W and SRW treatments increased by 1.19 and 1.20 times, respectively. The PNR was significantly positively correlated with AOB abundance (path coefficient = 0.712, p < 0.05) and negatively correlated with clade-B abundance (path coefficient = -0.106, p < 0.05). Discussion This study provides scientific support for the application of straw returning combined with earthworm addition to improve soil nitrification with respect to soil ammonia-oxidizing microorganisms.
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Affiliation(s)
- Xiangqian Chu
- Shanghai Academy of Agricultural Sciences, Eco-environmental Protection Institute, Shanghai, China
- Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Naling Bai
- Shanghai Academy of Agricultural Sciences, Eco-environmental Protection Institute, Shanghai, China
- Shanghai Agricultural Academy of Sciences, Key Laboratory of Integrated Rice-Fish Farming Ecosystem, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Xianqing Zheng
- Shanghai Academy of Agricultural Sciences, Eco-environmental Protection Institute, Shanghai, China
- Shanghai Agricultural Academy of Sciences, Key Laboratory of Integrated Rice-Fish Farming Ecosystem, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Quanhua Wang
- Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Xi Pan
- Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Shuangxi Li
- Shanghai Academy of Agricultural Sciences, Eco-environmental Protection Institute, Shanghai, China
- Shanghai Agricultural Academy of Sciences, Key Laboratory of Integrated Rice-Fish Farming Ecosystem, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Juanqin Zhang
- Shanghai Academy of Agricultural Sciences, Eco-environmental Protection Institute, Shanghai, China
- Shanghai Agricultural Academy of Sciences, Key Laboratory of Integrated Rice-Fish Farming Ecosystem, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Haiyun Zhang
- Shanghai Academy of Agricultural Sciences, Eco-environmental Protection Institute, Shanghai, China
- Shanghai Agricultural Academy of Sciences, Key Laboratory of Integrated Rice-Fish Farming Ecosystem, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Wenjie He
- Faculty of Resources and Environmental Science, Hubei University, Wuhan, China
| | - Feng Zhong
- Faculty of Resources and Environmental Science, Hubei University, Wuhan, China
| | - Weiguang Lv
- Shanghai Academy of Agricultural Sciences, Eco-environmental Protection Institute, Shanghai, China
- Shanghai Agricultural Academy of Sciences, Key Laboratory of Integrated Rice-Fish Farming Ecosystem, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Hanlin Zhang
- Shanghai Academy of Agricultural Sciences, Eco-environmental Protection Institute, Shanghai, China
- Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
- Agricultural Environment and Farmland Conservation Experiment Station of Ministry Agriculture, Shanghai, China
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21
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Carreras-Sempere M, Biel C, Viñas M, Guivernau M, Caceres R. The use of recovered struvite and ammonium nitrate in fertigation in a horticultural rotation: agronomic and microbiological assessment. ENVIRONMENTAL TECHNOLOGY 2022:1-17. [PMID: 36453585 DOI: 10.1080/09593330.2022.2154172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Phosphorus and nitrogen recovery from wastewater as struvite and ammonium nitrate (AN) may be viable alternative fertilizers to boost circularity in horticulture. A 2-year fertigated crop rotation in soil under greenhouse conditions was evaluated to determine the efficiency of both recovered products as raw materials for a nutrient solution (NS) manufacture. The effects of these treatments versus synthetic fertilizers were compared in terms of crop performance, plant nutrient uptake, soil chemistry and microbiota. This is the first study to implement struvite through fertigation as the sole source of P in soil crops. Results showed that both recovered products can be used as fertilizers in NS, due to the similar response to the control for different parameters and crops (tomato, lettuce, and cauliflower). However, the AN treatment showed lower yield in the first tomato crop, which results may depend on the cultivar ammonium tolerance. Besides, the concentration of heavy metals in fruits/leaves was below the permissible limits. Total and Olsen phosphorus soil analysis revealed no differences among treatments, resulting in a similar performance of P-struvite to commercial phosphate. Bulk soil bacteria structure, richness and relative dominance were increased over time, while archaea only showed lower evenness, both despite the fertilization strategy. Shannon diversity was not significantly affected. A predominance of ammonia-oxidizing bacteria (AOB) versus archaea (AOA) was observed, while nitrite-oxidizing bacteria (NOB), dominated by Nitrospira, increased with fertigation. Our results demonstrate that fertilizer blends for NS containing recovered nutrients are a feasible alternative to synthetic fertilizers.
