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Li S, Liu T, Liu C, Sun D, Yan Q, Gao D, Zhang Z. Impact of soil inorganic nitrogen on bacterial phylogeny in estuarine intertidal zones: a study of nitrogen metabolism. Front Microbiol 2024; 14:1341564. [PMID: 38249472 PMCID: PMC10797050 DOI: 10.3389/fmicb.2023.1341564] [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: 11/20/2023] [Accepted: 12/13/2023] [Indexed: 01/23/2024] Open
Abstract
Here we investigated the potential impacts of soil inorganic nitrogen (SIN) content on the phylogenetic characteristics and ecological functions of soil bacterial communities in estuarine intertidal zones in China, aiming to comprehend the response mechanism of soil microorganisms to variations in SIN content within estuarine wetlands. Our results show that SIN in estuarine areas has a significant spatiotemporal variation on spatial and seasonal scales, in this study and is significantly associated with the phylogenetic diversity and phylogenetic turnover of soil bacterial communities. In addition, the results of the metagenomic analysis showed that the relative abundance of nitrogen-cycling functional genes in bacterial communities did not differ significantly in sampling sites and seasons, and weakly correlated with SIN content. Further, the results based on structural equation modeling (SEM) analysis showed that SIN directly and significantly regulated the phylogenetic characteristics of bacterial communities, thereby indirectly affecting the potential of bacterial nitrogen metabolism. This study emphasizes the key influence of SIN variations on the phylogenetic dissimilarity in soil bacterial communities. Moreover, although there was a weak direct relationship between the functional characteristics of the bacterial nitrogen metabolism and SIN content, the spatiotemporal variation of bacterial nitrogen metabolic potential may be indirectly regulated by SIN content by influencing the phylogenetic diversity in bacterial communities. Our study unravels the pivotal mechanisms through which SIN content influences bacterial communities, thereby offering novel insights into the microbial intricacies governing nitrogen metabolism within estuaries.
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Affiliation(s)
- Siqi Li
- Department of Military Oceanography and Hydrography and Cartography, Dalian Naval Academy, Dalian, China
| | - Tianyang Liu
- Department of Military Oceanography and Hydrography and Cartography, Dalian Naval Academy, Dalian, China
| | - Cheng Liu
- Shandong Key Laboratory of Eco-Environmental Science for the Yellow River Delta, Binzhou University, Binzhou, Shandong, China
| | - Donglei Sun
- Department of Military Oceanography and Hydrography and Cartography, Dalian Naval Academy, Dalian, China
| | - Qin Yan
- Department of Military Oceanography and Hydrography and Cartography, Dalian Naval Academy, Dalian, China
| | - Dengzhou Gao
- Key Laboratory of Humid Subtropical Eco-geographical Process of Ministry of Education, College of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Zongxiao Zhang
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
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Ren B, Wang W, Shen L, Yang W, Yang Y, Jin J, Geng C. Nitrogen fertilization rate affects communities of ammonia-oxidizing archaea and bacteria in paddy soils across different climatic zones of China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 902:166089. [PMID: 37549709 DOI: 10.1016/j.scitotenv.2023.166089] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/02/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023]
Abstract
Nitrogen fertilization has important effects on nitrification. However, how the rate of nitrogen fertilization affects nitrification potential, as well as the communities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), remains unclear. We performed a large-scale investigation of nitrification potential and ammonia-oxidizer communities in Chinese paddy fields at different nitrogen fertilization rates across different climatic zones. It was found that the nitrification potential at the high nitrogen fertilization rate (≥150 kg-1 N ha-1) was 23.35 % higher than that at the intermediate rate (100-150 kg-1 N ha-1) and 20.77 % higher than that at the low rate (< 100 kg-1 N ha-1). The nitrification potential showed no significant variation among different nitrogen fertilization rates across climatic zones. Furthermore, the AOA and AOB amoA gene abundance at the high nitrogen fertilization rate was 481.67 % and 292.74 % higher (p < 0.05) than that at the intermediate rate, respectively. Correlation analysis demonstrated a significant positive correlation between AOB abundance and nitrification potential. AOA and AOB community composition differed significantly among nitrogen fertilization rates. Moreover, soil NH4+ content, pH, water content, bulk density, and annual average temperature were regarded as key environmental factors influencing the community structure of ammonia-oxidizers. Taken together, the nitrogen fertilization rate had a significant impact on the communities of AOA and AOB but did not significantly alter the nitrification potential. Our findings provide new insights into the impact of nitrogen fertilization management on nitrification in rice paddy fields.
