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Ren B, Wang W, Shen L, Yang W, Yang Y, Jin J, Geng C. Nitrogen fertilization rate affects communities of ammonia-oxidizing archaea and bacteria in paddy soils across different climatic zones of China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 902:166089. [PMID: 37549709 DOI: 10.1016/j.scitotenv.2023.166089] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/02/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023]
Abstract
Nitrogen fertilization has important effects on nitrification. However, how the rate of nitrogen fertilization affects nitrification potential, as well as the communities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), remains unclear. We performed a large-scale investigation of nitrification potential and ammonia-oxidizer communities in Chinese paddy fields at different nitrogen fertilization rates across different climatic zones. It was found that the nitrification potential at the high nitrogen fertilization rate (≥150 kg-1 N ha-1) was 23.35 % higher than that at the intermediate rate (100-150 kg-1 N ha-1) and 20.77 % higher than that at the low rate (< 100 kg-1 N ha-1). The nitrification potential showed no significant variation among different nitrogen fertilization rates across climatic zones. Furthermore, the AOA and AOB amoA gene abundance at the high nitrogen fertilization rate was 481.67 % and 292.74 % higher (p < 0.05) than that at the intermediate rate, respectively. Correlation analysis demonstrated a significant positive correlation between AOB abundance and nitrification potential. AOA and AOB community composition differed significantly among nitrogen fertilization rates. Moreover, soil NH4+ content, pH, water content, bulk density, and annual average temperature were regarded as key environmental factors influencing the community structure of ammonia-oxidizers. Taken together, the nitrogen fertilization rate had a significant impact on the communities of AOA and AOB but did not significantly alter the nitrification potential. Our findings provide new insights into the impact of nitrogen fertilization management on nitrification in rice paddy fields.
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Affiliation(s)
- Bingjie Ren
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Weiqi Wang
- Key Laboratory of Humid Subtropical Eco-geographical Process, Ministry of Education, Fujian Normal University, Fuzhou 350117, China
| | - Lidong Shen
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China.
| | - Wangting Yang
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Yuling Yang
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Jinghao Jin
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Caiyu Geng
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
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2
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Zhang D, Li M, Yang Y, Yu H, Xiao F, Mao C, Huang J, Yu Y, Wang Y, Wu B, Wang C, Shu L, He Z, Yan Q. Nitrite and nitrate reduction drive sediment microbial nitrogen cycling in a eutrophic lake. WATER RESEARCH 2022; 220:118637. [PMID: 35617789 DOI: 10.1016/j.watres.2022.118637] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 05/05/2023]
Abstract
The anaerobic microbial nitrogen (N) removal in lake sediments is one of the most important processes driving the nitrogen cycling in lake ecosystems. However, the N removal and its underlying mechanisms regulated by denitrifying and anaerobic ammonia oxidation (anammox) bacteria in lake sediments remain poorly understood. With the field sediments collected from different areas of Lake Donghu (a shallow eutrophic lake), we examined the denitrifying and anammox bacterial communities by sequencing the nirS/K and hzsB genes, respectively. The results indicated that denitrifiers in sediments were affiliated to nine clusters, which are involved in both heterotrophic and autotrophic denitrification. However, anammox bacteria were only dominated by Candidatus Brocadia. We found that NO3- and NO2- concentrations, as well as Nar enzyme activity were the key factors affecting denitrifying and anammox communities in this eutrophic lake. The enrichment experiments in bioreactors confirmed the divergence of denitrification and anammox rates with an additional complement of NO2-, especially under a condition low nitrate reductase activity. The coupled denitrification and anammox may play significant roles in N removal, and the availability of electronic acceptors (i.e., NO2- and NO3-) strongly influenced the N loss in lake sediments. Further path analysis indicated that NO2-, NO3- and some N-related enzymes were the key factors affecting microbial N removal in lake sediments. This study advances our understanding of the mechanisms driving the of denitrification and anammox in lake sediments, which also provides new insights into coupled denitrification-anammox N removal in eutrophic lake ecosystems.
