1
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Wang Z, Li Y, Zheng W, Ji Y, Duan M, Ma L. Ammonia oxidizing archaea and bacteria respond to different manure application rates during organic vegetable cultivation in Northwest China. Sci Rep 2023; 13:8064. [PMID: 37202434 DOI: 10.1038/s41598-023-35134-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 05/12/2023] [Indexed: 05/20/2023] Open
Abstract
Ammonia oxidization is a critical process in nitrogen cycling that involves ammonia oxidizing archaea (AOA) and bacteria (AOB). However, the effects of different manure amounts on ammonia-oxidizing microorganisms (AOMs) over the course of organic vegetables production remains unclear. We used the amoA gene to evaluated AOMs abundance and community structure in organic vegetable fields. Quantitative PCR revealed that AOB were more abundant than AOA. Among them, the amoA copy number of AOB treated with 900 kgN ha-1 was 21.3 times that of AOA. The potential nitrification rate was significantly correlated with AOB abundance (P < 0.0001) but not with AOA, suggesting that AOB might contribute more to nitrification than AOA. AOB sequences were classified into Nitrosomonas and Nitrosospira, and AOA into Nitrosopumilus and Nitrososphaera. Nitrosomonas and Nitrosopumilus were predominant in treatments that received manure nitrogen at ≥ 900 kg ha-1 (52.7-56.5%) and when manure was added (72.7-99.8%), respectively, whereas Nitrosospira and Nitrososphaera occupied more than a half percentage in those that received ≤ 600 kg ha-1 (58.4-84.9%) and no manure (59.6%). A similar manure rate resulted in more identical AOMs' community structures than greater difference manure rate. The bacterial amoA gene abundances and ratios of AOB and AOA showed significantly positive correlations with soil electrical conductivity, total carbon and nitrogen, nitrate, phosphorus, potassium, and organic carbon, indicating that these were potential key factors influencing AOMs. This study explored the AOMs' variation in organic vegetable fields in Northwest China and provided a theoretical basis and reference for the subsequent formulation of proper manure management.
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Affiliation(s)
- Zhan Wang
- Research Centre of Intelligent Equipment, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
- Guyuan Branch, Ningxia Academy of Agricultural and Forestry Sciences, Guyuan, 756000, China
| | - Yinkun Li
- Research Centre of Intelligent Equipment, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Wengang Zheng
- Research Centre of Intelligent Equipment, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Yuru Ji
- Research Centre of Intelligent Equipment, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Minjie Duan
- Beijing Key Laboratory of Ecological Function Assessment and Regulation Technology of Green Space, Beijing Urban Ecosystem Positioning Observation and Research Station, Beijing Institute of Landscape Architecture, Beijing, 100102, China
| | - Li Ma
- Wuzhong National Agricultural Science and Technology Park Management Committee, Wuzhong, 751100, Ningxia, China
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2
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Yue Y, Wang F, Pan J, Chen XP, Tang Y, Yang Z, Ma J, Li M, Yang M. Spatiotemporal dynamics, community assembly and functional potential of sedimentary archaea in reservoirs: coaction of stochasticity and nutrient load. FEMS Microbiol Ecol 2022; 98:6701916. [PMID: 36111740 DOI: 10.1093/femsec/fiac109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 08/16/2022] [Accepted: 09/14/2022] [Indexed: 01/21/2023] Open
Abstract
Archaea participate in biogeochemical cycles in aquatic ecosystems, and deciphering their community dynamics and assembly mechanisms is key to understanding their ecological functions. Here, sediments from 12 selected reservoirs from the Wujiang and Pearl River basins in southwest China were investigated using 16S rRNA Illumina sequencing and quantitative PCR for archaeal abundance and richness in all seasons. Generally, archaeal abundance and α-diversity were significantly correlated with temperature; however, β-diversity analysis showed that community structures varied greatly among locations rather than seasons, indicating a distance-decay pattern with geographical variation. The null model revealed the major contribution of stochasticity to archaeal community assembly, which was further confirmed by the neutral community model that could explain 71.7% and 90.2% of the variance in archaeal assembly in the Wujiang and Pearl River basins, respectively. Moreover, sediment total nitrogen and organic carbon levels were significantly correlated with archaeal abundance and α-diversity. Interestingly, these nutrient levels were positively and negatively correlated, respectively, with the abundance of methanogenic and ammonia-oxidized archaea: the dominant sedimentary archaea in these reservoirs. Taken together, this work systematically characterized archaeal community profiles in reservoir sediments and demonstrated the combined action of stochastic processes and nutrient load in shaping archaeal communities in reservoir ecosystems.
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Affiliation(s)
- Yihong Yue
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Fushun Wang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, 518060, China.,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Xue-Ping Chen
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Yi Tang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Zhihong Yang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Jing Ma
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, 518060, China.,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Ming Yang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
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3
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He S, Zhao Z, Tian Z, Xu C, Liu Y, He D, Zhang Y, Zheng M. Comammox bacteria predominate among ammonia-oxidizing microorganisms in municipal but not in refinery wastewater treatment plants. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 316:115271. [PMID: 35594823 DOI: 10.1016/j.jenvman.2022.115271] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 05/03/2022] [Accepted: 05/07/2022] [Indexed: 06/15/2023]
Abstract
Comammox bacteria have proved to be one dominant and significant ammonia-oxidizing microorganisms (AOMs) in municipal wastewater treatment plants (WWTPs), however, it still remains unknown about their abundance and diversity in industrial WWTPs. In this study, activated sludge samples from 8 municipal WWTPs and 6 industrial WWTPs treating refinery wastewater were taken and analyzed using qPCR and amoA gene sequencing. Intriguingly, quantitative real-time PCR (qPCR) results suggested that comammox bacteria had a higher numerical abundance compared with ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in municipal WWTPs but did not in refinery WWTPs. Moreover, comammox amoA sequences obtained from high-throughput sequencing were retrieved from all the 8 municipal samples but only 1 industrial sample. Further phylogenetic analysis revealed that N. nitrosa cluster accounted for as high as 79.56% of the total comammox affiliated sequences, which was the most numerically abundant comammox species in municipal WWTPs. This study provided new insights into the abundance and diversity of comammox bacteria in the biological nitrification process in municipal and refinery wastewater treatment systems.
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Affiliation(s)
- Shishi He
- The Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, Main Building G619, North China Electric Power University, Beijing, 102206, China
| | - Zhirong Zhao
- The Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, Main Building G619, North China Electric Power University, Beijing, 102206, China
| | - Zhichao Tian
- The Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, Main Building G619, North China Electric Power University, Beijing, 102206, China
| | - Chi Xu
- The Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, Main Building G619, North China Electric Power University, Beijing, 102206, China
| | - Yuan Liu
- The Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, Main Building G619, North China Electric Power University, Beijing, 102206, China
| | - Da He
- Key Laboratory of Ecological Impacts of Hydraulic Projects and Restoration of Aquatic Ecosystem of Ministry of Water Resources, Institute of Hydroecology, Ministry of Water Resources & Chinese Academy of Sciences, Wuhan, China
| | - Yinghui Zhang
- Guangxi Huantou Water Group Co. LTD, Nanning, 530015, China
| | - Maosheng Zheng
- The Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, Main Building G619, North China Electric Power University, Beijing, 102206, China.
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4
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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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5
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Wei H, Lin X. Shifts in the relative abundance and potential rates of sediment ammonia-oxidizing archaea and bacteria along environmental gradients of an urban river-estuary-adjacent sea continuum. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 771:144824. [PMID: 33545473 DOI: 10.1016/j.scitotenv.2020.144824] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in N cycling in sediments globally. However, little is known about their ammonia oxidation rates along a river-estuary-sea continuum. In this study, we investigated how the potential ammonia oxidation rates (PARs) of AOA and AOB changed spatially along a continuum comprising three habitats: the Shanghai urban river network, the Yangtze Estuary, and the adjacent East China Sea, in summer and winter. The AOA and AOB PARs (0.53 ± 0.49 and 0.72 ± 0.69 μg N g-1 d-1, mean ± SD, respectively) and their amoA gene abundance (0.47 ± 0.85 × 106 and 2.4 ± 3.54 × 106 copies g-1, respectively) decreased along the continuum, particularly from the urban river to the estuary, driven by decreasing sediment total organic C and N and other correlated inorganic nutrients (e.g., NH4+) along the gradient of anthropogenic influences. These spatial patterns were consistent between the seasons. The urban river network, where the anthropogenic influences were strongest, saw the largest seasonal differences, as both AOA and AOB had higher PARs and abundance in summer than in winter. The ratios between AOA and AOB PARs (~0.87 ± 0.51) and gene abundances (~0.25 ± 0.24), however, were predominantly <1, indicating an AOB-dominated community. Comparing the different NH4+ consumption pathways, total aerobic oxidation accounted for 12-26% of the total consumption, with the largest proportion in the estuary, where the system was well oxygenated, and the lowest in the adjacent sea, where inorganic N was highly depleted. This study revealed the spatiotemporal patterns of AOA and AOB potential rates and gene abundance along gradients of human influences and identified organic matter and nutrients as key environmental factors that shaped the variation of AOA and AOB along the continuum.
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Affiliation(s)
- Hengchen Wei
- The University of Texas at Austin Marine Science Institute, 750 Channel View Drive, Port Aransas, TX 78373, USA
| | - Xianbiao Lin
- Laboratory of Microbial Ecology and Matter Cycles, School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China; School of Geographic Sciences, Key Laboratory of Geographic Information Science of the Ministry of Education, East China Normal University, Shanghai 200241, China; Southern Laboratory of Ocean Science and Engineering (Guangdong, Zhuhai), Zhuhai 519000, China.