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Affiliation(s)
- Bingjie Ren
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Weiqi Wang
- Key Laboratory of Humid Subtropical Eco-geographical Process, Ministry of Education, Fujian Normal University, Fuzhou 350117, China
| | - Lidong Shen
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China.
| | - Wangting Yang
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Yuling Yang
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Jinghao Jin
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Caiyu Geng
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
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Gu Q, Ma J, Zhang J, Guo W, Wu H, Sun M, Wang J, Wei X, Zhang Y, Chen M, Xue L, Ding Y, Wu Q. Nitrogen-metabolising microorganism analysis in rapid sand filters from drinking water treatment plant. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:29458-29475. [PMID: 36417065 DOI: 10.1007/s11356-022-23963-0] [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: 10/24/2021] [Accepted: 10/29/2022] [Indexed: 06/16/2023]
Abstract
Sand filters (SFs) are common treatment processes for nitrogen pollutant removal in drinking water treatment plants (DWTPs). However, the mechanisms on the nitrogen-cycling role of SFs are still unclear. In this study, 16S rRNA gene amplicon sequencing was used to characterise the diversity and composition of the bacterial community in SFs from DWTPs. Additionally, metagenomics approach was used to determine the functional microorganisms involved in nitrogen cycle in SFs. Our results showed that Pseudomonadota, Acidobacteria, Nitrospirae and Chloroflexi dominated in SFs. Subsequently, 85 high-quality metagenome-assembled genomes (MAGs) were retrieved from metagenome datasets of selected SFs involving nitrification, assimilatory nitrogen reduction, denitrification and anaerobic ammonia oxidation (anammox) processes. Read mapping to reference genomes of Nitrospira and the phylogenetic tree of the ammonia monooxygenase subunit A gene, amoA, suggested that Nitrospira is abundantly found in SFs. Furthermore, according to their genetic content, a nitrogen metabolic model in SFs was proposed using representative MAGs and pure culture isolate. Quantitative real-time polymerase chain reaction (qPCR) showed that ammonia-oxidising bacteria (AOB) and archaea (AOA), and complete ammonia oxidisers (comammox) were ubiquitous in the SFs, with the abundance of comammox being higher than that of AOA and AOB. Moreover, we identified a bacterial strain with a high NO3-N removal rate as Pseudomonas sp. DW-5, which could be applied in the bioremediation of micro-polluted drinking water sources. Our study provides insights into functional nitrogen-metabolising microbes in SFs of DWTPs.
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Affiliation(s)
- Qihui Gu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Jun Ma
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, People's Republic of China
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Weipeng Guo
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Huiqing Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Ming Sun
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Juan Wang
- College of Food Science, South China Agricultural University, Guangzhou, 510640, People's Republic of China
| | - Xianhu Wei
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Youxiong Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Montong Chen
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Liang Xue
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Yu Ding
- Department of Food Science & Technology, Institute of Food Safety and Nutrition, Jinan University, Huangpu Ave. 601, Guangzhou, 510632, People's Republic of China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China.
