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Cui K, Wang Y, Zhang X, Zhang X, Zhang X, Li Y, Shi W, Xie X. Archaeal communities change responding to anthropogenic and natural treatments of freeze-thawed soils. ENVIRONMENTAL RESEARCH 2024; 255:119150. [PMID: 38763282 DOI: 10.1016/j.envres.2024.119150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 05/21/2024]
Abstract
The coverage of accumulated snow plays a significant role in inducing changes in both microbial activity and environmental factors within freeze-thaw soil systems. This study aimed to analyze the impact of snow cover on the dynamics of archeal communities in freeze-thaw soil. Furthermore, it seeks to investigate the role of fertilization in freeze-thaw soil. Four treatments were established based on snow cover and fertilization:No snow and no fertilizer (CK-N), snow cover without fertilizer (X-N), fertilizer without snow cover (T-N), and both fertilizer and snow cover (T-X). The research findings indicated that after snow cover treatment, the carbon, nitrogen, and phosphorus content in freeze-thaw soil exhibit periodic fluctuations. Snow covered effectively altered the community composition of bacteria and archaea in the soil, with a greater impact on archaeal communities than on bacterial communities. Snow covered improves the stability of archaeal communities in freeze-thaw soil. Additionally, the arrival of snow also enhanced the correlation between archaea and environmental factors, with the key archaeal phyla involved being Nanoarchaeota and Crenarchaeota. Further research showed that the application of organic fertilizers also had some impact on freeze-thaw soil, but this impact was smaller compared to snow cover. In summary, the arrival of snow could alter the archaeal community and protect nutrient elements in freeze-thaw soil, reducing their loss, and its effect is more pronounced compared to the application of organic fertilizers.
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Affiliation(s)
- Kunxue Cui
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Yumeng Wang
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Xiaoxu Zhang
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Xu Zhang
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China.
| | - Xinlin Zhang
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Yu Li
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Wenjing Shi
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Xinyu Xie
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China
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Gao F, Li Y, Fan H, Luo D, Chapman SJ, Yao H. 15N-DNA stable isotope probing reveals niche differentiation of ammonia oxidizers in paddy soils. Appl Microbiol Biotechnol 2024; 108:342. [PMID: 38789552 PMCID: PMC11126484 DOI: 10.1007/s00253-024-13170-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 03/14/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024]
Abstract
Chemoautotrophic canonical ammonia oxidizers (ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB)) and complete ammonia oxidizers (comammox Nitrospira) are accountable for ammonia oxidation, which is a fundamental process of nitrification in terrestrial ecosystems. However, the relationship between autotrophic nitrification and the active nitrifying populations during 15N-urea incubation has not been totally clarified. The 15N-labeled DNA stable isotope probing (DNA-SIP) technique was utilized in order to study the response from the soil nitrification process and the active nitrifying populations, in both acidic and neutral paddy soils, to the application of urea. The presence of C2H2 almost completely inhibited NO3--N production, indicating that autotrophic ammonia oxidation was dominant in both paddy soils. 15N-DNA-SIP technology could effectively distinguish active nitrifying populations in both soils. The active ammonia oxidation groups in both soils were significantly different, AOA (NS (Nitrososphaerales)-Alpha, NS-Gamma, NS-Beta, NS-Delta, NS-Zeta and NT (Ca. Nitrosotaleales)-Alpha), and AOB (Nitrosospira) were functionally active in the acidic paddy soil, whereas comammox Nitrospira clade A and Nitrosospira AOB were functionally active in the neutral paddy soil. This study highlights the effective discriminative effect of 15N-DNA-SIP and niche differentiation of nitrifying populations in these paddy soils. KEY POINTS: • 15N-DNA-SIP technology could effectively distinguish active ammonia oxidizers. • Comammox Nitrospira clade A plays a lesser role than canonical ammonia oxidizers. • The active groups in the acidic and neutral paddy soils were significantly different.
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Affiliation(s)
- Fuyun Gao
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yaying Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, People's Republic of China.
| | - Haoxin Fan
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430073, People's Republic of China
| | - Dan Luo
- College of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, 730050, People's Republic of China
| | | | - Huaiying Yao
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, People's Republic of China.
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430073, People's Republic of China.
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Yang X, Shi Y, Ying G, Li M, He Z, Shu L. Cooperation among nitrifying microorganisms promotes the irreversible biotransformation of sulfamonomethoxine. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 923:171395. [PMID: 38447730 DOI: 10.1016/j.scitotenv.2024.171395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/08/2024]
Abstract
Ammonia-oxidizing microorganisms, including AOA (ammonia-oxidizing archaea), AOB (ammonia-oxidizing bacteria), and Comammox (complete ammonia oxidization) Nitrospira, have been reported to possess the capability for the biotransformation of sulfonamide antibiotics. However, given that nitrifying microorganisms coexist and operate as communities in the nitrification process, it is surprising that there is a scarcity of studies investigating how their interactions would affect the biotransformation of sulfonamide antibiotics. This study aims to investigate the sulfamonomethoxine (SMM) removal efficiency and mechanisms among pure cultures of phylogenetically distinct nitrifiers and their combinations. Our findings revealed that AOA demonstrated the highest SMM removal efficiency and rate among the pure cultures, followed by Comammox Nitrospira, NOB, and AOB. However, the biotransformation of SMM by AOA N. gargensis is reversible, and the removal efficiency significantly decreased from 63.84 % at 167 h to 26.41 % at 807 h. On the contrary, the co-culture of AOA and NOB demonstrated enhanced and irreversible SMM removal efficiency compared to AOA alone. Furthermore, the presence of NOB altered the SMM biotransformation of AOA by metabolizing TP202 differently, possibly resulting from reduced nitrite accumulation. This study offers novel insights into the potential application of nitrifying communities for the removal of sulfonamide antibiotics (SAs) in engineered ecosystems.