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6
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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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7
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Wang X, Lu L, Zhou X, Tang X, Kuang L, Chen J, Shan J, Lu H, Qin H, Adams J, Wang B. Niche Differentiation of Comammox Nitrospira in the Mudflat and Reclaimed Agricultural Soils Along the North Branch of Yangtze River Estuary. Front Microbiol 2021; 11:618287. [PMID: 33584582 PMCID: PMC7873905 DOI: 10.3389/fmicb.2020.618287] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/15/2020] [Indexed: 01/13/2023] Open
Abstract
The discovery of complete ammonia oxidation (comammox), oxidizing ammonia to nitrate via nitrite in a single organism, has redefined the traditional recognition of the two-step nitrification driven by two functional groups (ammonia-oxidizing and nitrite-oxidizing microorganisms). However, the understanding of the distribution and niche differentiation of comammox Nitrospira in the estuarine mudflats and their reclaimed agricultural soils is still limited. Here, we investigated the abundance, diversity and community structures of comammox Nitrospira in the mudflats and the reclaimed agricultural soils in the northern Yangtze River estuary. Quantitative PCR showed the abundances of amoA genes of comammox were lower than that of ammonia-oxidizing bacteria (AOB) in nearly all samples. Amplicon sequencing of amoA genes revealed that the community structures of comammox Nitrospira were significantly (P < 0.001) different between the original mudflats and the reclaimed agricultural soils, indicating niche differentiation among comammox Nitrospira clades (clade A.1, clade A.2, and clade B). The clade A.1 was the dominant group of comammox Nitrospira in the mudflats, while clade B predominated in the agricultural soils. However, the members of clade A.2 could be clearly divided into two groups, the mudflat-preferred and agricultural soil-preferred groups, suggesting more complicated ecological preferences within this sub-clade. Furthermore, it was demonstrated that salinity, organic matter (OM) and NO3–-N had a significantly influence on the distribution of comammox Nitrospira in the estuarine environment. Clade A.1 and nearly half members of clade A.2 were positively correlated with salinity, and negatively correlated with the concentrations of OM and NO3–-N. In contrast, the clade B and the other half members of clade A.2 showed the exact opposite pattern: a negative correlation with salinity and positive correlation with OM and NO3–-N. The co-occurrence network demonstrated that the operational taxonomic units (OTUs) within the same (sub-)clade were mostly positively correlated, indicating the similar niche preferences among the members from the same (sub-)clade of comammox Nitrospira. Taken together, our results revealed the niche differentiation of comammox Nitrospira in estuarine ecosystems where salinity and OM were the primary factors responsible for the distinct ecological distribution patterns.
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Affiliation(s)
- Xinxin Wang
- College of Environmental Science and Engineering, China West Normal University, Nanchong, China.,Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China.,State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Lu Lu
- College of Environmental Science and Engineering, China West Normal University, Nanchong, China
| | - Xue Zhou
- College of Agricultural Engineering, Hohai University, Nanjing, China
| | - Xiufeng Tang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Lu Kuang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Junhui Chen
- Key State Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Jun Shan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Huijie Lu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China
| | - Hua Qin
- Key State Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Jonathan Adams
- School of Geography and Ocean Science, Nanjing University, Nanjing, China
| | - Baozhan Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
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8
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Wang C, Wu R, Song Y, Guo J, Liu R, Cui Y. Differences in nitrification and ammonium-oxidising prokaryotes in the process of wetland restoration. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2020; 56:136-144. [PMID: 33259261 DOI: 10.1080/10934529.2020.1852845] [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: 05/16/2020] [Revised: 11/06/2020] [Accepted: 11/12/2020] [Indexed: 06/12/2023]
Abstract
Ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB) are ammonium oxidising prokaryotes that can drive soil nitrification in wetlands. During the restoration of wetlands, different types of land use soils (agricultural soil [AS], restored wetland soil [RS], and natural wetland soil [NWS]) are present. However, studies on the effects of changes in the types of land use in wetlands during restoration on nitrification and the community composition of AOA and AOB are still not well understood. In this study, the differences in the potential nitrification rate (PNR) and community composition of AOA and AOB in AS, RS, and NWS were compared and discussed. The results indicated that the PNRs in the AS, RS, and NWS were on the same order of magnitude. Nitrification was mainly driven by AOB. High-throughput sequencing results showed that the genus Nitrososphaera of AOA and unclassified_o_Nitrosomonadales of AOB were only detected in the AS. Redundancy analysis (RDA) results indicated that the community composition of AOA was mostly influenced by pH, while TC was the most influential variable on the community composition of AOB. Our study provides a basis for distinguishing the roles of ammonium-oxidising prokaryotes in nitrification and further understanding the changes in nitrifying activity in wetlands during restoration.
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Affiliation(s)
- Chunyong Wang
- School of Chemical and Environmental Engineering, Liaoning University of Technology, Jinzhou, PR China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, PR China
| | - Rui Wu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, PR China
| | - Yi Song
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, PR China
| | - Jianbo Guo
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, PR China
| | - Ruyin Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, PR China
| | - Yanshan Cui
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, PR China
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9
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Lin J, Chen N, Yuan X, Tian Q, Hu A, Zheng Y. Impacts of human disturbance on the biogeochemical nitrogen cycle in a subtropical river system revealed by nitrifier and denitrifier genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 746:141139. [PMID: 32745858 DOI: 10.1016/j.scitotenv.2020.141139] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 07/15/2020] [Accepted: 07/19/2020] [Indexed: 06/11/2023]
Abstract
Human activities have largely modified nitrogen (N) sources supply, cycling and export from land to ocean. Nitrification and denitrification are vital processes alleviating N pollution in aquatic ecosystems but the diverse responses and niche of microbial N retention to human disturbance are still understudied. Here we investigated the changes in N species and functional genes in the urban, agriculture and reservoir river sections of the Jiulong River (southeast China). Our results show that ammonia-oxidizing bacteria (AOB) (Nitrosomonas) were dominant in the urban river section receiving ammonium-rich sewage that enhanced nitrification and subsequent denitrification, while ammonia-oxidizing archaea (AOA) was more abundant than AOB in the river section flowing through areas of pomelo (Citrus maxima) agriculture with low pH, low ammonium and very high nitrate input. Warm temperatures and large total suspended matter (TSM) in the wet season promoted growth of nitrifiers and denitrifiers, which were mostly particle-attached. The potential river N retention through gaseous N removal (PRN2O and PRN2) in the agriculture section with huge N loading was among the lowest. Strong nitrification and denitrification were suspected to occur in the agricultural acid soil system rather than in the river network. In addition, the decreased TSM and N concentration promoted free-living microbes in the reservoir. The highest PRN2 and N2 production observed in the reservoir in the dry season implied that denitrification and anammox occurring in sediments was likely to increase N retention. This study suggests the diverse factors involved in processing of N pollution among diverse landscapes.
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Affiliation(s)
- Jingjie Lin
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Nengwang Chen
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen, China; State Key Laboratory of Marine Environment Science, Xiamen University, Xiamen, China.
| | - Xin Yuan
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Qing Tian
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Yi Zheng
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, China
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10
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Monthly distribution of ammonia-oxidizing microbes in a tropical bay. J Microbiol 2020; 59:10-19. [PMID: 33201437 DOI: 10.1007/s12275-021-0287-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 09/28/2020] [Accepted: 09/28/2020] [Indexed: 10/23/2022]
Abstract
Ammonia oxidation, performed by ammonia-oxidizing archaea (AOA) and bacteria (AOB), plays a critical role in the cycle of nitrogen in the ocean. For now, environmental variables controlling distribution of ammonia-oxidizing microbes are still largely unknown in oceanic environments. In this study, we used real-time quantitative PCR and high-throughput sequencing methods to investigate the abundance and diversity of AOA and AOB from sediment and water in Zhanjiang Bay. Phylogenic analysis revealed that the majority of AOA amoA sequences in water and sediment were affiliated with the genus Nitrosopumilus, whereas the Nitrosotalea cluster was only detected with low abundance in water. Nitrosomonas and Nitrosospira dominated AOB amoA sequences in water and sediment, respectively. The amoA copy numbers of both AOA and AOB varied significantly with month for both sediment and water. When water and sediment temperature dropped to 17-20°C in December and February, respectively, the copy number of AOB amoA genes increased markedly and was much higher than for AOA amoA genes. Also, AOA abundance in water peaked in December when water temperature was lowest (17-20°C). Stepwise multiple regression analyses revealed that temperature was the most key factor driving monthly changes of AOA or AOB abundance. It is inferred that low water temperature may inhibit growth of phytoplankton and other microbes and so reduce competition for a common substrate, ammonium.
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11
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Chi Y, Yang P, Ren S, Yang J. Finding the optimal fertilizer type and rate to balance yield and soil GHG emissions under reclaimed water irrigation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 729:138954. [PMID: 32387773 DOI: 10.1016/j.scitotenv.2020.138954] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/20/2020] [Accepted: 04/22/2020] [Indexed: 06/11/2023]
Abstract
Water and inorganic nitrogen fertilizer have a notable impact on crop yield and greenhouse gas (GHG) emissions from soil. Reclaimed water (RW) is widely used for irrigation when there are shortages of water resources. It is very important to control yield and greenhouse gas emissions by fertilization under reclaimed water irrigation (RWI). The study consisted of a continuous test that evaluated three types of fertilizer treatments (urea, amine, and slow-release fertilizer) and a no-fertilizer treatment under three-year RWI and four fertilizer levels (150, 200, 250 and 300 kg.N.ha-1) under one-year RWI to determine the best fertilizer to support maize production and reduce GHG (CO2 and N2O) emissions from soil; further, the applicability of RWI in the DNDC model was verified. For many years, GHG emissions under RWI showed an increasing trend, but the effect was not significant. A strong correlation was found between the GHG emissions flux and fertilizer amount, and a threshold fertilization amount existed between 220 and 260 kg.N.ha-1 that minimized yield-scaled N2O emissions and the ratio of GHG cumulative emission to yield (GHG/Y). The results indicated that the optimal amounts of SF and UF under RWI were 240 and 225 kg.N.ha-1 by second-order equation and the DNDC model, respectively, and the rate better balanced the yield and GHG emissions.