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Affiliation(s)
- Dandan Zhang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, School of Ecology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Mingyue Li
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, School of Ecology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Yuchun Yang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, School of Ecology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Huang Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, School of Ecology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Fanshu Xiao
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, School of Ecology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China; Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Chengzhi Mao
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Jie Huang
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yuhe Yu
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yunfeng Wang
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; Institute of Evolution & Marine Biodiversity, College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Bo Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, School of Ecology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, School of Ecology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, School of Ecology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, School of Ecology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China; College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, School of Ecology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China.
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3
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Silveira R, Silva MRSS, de Roure Bandeira de Mello T, Alvim EACC, Marques NCS, Kruger RH, da Cunha Bustamante MM. Bacteria and Archaea Communities in Cerrado Natural Pond Sediments. MICROBIAL ECOLOGY 2021; 81:563-578. [PMID: 32829441 DOI: 10.1007/s00248-020-01574-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 08/07/2020] [Indexed: 06/11/2023]
Abstract
Natural ponds in the Brazilian Cerrado harbor high biodiversity but are still poorly studied, especially their microbial assemblage. The characterization of the microbial community in aquatic environments is fundamental for understanding its functioning, particularly under the increasing pressure posed by land conversion and climate change. Here, we aim to characterize the structure (abundance, richness, and diversity) and composition of the Bacteria and Archaea in the sediment of two natural ponds belonging to different basins that primarily differ in size and depth in the Cerrado. Sediment samples were collected in the dry and rainy seasons and the transition periods between both. The structure and composition of Bacteria and Archaea were assessed by 16S rRNA gene pyrosequencing. We identified 45 bacterial and four archaeal groups. Proteobacteria and Acidobacteria dominated the bacterial community, while Euryarchaeota and Thaumarchaeota dominated the archaeal community. Seasonal fluctuations in the relative abundance of microbial taxa were observed, but pond characteristics were more determinant to community composition differences. Microbial communities are highly diverse, and local variability could partially explain the microbial structure's main differences. Functional predictions based in 16S rRNA gene accessed with Tax4Fun indicated an enriched abundance of predicted methane metabolism in the deeper pond, where higher abundance of methanogenic archaea Methanocella, Methanosaeta, and Methanomicrobiaceae was detected. Our dataset encompasses the more comprehensive survey of prokaryotic microbes in Cerrado's aquatic environments. Here, we present basic and essential information about composition and diversity, for initial insights into the ecology of Bacteria and Archaea in these environments.
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Affiliation(s)
- Rafaella Silveira
- Microbial Biology, Cellular Biology Department, Biology Institute, University of Brasília, Brasilia, DF, 70919-970, Brazil.
- Enzymology Laboratory, Cellular Biology Department, Biology Institute, University of Brasília, Brasilia, DF, 70919-970, Brazil.
- Ecosystems Laboratory, Ecology Department, Biology Institute, University of Brasília, Brasilia, DF, 70919-970, Brazil.
| | | | | | | | - Nubia Carla Santos Marques
- Ecosystems Laboratory, Ecology Department, Biology Institute, University of Brasília, Brasilia, DF, 70919-970, Brazil
| | - Ricardo Henrique Kruger
- Microbial Biology, Cellular Biology Department, Biology Institute, University of Brasília, Brasilia, DF, 70919-970, Brazil
- Enzymology Laboratory, Cellular Biology Department, Biology Institute, University of Brasília, Brasilia, DF, 70919-970, Brazil
| | - Mercedes Maria da Cunha Bustamante
- Microbial Biology, Cellular Biology Department, Biology Institute, University of Brasília, Brasilia, DF, 70919-970, Brazil.
- Ecosystems Laboratory, Ecology Department, Biology Institute, University of Brasília, Brasilia, DF, 70919-970, Brazil.