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Affiliation(s)
- Mar Carreras-Sempere
- Sustainable Plant Protection Program, Institute of Agrifood Research and Technology (IRTA), Cabrils, Spain
- Sustainability in Biosystems Program, Institute of Agrifood Research and Technology (IRTA), Caldes de Montbui, Spain
| | - Carmen Biel
- Sustainable Plant Protection Program, Institute of Agrifood Research and Technology (IRTA), Cabrils, Spain
| | - Marc Viñas
- Sustainability in Biosystems Program, Institute of Agrifood Research and Technology (IRTA), Caldes de Montbui, Spain
| | - Miriam Guivernau
- Sustainability in Biosystems Program, Institute of Agrifood Research and Technology (IRTA), Caldes de Montbui, Spain
| | - Rafaela Caceres
- Sustainable Plant Protection Program, Institute of Agrifood Research and Technology (IRTA), Cabrils, Spain
- Sustainability in Biosystems Program, Institute of Agrifood Research and Technology (IRTA), Caldes de Montbui, Spain
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22
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Palomo A, Dechesne A, Pedersen AG, Smets BF. Genomic profiling of Nitrospira species reveals ecological success of comammox Nitrospira. MICROBIOME 2022; 10:204. [PMID: 36451244 PMCID: PMC9714041 DOI: 10.1186/s40168-022-01411-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/03/2022] [Indexed: 05/19/2023]
Abstract
BACKGROUND The discovery of microorganisms capable of complete ammonia oxidation to nitrate (comammox) has prompted a paradigm shift in our understanding of nitrification, an essential process in N cycling, hitherto considered to require both ammonia oxidizing and nitrite oxidizing microorganisms. This intriguing metabolism is unique to the genus Nitrospira, a diverse taxon previously known to only contain canonical nitrite oxidizers. Comammox Nitrospira have been detected in diverse environments; however, a global view of the distribution, abundance, and diversity of Nitrospira species is still incomplete. RESULTS In this study, we retrieved 55 metagenome-assembled Nitrospira genomes (MAGs) from newly obtained and publicly available metagenomes. Combined with publicly available MAGs, this constitutes the largest Nitrospira genome database to date with 205 MAGs, representing 132 putative species, most without cultivated representatives. Mapping of metagenomic sequencing reads from various environments against this database enabled an analysis of the distribution and habitat preferences of Nitrospira species. Comammox Nitrospira's ecological success is evident as they outnumber and present higher species-level richness than canonical Nitrospira in all environments examined, except for marine and wastewaters samples. The type of environment governs Nitrospira species distribution, without large-scale biogeographical signal. We found that closely related Nitrospira species tend to occupy the same habitats, and that this phylogenetic signal in habitat preference is stronger for canonical Nitrospira species. Comammox Nitrospira eco-evolutionary history is more complex, with subclades achieving rapid niche divergence via horizontal transfer of genes, including the gene encoding hydroxylamine oxidoreductase, a key enzyme in nitrification. CONCLUSIONS Our study expands the genomic inventory of the Nitrospira genus, exposes the ecological success of complete ammonia oxidizers within a wide range of habitats, identifies the habitat preferences of (sub)lineages of canonical and comammox Nitrospira species, and proposes that horizontal transfer of genes involved in nitrification is linked to niche separation within a sublineage of comammox Nitrospira. Video Abstract.