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Wen Y, Zhang W, Shan B, Qu J. Evidence of temperature-controlled dissolved inorganic nitrogen distribution in a shallow lake. J Environ Sci (China) 2022; 122:105-114. [PMID: 35717076 DOI: 10.1016/j.jes.2021.09.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/28/2021] [Accepted: 09/28/2021] [Indexed: 11/26/2022]
Abstract
Dissolved inorganic nitrogen (DIN) plays an important role in aquatic ecosystems as an available source of nitrogen (N). Despite recent advances in our understanding of the effects of climate change on DIN in coastal waters, shallow high-latitude lakes exposed to large seasonal temperature differences have received limited research attention. Therefore, in the present study, Baiyangdian Lake (BYDL) was selected as the study area, as a typical high latitude shallow lake in North China. Based on water and sediment samples collected in spring, summer and winter seasons, DIN accumulation in sedimentary pore water and DIN diffusion fluxes at the sediment-water interface were quantified under different temperature conditions. Correlation analysis was used to establish the effects of temperature on DIN concentration and diffusion in different media. Results show that the diffusion of DIN at the lake sediment-water interface exhibited a strongly positive relationship with temperature, suggesting that high temperature conditions lead to greater DIN release from sediments. Cold temperatures cause DIN accumulation in sedimentary pore water, providing sufficient substrate for N-related bacteria in the sediment under cold temperature conditions. Temperature controls the vertical distribution of DIN by affecting its migratory diffusion and transformation at the sediment-water interface. These findings are valuable for understanding the impact of climate change on the distribution of N in inland shallow lakes, especially in high latitude shallow lakes subjected to large seasonal temperature differences throughout the year.
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Affiliation(s)
- Yan Wen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenqiang Zhang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Baoqing Shan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jie Qu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
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5
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Li W, Zhang W, Shan B, Sun B, Guo X, Li Z. Risk assessment of heavy metals in suspended particulate matter in a typical urban river. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:46649-46664. [PMID: 35171423 DOI: 10.1007/s11356-022-18966-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
Suspended particulate matter (SPM) is a major source of contamination in urban rivers as it serves as a carrier for pollutants, such as heavy metals. In this study, the Beiyun River, northern China, was used as a case study to determine the characteristics of SPM-associated heavy metal spatial distribution, to evaluate the potential ecological risks and identify heavy metal sources. The concentrations of seven heavy metals and other associated indicators (TC, TN, TP, and OM) were measured at 12 sites and analyzed by Pearson correlation (PC) and principal component analyses (PCA). The average concentrations of Cr, Ni, Cu, Zn, As, Cd, and Pb were 70.72, 27.88, 31.35, 115.70, 27.77, 0.23, and 29.62 mg/kg, respectively, with significant spatial differences occurring between some elements. Igeo values established the ranked order of heavy metal pollutant concentrations in SPM as As > Cd > Zn > Cu > Pb > Cr > Ni. [Formula: see text] analysis demonstrated that the ranked order of potential ecological risk from the seven metals was Cd > As > Cu > Pb > Ni > Cr > Zn. Potential ecological risk index (RI) results confirmed the high potential ecological risk in the study area. Among the measured heavy metals, Cd represented the highest pollution risk, as shown by its highest [Formula: see text] value. Correlation analysis (CA) showed that Zn had a strong correlation with Cu and Pb. Significant positive correlations were found between TC, TN, TP, and Cu. Three element pairs, Zn-Cd, Cr-Cu, and Cr-Ni, were also found to have strong correlations. Zn, Cu, and Ni were mainly introduced by human activities including urban industrial sewage discharge (such as metallurgy and electroplating industrial wastewater), agricultural drainage, and landfill wastewater, while Cr mainly originated from natural processes like mineral weathering and atmospheric precipitation. This information on the concentration, risk, and sources of SPM in Beiyun River provides an important reference for the reduction of heavy metal pollution in SPM in a typical river in the Haihe River Basin (China).