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4
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Sodhi KK, Kumar M, Balan B, Dhaulaniya AS, Shree P, Sharma N, Singh DK. Perspectives on the antibiotic contamination, resistance, metabolomics, and systemic remediation. SN APPLIED SCIENCES 2021. [DOI: 10.1007/s42452-020-04003-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
AbstractAntibiotics have been regarded as the emerging contaminants because of their massive use in humans and veterinary medicines and their persistence in the environment. The global concern of antibiotic contamination to different environmental matrices and the emergence of antibiotic resistance has posed a severe impact on the environment. Different mass-spectrometry-based techniques confirm their presence in the environment. Antibiotics are released into the environment through the wastewater steams and runoff from land application of manure. The microorganisms get exposed to the antibiotics resulting in the development of antimicrobial resistance. Consistent release of the antibiotics, even in trace amount into the soil and water ecosystem, is the major concern because the antibiotics can lead to multi-resistance in bacteria which can cause hazardous effects on agriculture, aquaculture, human, and livestock. A better understanding of the correlation between the antibiotic use and occurrence of antibiotic resistance can help in the development of policies to promote the judicious use of antibiotics. The present review puts a light on the remediation, transportation, uptake, and antibiotic resistance in the environment along with a novel approach of creating a database for systemic remediation, and metabolomics for the cleaner and safer environment.
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5
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Zhou W, Jiang X, Ouyang J, Lu B, Liu W, Liu G. Environmental Factors, More Than Spatial Distance, Explain Community Structure of Soil Ammonia-Oxidizers in Wetlands on the Qinghai-Tibetan Plateau. Microorganisms 2020; 8:E933. [PMID: 32575850 PMCID: PMC7355592 DOI: 10.3390/microorganisms8060933] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/08/2020] [Accepted: 06/18/2020] [Indexed: 11/17/2022] Open
Abstract
In wetland ecosystems, ammonia oxidation highly depends on the activity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), which are, therefore, important for studying nitrogen cycling. However, the ammonia-oxidizer communities in the typical high-elevation wetlands are poorly understood. Here, we examined ammonia-oxidizer communities in soils from three wetland types and 31 wetland sites across the Qinghai-Tibetan Plateau. The amoA gene of AOA and AOB was widespread across all wetland types. Nitrososphaera clade (Group I.1b) overwhelmingly dominated in AOA community (90.36%), while Nitrosospira was the principal AOB type (64.96%). The average abundances of AOA and AOB were 2.63 × 104 copies g-1 and 9.73 × 103 copies g-1. The abundance of AOA amoA gene was higher in riverine and lacustrine wetlands, while AOB amoA gene dominated in palustrine wetlands. The environmental conditions, but not spatial distance, have a dominant role in shaping the pattern of ammonia-oxidizer communities. The AOA community composition was influenced by mean annual temperature (MAT) and mean annual precipitation (MAP), while MAT, conductivity and plant richness, pH, and TN influenced the AOB community composition. The net nitrification rate had a significant correlation to AOB, but not AOA abundance. Our results suggest a dominant role for climate factors (MAT and MAP) in shaping community composition across a wide variety of wetland sites and conditions.
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Affiliation(s)
- Wen Zhou
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (W.Z.); (X.J.); (J.O.); (B.L.)
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Xiaoliang Jiang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (W.Z.); (X.J.); (J.O.); (B.L.)
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Ouyang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (W.Z.); (X.J.); (J.O.); (B.L.)
- Research Center for Ecology and Environment of Qinghai–Tibetan Plateau, Tibet University, Lhasa 850000, China
- College of Science, Tibet University, Lhasa 850000, China
| | - Bei Lu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (W.Z.); (X.J.); (J.O.); (B.L.)
| | - Wenzhi Liu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (W.Z.); (X.J.); (J.O.); (B.L.)
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Center for Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
| | - Guihua Liu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (W.Z.); (X.J.); (J.O.); (B.L.)