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Affiliation(s)
- Alejandro Palomo
- Department of Environmental and Resource Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Arnaud Dechesne
- Department of Environmental and Resource Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Anders G. Pedersen
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Copenhagen, Denmark
| | - Barth F. Smets
- Department of Environmental and Resource Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
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23
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Tawfik A, Al-Sayed A, Hassan GK, Nasr M, El-Shafai SA, Alhajeri NS, Khan MS, Akhtar MS, Ahmad Z, Rojas P, Sanz JL. Electron donor addition for stimulating the microbial degradation of 1,4 dioxane by sequential batch membrane bioreactor: A techno-economic approach. CHEMOSPHERE 2022; 306:135580. [PMID: 35810864 DOI: 10.1016/j.chemosphere.2022.135580] [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: 05/06/2022] [Revised: 06/27/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
The presence of 1,4 dioxane in wastewater is associated with severe health and environmental issues. The removal of this toxic contaminant from the industrial effluents prior to final disposal is necessary. The study comprehensively evaluates the performance of sequential batch membrane bioreactor (MBR) for treating wastewater laden with 1,4 dioxane. Acetate was supplemented to the wastewater feed as an electron donor for enhancing and stimulating the microbial growing activities towards the degradation of 1,4 dioxane. The removal efficiency of 1,4 dioxane was maximized to 87.5 ± 6.8% using an acetate to dioxane (A/D) ratio of 4.0, which was substantially dropped to 31.06 ± 3.7% without acetate addition. Ethylene glycol, glyoxylic acid, glycolic acid, and oxalic acid were the main metabolites of 1,4 dioxane biodegradation using mixed culture bacteria. The 1,4 dioxane degrading bacteria, particularly the genus of Acinetobacter, were promoted to 92% at the A/D ratio of 4.0. This condition encouraged as well the increase of the main 1,4 dioxane degraders, i.e., Xanthomonadales (12.5%) and Pseudomonadales (9.1%). However, 50% of the Sphingobacteriales and 82.5% of Planctomycetes were reduced due to the inhibition effect of the 1,4 dioxane contaminate. Similarly, the relative abundance of Firmicutes, Verrucomicrobia, Chlamydiae, Actinobacteria, Chloroflexi, and Nitrospirae was reduced in the MBR at the A/D ratio of 4.0. The results derived from the microbial analysis and metabolites detection at different A/D ratios indicated that acetate supplementation (as an electron donor) maintained an essential role in encouraging the microorganisms to produce the monooxygenase enzymes responsible for the biodegradation process. Economic feasibility of such a MBR system showed that for a designed flow rate of 30 m3∙d-1, the payback period from reusing the treated wastewater would reach 6.6 yr. The results strongly recommend the utilization of mixed culture bacteria growing on acetate for removing 1,4 dioxane from the wastewater industry, achieving dual environmental and economic benefits.
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Affiliation(s)
- Ahmed Tawfik
- National Research Centre, Water Pollution Research Department, 33 El-Bohouth St., Dokki, P.O. 12622, Giza, Egypt.
| | - Aly Al-Sayed
- National Research Centre, Water Pollution Research Department, 33 El-Bohouth St., Dokki, P.O. 12622, Giza, Egypt
| | - Gamal K Hassan
- National Research Centre, Water Pollution Research Department, 33 El-Bohouth St., Dokki, P.O. 12622, Giza, Egypt
| | - Mahmoud Nasr
- Sanitary Engineering Department, Faculty of Engineering, Alexandria University, Alexandria, 21544, Egypt
| | - Saber A El-Shafai
- National Research Centre, Water Pollution Research Department, 33 El-Bohouth St., Dokki, P.O. 12622, Giza, Egypt
| | - Nawaf S Alhajeri
- Department of Environmental Technology Management, College of Life Sciences, Kuwait University, P.O. Box 5969, Safat 13060, Kuwait.
| | - Mohd Shariq Khan
- Department of Chemical Engineering, Dhofar University, Salalah, 211, Oman
| | - Muhammad Saeed Akhtar
- School of Chemical Engineering, Yeungnam University, 280 Daehak-ro, Gyeongsan, Gyeongbuk, 38541, Republic of Korea.
| | - Zubair Ahmad
- School of Chemical Engineering, Yeungnam University, 280 Daehak-ro, Gyeongsan, Gyeongbuk, 38541, Republic of Korea.