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Affiliation(s)
- Wenye Li
- School of Water and Soil Conservation, Beijing Forestry University, Beijing, 100038, China
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Wenqiang Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
| | - Baoqing Shan
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Baoping Sun
- School of Water and Soil Conservation, Beijing Forestry University, Beijing, 100038, China
| | - Xiaoping Guo
- School of Water and Soil Conservation, Beijing Forestry University, Beijing, 100038, China
| | - Zhenhan Li
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
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He Y, Zhou Y, Weng R, Wang J, Chen J, Huang M. Responses of Ammonia-Oxidizing Archaea and Bacteria in Malodorous River Sediments to Different Remediation Techniques. MICROBIAL ECOLOGY 2021; 81:314-322. [PMID: 32935184 DOI: 10.1007/s00248-020-01597-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 09/01/2020] [Indexed: 06/11/2023]
Abstract
In this study, the joint use of high throughput sequencing, real-time quantitative PCR, and ammonia-oxidizing bacteria (AOB)-inhibiting allylthiourea was used to differentiate between the contributions of ammonia-oxidizing archaea (AOA) vs AOB to ammonia oxidation and ascertain how AOA and AOB responded to two widely used river remediation techniques (aeration and Ca(NO3)2 injection). Results showed that ammonia oxidation was largely attributed to ATU-sensitive AOB rather than AOA and Nitrosomonas was the predominant AOB-related genus (53.86%) in the malodorous river. The contribution of AOB to ammonia oxidation in the context of aeration and Ca(NO3)2 injection was 75.51 ± 2.77% and 60.19 ± 10.44%, respectively. The peak of AOB/AOA ratio and the marked increase of relative abundances of Nitrosomonas and Nitrosospira in aeration runs further demonstrated aeration favored the ammonia oxidation of AOB. Comparatively, Ca(NO3)2 injection could increase the ammonia oxidation contribution of AOA from 31.32 ± 6.06 to 39.81 ± 10.44% and was significantly correlated with Nitrosococcus of AOB (r = 0.796, p < 0.05), Candidatus_Nitrosopelagicus of AOA (r = 0.986, p < 0.01), and AOA Simpson diversity (r = - 0.791, p < 0.05). Moreover, Candidatus_Nitrosopelagicus was only present in Ca(NO3)2 runs. Taken together, Ca(NO3)2 was recognized as an important factor in mediating the growth and ecological niches of ammonia oxidizers.Graphical abstract.
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Affiliation(s)
- Yan He
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, Institute of Eco-Chongming, Technology Innovation Center for Land Spatial Eco-restoration in Metropolitan Area, Ministry of Natural Resources, East China Normal University, Shanghai, 200241, China.
| | - Yunchang Zhou
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, Institute of Eco-Chongming, Technology Innovation Center for Land Spatial Eco-restoration in Metropolitan Area, Ministry of Natural Resources, East China Normal University, Shanghai, 200241, China
| | - Rui Weng
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, Institute of Eco-Chongming, Technology Innovation Center for Land Spatial Eco-restoration in Metropolitan Area, Ministry of Natural Resources, East China Normal University, Shanghai, 200241, China
| | - Jianhua Wang
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, Institute of Eco-Chongming, Technology Innovation Center for Land Spatial Eco-restoration in Metropolitan Area, Ministry of Natural Resources, East China Normal University, Shanghai, 200241, China
| | - Jinghan Chen
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, Institute of Eco-Chongming, Technology Innovation Center for Land Spatial Eco-restoration in Metropolitan Area, Ministry of Natural Resources, East China Normal University, Shanghai, 200241, China
| | - Minsheng Huang
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, Institute of Eco-Chongming, Technology Innovation Center for Land Spatial Eco-restoration in Metropolitan Area, Ministry of Natural Resources, East China Normal University, Shanghai, 200241, China
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Li Y, Gao L, Niu L, Zhang W, Yang N, Du J, Gao Y, Li J. Developing a statistical-weighted index of biotic integrity for large-river ecological evaluations. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 277:111382. [PMID: 33069143 DOI: 10.1016/j.jenvman.2020.111382] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 06/14/2020] [Accepted: 09/13/2020] [Indexed: 06/11/2023]