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Center for Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
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Wang R, Han R, Long Q, Gao X, Xing J, Shen G, Zhu D. Bacterial and Archaeal Communities within an Ultraoligotrophic, High-altitude Lake in the Pre-Himalayas of the Qinghai-Tibet Plateau. Indian J Microbiol 2020; 60:363-373. [PMID: 32655200 DOI: 10.1007/s12088-020-00881-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 05/06/2020] [Indexed: 11/25/2022] Open
Abstract
Puma Yumco Lake (PYL) is an ultraoligotrophic freshwater lake that sits an altitude of 5030 m within the Qinghai-Tibet Plateau of China. The bacterial and archaeal diversity of the lake remains poorly understood, despite their potential to inform on biogeochemical cycling and environment-microbial associations in these unique environments. Here, the bacterial and archaeal communities of PYL were investigated using high-throughput sequencing analysis of community 16S rRNA gene sequences. Further, the relationships among dominant taxa and environmental factors were comprehensively evaluated. Bacterial diversity comprised 31 phyla and 371 genera (10,645 operational taxonomic units [OTUs], Shannon index values of 5.21-6.16) and was significantly higher than that of Archaea (five phyla and 24 genera comprising 1141 OTUs and Shannon index values of 1.18-3.28). The bacterial communities were dominated by Proteobacteria (48.42-59.97% relative abundances), followed by Bacteroidetes (12.5-32.51%), Acidobacteria (2.07-11.56%), Firmicutes (0.65-6.32%), Planctomycetes (0.99-3.56%), Gemmatimonadetes (0.38-3.57%), Actinobacteria (1.67-3.52%), Verrucomicrobia (0.87-2.01%), and Chloroflexi (0.5-1.17%). In addition, archaeal communities were dominated by Thaumarchaeota (33.22-93.00%), followed by Euryarchaeota (2.89-35.47%), Woesearchaeota (0.99-31.04%), and Pacearchaeota (0.01-1.14%). The most abundant bacterial genus was Rhodoferax (5.73-26.62%) and the most abundant archaeal genus was the ammonia-oxidizing Nitrososphaera (29.18-91.46%). These results suggest that the Rhodoferax and Nitrososphaera are likely to participate in biogeochemical cycles in these environments through photoheterotrophy and nitrification, respectively. Taken together, these results provide valuable data for better understanding microbial interactions with each other and with these unique environments.
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Affiliation(s)
- Rong Wang
- Research Center of Basic Medical Science, Medical College of Qinghai University, Xining, 810016 Qinghai China
| | - Rui Han
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, 810016 Qinghai China
| | - Qifu Long
- Research Center of Basic Medical Science, Medical College of Qinghai University, Xining, 810016 Qinghai China
| | - Xiang Gao
- Research Center of Basic Medical Science, Medical College of Qinghai University, Xining, 810016 Qinghai China
| | - Jiangwa Xing
- Research Center of Basic Medical Science, Medical College of Qinghai University, Xining, 810016 Qinghai China
| | - Guoping Shen
- Research Center of Basic Medical Science, Medical College of Qinghai University, Xining, 810016 Qinghai China
| | - Derui Zhu
- Research Center of Basic Medical Science, Medical College of Qinghai University, Xining, 810016 Qinghai China
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Yang X, Liu L, Wang S. A strategy of high-efficient nitrogen removal by an ammonia-oxidizing bacterium consortium. BIORESOURCE TECHNOLOGY 2019; 275:216-224. [PMID: 30590208 DOI: 10.1016/j.biortech.2018.12.057] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 12/09/2018] [Accepted: 12/16/2018] [Indexed: 06/09/2023]
Abstract
An ammonia-oxidizing bacterium consortium showed approximately 100% removal of NH4+-N with an initial concentration of 262.28 ± 8.21 mg·L-1 within 10 days, and only 16.54 ± 0.52% of NH4+-N was converted to NO2--N in this study. The consortium removed ammonium by heterotrophic nitrification and aerobic denitrification (HNAD) without N2O emission. The activity of AOB was not affected by low concentrations of FA or FNA, but completely inhibited by 0.04 mg HNO2·L-1. In a bioaugmentation treatment of eutrophic wastewater using the consortium, the removal efficiency of NH4+-N reached 90.85 ± 0.8% and 77.88 ± 1.86% at initial concentrations of 1.80 ± 0.04 mg·L-1 and 40.31 ± 0.57 mg·L-1, respectively, and the dissolved oxygen level had a significant impact on the consortium activity. No significant changes in the bacterial community structure were observed after the consortium addition, and local functional bacteria were enriched by aeration and contributed to ammonium nitrogen removal with AOB.