| | - Patricia Rojas
- Universidad Autonoma de Madrid, Department of Molecular Biology, Madrid, 28049, Spain
| | - Jose L Sanz
- Universidad Autonoma de Madrid, Department of Molecular Biology, Madrid, 28049, Spain
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24
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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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25
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Lin S, Liu Z, Wang Y, Li J, Wang G, Ye J, Wang H, He H. Soil metagenomic analysis on changes of functional genes and microorganisms involved in nitrogen-cycle processes of acidified tea soils. FRONTIERS IN PLANT SCIENCE 2022; 13:998178. [PMID: 36311106 PMCID: PMC9614370 DOI: 10.3389/fpls.2022.998178] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/26/2022] [Indexed: 06/01/2023]
Abstract
Nitrogen (N) is the first essential nutrient for tea growth. However, the effect of soil acidification on soil N cycle and N forms in tea plantation are unclear. In this study, the nitrogen contents, soil enzyme activity and N mineralization rate in acidified soil of tea plantation were measured. Moreover, the effects of soil acidification on N cycling functional genes and functional microorganisms were explored by soil metagenomics. The results showed that the NH4 +-N, available N and net N mineralization rate in the acidified tea soil decreased significantly, while the NO3 --N content increased significantly. The activities of sucrase, protease, catalase and polyphenol oxidase in the acidified tea soil decreased significantly. The abundance of genes related to ammonification, dissimilatory N reduction, nitrification and denitrification pathway in the acidified tea soil increased significantly, but the abundance of functional genes related to glutamate synthesis and assimilatory N reduction pathway were opposite. In addition, the abundance of Proteobacteria, Actinobacteria, Chloroflexi, Nitrospirae, Actinomadura, Nitrospira etc. microorganisms related to nitrification, denitrification and pathogenic effect increased significantly in the acidified tea soil. The correlation results showed that soil pH and N forms were correlated with soil enzyme activity, N cycling function genes and microbial changes. In conclusion, soil acidification results in significant changes in enzyme activity, gene abundance and microorganism involved in various N cycle processes in acidified tea soil, which leads to imbalance of soil N form ratio and is not conducive to N transformation and absorption of tea trees.
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Affiliation(s)
- Shunxian Lin
- Key Laboratory of Agroecological Processing and Safety Monitoring of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhijun Liu
- Key Laboratory of Agroecological Processing and Safety Monitoring of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuchao Wang
- Key Laboratory of Agroecological Processing and Safety Monitoring of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiayu Li
- Key Laboratory of Agroecological Processing and Safety Monitoring of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Gege Wang
- Key Laboratory of Agroecological Processing and Safety Monitoring of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jianghua Ye
- Key Laboratory of Agroecological Processing and Safety Monitoring of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Tea and Food Science, Wuyi University, Wuyishan, China
| | - Haibin Wang
- Key Laboratory of Agroecological Processing and Safety Monitoring of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Sciences, Longyan University, Longyan, China
| | - Haibin He
- Key Laboratory of Agroecological Processing and Safety Monitoring of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
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Zhao Y, Chen W, Zhang P, Cai J, Lou Y, Hu B. Microbial cooperation promotes humification to reduce antibiotic resistance genes abundance in food waste composting. BIORESOURCE TECHNOLOGY 2022; 362:127824. [PMID: 36028052 DOI: 10.1016/j.biortech.2022.127824] [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: 07/13/2022] [Revised: 08/18/2022] [Accepted: 08/20/2022] [Indexed: 06/15/2023]
Abstract
Antibiotic resistance genes (ARGs) fate in a full-scale Food waste (FW) facility was investigated. Results showed that with the changes in ARGs, microbial networks could be naturally divided into two clusters, named as the ARGs increasing group (AI group) and the ARGs decreasing group (AD group). The significant difference between two groups (i.e. stronger microbial competition in the AI group and stronger microbial cooperation in the AD group) implied that the variation in ARGs over time were caused by a switch between competition and cooperation. These results indicated that microbial competition might increase ARGs abundance, while cooperation might reduce it. Meanwhile, structural-equation-model (SEM model) showed that humification indexes (e.g. GI value) was an indicator for characterizing microbial interactions and ARGs. The results of the linear model further confirmed that mature compost (GI values > 92.6 %) could reduce the risk of ARGs.