Abstract
The efficiency, accuracy and universality of ecological assessment methods comprise an important foundation for comprehensive assessment and restoration of large river ecological health at the watershed scale. New evaluation metrics and methods are urgently needed to be developed to adapt the characteristics of large rivers, including geographical differences in surface runoff, regional ecological complexity, and seasonal changes. In this study, a bacteria-weighted index of biotic integrity was developed to assess the ecological health of large rivers (lrBW-IBI) based on compositional and functional characteristics of sediment bacterial communities from 33 sections of the lower mainstream of Yangtze River. Five key metrics were determined by range, responsiveness, and redundancy tests. Principal component analysis (PCA), entropy method, criteria importance through intercriteria correlation and random forest were applied to calculate weighted coefficients of key metrics. The optimal lrBW-IBI was observed through the sum of PCA weighted-metrics: the relative abundance of Latescibacteria (0.234), Gemmatimonadaceae (0.149), Nitrospira spp. (0.234), Rhizobiales (0.228), and nitrogenase NifH (0.156). According to PCA based lrBW-IBI, 12.12%, 24.24%, 39.39%, and 24.24% of river sections were labeled excellent, good, moderate, and relatively poor, respectively. The ecological status of the lower mainstream of the Yangtze River did not change significantly across seasons but declined gradually from upstream to downstream. This study provides a new assessment tool for the ecological health of large rivers and highlights the importance of microbial ecological index in river ecology.
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Affiliation(s)
- Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, PR China
| | - Lin Gao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, PR China
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, PR China.
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, PR China
| | - Nan Yang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, PR China
| | - Jiming Du
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, PR China
| | - Yu Gao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, PR China
| | - Jie Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, PR China
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Wei D, Zeng S, Hou D, Zhou R, Xing C, Deng X, Yu L, Wang H, Deng Z, Weng S, Huang Z, He J. Community diversity and abundance of ammonia-oxidizing archaea and bacteria in shrimp pond sediment at different culture stages. J Appl Microbiol 2020; 130:1442-1455. [PMID: 33021028 DOI: 10.1111/jam.14846] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 08/25/2020] [Accepted: 09/02/2020] [Indexed: 02/06/2023]
Abstract
AIMS Ammonia oxidation is a significant process of nitrogen cycles in a lot of ecosystems sediments while there are few studies in shrimp culture pond (SCP) sediments. This paper attempted to explore the community diversity and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in SCP sediments at different culture stages. METHODS AND RESULTS We collected SCP sediments and analysed the community diversity and abundance of AOA and bacteria in shrimp pond sediment at different culture stages using the ammonia monooxygenase (amoA) gene with quantitative PCR (qPCR) and 16S rRNA gene sequencing. The AOB-amoA gene abundance was showed higher than AOA-amoA gene abundance in SCP sediments on Day 50 and Day 60 after shrimp larvae introducing into the pond, and the diversity of AOA in SCP sediments was higher than that of AOB. The phylogenetic tree revealed that the most of AOA were the member of Nitrosopumilus and Nitrososphaera, and the majority of AOB sequences were clustered into Nitrosospira, Nitrosomonas clusters 6a and 7. The AOA community has close relationship with total organic carbon (TOC), pH, total phosphorus (TP), nitrate reductase, urease, acid phosphatase and β-glucosidase. The AOB community was related to TOC, C/N and nitrate reductase. CONCLUSIONS AOA and AOB play the different ecological roles in SCP sediments at different culture stages. SIGNIFICANCE AND IMPACT OF THE STUDY Our results suggested that the different community diversity and abundance of AOA and AOB in SCP sediments, which may improve our ecological cognition of shrimp culture stages in SCP ecosystems.