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Affiliation(s)
- Xiaolong Yang
- Department of Environmental Science and Engineering, Fudan University, 2005 Songhu Road, Shanghai 200433, PR China
| | - Lihua Liu
- Maths & Physics College, Jinggangshan University, 28 Xueyuan Road, Ji'an 343009, PR China
| | - Shoubing Wang
- Department of Environmental Science and Engineering, Fudan University, 2005 Songhu Road, Shanghai 200433, PR China.
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Variation of Bacterial and Archaeal Community Structures in a Full-Scale Constructed Wetlands for Wastewater Treatment. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2018; 2018:9319345. [PMID: 30410420 PMCID: PMC6206559 DOI: 10.1155/2018/9319345] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/22/2018] [Indexed: 11/18/2022]
Abstract
Microorganisms play important roles in the reduction of organic and inorganic pollutants in constructed wetlands used for the treatment of wastewater. However, the diversity and structure of microbial community in constructed wetland system remain poorly known. In this study, the Illumina MiSeq Sequencing of 16S rDNA was used to analyze the bacterial and archaeal microbial community structures of soil and water in a free surface flow constructed wetland, and the differences of bacterial communities and archaeal compositions between soil and water were compared. The results showed that the Proteobacteria were the dominant bacteria, making up 35.38%~48.66% relative abundance. Euryarchaeotic were the absolute dominant archaea in the influent sample with the relative abundance of 93.29%, while Thaumarchaeota showed dominance in the other three samples, making up 50.58%~75.70%. The relative abundances of different species showed great changes in bacteria and archaea, and the number of dominant species in bacteria was much higher than that in archaea. Compared to archaea, the community compositions of bacteria were more abundant and the changes were more significant. Meanwhile, bacteria and archaea had large differences in compositions between water and soil. The microbial richness in water was significantly higher than that in soil. Simultaneously, soil had a significant enrichment effect on some microbial flora.
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9
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Dai L, Liu C, Yu L, Song C, Peng L, Li X, Tao L, Li G. Organic Matter Regulates Ammonia-Oxidizing Bacterial and Archaeal Communities in the Surface Sediments of Ctenopharyngodon idellus Aquaculture Ponds. Front Microbiol 2018; 9:2290. [PMID: 30319588 PMCID: PMC6165866 DOI: 10.3389/fmicb.2018.02290] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 09/07/2018] [Indexed: 01/28/2023] Open
Abstract
Ammonia-oxidizing bacteria (AOB) and archaea (AOA) play important roles in nitrogen removal in aquaculture ponds, but their distribution and the environmental factors that drive their distribution are largely unknown. In this study, we collected surface sediment samples from Ctenopharyngodon idellus ponds in three different areas in China that practice aquaculture. The community structure of AOB and AOA and physicochemical characteristics in the ponds were investigated. The results showed that AOA were more abundant than AOB in all sampling ponds except one, but sediment AOB and AOA numbers varied greatly between ponds. Correlation analyses indicated a significant correlation between the abundance of AOB and arylsulfatase, as well as the abundance of AOA and total nitrogen (TN) and arylsulfatase. In addition, AOB/AOA ratio was found to be significantly correlated with the microbial biomass carbon. AOB were grouped into seven clusters affiliated to Nitrosospira and Nitrosomonas, and AOA were grouped into six clusters affiliated to Nitrososphaera, Nitrososphaera sister group, and Nitrosopumilus. AOB/AOA diversity in the surface sediments of aquaculture ponds varied according to the levels of total organic carbon (TOC), and AOB and AOA diversity was significantly correlated with arylsulfatase and β-glucosidase, respectively. The compositions of the AOB communities were also found to be significantly influenced by sediment eutrophic status (TOC and TN levels), and pH. In addition, concentrations of acid phosphatase and arylsulfatase in surface sediments were significantly correlated with the prominent bacterial amoA genotypes, and concentrations of TOC and urease were found to be significantly correlated with the prominent archaeal amoA genotype compositions. Taken together, our results indicated that AOB and AOA communities in the surface sediments of Ctenopharyngodon idellus aquaculture ponds are regulated by organic matter and its availability to the microorganisms.