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Affiliation(s)
- Yanbing Chi
- College of Water Resources & Civil Engineering, China Agricultural University, No. 17 Tsinghua East Road, Haidian District, 100083 Beijing, China
| | - Peiling Yang
- College of Water Resources & Civil Engineering, China Agricultural University, No. 17 Tsinghua East Road, Haidian District, 100083 Beijing, China.
| | - Shumei Ren
- College of Water Resources & Civil Engineering, China Agricultural University, No. 17 Tsinghua East Road, Haidian District, 100083 Beijing, China
| | - Jing Yang
- College of Water Resources & Civil Engineering, China Agricultural University, No. 17 Tsinghua East Road, Haidian District, 100083 Beijing, China
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12
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Ginawi A, Wang L, Wang H, Yu B, Yunjun Y. Effects of environmental variables on abundance of ammonia-oxidizing communities in sediments of Luotian River, China. PeerJ 2020; 8:e8256. [PMID: 31934502 PMCID: PMC6951284 DOI: 10.7717/peerj.8256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 11/20/2019] [Indexed: 12/14/2022] Open
Abstract
Ammonia-oxidizing communities play important functional roles in the nitrification. However, environmental stresses can significantly affect this process by controlling the abundant communities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities. In this study, we examined the abundance variations of ammonia-oxidizing communities using quantitative polymerase chain reaction (qPCR) and terminal-restriction fragment length polymorphism (T-RFLP) in a typical subtropical river, Luotian County, South Dabie Mountains, China. Clone libraries were conducted to evaluate the community structure and abundance of AOA and AOB in sediments. Results showed that Nitrososphaera sp and Nitrosopumilus sp were the most dominant AOA. The abundance of the AOA and AOB amoA gene ranged from 5.28 × 108 gene copies (g-soil−1) to 2.23 × 108 gene copies (g-soil−1) and 5.45 × 108 gene copies (g-soil−1) to 3.30 × 107 gene copies (g-soil−1), respectively. Five environmental variables, namely, ORP, DO, NO\documentclass[12pt]{minimal}
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}{}${}_{4}^{+}$\end{document}4+ were played a major function in microbial communities of AOA and AOB in sediments. The T-RFLP profiles of AOA showed that 488 and 116 bp T-RFs were dominated. Overall, the results of this study showed that anthropogenic activities andenvironmental stress in rivers can alter the structure and function of microbes in their variable environment.
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Affiliation(s)
- Amjed Ginawi
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Faculty of Marine Science and Fisheries, Red Sea University, Port Sudan, Red Sea State, Sudan
| | - Lixiao Wang
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Huading Wang
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Bingbing Yu
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yan Yunjun
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
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13
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Hu J, Liu S, Yang W, He Z, Wang J, Liu H, Zheng P, Xi C, Ma F, Hu B. Ecological Success of the Nitrosopumilus and Nitrosospira Clusters in the Intertidal Zone. MICROBIAL ECOLOGY 2019; 78:555-564. [PMID: 30903203 DOI: 10.1007/s00248-019-01359-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 03/07/2019] [Indexed: 06/09/2023]
Abstract
The intertidal zone is an important buffer and a nitrogen sink between land and sea. Ammonia oxidation is the rate-limiting step of nitrification, conducted by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). However, it remains a debatable issue regarding dominant ammonia oxidizers in this region, and environmental factors driving their spatiotemporal niche differentiation have yet to be identified. In this study, intertidal and subtidal zones of Zhoushan Islands were selected for seasonal sampling. Ammonia-oxidizing activity, quantitative PCR, and 454 high-throughput sequencing were performed to study the nitrification potential, abundance, and community structure of ammonia-oxidizing archaea and bacteria. AOA and AOB amoA abundance (107-108amoA gene copies/g dry weight sediment) varied spatiotemporally independently of environmental factors. AOA surpassed AOB in most samples, driven by sediment temperature, moisture, and total nitrogen. The diversity of both AOA and AOB differed spatiotemporally. The Nitrosopumilus and Nitrosospira clusters accounted for an absolutely dominant percentage of AOA (> 99%) and AOB (> 99%) respectively, indicating a negligible contribution of other clusters to ammonia oxidation. However, there was no significant correlation between nitrification potential and the abundance of AOA or AOB. Overall, the present study showed that AOA dominated over AOB spatiotemporally in the intertidal zone of Zhoushan Islands due to fluctuations in environmental factors, and the Nitrosopumilus and Nitrosospira clusters ecologically succeeded in the intertidal zone of Zhoushan Islands.
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Affiliation(s)
- Jiajie Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Shuai Liu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Weiling Yang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Zhanfei He
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Huan Liu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Chuanwu Xi
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Fang Ma
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China.
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China.
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China.
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14
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Fang J, Zhao R, Cao Q, Quan Q, Sun R, Liu J. Effects of emergent aquatic plants on nitrogen transformation processes and related microorganisms in a constructed wetland in northern China. PLANT AND SOIL 2019; 443:473-492. [DOI: 10.1007/s11104-019-04249-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 08/01/2019] [Indexed: 06/14/2024]
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15
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Imchen M, Kumavath R, Vaz ABM, Góes-Neto A, Barh D, Ghosh P, Kozyrovska N, Podolich O, Azevedo V. 16S rRNA Gene Amplicon Based Metagenomic Signatures of Rhizobiome Community in Rice Field During Various Growth Stages. Front Microbiol 2019; 10:2103. [PMID: 31616390 PMCID: PMC6764247 DOI: 10.3389/fmicb.2019.02103] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 08/26/2019] [Indexed: 11/21/2022] Open
Abstract
Rice is a major staple food across the globe. Its growth and productivity is highly dependent on the rhizobiome where crosstalk takes place between plant and the microbial community. Such interactions lead to selective enrichment of plant beneficial microbes which ultimately defines the crop health and productivity. In this study, rhizobiome modulation is documented throughout the development of rice plant. Based on 16S rRNA gene affiliation at genus level, abundance, and diversity of plant growth promoting bacteria increased during the growth stages. The observed α diversity and rhizobiome complexity increased significantly (p < 0.05) during plantation. PCoA indicates that different geographical locations shared similar rhizobiome diversity but exerted differential enrichment (p < 0.001). Diversity of enriched genera represented a sigmoid curve and subsequently declined after harvest. A major proportion of dominant enriched genera (p < 0.05, abundance > 0.1%), based on 16S rRNA gene, were plant growth promoting bacteria that produces siderophore, indole-3-acetic acid, aminocyclopropane-1-carboxylic acid, and antimicrobials. Hydrogenotrophic methanogens dominated throughout cultivation. Type I methanotrophs (n = 12) had higher diversity than type II methanotrophs (n = 6). However, the later had significantly higher abundance (p = 0.003). Strong enrichment pattern was also observed in type I methanotrophs being enriched during water logged stages. Ammonia oxidizing Archaea were several folds more abundant than ammonia oxidizing bacteria. K-strategists Nitrosospira and Nitrospira dominated ammonia and nitrite oxidizing bacteria, respectively. The study clarifies the modulation of rhizobiome according to the rice developmental stages, thereby opening up the possibilities of bio-fertilizer treatment based on each cultivation stages.
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Affiliation(s)
- Madangchanok Imchen
- Department of Genomic Sciences, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Ranjith Kumavath
- Department of Genomic Sciences, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Aline B M Vaz
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Aristóteles Góes-Neto
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Debmalya Barh
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil.,Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Purba Medinipur, India
| | - Preetam Ghosh
- Department of Computer Sciences, Virginia Commonwealth University, Richmond, VA, United States
| | - Natalia Kozyrovska
- Institute of Molecular Biology and Genetics, National Academy of Sciences, Kyiv, Ukraine
| | - Olga Podolich
- Institute of Molecular Biology and Genetics, National Academy of Sciences, Kyiv, Ukraine
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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16
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Li X, Li Y, Li Y, Wu J. Enhanced nitrogen removal and quantitative analysis of removal mechanism in multistage surface flow constructed wetlands for the large-scale treatment of swine wastewater. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 246:575-582. [PMID: 31202022 DOI: 10.1016/j.jenvman.2019.06.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 05/31/2019] [Accepted: 06/05/2019] [Indexed: 06/09/2023]
Abstract
Constructed wetlands have recently been studied as a form of green infrastructure for the enhanced removal of nitrogen (N). This study aimed to demonstrate the use of multistage surface flow constructed wetland (SFCW) for treatment of swine wastewater. The results showed chemical oxygen demand (COD), total nitrogen (TN), NH4+, and NO3- removal rates of 16.3 g m-2 d-1, 9.14 g m-2 d-1, 7.75 g m-2 d-1, and 45.49 mg m-2 d-1, respectively. The sediment and plant absorption N rates were 2.44 g m-2 d-1, and 1.24 g m-2 d-1, respectively. Moreover, the microbial process which is the primary process, by which N is removed, accounted for 56.75-65.35%. Quantitative polymerase chain reaction (qPCR) revealed the highest microbial abundance in the segment of the SFCW with high N concentration. Ammonia-oxidizing bacteria (AOB) and nirK could be primarily responsible for the high removal rate of N. Factors like pH, DO, COD, N, and OM play an important role in influencing microbial abundance. It is suggested that the multistage SFCW has a promising future for the large scale treatment of swine wastewater.