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Affiliation(s)
- D Wei
- State Key Laboratory of Biocontrol/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences/School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China.,Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
| | - S Zeng
- State Key Laboratory of Biocontrol/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences/School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China.,Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
| | - D Hou
- State Key Laboratory of Biocontrol/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences/School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China.,Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
| | - R Zhou
- State Key Laboratory of Biocontrol/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences/School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China.,Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
| | - C Xing
- State Key Laboratory of Biocontrol/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences/School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
| | - X Deng
- Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
| | - L Yu
- State Key Laboratory of Biocontrol/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences/School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China.,Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
| | - H Wang
- State Key Laboratory of Biocontrol/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences/School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
| | - Z Deng
- State Key Laboratory of Biocontrol/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences/School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China.,Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
| | - S Weng
- State Key Laboratory of Biocontrol/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences/School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China.,Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
| | - Z Huang
- State Key Laboratory of Biocontrol/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences/School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China.,Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
| | - J He
- State Key Laboratory of Biocontrol/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences/School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China.,Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
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9
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Yu L, Liu S, Jiang L, Wang X, Xiao L. Insight into the nitrogen accumulation in urban center river from functional genes and bacterial community. PLoS One 2020; 15:e0238531. [PMID: 32877444 PMCID: PMC7467313 DOI: 10.1371/journal.pone.0238531] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 08/18/2020] [Indexed: 01/26/2023] Open
Abstract
Along with urbanization, the intensified nitrogen pollution in urban rivers and the form of black-odor rivers has become one of the biggest concerns. Better understanding of the nitrogen transformations and microbial mechanisms occurring within urban rivers could help to manage their water quality. In this study, pollution characteristics, potential nitrogen removal rate, composition and function of bacterial community, and abundance of functional genes associated with nitrogen transformation were comparatively investigated in a typical urban river (FC) and a suburban river (LH). Compared with LH, FC was characterized by higher content of nutrients, lower potential nitrogen removal rate and lower abundance of functional genes associated with nitrogen transformation in both overlying water and sediment, especially in summer. Sediment dissolved organic matter characterized by excitation−emission matrix (EEM) showed that FC was more severely polluted by high nitrogen organic matter. Our results revealed that anammox was the main nitrogen removal pathway in both rivers and potential nitrogen removal rates decreased significantly in summer. Bacterial community analysis showed that the benthic communities were more severely influenced by the pollutant than aquatic ones in both rivers. Furthermore, the FC benthic community was dominated by anaerobic respiring, fermentative, sulfate reduction bacteria. Quantitatively, the denitrification rate showed a significant positive correlation with the abundance of denitrification genes, whilst the anammox rate was significantly negatively correlated with bacterial diversity. Meanwhile, NH4+-N had a significant negative correlation to both denitrification and anammox in sediment. Taken together, the results indicated that the increased nitrogen pollutants in an urban river altered nitrogen removal pathways and bacterial communities, which could in turn exacerbate the nitrogen pollution to this river.
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Affiliation(s)
- Lei Yu
- School of the Environment, State Key Laboratory for Pollution Control and Resource Reuse (SKL-PCRR), Nanjing University, Nanjing, China
| | - ShuLei Liu
- School of the Environment, State Key Laboratory for Pollution Control and Resource Reuse (SKL-PCRR), Nanjing University, Nanjing, China
| | - LiJuan Jiang