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Affiliation(s)
- Lili Dai
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China.,College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Chengqing Liu
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China.,College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Liqin Yu
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Chaofeng Song
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Liang Peng
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Xiaoli Li
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Ling Tao
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Gu Li
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
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10
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Geochemical and Microbial Community Attributes in Relation to Hyporheic Zone Geological Facies. Sci Rep 2017; 7:12006. [PMID: 28931901 PMCID: PMC5607297 DOI: 10.1038/s41598-017-12275-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 08/30/2017] [Indexed: 11/18/2022] Open
Abstract
The hyporheic zone (HZ) is the active ecotone between the surface stream and groundwater, where exchanges of nutrients and organic carbon have been shown to stimulate microbial activity and transformations of carbon and nitrogen. To examine the relationship between sediment texture, biogeochemistry, and biological activity in the Columbia River HZ, the grain size distributions for sediment samples were characterized to define geological facies, and the relationships among physical properties of the facies, physicochemical attributes of the local environment, and the structure and activity of associated microbial communities were examined. Mud and sand content and the presence of microbial heterotrophic and nitrifying communities partially explained the variability in many biogeochemical attributes such as C:N ratio and %TOC. Microbial community analysis revealed a high relative abundance of putative ammonia-oxidizing Thaumarchaeota and nitrite-oxidizing Nitrospirae. Network analysis showed negative relationships between sets of co-varying organisms and sand and mud contents, and positive relationships with total organic carbon. Our results indicate grain size distribution is a good predictor of biogeochemical properties, and that subsets of the overall microbial community respond to different sediment texture. Relationships between facies and hydrobiogeochemical properties enable facies-based conditional simulation/mapping of these properties to inform multiscale modeling of hyporheic exchange and biogeochemical processes.
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Zhao K, Kong W, Khan A, Liu J, Guo G, Muhanmmad S, Zhang X, Dong X. Elevational diversity and distribution of ammonia-oxidizing archaea community in meadow soils on the Tibetan Plateau. Appl Microbiol Biotechnol 2017; 101:7065-7074. [PMID: 28776097 DOI: 10.1007/s00253-017-8435-x] [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: 06/16/2017] [Revised: 07/12/2017] [Accepted: 07/19/2017] [Indexed: 10/19/2022]
Abstract
Unraveling elevational diversity patterns of plants and animals has long been attracting scientific interests. However, whether soil microorganisms exhibit similar elevational patterns remains largely less explored, especially for functional microbial communities, such as ammonia oxidizers. Here, we investigated the diversity and distribution pattern of ammonia-oxidizing archaea (AOA) in meadow soils along an elevation gradient from 4400 m to the grassline at 5100 m on the Tibetan Plateau using terminal restriction fragment length polymorphism (T-RFLP) and sequencing methods by targeting amoA gene. Increasing elevations led to lower soil temperature and pH, but higher nutrients and water content. The results showed that AOA diversity and evenness monotonically increased with elevation, while richness was relatively stable. The increase of diversity and evenness was attributed to the growth inhibition of warm-adapted AOA phylotypes by lower temperature and the growth facilitation of cold-adapted AOA phylotypes by richer nutrients at higher elevations. Low temperature thus played an important role in the AOA growth and niche separation. The AOA community variation was explained by the combined effect of all soil properties (32.6%), and 8.1% of the total variation was individually explained by soil pH. The total AOA abundance decreased, whereas soil potential nitrification rate (PNR) increased with increasing elevations. Soil PNR positively correlated with the abundance of cold-adapted AOA phylotypes. Our findings suggest that low temperature plays an important role in AOA elevational diversity pattern and niche separation, rising the negative effects of warming on AOA diversity and soil nitrification process in the Tibetan region.