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Affiliation(s)
- Yuxiang Zhao
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Weizhen Chen
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Pan Zhang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Jingjie Cai
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Yicheng Lou
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Baolan Hu
- College of Environmental and Resource Sciences, 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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27
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Yuan Z, Liu Q, Pang Z, Fallah N, Liu Y, Hu C, Lin W. Sugarcane Rhizosphere Bacteria Community Migration Correlates with Growth Stages and Soil Nutrient. Int J Mol Sci 2022; 23:ijms231810303. [PMID: 36142216 PMCID: PMC9499485 DOI: 10.3390/ijms231810303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 11/25/2022] Open
Abstract
Plants and rhizosphere bacterial microbiota have intimate relationships. As neighbors of the plant root system, rhizosphere microorganisms have a crucial impact on plant growth and health. In this study, we sampled rhizosphere soil of sugarcane in May (seedling), July (tillering), September (elongation) and November (maturity), respectively. We employ 16S rRNA amplicon sequencing to investigate seasonal variations in rhizosphere bacteria community structure and abundance, as well as their association with soil edaphic factors. The results demonstrate that soil pH, total nitrogen (TN) and available nitrogen (AN) decrease substantially with time. Rhizosphere bacteria diversity (Shannon) and the total enriched OTUs are also significantly higher in July relative to other months. Bacteria OTUs and functional composition exhibit a strong and significant correlation with soil temperature (Tem), suggesting that Tem was the potential determinant controlling rhizosphere bacteria diversity, enriched OTUs as well as functional composition. Redundancy analysis (RDA) point toward soil total potassium (TK), pH, TN, Tem and AN as principal determinant altering shifting bacteria community structure. Variation partitioning analysis (VPA) analysis further validate that a substantial proportion of variation (70.79%) detected in the rhizosphere bacteria community structure was attributed to edaphic factors. Mfuzz analysis classified the bacterial genera into four distinct clusters, with cluster two exhibiting a distinct and dramatic increase in July, predominantly occupied by Allocatelliglobosispora. The stochastic forest model found the key characteristic bacterial populations that can distinguish the four key growth periods of sugarcane. It may help us to answer some pending questions about the interaction of rhizosphere microorganisms with plants in the future.
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Affiliation(s)
- Zhaonian Yuan
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Province and Ministry Co-Sponsored Collaborative Innovation Center of Sugar Industry, Nanning 530000, China
- Correspondence:
| | - Qiang Liu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ziqin Pang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Agro-Ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Nyumah Fallah
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Agro-Ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yueming Liu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chaohua Hu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wenxiong Lin
- Fujian Provincial Key Laboratory of Agro-Ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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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: 3] [Impact Index Per Article: 1.5] [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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29
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Wang Q, Feng X, Liu Y, Cui W, Sun Y, Zhang S, Wang F. Effects of microplastics and carbon nanotubes on soil geochemical properties and bacterial communities. JOURNAL OF HAZARDOUS MATERIALS 2022; 433:128826. [PMID: 35381513 DOI: 10.1016/j.jhazmat.2022.128826] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 03/19/2022] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
A 100-day soil incubation experiment was conducted to explore the effects of conventional (high-density polyethylene, HDPE) and biodegradable (polylactic acid, PLA) microplastics (MPs) and multiwall carbon nanotubes (MWCNTs) on soil geochemical properties and bacterial communities. Generally, soil pH was increased by 10% HDPE and 10% PLA, but decreased by increasing MWCNTs. Soil dissolved organic carbon content was only increased by 10% PLA. NO3--N content was significantly decreased by MPs, with a decrement of 99% by 10% PLA. Similarly, available P content was reduced by 10% MPs. The activities of urease and alkaline phosphatase were stimulated by 10% PLA, but generally inhibited by HDPE. Conversely, FDAse activity was stimulated by HDPE, but inhibited by 10% PLA, whereas invertase activity decreased with increasing MWCNTs. Overall, both MPs and MWCNTs changed soil bacterial diversity. Co-exposure to 10% MPs and MWCNTs of 1 and 10 mg/kg caused the lowest species richness and Shannon indexes. MPs especially at the 10% dose changed bacterial community composition and the associated metabolic pathways, causing the enrichment of specific taxa and functional genes. Our findings show that conventional and biodegradable MPs differently change soil geochemical properties and microbial community structure and functions, which can be further modified by co-existing MWCNTs.