- School of the Environment, State Key Laboratory for Pollution Control and Resource Reuse (SKL-PCRR), Nanjing University, Nanjing, China
| | - XiaoLin Wang
- School of the Environment, State Key Laboratory for Pollution Control and Resource Reuse (SKL-PCRR), Nanjing University, Nanjing, China
| | - Lin Xiao
- School of the Environment, State Key Laboratory for Pollution Control and Resource Reuse (SKL-PCRR), Nanjing University, Nanjing, China
- * E-mail:
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10
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Chen J, He Y, Wang J, Huang M, Guo C. Dynamics of nitrogen transformation and bacterial community with different aeration depths in malodorous river. World J Microbiol Biotechnol 2019; 35:196. [DOI: 10.1007/s11274-019-2773-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 11/21/2019] [Indexed: 11/28/2022]
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11
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Dai L, Liu C, Yu L, Song C, Peng L, Li X, Tao L, Li G. Organic Matter Regulates Ammonia-Oxidizing Bacterial and Archaeal Communities in the Surface Sediments of Ctenopharyngodon idellus Aquaculture Ponds. Front Microbiol 2018; 9:2290. [PMID: 30319588 PMCID: PMC6165866 DOI: 10.3389/fmicb.2018.02290] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 09/07/2018] [Indexed: 01/28/2023] Open
Abstract
Ammonia-oxidizing bacteria (AOB) and archaea (AOA) play important roles in nitrogen removal in aquaculture ponds, but their distribution and the environmental factors that drive their distribution are largely unknown. In this study, we collected surface sediment samples from Ctenopharyngodon idellus ponds in three different areas in China that practice aquaculture. The community structure of AOB and AOA and physicochemical characteristics in the ponds were investigated. The results showed that AOA were more abundant than AOB in all sampling ponds except one, but sediment AOB and AOA numbers varied greatly between ponds. Correlation analyses indicated a significant correlation between the abundance of AOB and arylsulfatase, as well as the abundance of AOA and total nitrogen (TN) and arylsulfatase. In addition, AOB/AOA ratio was found to be significantly correlated with the microbial biomass carbon. AOB were grouped into seven clusters affiliated to Nitrosospira and Nitrosomonas, and AOA were grouped into six clusters affiliated to Nitrososphaera, Nitrososphaera sister group, and Nitrosopumilus. AOB/AOA diversity in the surface sediments of aquaculture ponds varied according to the levels of total organic carbon (TOC), and AOB and AOA diversity was significantly correlated with arylsulfatase and β-glucosidase, respectively. The compositions of the AOB communities were also found to be significantly influenced by sediment eutrophic status (TOC and TN levels), and pH. In addition, concentrations of acid phosphatase and arylsulfatase in surface sediments were significantly correlated with the prominent bacterial amoA genotypes, and concentrations of TOC and urease were found to be significantly correlated with the prominent archaeal amoA genotype compositions. Taken together, our results indicated that AOB and AOA communities in the surface sediments of Ctenopharyngodon idellus aquaculture ponds are regulated by organic matter and its availability to the microorganisms.
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Affiliation(s)
- Lili Dai
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China.,College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Chengqing Liu
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China.,College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Liqin Yu
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Chaofeng Song
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Liang Peng
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Xiaoli Li
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Ling Tao
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Gu Li
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
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12
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Yin X, Liu G, Peng L, Hua Y, Wan X, Zhou W, Zhao J, Zhu D. Microbial community of nitrogen cycle-related genes in aquatic plant rhizospheres of Lake Liangzi in winter. J Basic Microbiol 2018; 58:998-1006. [DOI: 10.1002/jobm.201800220] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 07/18/2018] [Accepted: 07/31/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Xingjia Yin
- Laboratory of Eco-Environmental Engineering Research; Huazhong Agricultural University; Wuhan P. R. China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River); Ministry of Agriculture; Wuhan China
| | - Guanglong Liu
- Laboratory of Eco-Environmental Engineering Research; Huazhong Agricultural University; Wuhan P. R. China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River); Ministry of Agriculture; Wuhan China
| | - Lei Peng
- Laboratory of Eco-Environmental Engineering Research; Huazhong Agricultural University; Wuhan P. R. China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River); Ministry of Agriculture; Wuhan China
| | - Yumei Hua
- Laboratory of Eco-Environmental Engineering Research; Huazhong Agricultural University; Wuhan P. R. China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River); Ministry of Agriculture; Wuhan China