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Affiliation(s)
- Kang Zhao
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Building 3, Courtyard 16, Lincui Road, Chaoyang District, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Weidong Kong
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Building 3, Courtyard 16, Lincui Road, Chaoyang District, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100101, China.
| | - Ajmal Khan
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Building 3, Courtyard 16, Lincui Road, Chaoyang District, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinbo Liu
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Building 3, Courtyard 16, Lincui Road, Chaoyang District, Beijing, 100101, China
| | - Guangxia Guo
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Building 3, Courtyard 16, Lincui Road, Chaoyang District, Beijing, 100101, China
| | - Said Muhanmmad
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Building 3, Courtyard 16, Lincui Road, Chaoyang District, Beijing, 100101, China
| | - Xianzhou Zhang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaobin Dong
- State Key Laboratory of Earth Surface Processes and Resource Ecology, College of Resources Science and Technology, Beijing Normal University, Beijing, 100875, China
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Long Y, Yi H, Chen S, Zhang Z, Cui K, Bing Y, Zhuo Q, Li B, Xie S, Guo Q. Influences of plant type on bacterial and archaeal communities in constructed wetland treating polluted river water. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:19570-9. [PMID: 27392623 DOI: 10.1007/s11356-016-7166-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 06/28/2016] [Indexed: 05/12/2023]
Abstract
Both bacteria and archaeal communities can play important roles in biogeochemical processes in constructed wetland (CW) system. However, the influence of plant type on microbial community in surface water CW remains unclear. The present study investigated bacterial and archaeal communities in five surface water CW systems with different plant species. The abundance, richness, and diversity of both bacterial and archaeal communities considerably differed in these five CW systems. Compared with the other three CW systems, the CW systems planted with Vetiveria zizanioides or Juncus effusus L. showed much higher bacterial abundance but lower archaeal abundance. Bacteria outnumbered archaea in each CW system. Moreover, the CW systems planted with V. zizanioides or J. effusus L. had relatively lower archaeal but higher bacterial richness and diversity. In each CW system, bacterial community displayed much higher richness and diversity than archaeal community. In addition, a remarkable difference of both bacterial and archaeal community structures was observed in the five studied CW systems. Proteobacteria was the most abundant bacterial group (accounting for 33-60 %). Thaumarchaeota organisms (57 %) predominated in archaeal communities in CW systems planted with V. zizanioides or J. effusus L., while Woesearchaeota (23 or 24 %) and Euryarchaeota (23 or 15 %) were the major archaeal groups in CW systems planted with Cyperus papyrus or Canna indica L. Archaeal community in CW planted with Typha orientalis Presl was mainly composed of unclassified archaea. Therefore, plant type exerted a considerable influence on microbial community in surface water CW system.
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Affiliation(s)
- Yan Long
- Key Laboratory of Water/Soil Toxic Pollutants Control and Bioremediation of Guangdong Higher Education Institutes, School of Environment, Jinan University, Guangzhou, 510632, China
| | - Hao Yi
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou, 510655, China
| | - Sili Chen
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou, 510655, China
| | - Zhengke Zhang
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou, 510655, China
| | - Kai Cui
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou, 510655, China
| | - Yongxin Bing
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou, 510655, China
| | - Qiongfang Zhuo
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou, 510655, China
| | - Bingxin Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
| | - Qingwei Guo
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou, 510655, China.
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Yang Y, Li N, Zhao Q, Yang M, Wu Z, Xie S, Liu Y. Ammonia-oxidizing archaea and bacteria in water columns and sediments of a highly eutrophic plateau freshwater lake. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:15358-15369. [PMID: 27109114 DOI: 10.1007/s11356-016-6707-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 04/17/2016] [Indexed: 06/05/2023]
Abstract
Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) can play important roles in the microbial oxidation of ammonia nitrogen in freshwater lake, but information on spatiotemporal variation in water column and sediment community structure is still limited. Additionally, the drivers of the differences between sediment and water assemblages are still unclear. The present study investigated the variation of AOA and AOB communities in both water columns and sediments of eutrophic freshwater Dianchi Lake. The abundance, diversity, and structure of both planktonic and sediment ammonia-oxidizing microorganisms in Dianchi Lake showed the evident changes with sampling site and time. In both water columns and sediments, AOB amoA gene generally outnumbered AOA, and the AOB/AOA ratio was much higher in summer than in autumn. The total AOA amoA abundance was relatively great in autumn, while sediment AOB was relatively abundant in summer. Sediment AOA amoA abundance was likely correlated with ammonia nitrogen (rs = 0.963). The AOB/AOA ratio in lake sediment was positively correlated with total phosphorus (rs = 0.835), while pH, dissolved organic carbon, and ammonia nitrogen might be the key driving forces for the AOB/AOA ratio in lake water. Sediment AOA and AOB diversity was correlated with nitrate nitrogen (rs = -0.786) and total organic carbon (rs = 0.769), respectively, while planktonic AOB diversity was correlated with ammonia nitrogen (rs = 0.854). Surface water and sediment in the same location had a distinctively different microbial community structure. In addition, sediment AOB community structure was influenced by total phosphorus, while total phosphorus might be a key determinant of planktonic AOB community structure.