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Affiliation(s)
- Xi Li
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, PR China; Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, PR China
| | - Yuyuan Li
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, PR China; Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, PR China.
| | - Yong Li
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, PR China; Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, PR China
| | - Jinshui Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, PR China; Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, PR China
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17
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Spatial and Seasonal Variations in the Abundance of Nitrogen-Transforming Genes and the Microbial Community Structure in Freshwater Lakes with Different Trophic Statuses. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16132298. [PMID: 31261730 PMCID: PMC6651097 DOI: 10.3390/ijerph16132298] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 06/25/2019] [Accepted: 06/26/2019] [Indexed: 12/27/2022]
Abstract
Identifying nitrogen-transforming genes and the microbial community in the lacustrine sedimentary environment is critical for revealing nitrogen cycle processes in eutrophic lakes. In this study, we examined the diversity and abundance of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), denitrifying bacteria (DNB), and anammox bacteria (AAOB) in different trophic status regions of Lake Taihu using the amoA, Arch-amoA, nirS, and hzo genes as functional markers. Quantitative Polymerase Chain Reaction (qPCR) results indicated that the abundance of the nirS gene was the highest, while the amoA gene had the lowest abundance in all regions. Except for the primary inflow area of Lake Taihu, Arch-amoA gene abundance was higher than the hzo gene in three lake bays, and the abundance of the nirS gene increased with decreasing trophic status. The opposite pattern was observed for the amoA, Arch-amoA, and hzo genes. Phylogenetic analyses showed that the predominant AOB and AOA were Nitrosomonas and Nitrosopumilus maritimus, respectively, and the proportion of Nitrosomonas in the eutrophic region (87.9%) was higher than that in the mesotrophic region (71.1%). Brocadia and Anammoxoglobus were the two predominant AAOB in Lake Taihu. Five novel unknown phylotypes of AAOB were observed, and Cluster AAOB-B was only observed in the inflow area with a proportion of 32%. In the DNB community, Flavobacterium occurred at a higher proportion (22.6–38.2%) in all regions, the proportion of Arthrobacter in the mesotrophic region (3.6%) was significantly lower than that in the eutrophic region (15.6%), and the proportions of Cluster DNB-E in the inflow area (24.5%) was significantly higher than that in the lake bay (7.3%). The canonical correspondence analysis demonstrated that the substrate concentration in sedimentary environments, such as NOx--N in the sediment, NH4+-N in the pore water, and the total organic matter, were the key factors that determined the nitrogen-transforming microbial community. However, the temperature was also a predominant factor affecting the AOA and AAOB communities.
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18
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Liu H, Hu Z, Zhou M, Hu J, Yao X, Zhang H, Li Z, Lou L, Xi C, Qian H, Li C, Xu X, Zheng P, Hu B. The distribution variance of airborne microorganisms in urban and rural environments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 247:898-906. [PMID: 30823344 DOI: 10.1016/j.envpol.2019.01.090] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 10/26/2018] [Accepted: 01/21/2019] [Indexed: 06/09/2023]
Abstract
Microorganisms are ubiquitous in the atmosphere, where they can disperse for a long distance. However, it remains poorly understood how these airborne microorganisms vary and which factors influence the microbial distribution in different anthropogenic activity regions. To explore the regional differences of bacteria and fungi in airborne particles, PM2.5 and PM10 samples were collected in the urban and rural areas of Hangzhou. The bacterial and fungal communities in the urban atmosphere was more similar to each other than those in the rural atmosphere. Analyses conducted by the concentration weighted trajectory model demonstrated that the local environment contributed more to the similarity of airborne bacteria and fungi compared with the atmospheric transport. The concentrations of local air pollutants (PM2.5, PM10, NO2, SO2 and CO) were positively correlated with the similarity of the bacterial and fungal communities. Additionally, the concentrations of these air pollutants in the urban site were about 1.5 times than those in the rural site. This implicated that anthropogenic activity, which is the essential cause of air pollutants, influenced the similarity of airborne bacteria and fungi in the urban area. This work ascertains the outdoor bacterial and fungal distribution in the urban and the rural atmosphere and provides a prospective model for studying the contributing factors of airborne bacteria and fungi.
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Affiliation(s)
- Huan Liu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Zhichao Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Meng Zhou
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Jiajie Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Xiangwu Yao
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Hao Zhang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Zheng Li
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Liping Lou
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Chuanwu Xi
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, China
| | - Chunyan Li
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Xiangyang Xu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China; Research Center for Air Pollution and Health, Zhejiang University, Hangzhou, 310058, China.
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19
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Nsenga Kumwimba M, Meng F. Roles of ammonia-oxidizing bacteria in improving metabolism and cometabolism of trace organic chemicals in biological wastewater treatment processes: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 659:419-441. [PMID: 31096373 DOI: 10.1016/j.scitotenv.2018.12.236] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 11/20/2018] [Accepted: 12/15/2018] [Indexed: 05/27/2023]
Abstract
While there has been a significant recent improvement in the removal of pollutants in natural and engineered systems, trace organic chemicals (TrOCs) are posing a major threat to aquatic environments and human health. There is a critical need for developing potential strategies that aim at enhancing metabolism and/or cometabolism of these compounds. Recently, knowledge regarding biodegradation of TrOCs by ammonia-oxidizing bacteria (AOB) has been widely developed. This review aims to delineate an up-to-date version of the ecophysiology of AOB and outline current knowledge related to biodegradation efficiencies of the frequently reported TrOCs by AOB. The paper also provides an insight into biodegradation pathways by AOB and transformation products of these compounds and makes recommendations for future research of AOB. In brief, nitrifying WWTFs (wastewater treatment facilities) were superior in degrading most TrOCs than non-nitrifying WWTFs due to cometabolic biodegradation by the AOB. To fully understand and/or enhance the cometabolic biodegradation of TrOCs by AOB, recent molecular research has focused on numerous crucial factors including availability of the compounds to AOB, presence of growth substrate (NH4-N), redox potentials, microorganism diversity (AOB and heterotrophs), physicochemical properties and operational parameters of the WWTFs, molecular structure of target TrOCs and membrane-based technologies, may all significantly impact the cometabolic biodegradation of TrOCs. Still, further exploration is required to elucidate the mechanisms involved in biodegradation of TrOCs by AOB and the toxicity levels of formed products.
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Affiliation(s)
- Mathieu Nsenga Kumwimba
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China; Faculty of Agronomy, Department of Natural Resources and Environmental Management, University of Lubumbashi, Democratic Republic of the Congo
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China.
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20
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Wang X, Wang S, Shi G, Wang W, Zhu G. Factors driving the distribution and role of AOA and AOB in Phragmites communis
rhizosphere in riparian zone. J Basic Microbiol 2019; 59:425-436. [DOI: 10.1002/jobm.201800581] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/01/2018] [Accepted: 12/16/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Xiaomin Wang
- Key Laboratory of Drinking Water Science and Technology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Shanyun Wang
- Key Laboratory of Drinking Water Science and Technology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
| | - Guoshuai Shi
- Key Laboratory of Drinking Water Science and Technology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
| | - Weidong Wang
- Key Laboratory of Drinking Water Science and Technology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
- University of Chinese Academy of Sciences; Beijing 100049 China
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21
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Vipindas PV, Jabir T, Jasmin C, Balu T, Rehitha TV, Adarsh BM, Nair S, Abdulla MH, Abdulaziz A. Diversity and seasonal distribution of ammonia-oxidizing archaea in the water column of a tropical estuary along the southeast Arabian Sea. World J Microbiol Biotechnol 2018; 34:188. [PMID: 30511184 DOI: 10.1007/s11274-018-2570-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 11/27/2018] [Indexed: 01/28/2023]
Abstract
Diversity and distribution pattern of ammonia-oxidizing archaea (AOA) were studied across a salinity gradient in the water column of Cochin Estuary (CE), a tropical monsoonal estuary along the southeast Arabian Sea. The water column of CE was found to be nutrient rich with high bacterial (3.7-6.7 × 108 cells L-1) and archaeal abundance (1.9-4.5 × 108 cells L-1). Diversity and seasonal variation in the distribution pattern of AOA were studied using clone library analysis and Denaturing gradient gel electrophoresis (DGGE). Clone library analysis of both the amoA and 16S rRNA gene sequences showed similar diversity pattern, however the diversity was more clear when the 16S rRNA gene sequences were analyzed. More than 70% of the sequences retrieved were clustered under uncultured Thaumarchaeota group 1 lineage and the major fractions of the remaining sequences were grouped into the Nitrosopumilus lineage and Nitrosopelagicus lineage. The AOA community in the CE was less adaptable to changing environmental conditions and its distribution showed seasonal variations within the DGGE banding pattern with higher diversity during the pre-monsoon period. The distribution of AOA also showed its preference to intermediate salinity for their higher diversity. Summer monsoon associated runoff and flushing played a critical role in regulating the seasonality of AOA distribution.
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Affiliation(s)
- Puthiya Veettil Vipindas
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Cochin, Kerala, 682016, India. .,Cryobiology Laboratory, National Centre for Polar and Ocean Research, Vasco-da-Gama, Goa, 403 804, India.
| | - Thajudeen Jabir
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
| | - Chekidhenkuzhiyil Jasmin
- Council of Scientific and Industrial Research (CSIR) - National Institute of Oceanography, Regional Centre, Cochin, Kerala, 682018, India
| | - Tharakan Balu
- Council of Scientific and Industrial Research (CSIR) - National Institute of Oceanography, Regional Centre, Cochin, Kerala, 682018, India
| | - Thekkendavida Velloth Rehitha
- Council of Scientific and Industrial Research (CSIR) - National Institute of Oceanography, Regional Centre, Cochin, Kerala, 682018, India
| | - Balakrishnan Meenakshikutty Adarsh
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
| | - Shanta Nair
- Council of Scientific and Industrial Research (CSIR) - National Institute of Oceanography, Regional Centre, Cochin, Kerala, 682018, India
| | - Mohamed Hatha Abdulla
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
| | - Anas Abdulaziz
- Council of Scientific and Industrial Research (CSIR) - National Institute of Oceanography, Regional Centre, Cochin, Kerala, 682018, India
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22
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Liu Y, Liu J, Yao P, Ge T, Qiao Y, Zhao M, Zhang XH. Distribution patterns of ammonia-oxidizing archaea and bacteria in sediments of the eastern China marginal seas. Syst Appl Microbiol 2018; 41:658-668. [PMID: 30172418 DOI: 10.1016/j.syapm.2018.08.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 07/26/2018] [Accepted: 08/13/2018] [Indexed: 01/19/2023]
Abstract
Ammonia-oxidizing archaea (AOA) and bacteria (AOB) vary in their contribution to nitrification in different environments. The eastern China marginal seas (ECMS) are featured by complex river runoffs and ocean currents, forming different sediment patches. Here, via quantitative PCR and clone library analysis of the amoA genes, we showed that AOB were more abundant than AOA in ECMS sediments. The abundance, diversity and richness of AOA, but not AOB, were higher in the East China Sea (ECS) than in the Yellow Sea (YS) and Bohai Sea (BS). Nitrosopumilus (AOA) and Nitrosospira (AOB) were predominant lineages, but their abundances varied significantly between ECS, and BS and YS. This was mainly attributed to salinity and dissolved oxygen of the bottom water. The discovery of a high abundance of Nitrosophaera at estuarine sites suggested strong terrigenous influence exerted on the AOA community. In contrast, variations in ocean conditions played more important roles in structuring the AOB community, which was separated by bottom water dissolved oxygen into two groups: the south YS, and the north YS and BS. This study provides a comprehensive insight into the spatial distribution pattern of ammonia-oxidizing prokaryotes in ECMS sediments, laying a foundation for understanding their relative roles in nitrification.