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Affiliation(s)
- Quanlong Wang
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, PR China
| | - Xueying Feng
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, PR China
| | - Yingying Liu
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, PR China
| | - Wenzhi Cui
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, PR China
| | - Yuhuan Sun
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, PR China
| | - Shuwu Zhang
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, PR China
| | - Fayuan Wang
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, PR China.
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30
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Zhao Y, Weng Q, Hu B. Microbial interaction promote the degradation rate of organic matter in thermophilic period. WASTE MANAGEMENT (NEW YORK, N.Y.) 2022; 144:11-18. [PMID: 35299060 DOI: 10.1016/j.wasman.2022.03.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/19/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
Composting is an efficient, microbe-driven method for the biodegradation of solid organic substrates. In such a complex engineering ecosystem, microbial interaction is more important to function than relative abundance and alpha diversity. However, microbial interaction and its driving force in the composting process has been rarely reported. Thus, we combined network analysis and positive cohesion to analyze the relationship between cooperation among bacteria taxa and the degradation of organic matter in ten industrial-scale food waste composting piles. The results showed that although the complexity of network and microbial diversity were inhibited by high temperature, microbial cooperation was stimulated in the thermophilic period. The positive cohesion, which reflected the degree of microbial cooperation, tended to be positively correlated with the degradation rate of organic matter, functional genera, and genes associated with organic matter degradation. Thus, microbial cooperation was a key factor in the promotion of the degradation of organic matter. From the insight microbial community, Thermobifida was the genera with high abundance, high occurrence frequency, and high contributions to microbial structure. Additionally, it was not only highly associated with the degree of cooperation but was also highly linked with the functional genera in the composting, implying that it might play an important role in regulating cooperation to promote the functional genera. Our research provides a deep understanding of the interaction among bacteria taxa during the composting process. Focusing on the abundance of Thermobifida might be an efficient way to improve composting quality by enhancing the cooperation of microbes.
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Affiliation(s)
- Yuxiang Zhao
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Qin Weng
- Department of Environmental Engineering, Zhejiang University, 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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31
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Hu Z, Yang L, Han J, Liu Z, Zhao Y, Jin Y, Sheng Y, Zhu L, Hu B. Human viruses lurking in the environment activated by excessive use of COVID-19 prevention supplies. ENVIRONMENT INTERNATIONAL 2022; 163:107192. [PMID: 35354102 PMCID: PMC8938188 DOI: 10.1016/j.envint.2022.107192] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 02/24/2022] [Accepted: 03/17/2022] [Indexed: 05/09/2023]
Abstract
Due to extensive COVID-19 prevention measures, millions of tons of chemicals penetrated into natural environment. Alterations of human viruses in the environment, the neglected perceiver of environmental fluctuations, remain obscure. To decipher the interaction between human viruses and COVID-19 related chemicals, environmental samples were collected on March 2020 from surroundings of designated hospitals and receivers of wastewater treatment plant effluent in Wuhan. The virus community and chemical concentration were respectively unveiled in virtue of virome and ultra-high-performance liquid chromatography-tandem mass spectrometry. The complex relationship between virus and chemical was ulteriorly elaborated by random forest model. As an indicator, environmental viruses were corroborated to sensitively reflect the ecological disturbance originated from pandemic prevention supplies. Chemicals especially trihalomethanes restrained the virus community diversity. Confronting this adverse scenario, Human gammaherpesvirus 4 and Orf virus with resistance to trihalomethanes flourished while replication potential of Macacine alphaherpesvirus 1 ascended under glucocorticoids stress. Consequently, human viruses lurking in the environment were actuated by COVID-19 prevention chemicals, which was a constant burden to public health in this ongoing pandemic. Besides, segments of SARS-CoV-2 RNA were detected near designated hospitals, suggesting environment as a missing link in the transmission route. This research innovatively underlined the human health risk of pandemic prevention supplies from the virus - environment interaction, appealing for monitoring of environmental viruses in long term.
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Affiliation(s)
- Zhichao Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Lihua Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Jian Han
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zishu Liu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Yuxiang Zhao
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Yihao Jin
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Yaqi Sheng
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, 310058 China
| | - Lizhong Zhu
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, 310058 China.
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China.
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32
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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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