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Affiliation(s)
- Xueqin Yang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Yijing Shi
- SCNU Environmental Research Institute, School of Environment, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China.
| | - Guangguo Ying
- SCNU Environmental Research Institute, School of Environment, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Mengyuan Li
- SCNU Environmental Research Institute, School of Environment, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China.
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Dai Y, Li J, Wang S, Cai X, Zhao X, Cheng X, Huang Q, Yang X, Luo C, Zhang G. Unveiling the synergistic mechanism of autochthonous fungal bioaugmentation and ammonium nitrogen biostimulation for enhanced phenanthrene degradation in oil-contaminated soils. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133293. [PMID: 38141301 DOI: 10.1016/j.jhazmat.2023.133293] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/22/2023] [Accepted: 12/14/2023] [Indexed: 12/25/2023]
Abstract
Autochthonous bioaugmentation and nutrient biostimulation are promising bioremediation methods for polycyclic aromatic hydrocarbons (PAHs) in contaminated agricultural soils, but little is known about their combined working mechanism. In this study, a microcosm trial was conducted to explore the combined mechanism of autochthonous fungal bioaugmentation and ammonium nitrogen biostimulation, using DNA stable-isotope-probing (DNA-SIP) and microbial network analysis. Both treatments significantly improved phenanthrene (PHE) removal, with their combined application producing the best results. The microbial community composition was notably altered by all bioremediation treatments, particularly the PHE-degrading bacterial and fungal taxa. Fungal bioaugmentation removed PAHs through extracellular enzyme secretion but reduced soil microbial diversity and ecological stability, while nitrogen biostimulation promoted PAH dissipation by stimulating indigenous soil degrading microbes, including fungi and key bacteria in the soil co-occurrence networks, ensuring the ecological diversity of soil microorganisms. The combination of both approaches proved to be the most effective strategy, maintaining a high degradation efficiency and relatively stable soil biodiversity through the secretion of lignin hydrolytic enzymes by fungi, and stimulating the reproduction of soil native degrading microbes, especially the key degraders in the co-occurrence networks. Our findings provide a fresh perspective of the synergy between fungal bioaugmentation and nitrogen biostimulation, highlighting the potential of this combined bioremediation approach for in situ PAH-contaminated soils.
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Affiliation(s)
- Yeliang Dai
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jibing Li
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China.
| | - Shuang Wang
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Xixi Cai
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Xuan Zhao
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Xianghui Cheng
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Qihui Huang
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Xiumin Yang
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Chunling Luo
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China.
| | - Gan Zhang
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China
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5
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Wen S, Liu H, Yang R, Wang L, Zhu L, Wang J, Kim YM, Wang J. Immobilization of Bacillus Thuringiensis and applicability in removal of sulfamethazine from soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 333:122080. [PMID: 37390917 DOI: 10.1016/j.envpol.2023.122080] [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: 02/10/2023] [Revised: 06/13/2023] [Accepted: 06/17/2023] [Indexed: 07/02/2023]
Abstract
Microbial degradation is considered an essential and promising treatment for sulfadimidine contamination of soil. To address the low colonization rates and inefficiencies of typical antibiotic-degrading bacteria, sulfamethazine (SM2)-degrading strain H38 is converted into immobilized bacteria in this study. Results show that the removal rate of SM2 by immobilized strain H38 reaches 98% at 36 h, whereas the removal rate of SM2 by free bacteria reaches 75.2% at 60 h. In addition, the immobilized bacteria H38 exhibits tolerance to a wide range of pH (5-9) and temperature (20 °C-40 °C). As the amount of inoculation increases and the initial concentration of SM2 decreases, the removal rate of SM2 by the immobilized strain H38 increases gradually. Laboratory soil remediation tests show that the immobilized strain H38 can remove 90.0% of SM2 from the soil on the 12th day, which exceeds the removal by free bacteria by 23.9% in the same period. Additionally, the results show that the immobilized strain H38 enhances the overall activity of microorganisms in SM2-contaminated soil. Compared with the SM2 only (control group containing no bacteria) and free bacterial treatment groups, the gene expression levels of ammonia-oxidizing archaea, ammonia-oxidizing bacteria, cbbLG, and cbbM increased significantly in the treatment group with immobilized strain H38. This study shows that immobilized strain H38 can reduce the effect of SM2 on soil ecology to a greater extent than free bacteria, while providing safe and effective remediation.