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Affiliation(s)
- Yuyang Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Jiwen Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Peng Yao
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Tiantian Ge
- College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
| | - Yanlu Qiao
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Meixun Zhao
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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23
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Kerfahi D, Tripathi BM, Slik JWF, Sukri RS, Jaafar S, Adams JM. Distinctive Soil Archaeal Communities in Different Variants of Tropical Equatorial Forest. MICROBIAL ECOLOGY 2018; 76:215-225. [PMID: 29184976 DOI: 10.1007/s00248-017-1118-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 11/20/2017] [Indexed: 06/07/2023]
Abstract
Little is known of how soil archaeal community composition and diversity differ between local variants of tropical rainforests. We hypothesized that (1) as with plants, animals, fungi, and bacteria, the soil archaeal community would differ between different variants of tropical forest; (2) that spatially rarer forest variants would have a less diverse archaeal community than common ones; (3) that a history of forest disturbance would decrease archaeal alpha- and beta-diversity; and (4) that archaeal distributions within the forest would be governed more by deterministic than stochastic factors. We sampled soil across several different forest types within Brunei, Northwest Borneo. Soil DNA was extracted, and the 16S rRNA gene of archaea was sequenced using Illumina MiSeq. We found that (1) as hypothesized, there are distinct archaeal communities for each forest type, and community composition significantly correlates with soil parameters including pH, organic matter, and available phosphorous. (2) As hypothesized, the "rare" white sand forest variants kerangas and inland heath had lower archaeal diversity. A nestedness analysis showed that archaeal community in inland heath and kerangas was mainly a less diverse subset of that in dipterocarp forests. However, primary dipterocarp forest had the lowest beta-diversity among the other tropical forest types. (3) Also, as predicted, forest disturbance resulted in lower archaeal alpha-diversity-but increased beta-diversity in contrast with our predictions. (4) Contrary to our predictions, the BetaNTI of the various primary forest types indicated community assembly was mainly stochastic. The possible effects of these habitat and disturbance-related effects on N cycling should be investigated.
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Affiliation(s)
- Dorsaf Kerfahi
- Department of Biological Sciences, Seoul National University, Gwanak-Gu, Seoul, 151-747, Republic of Korea
- Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Seestrasse 15, 18119, Rostock, Germany
| | - Binu M Tripathi
- Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon, 21990, Republic of Korea
| | - J W Ferry Slik
- Faculty of Science, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
| | - Rahayu S Sukri
- Faculty of Science, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
| | - Salwana Jaafar
- Faculty of Science, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
| | - Jonathan M Adams
- Division of Agrifood and Environment, Cranfield University, College Rd, Cranfield, MK43 0AL, UK.
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24
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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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25
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Dang C, Liu W, Lin Y, Zheng M, Jiang H, Chen Q, Ni J. Dominant role of ammonia-oxidizing bacteria in nitrification due to ammonia accumulation in sediments of Danjiangkou reservoir, China. Appl Microbiol Biotechnol 2018; 102:3399-3410. [PMID: 29497800 DOI: 10.1007/s00253-018-8865-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 01/31/2018] [Accepted: 02/12/2018] [Indexed: 11/29/2022]
Abstract
Surface sediments are the inner source of contaminations in aquatic systems and usually maintain aerobic conditions. As the key participators of nitrification process, little is known about the activities and contributions of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in the surface sediments. In this study, we determined the net and potential nitrification rates and used 1-octyne as an AOB specific inhibitor to detect the contributions of AOA and AOB to nitrification in surface sediments of Danjiangkou reservoir, which is the water source area of the middle route of South-to-North Water Diversion Project in China. Quantitative PCR and Illumina high-throughput sequencing were used to evaluate the abundance and diversity of the amoA gene. The net and potential nitrification rates ranged from 0.42 to 1.93 and 2.06 to 8.79 mg N kg-1 dry sediments d-1, respectively. AOB dominated in both net and potential nitrification, whose contribution accounted for 52.7-78.6% and 59.9-88.1%, respectively. The cell-specific ammonia oxidation rate calculation also revealed the cell-specific rates of AOB were higher than that of AOA. The Spearman's rank correlation analysis suggested that ammonia accumulation led to the AOB predominant role in net nitrification activity, and AOB abundance played the key role in potential nitrification activity. Furthermore, phylogenetic analysis suggested AOB were predominantly characterized by the Nitrosospira cluster, while AOA by the Nitrososphaera and Nitrososphaera sister clusters. This study will help us to better understand the contributions and characteristics of AOA and AOB in aquatic sediments and provide improved strategies for nitrogen control in large reservoirs.
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Affiliation(s)
- Chenyuan Dang
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, 100871, People's Republic of China
| | - Wen Liu
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, 100871, People's Republic of China.,School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Yaxuan Lin
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, 100871, People's Republic of China
| | - Maosheng Zheng
- MOE Key Laboratory of Regional Energy Systems Optimization, Sino-Canada Resources and Environmental Research Academy, North China Electric Power University, Beijing, 102206, People's Republic of China
| | - Huan Jiang
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, 100871, People's Republic of China
| | - Qian Chen
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, 100871, People's Republic of China
| | - Jinren Ni
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, 100871, People's Republic of China.
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26
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Liu H, Zhang X, Zhang H, Yao X, Zhou M, Wang J, He Z, Zhang H, Lou L, Mao W, Zheng P, Hu B. Effect of air pollution on the total bacteria and pathogenic bacteria in different sizes of particulate matter. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 233:483-493. [PMID: 29101891 DOI: 10.1016/j.envpol.2017.10.070] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 10/16/2017] [Accepted: 10/17/2017] [Indexed: 05/21/2023]
Abstract
In recent years, air pollution events have occurred frequently in China during the winter. Most studies have focused on the physical and chemical composition of polluted air. Some studies have examined the bacterial bioaerosols both indoors and outdoors. But few studies have focused on the relationship between air pollution and bacteria, especially pathogenic bacteria. Airborne PM samples with different diameters and different air quality index values were collected in Hangzhou, China from December 2014 to January 2015. High-throughput sequencing of 16S rRNA was used to categorize the airborne bacteria. Based on the NCBI database, the "Human Pathogen Database" was established, which is related to human health. Among all the PM samples, the diversity and concentration of total bacteria were lowest in the moderately or heavily polluted air. However, in the PM2.5 and PM10 samples, the relative abundances of pathogenic bacteria were highest in the heavily and moderately polluted air respectively. Considering the PM samples with different particle sizes, the diversities of total bacteria and the proportion of pathogenic bacteria in the PM10 samples were different from those in the PM2.5 and TSP samples. The composition of PM samples with different sizes range may be responsible for the variances. The relative humidity, carbon monoxide and ozone concentrations were the main factors, which affected the diversity of total bacteria and the proportion of pathogenic bacteria. Among the different environmental samples, the compositions of the total bacteria were very similar in all the airborne PM samples, but different from those in the water, surface soil, and ground dust samples. Which may be attributed to that the long-distance transport of the airflow may influence the composition of the airborne bacteria. This study of the pathogenic bacteria in airborne PM samples can provide a reference for environmental and public health researchers.
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Affiliation(s)
- Huan Liu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Xu Zhang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Hao Zhang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Xiangwu Yao
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Meng Zhou
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Zhanfei He
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Huihui Zhang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Liping Lou
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Weihua Mao
- The Center of Analysis and Measurement, Zhejiang University, Hangzhou, 310058, China
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China; Research Center for Air Pollution and Health, Zhejiang University, Hangzhou, 310058, China.
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Distinct distribution patterns of ammonia-oxidizing archaea and bacteria in sediment and water column of the Yellow River estuary. Sci Rep 2018; 8:1584. [PMID: 29371667 PMCID: PMC5785527 DOI: 10.1038/s41598-018-20044-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 01/12/2018] [Indexed: 11/20/2022] Open
Abstract
Ammonia oxidation is a critical process of estuarine nitrogen cycling involving ammonia-oxidizing archaea (AOA) and bacteria (AOB). However, the distribution patterns of ammonia-oxidizing microorganisms (AOMs) between different habitats in the same area remain unclear. The present study investigated the AOMs’ abundance and community compositions in both sediment and water habitats of the Yellow River estuary. Quantitative PCR (qPCR) revealed that AOA showed significant higher abundance than AOB both in sediment and water samples. AOA and AOB abundance distribution trends were consistent in sediment but distinct in water along the sampling sites. Clone library-based analyses showed that AOA sequences were affiliated with Nitrososphaera, Nitrosopumilus and Nitrosotalea clusters. Generally, Nitrososphaera was predominant in sediment, while Nitrosopumilus and Nitrosotalea dominated in water column. AOB sequences were classified into genera Nitrosospira and Nitrosomonas, and Nitrosospira dominated in both habitats. Principal coordinate analysis (PCoA) also indicated AOA community structures exhibited significant differences between two habitats, while AOB were not. Ammonium and carbon contents were the potential key factors to influence AOMs’ abundance and compositions in sediment, while no measured variables were determined to have major influences on communities in water habitat. These findings increase the understanding of the AOMs’ distribution patterns in estuarine ecosystems.