| | - Xiaoqiong Wan
- Laboratory of Eco-Environmental Engineering Research; Huazhong Agricultural University; Wuhan P. R. China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River); Ministry of Agriculture; Wuhan China
| | - Wenbing Zhou
- Laboratory of Eco-Environmental Engineering Research; Huazhong Agricultural University; Wuhan P. R. China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River); Ministry of Agriculture; Wuhan China
| | - Jianwei Zhao
- Laboratory of Eco-Environmental Engineering Research; Huazhong Agricultural University; Wuhan P. R. China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River); Ministry of Agriculture; Wuhan China
| | - Duanwei Zhu
- Laboratory of Eco-Environmental Engineering Research; Huazhong Agricultural University; Wuhan P. R. China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River); Ministry of Agriculture; Wuhan China
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13
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Xia X, Zhang S, Li S, Zhang L, Wang G, Zhang L, Wang J, Li Z. The cycle of nitrogen in river systems: sources, transformation, and flux. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2018; 20:863-891. [PMID: 29877524 DOI: 10.1039/c8em00042e] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Nitrogen is a requisite and highly demanded element for living organisms on Earth. However, increasing human activities have greatly altered the global nitrogen cycle, especially in rivers and streams, resulting in eutrophication, formation of hypoxic zones, and increased production of N2O, a powerful greenhouse gas. This review focuses on three aspects of the nitrogen cycle in streams and rivers. We firstly introduce the distributions and concentrations of nitrogen compounds in streams and rivers as well as the techniques for tracing the sources of nitrogen pollution. Secondly, the overall picture of nitrogen transformations in rivers and streams conducted by organisms is described, especially focusing on the roles of suspended particle-water surfaces in overlying water, sediment-water interfaces, and riparian zones in the nitrogen cycle of streams and rivers. The coupling of nitrogen and other element (C, S, and Fe) cycles in streams and rivers is also briefly covered. Finally, we analyze the nitrogen budget of river systems as well as nitrogen loss as N2O and N2 through the fluvial network and give a summary of the effects and consequences of human activities and climate change on the riverine nitrogen cycle. In addition, future directions for the research on the nitrogen cycle in river systems are outlined.
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Affiliation(s)
- Xinghui Xia
- School of Environment, Beijing Normal University, State Key Joint Laboratory of Environmental Simulation and Pollution Control, Beijing, 100875, China.
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14
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Spatiotemporal variation of bacterial and archaeal communities in sediments of a drinking reservoir, Beijing, China. Appl Microbiol Biotechnol 2016; 101:3379-3391. [PMID: 27942905 DOI: 10.1007/s00253-016-8019-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 11/13/2016] [Accepted: 11/16/2016] [Indexed: 01/01/2023]
Abstract
Bacterial and archaeal assemblages are one of the most important contributors to the recycling of nutrients and the decomposition of organic matter in aquatic sediments. However, their spatiotemporal variation and its driving factors remain unclear, especially for drinking reservoirs, which are strongly affected by human consumption. Using quantitative PCR and Illumina MiSeq sequencing, we investigated the bacterial and archaeal communities in the sediments of a drinking reservoir, the Miyun Reservoir, one of the most important drinking sources for Beijing City. The abundance of bacteria and archaea presented no spatiotemporal variation. With respect to community diversity, visible spatial and temporal differences were observed in archaea, whereas the bacterial community showed minor variation. The bacterial communities in the reservoir sediment mainly included Proteobacteria, Bacteroidetes, Nitrospirae, Acidobacteria, and Verrucomicrobia. The bacterial community structure showed obvious spatial variation. The composition of the bacterial operational taxonomic units (OTUs) and main phyla were dam-specific; the composition of samples in front of the dam were significantly different from the composition of the other samples. The archaeal communities were mainly represented by Woesearchaeota and Euryarchaeota. Distinctly spatial and seasonal variation was observed in the archaeal community structure. The sediment NH4+-N, pH, and water depth were identified as the key driving factors of changes in the composition of the bacterial and archaeal communities. Water depth might have the greatest influence on the microbial community structure. The dam-specific community structure may be related to the greater water depth in front of the dam. This finding indicates that water depth might be the greatest contributor to the microbial community structure in the Miyun Reservoir.
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