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Affiliation(s)
- Yuyin Yang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Ningning Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Qun Zhao
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Mengxi Yang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Zhen Wu
- Key Laboratory of Water and Sediment Sciences (Ministry of Education), College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
| | - Yong Liu
- Key Laboratory of Water and Sediment Sciences (Ministry of Education), College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
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Yang Y, Zhang J, Zhao Q, Zhou Q, Li N, Wang Y, Xie S, Liu Y. Sediment Ammonia-Oxidizing Microorganisms in Two Plateau Freshwater Lakes at Different Trophic States. MICROBIAL ECOLOGY 2016; 71:257-265. [PMID: 26111964 DOI: 10.1007/s00248-015-0642-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 06/15/2015] [Indexed: 06/04/2023]
Abstract
Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) can contribute to ammonia biotransformation in freshwater lake ecosystems. However, the factors shaping the distribution of sediment AOA and AOB in plateau freshwater lake remains unclear. The present study investigated sediment AOA and AOB communities in two freshwater lakes (hypertrophic Dianchi Lake and mesotrophic Erhai Lake) on the Yunnan Plateau (China). A remarkable difference in the abundance, diversity, and composition of sediment AOA and AOB communities was observed between Dianchi Lake and Erhai Lake. AOB usually outnumbered AOA in Dianchi Lake, but AOA showed the dominance in Erhai Lake. Organic matter (OM), total nitrogen (TN), and total phosphorus (TP) might be the key determinants of AOB abundance, while AOA abundance was likely influenced by the ration of OM to TN (C/N). AOA or AOB community structure was found to be relatively similar in the same lake. TN and TP might play important roles in shaping sediment AOA and AOB compositions in Dianchi Lake and Erhai Lake. Moreover, Nitrososphaera-like AOA were detected in Dianchi Lake. Nitrosospira- and Nitrosomonas-like AOB were dominant in Dianchi Lake and Erhai Lake, respectively. Sediment AOA and AOB communities in Dianchi Lake and Erhai Lake were generally regulated by trophic state.
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Affiliation(s)
- Yuyin Yang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Jingxu Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Qun Zhao
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Qiheng Zhou
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Ningning Li
- Yuanpei College, Peking University, Beijing, 100871, China
| | - Yilin Wang
- Key Laboratory of Water and Sediment Sciences (Ministry of Education), College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
| | - Yong Liu
- Key Laboratory of Water and Sediment Sciences (Ministry of Education), College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
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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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16
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Huang R, Zhao DY, Zeng J, Tian MY, Shen F, Jiang CL, Huang F, Yu ZB, Wu QL. Bioturbation of Tubificid worms affects the abundance and community composition of ammonia-oxidizing archaea and bacteria in surface lake sediments. ANN MICROBIOL 2016. [DOI: 10.1007/s13213-016-1192-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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17
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Antibiotic sulfanilamide biodegradation by acclimated microbial populations. Appl Microbiol Biotechnol 2015; 100:2439-47. [DOI: 10.1007/s00253-015-7133-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 10/26/2015] [Accepted: 10/29/2015] [Indexed: 11/27/2022]
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Spatiotemporal variation of bacterial and archaeal communities in a pilot-scale constructed wetland for surface water treatment. Appl Microbiol Biotechnol 2015; 100:1479-1488. [DOI: 10.1007/s00253-015-7072-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 09/30/2015] [Accepted: 10/06/2015] [Indexed: 01/29/2023]
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