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28
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Wang J, Gong B, Wang Y, Wen Y, Zhou J, He Q. The potential multiple mechanisms and microbial communities in simultaneous nitrification and denitrification process treating high carbon and nitrogen concentration saline wastewater. BIORESOURCE TECHNOLOGY 2017; 243:708-715. [PMID: 28710998 DOI: 10.1016/j.biortech.2017.06.131] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Revised: 06/20/2017] [Accepted: 06/22/2017] [Indexed: 06/07/2023]
Abstract
A simultaneous nitrification and denitrification (SND) process in sequencing batch biofilm reactor (SBBR) was established to treat high carbon and nitrogen saline wastewater in this study. Acetate, glucose and an organic mixture were applied as organic sources in three SBBRs, achieving average total nitrogen removal efficiency of 97.15%, 63.94% and 94.99% during 120days' operation, respectively. The underlying nitrogen removal mechanisms were investigated by 16S rRNA sequencing and batch tests. Results showed different carbon sources had great impact on microbial communities, and led to different nitrogen removal mechanism. Autotrophic and heterotrophic nitrification together contributed to the well performance of nitrification process. And denitrification was carried out by a combined anoxic and aerobic denitrificans. Furthermore, the SND process was mainly via nitrite not nitrate. Compared with ammonia-oxidizing bacteria, ammonia-oxidizing archaea with a much higher abundance contributed more to autotrophic nitrification. Pseudomonas_stutzeri and Bacillus_cereus were the predominant detected heterotrophic nitrification-aerobic denitrification bacterium.
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Affiliation(s)
- Jiale Wang
- Faculty of Urban Construction and Environmental Engineering, Chongqing University, Chongqing 400045, PR China
| | - Benzhou Gong
- Faculty of Urban Construction and Environmental Engineering, Chongqing University, Chongqing 400045, PR China
| | - Yingmu Wang
- Faculty of Urban Construction and Environmental Engineering, Chongqing University, Chongqing 400045, PR China
| | - Yuhui Wen
- Faculty of Urban Construction and Environmental Engineering, Chongqing University, Chongqing 400045, PR China
| | - Jian Zhou
- Faculty of Urban Construction and Environmental Engineering, Chongqing University, Chongqing 400045, PR China; Key Laboratory of the Three Gorges Reservoir's Eco-Environments, Ministry of Education, Chongqing University, Chongqing 400045, PR China.
| | - Qiang He
- Faculty of Urban Construction and Environmental Engineering, Chongqing University, Chongqing 400045, PR China; Key Laboratory of the Three Gorges Reservoir's Eco-Environments, Ministry of Education, Chongqing University, Chongqing 400045, PR China
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29
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Effect of Sewage and Industrial Effluents on Bacterial and Archaeal Communities of Creek Sediments in the Taihu Basin. WATER 2017. [DOI: 10.3390/w9060373] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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30
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Screening and optimizing of inhibitors for ammonia-oxidizing bacteria in sediments of malodorous river. Appl Microbiol Biotechnol 2017; 101:6193-6203. [PMID: 28540424 DOI: 10.1007/s00253-017-8318-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 04/26/2017] [Accepted: 04/29/2017] [Indexed: 10/19/2022]
Abstract
The proper use of selective ammonia-oxidizing archaea (AOA) and/or ammonia-oxidizing bacteria (AOB) inhibitors is critical to distinguish AOA and AOB contribution. In this research, three inhibitors including ampicillin, dicyandiamide (DCD), and allylthiourea (ATU) were examined mainly focusing on inhibiting dosage, adaptability, and effects. The results showed that the optimized inhibitory dosage of ampicillin, DCD, and ATU was separately 1.5 g L-1, 1 mM, and 25 μM. Among the three inhibitors, ATU exhibited the strongest and persistent inhibition effects and resulted in up to 90% inhibition in the AOB-enriched culture. The seemingly weakening inhibiting effects of ATU in the simulated river systems can be attributed to the involved role of AOA, the uneven spatial distribution of ATU, and protection by sediment structure in complex malodorous rivers. The high-throughput pyrosequencing analysis showed the AOB-related genus Nitrosomonas and Nitrosococcus were mostly affected by ATU in the enrichments and the river systems, respectively. The inhibition of ATU was realized mainly by reducing the abundance and activity of AOB. The decrease of the ratio of AOB/AOA amoA gene copy numbers after addition of ATU further confirmed the inhibiting effectiveness of ATU in complex microbial community of malodorous rivers.
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31
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Reisinger AJ, Groffman PM, Rosi-Marshall EJ. Nitrogen-cycling process rates across urban ecosystems. FEMS Microbiol Ecol 2016; 92:fiw198. [DOI: 10.1093/femsec/fiw198] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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32
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Zhang Y, Chen L, Sun R, Dai T, Tian J, Zheng W, Wen D. Population and diversity of ammonia-oxidizing archaea and bacteria in a pollutants' receiving area in Hangzhou Bay. Appl Microbiol Biotechnol 2016; 100:6035-45. [PMID: 26960319 DOI: 10.1007/s00253-016-7421-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 02/20/2016] [Accepted: 02/24/2016] [Indexed: 12/19/2022]
Abstract
The community structure of ammonia-oxidizing microorganisms is sensitive to various environmental factors, including pollutions. In this study, real-time PCR and 454 pyrosequencing were adopted to investigate the population and diversity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) temporally and spatially in the sediments of an industrial effluent receiving area in the Qiantang River's estuary, Hangzhou Bay. The abundances of AOA and AOB amoA genes fluctuated in 10(5)-10(7) gene copies per gram of sediment; the ratio of AOA amoA/AOB amoA ranged in 0.39-5.52. The AOA amoA/archaeal 16S rRNA, AOB amoA/bacterial 16S rRNA, and AOA amoA/AOB amoA were found to positively correlate with NH4 (+)-N concentration of the seawater. Nitrosopumilus cluster and Nitrosomonas-like cluster were the dominant AOA and AOB, respectively. The community structures of both AOA and AOB in the sediments exhibited significant seasonal differences rather than spatial changes in the effluent receiving area. The phylogenetic distribution of AOB in this area was consistent with the wastewater treatment plants (WWTPs) discharging the effluent but differed from the Qiantang River and other estuaries, which might be an outcome of long-term effluent discharge.
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Affiliation(s)
- Yan Zhang
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Lujun Chen
- School of Environment, Tsinghua University, Beijing, 100084, China.,Zhejiang Provincial Key Laboratory of Water Science and Technology, Department of Environmental Technology and Ecology, Yangtze Delta Region Institute of Tsinghua University, Jiaxing, Zhejiang, 314050, China
| | - Renhua Sun
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.,Rural Energy & Environment Agency, Ministry of Agriculture, Beijing, 100125, China
| | - Tianjiao Dai
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Jinping Tian
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Wei Zheng
- Zhejiang Provincial Key Laboratory of Water Science and Technology, Department of Environmental Technology and Ecology, Yangtze Delta Region Institute of Tsinghua University, Jiaxing, Zhejiang, 314050, China
| | - Donghui Wen
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
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33
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Bao L, Wang X, Chen Y. Abundance and distribution of ammonia-oxidizing microorganisms in the sediments of Beiyun River, China. ANN MICROBIOL 2016. [DOI: 10.1007/s13213-016-1191-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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34
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Archaeal community in a human-disturbed watershed in southeast China: diversity, distribution, and responses to environmental changes. Appl Microbiol Biotechnol 2016; 100:4685-98. [PMID: 26810199 DOI: 10.1007/s00253-016-7318-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 01/11/2016] [Accepted: 01/12/2016] [Indexed: 10/22/2022]
Abstract
The response of freshwater bacterial community to anthropogenic disturbance has been well documented, yet the studies of freshwater archaeal community are rare, especially in lotic environments. Here, we investigated planktonic and benthic archaeal communities in a human-perturbed watershed (Jiulong River Watershed, JRW) of southeast China by using Illumina 16S ribosomal RNA gene amplicon sequencing. The results of taxonomic assignments indicated that SAGMGC-1, Methanobacteriaceae, Methanospirillaceae, and Methanoregulaceae were the four most abundant families in surface waters, accounting for 12.65, 23.21, 18.58 and 10.97 % of planktonic communities, whereas Nitrososphaeraceae and Miscellaneous Crenarchaeotic Group occupied more than 49 % of benthic communities. The compositions of archaeal communities and populations in waters and sediments were significantly different from each other. Remarkably, the detection frequencies of families Methanobacteriaceae and Methanospirillaceae, and genera Methanobrevibacter and Methanosphaera in planktonic communities correlated strongly with bacterial fecal indicator, suggesting some parts of methanogenic Archaea may come from fecal contamination. Because soluble reactive phosphorus (SRP) and the ratio of dissolved inorganic nitrogen to SRP instead of nitrogen nutrients showed significant correlation with several planktonic Nitrosopumilus- and Nitrosotalea-like OTUs, Thaumarchaeota may play an unexplored role in biogeochemical cycling of river phosphorus. Multivariate statistical analyses revealed that the variation of α-diversity of planktonic archaeal community was best explained by water temperature, whereas nutrient concentrations and stoichiometry were the significant drivers of β-diversity of planktonic and benthic communities. Taken together, these results demonstrate that the structure of archaeal communities in the JRW is sensitive to anthropogenic disturbances caused by riparian human activities.
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Lu S, Liu X, Ma Z, Liu Q, Wu Z, Zeng X, Shi X, Gu Z. Vertical Segregation and Phylogenetic Characterization of Ammonia-Oxidizing Bacteria and Archaea in the Sediment of a Freshwater Aquaculture Pond. Front Microbiol 2016; 6:1539. [PMID: 26834709 PMCID: PMC4718984 DOI: 10.3389/fmicb.2015.01539] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Accepted: 12/21/2015] [Indexed: 11/19/2022] Open
Abstract
Pond aquaculture is the major freshwater aquaculture method in China. Ammonia-oxidizing communities inhabiting pond sediments play an important role in controlling culture water quality. However, the distribution and activities of ammonia-oxidizing microbial communities along sediment profiles are poorly understood in this specific environment. Vertical variations in the abundance, transcription, potential ammonia oxidizing rate, and community composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in sediment samples (0–50 cm depth) collected from a freshwater aquaculture pond were investigated. The concentrations of the AOA amoA gene were higher than those of the AOB by an order of magnitude, which suggested that AOA, as opposed to AOB, were the numerically predominant ammonia-oxidizing organisms in the surface sediment. This could be attributed to the fact that AOA are more resistant to low levels of dissolved oxygen. However, the concentrations of the AOB amoA mRNA were higher than those of the AOA by 2.5- to 39.9-fold in surface sediments (0–10 cm depth), which suggests that the oxidation of ammonia was mainly performed by AOB in the surface sediments, and by AOA in the deeper sediments, where only AOA could be detected. Clone libraries of AOA and AOB amoA sequences indicated that the diversity of AOA and AOB decreased with increasing depth. The AOB community consisted of two groups: the Nitrosospira and Nitrosomonas clusters, and Nitrosomonas were predominant in the freshwater pond sediment. All AOA amoA gene sequences in the 0–2 cm deep sediment were grouped into the Nitrososphaera cluster, while other AOA sequences in deeper sediments (10–15 and 20–25 cm depths) were grouped into the Nitrosopumilus cluster.
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Affiliation(s)
- Shimin Lu
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery SciencesShanghai, China; College of Fisheries and Life, Shanghai Ocean UniversityShanghai, China
| | - Xingguo Liu
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery Sciences Shanghai, China
| | - Zhuojun Ma
- Chinese Academy of Fishery Sciences Beijing, China
| | - Qigen Liu
- College of Fisheries and Life, Shanghai Ocean University Shanghai, China
| | - Zongfan Wu
- Tongren Municipal Agricultural Commission (Government, Public) Tongren, China
| | - Xianlei Zeng
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery SciencesShanghai, China; College of Fisheries and Life, Shanghai Ocean UniversityShanghai, China
| | - Xu Shi
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery Sciences Shanghai, China
| | - Zhaojun Gu
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery Sciences Shanghai, China
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Zhang Q, Tang F, Zhou Y, Xu J, Chen H, Wang M, Laanbroek HJ. Shifts in the pelagic ammonia-oxidizing microbial communities along the eutrophic estuary of Yong River in Ningbo City, China. Front Microbiol 2015; 6:1180. [PMID: 26579089 PMCID: PMC4621301 DOI: 10.3389/fmicb.2015.01180] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Accepted: 10/12/2015] [Indexed: 12/11/2022] Open
Abstract
Aerobic ammonia oxidation plays a key role in the nitrogen cycle, and the diversity of the responsible microorganisms is regulated by environmental factors. Abundance and composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were investigated in the surface waters along an environmental gradient of the Yong River in Ningbo, East China. Water samples were collected from three pelagic zones: (1) freshwaters in the urban canals of Ningbo, (2) brackish waters in the downstream Yong River, and (3) coastal marine water of Hangzhou Bay. Shifts in activity and diversity of the ammonia-oxidizing microorganisms occurred simultaneously with changes in environmental factors, among which salinity and the availabilities of ammonium and oxygen. The AOA abundance was always higher than that of AOB and was related to the ammonia oxidation activity. The ratios of AOA/AOB in the brackish and marine waters were significantly higher than those found in freshwaters. Both AOA and AOB showed similar community compositions in brackish and marine waters, but only 31 and 35% similarity, respectively, between these waters and the urban inland freshwaters. Most of AOA-amoA sequences from freshwater were affiliated with sequences obtained from terrestrial environments and those collected from brackish and coastal areas were ubiquitous in marine, coastal, and terrestrial ecosystems. All AOB from freshwaters belonged to Nitrosomonas, and the AOB from brackish and marine waters mainly belonged to Nitrosospira.
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Affiliation(s)
- Qiufang Zhang
- Faculty of Architectural Civil Engineering and Environment, Ningbo University Ningbo, China
| | - Fangyuan Tang
- Faculty of Architectural Civil Engineering and Environment, Ningbo University Ningbo, China
| | - Yangjing Zhou
- Faculty of Architectural Civil Engineering and Environment, Ningbo University Ningbo, China
| | - Jirong Xu
- Faculty of Architectural Civil Engineering and Environment, Ningbo University Ningbo, China
| | - Heping Chen
- Faculty of Architectural Civil Engineering and Environment, Ningbo University Ningbo, China
| | - Mingkuang Wang
- Faculty of Architectural Civil Engineering and Environment, Ningbo University Ningbo, China
| | - Hendrikus J Laanbroek
- Department of Microbial Wetland Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands ; Institute of Environmental Biology, Utrecht University Utrecht, Netherlands
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The influence of salinity on the abundance, transcriptional activity, and diversity of AOA and AOB in an estuarine sediment: a microcosm study. Appl Microbiol Biotechnol 2015. [DOI: 10.1007/s00253-015-6804-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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38
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Liu S, Hu B, He Z, Zhang B, Tian G, Zheng P, Fang F. Ammonia-oxidizing archaea have better adaptability in oxygenated/hypoxic alternant conditions compared to ammonia-oxidizing bacteria. Appl Microbiol Biotechnol 2015; 99:8587-96. [PMID: 26099334 DOI: 10.1007/s00253-015-6750-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 05/30/2015] [Accepted: 06/02/2015] [Indexed: 10/23/2022]
Abstract
Ammonia oxidation is performed by both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Few studies compared the adaptability of AOA and AOB for oxygenated/hypoxic alternant conditions in water-level-fluctuating zones. Here, using qPCR and 454 high-throughput sequencing of functional amoA genes of AOA and AOB, we examined the changes of abundances, diversities, and community structures of AOA and AOB in periodically flooded soils compared to the non-flooded soils in Three Gorges Reservoir. The increased AOA operational taxonomic unit (OTU) numbers and the higher ratios of abundance (AOA:AOB) in the periodically flooded soils suggested AOA have better adaptability for oxygenated/hypoxic alternant conditions in the water-level-fluctuating zones in the Three Gorges Reservoir and probably responsible for the ammonia oxidation there. Canonical correspondence analysis (CCA) showed that oxidation-reduction potential (ORP) had the most significant effect on the community distribution of AOA (p < 0.01). Pearson analysis also indicated that ORP was the most important factor influencing the abundances and diversities of ammonia-oxidizing microbes. ORP was significantly negatively correlated with AOA OTU numbers (p < 0.05), ratio of OTU numbers (AOA:AOB) (p < 0.01), and ratio of amoA gene abundances (AOA:AOB) (p < 0.05). ORP was also significantly positively correlated with AOB abundance (p < 0.05).
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Affiliation(s)
- Shuai Liu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China.
| | - Zhanfei He
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Bin Zhang
- Faculty of Urban Construction and Environmental Engineering, Chongqing University, Chongqing, China
| | - Guangming Tian
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Fang Fang
- Faculty of Urban Construction and Environmental Engineering, Chongqing University, Chongqing, China.
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Liu S, Ren H, Shen L, Lou L, Tian G, Zheng P, Hu B. pH levels drive bacterial community structure in sediments of the Qiantang River as determined by 454 pyrosequencing. Front Microbiol 2015; 6:285. [PMID: 25941515 PMCID: PMC4403504 DOI: 10.3389/fmicb.2015.00285] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 03/22/2015] [Indexed: 11/13/2022] Open
Abstract
The Qiantang River is a typical freshwater ecosystem that acts as an irreplaceable water source in Zhejiang Province in southeastern China. However, the effects of environmental factors on the bacterial community of this freshwater ecosystem have not been determined. In this study, seven sediment samples were collected along the river. Their bacterial communities were identified using 454 high-throughput sequencing, and the primary environmental factors responsible for shaping the community structure were analyzed. The number of bacterial operational taxonomic units (OTUs) ranged from 2637 to 3933. Using a linear-regression analysis, the OTU numbers were significantly positively correlated with pH (r = 0.832, p < 0.05) and negatively correlated with nitrate concentration (r = -0.805, p < 0.05). A redundancy analysis (RDA) was also performed to test the relationship between the environmental factors and bacterial community composition. The results indicated that pH (p < 0.05) and nitrate concentration (p < 0.05) were the most significant factors that determined the community distribution of sediment bacteria.
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Affiliation(s)
- Shuai Liu
- Department of Environmental Engineering, Zhejiang University Hangzhou, China
| | - Hongxing Ren
- Department of Environmental Engineering, Zhejiang University Hangzhou, China
| | - Lidong Shen
- Department of Environmental Engineering, Zhejiang University Hangzhou, China
| | - Liping Lou
- Department of Environmental Engineering, Zhejiang University Hangzhou, China
| | - Guangming Tian
- Department of Environmental Engineering, Zhejiang University Hangzhou, China
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University Hangzhou, China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University Hangzhou, China
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Zhang Y, Chen L, Dai T, Sun R, Wen D. Ammonia manipulates the ammonia-oxidizing archaea and bacteria in the coastal sediment-water microcosms. Appl Microbiol Biotechnol 2015; 99:6481-91. [PMID: 25797330 DOI: 10.1007/s00253-015-6524-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 03/02/2015] [Accepted: 03/03/2015] [Indexed: 12/14/2022]
Abstract
Ammonia was observed as a potential significant factor to manipulate the abundance and activity of ammonia-oxidizing microorganisms (AOMs) in water environments. For the first time, this study confirmed this phenomenon by laboratory cultivation. In a series of estuarine sediment-coastal water microcosms, we investigated the AOM's phylogenetic composition and activity change in response to ammonia concentration. Increase of ammonia concentration promoted bacterial amoA gene abundance in a linear pattern. The ratio of transcribed ammonia-oxidizing bacteria (AOB) amoA gene/ammonia-oxidizing archaea (AOA) amoA gene increased from 0.1 to 43 as NH4 (+)-N increased from less than 0.1 to 12 mg L(-1), and AOA amoA transcription was undetected under 20 mg NH4 (+)-N L(-1). The incubation of stable isotope probing (SIP) microcosms revealed a faster (13)C-NaHCO3 incorporation rate of AOA amoA gene under 0.1 mg NH4 (+)-N L(-1) and a sole (13)C-NaHCO3 utilization of the AOB amoA gene under 20 mg NH4 (+)-N L(-1). Our results indicate that ammonia concentration manipulates the structure of AOM. AOA prefers to live and perform higher amoA transcription activity than AOB in ammonia-limited water environments, and AOB tends to take the first contributor place in ammonia-rich ones.
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Affiliation(s)
- Yan Zhang
- School of Environment, Tsinghua University, Beijing, 100084, China
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41
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Chi XQ, Liu K, Zhou NY. Effects of bioaugmentation in para-nitrophenol-contaminated soil on the abundance and community structure of ammonia-oxidizing bacteria and archaea. Appl Microbiol Biotechnol 2015; 99:6069-82. [DOI: 10.1007/s00253-015-6462-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 02/03/2015] [Accepted: 02/05/2015] [Indexed: 10/23/2022]
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42
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Zhang Y, Chen L, Sun R, Dai T, Tian J, Wen D. Ammonia-oxidizing bacteria and archaea in wastewater treatment plant sludge and nearby coastal sediment in an industrial area in China. Appl Microbiol Biotechnol 2015; 99:4495-507. [DOI: 10.1007/s00253-014-6352-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 12/19/2014] [Accepted: 12/21/2014] [Indexed: 12/11/2022]
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43
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Liu Y, Zhang J, Zhao L, Li Y, Dai Y, Xie S. Distribution of sediment ammonia-oxidizing microorganisms in plateau freshwater lakes. Appl Microbiol Biotechnol 2015; 99:4435-44. [DOI: 10.1007/s00253-014-6341-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 12/15/2014] [Accepted: 12/17/2014] [Indexed: 01/16/2023]
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44
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Damashek J, Smith JM, Mosier AC, Francis CA. Benthic ammonia oxidizers differ in community structure and biogeochemical potential across a riverine delta. Front Microbiol 2015; 5:743. [PMID: 25620958 PMCID: PMC4287051 DOI: 10.3389/fmicb.2014.00743] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 12/08/2014] [Indexed: 11/17/2022] Open
Abstract
Nitrogen pollution in coastal zones is a widespread issue, particularly in ecosystems with urban or agricultural watersheds. California's Sacramento-San Joaquin Delta, at the landward reaches of San Francisco Bay, is highly impacted by both agricultural runoff and sewage effluent, leading to chronically high nutrient loadings. In particular, the extensive discharge of ammonium into the Sacramento River has altered this ecosystem by vastly increasing ammonium concentrations and thus changing the stoichiometry of inorganic nitrogen stocks, with potential effects throughout the food web. This debate surrounding ammonium inputs highlights the importance of understanding the rates of, and controls on, nitrogen (N) cycling processes across the delta. To date, however, there has been little research examining N biogeochemistry or N-cycling microbial communities in this system. We report the first data on benthic ammonia-oxidizing microbial communities and potential nitrification rates for the Sacramento-San Joaquin Delta, focusing on the functional gene amoA (which codes for the α-subunit of ammonia monooxygenase). There were stark regional differences in ammonia-oxidizing communities, with ammonia-oxidizing bacteria (AOB) outnumbering ammonia-oxidizing archaea (AOA) only in the ammonium-rich Sacramento River. High potential nitrification rates in the Sacramento River suggested these communities may be capable of oxidizing significant amounts of ammonium, compared to the San Joaquin River and the upper reaches of San Francisco Bay. Gene diversity also showed regional patterns, as well as phylogenetically unique ammonia oxidizers in the Sacramento River. The benthic ammonia oxidizers in this nutrient-rich aquatic ecosystem may be important players in its overall nutrient cycling, and their community structure and biogeochemical function appear related to nutrient loadings. Unraveling the microbial ecology and biogeochemistry of N cycling pathways, including benthic nitrification, is a critical step toward understanding how such ecosystems respond to the changing environmental conditions wrought by human development and climate change.
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Affiliation(s)
- Julian Damashek
- Department of Environmental Earth System Science, Stanford University Stanford, CA, USA
| | - Jason M Smith
- Department of Environmental Earth System Science, Stanford University Stanford, CA, USA
| | - Annika C Mosier
- Department of Environmental Earth System Science, Stanford University Stanford, CA, USA
| | - Christopher A Francis
- Department of Environmental Earth System Science, Stanford University Stanford, CA, USA
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Community structure and distribution of planktonic ammonia-oxidizing archaea and bacteria in the Dongjiang River, China. Res Microbiol 2014; 165:657-70. [DOI: 10.1016/j.resmic.2014.08.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 08/08/2014] [Indexed: 11/22/2022]
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46
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Impact of carbon source amendment on ammonia-oxidizing microorganisms in reservoir riparian soil. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-0979-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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47
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Baolan H, Shuai L, Wei W, Lidong S, Liping L, Weiping L, Guangming T, Xiangyang X, Ping Z. pH-dominated niche segregation of ammonia-oxidising microorganisms in Chinese agricultural soils. FEMS Microbiol Ecol 2014; 90:290-9. [DOI: 10.1111/1574-6941.12391] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 07/15/2014] [Accepted: 07/19/2014] [Indexed: 11/28/2022] Open
Affiliation(s)
- Hu Baolan
- Department of Environmental Engineering; Zhejiang University; Hangzhou China
| | - Liu Shuai
- Department of Environmental Engineering; Zhejiang University; Hangzhou China
| | - Wang Wei
- Department of Environmental Engineering; Zhejiang University; Hangzhou China
| | - Shen Lidong
- Department of Environmental Engineering; Zhejiang University; Hangzhou China
| | - Lou Liping
- Department of Environmental Engineering; Zhejiang University; Hangzhou China
| | - Liu Weiping
- College of Environmental & Resource Science; Ministry of Education; Key Laboratory for Environmental Remediation & Ecosystem Health; Zhejiang University; Hangzhou China
| | - Tian Guangming
- Department of Environmental Engineering; Zhejiang University; Hangzhou China
| | - Xu Xiangyang
- Department of Environmental Engineering; Zhejiang University; Hangzhou China
| | - Zheng Ping
- Department of Environmental Engineering; Zhejiang University; Hangzhou China
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Wang Z, Yang Y, Sun W, Xie S, Liu Y. Nonylphenol biodegradation in river sediment and associated shifts in community structures of bacteria and ammonia-oxidizing microorganisms. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2014; 106:1-5. [PMID: 24836870 DOI: 10.1016/j.ecoenv.2014.04.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 04/17/2014] [Accepted: 04/19/2014] [Indexed: 06/03/2023]
Abstract
Nonylphenol (NP) is one of commonly detected contaminants in the environment. Biological degradation is mainly responsible for remediation of NP-contaminated site. Knowledge about the structure of NP-degrading microbial community is still very limited. Microcosms were constructed to investigate the structure of microbial community in NP-contaminated river sediment and its change with NP biodegradation. A high level of NP was significantly dissipated in 6-9 days. Bacteria and ammonia-oxidizing archaea (AOA) were more responsive to NP amendment compared to ammonia-oxidizing bacteria (AOB). Gammaproteobacteria, Alphaproteobacteria and Bacteroidetes were the largest bacterial groups in NP-degrading sediment. Microorganisms from bacterial genera Brevundimonas, Flavobacterium, Lysobacter and Rhodobacter might be involved in NP degradation in river sediment. This study provides some new insights towards NP biodegradation and microbial ecology in NP-contaminated environment.
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Affiliation(s)
- Zhao Wang
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences (Ministry of Education), Peking University, Beijing 100871, China
| | - Yuyin Yang
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences (Ministry of Education), Peking University, Beijing 100871, China
| | - Weimin Sun
- Department of Environmental Science, Rutgers University, New Brunswick, NJ 08901, USA
| | - Shuguang Xie
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences (Ministry of Education), Peking University, Beijing 100871, China.
| | - Yong Liu
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences (Ministry of Education), Peking University, Beijing 100871, China.
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Xu W, Li M, Ding JF, Gu JD, Luo ZH. Bacteria dominate the ammonia-oxidizing community in a hydrothermal vent site at the Mid-Atlantic Ridge of the South Atlantic Ocean. Appl Microbiol Biotechnol 2014; 98:7993-8004. [DOI: 10.1007/s00253-014-5833-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 05/13/2014] [Accepted: 05/14/2014] [Indexed: 01/29/2023]
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50
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Bollmann A, Bullerjahn GS, McKay RM. Abundance and diversity of ammonia-oxidizing archaea and bacteria in sediments of trophic end members of the Laurentian Great Lakes, Erie and Superior. PLoS One 2014; 9:e97068. [PMID: 24819357 PMCID: PMC4018257 DOI: 10.1371/journal.pone.0097068] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 04/15/2014] [Indexed: 11/29/2022] Open
Abstract
Ammonia oxidation is the first step of nitrification carried out by ammonia-oxidizing Archaea (AOA) and Bacteria (AOB). Lake Superior and Erie are part of the Great Lakes system differing in trophic status with Lake Superior being oligotrophic and Lake Erie meso- to eutrophic. Sediment samples were collected from both lakes and used to characterize abundance and diversity of AOA and AOB based on the ammonia monooxygenase (amoA) gene. Diversity was accessed by a pyro-sequencing approach and the obtained sequences were used to determine the phylogeny and alpha and beta diversity of the AOA and AOB populations. In Lake Erie copy numbers of bacterial amoA genes were in the same order of magnitude or even higher than the copy numbers of the archaeal amoA genes, while in Lake Superior up to 4 orders of magnitude more archaeal than bacterial amoA copies were detected. The AOB detected in the samples from Lake Erie belonged to AOB that are frequently detected in freshwater. Differences were detected between the phylogenetic affiliations of the AOA from the two lakes. Most sequences detected in Lake Erie clustered in the Nitrososphaera cluster (Thaumarchaeal soil group I.1b) where as most of the sequences in Lake Superior were found in the Nitrosopumilus cluster (Thaumarchaeal marine group I.1a) and the Nitrosotalea cluster. Pearson correlations and canonical correspondence analysis (CCA) showed that the differences in abundance and diversity of AOA are very likely related to the sampling location and thereby to the different trophic states of the lakes.
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Affiliation(s)
- Annette Bollmann
- Department of Microbiology, Miami University, Oxford, Ohio, United States of America
- * E-mail: *
| | - George S. Bullerjahn
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, United States of America
| | - Robert Michael McKay
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, United States of America
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