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Affiliation(s)
- Shengfang Wen
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.
| | - Hunan Liu
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.
| | - Rui Yang
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.
| | - Lanjun Wang
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.
| | - Lusheng Zhu
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.
| | - Jun Wang
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.
| | - Young Mo Kim
- Department of Civil and Environmental Engineering, Hanyang University, Seongdong-gu, Seoul, 04763, Republic of Korea.
| | - Jinhua Wang
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.
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Shao P, Fang S, Rao L, Wang X, Zeng J, Zhang S, Wu Y, Yao J, Lin X. Contrasting responses of bacterial community to 4,4'-dibromodiphenyl ether (BDE-15) contamination in soil microcosms at different temperatures. CHEMOSPHERE 2023; 319:138056. [PMID: 36739991 DOI: 10.1016/j.chemosphere.2023.138056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Polybrominated diphenyl ethers (PBDEs) are biodegradable organic pollutants and pose potential risks to microorganisms exposed to the contamination, which are also affected by a variety of factors, such as temperature, in real environmental settings. A better understanding of the microbial community responses to PBDEs at different temperatures has practical significance for assessing ecological risks or possible degraders of these widely used flame retardants. In this study, soil microcosms spiked with or without 100 mg kg-1 4,4'-dibromodiphenyl ether (BDE-15) were established and incubated at four different temperatures (4 °C, 20 °C, 37 °C, and varying ambient temperature) for up to 180 days. Concentration and carbon isotope analyses were used to verify the transformation of BDE-15. Bacterial communities were monitored during the incubation to evaluate the community succession under the PBDE stress. The results showed the majority of added BDE-15 remained after the incubation period, with limited degradation occurred at all four temperatures. Temperature significantly shaped the richness, diversity, composition and co-occurrence network of soil bacterial community, while the impacts of PBDE on soil bacteria were temperature dependent. When incubated at 4 °C, BDE-15 substantially reduced the network complexity and changed the ratio of negative to positive interactions between taxa (nodes), highlighting the PBDE-associated risks at low temperature. At higher temperatures, BDE-15 had negligible influence on the community characteristics and network. Random forest model identified distinct taxa that might be related to PBDE degradation at different incubation temperatures. These findings demonstrate contrasting bacterial community effects of PBDE at different temperatures, thus attention should be paid to the ecological impacts of soil pollution under real environmental conditions.
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Affiliation(s)
- Pengfei Shao
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; College of Life Sciences, Henan Agricultural University, Zhengzhou, 450046, China; School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Shasha Fang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; College of Life Sciences, Henan Agricultural University, Zhengzhou, 450046, China
| | - Leizhen Rao
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xi Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Jun Zeng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Shimin Zhang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yucheng Wu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jun Yao
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Xiangui Lin
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
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Diao M, Balkema C, Suárez-Muñoz M, Huisman J, Muyzer G. Succession of bacteria and archaea involved in the nitrogen cycle of a seasonally stratified lake. FEMS Microbiol Lett 2023; 370:7043454. [PMID: 36796795 PMCID: PMC9990978 DOI: 10.1093/femsle/fnad013] [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: 12/05/2022] [Revised: 02/07/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023] Open
Abstract
Human-driven changes affect nutrient inputs, oxygen solubility, and the hydrodynamics of lakes, which affect biogeochemical cycles mediated by microbial communities. However, information on the succession of microbes involved in nitrogen cycling in seasonally stratified lakes is still incomplete. Here, we investigated the succession of nitrogen-transforming microorganisms in Lake Vechten over a period of 19 months, combining 16S rRNA gene amplicon sequencing and quantification of functional genes. Ammonia-oxidizing archaea (AOA) and bacteria (AOB) and anammox bacteria were abundant in the sediment during winter, accompanied by nitrate in the water column. Nitrogen-fixing bacteria and denitrifying bacteria emerged in the water column in spring when nitrate was gradually depleted. Denitrifying bacteria containing nirS genes were exclusively present in the anoxic hypolimnion. During summer stratification, abundances of AOA, AOB, and anammox bacteria decreased sharply in the sediment, and ammonium accumulated in hypolimnion. After lake mixing during fall turnover, abundances of AOA, AOB, and anammox bacteria increased and ammonium was oxidized to nitrate. Hence, nitrogen-transforming microorganisms in Lake Vechten displayed a pronounced seasonal succession, which was strongly determined by the seasonal stratification pattern. These results imply that changes in stratification and vertical mixing induced by global warming are likely to alter the nitrogen cycle of seasonally stratified lakes.
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Affiliation(s)
- Muhe Diao
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Cherel Balkema
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - María Suárez-Muñoz
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Jef Huisman
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Gerard Muyzer
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
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KHANGEMBAM CHERITADEVI, SINGH SAMARPAL, CHAKRABARTI RINA, SHARMA JAIGOPAL. Study of effect of various temperatures on the abundance of ammonia oxidizing archaea and bacteria. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2023. [DOI: 10.56093/ijans.v88i5.80023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Temperature plays significant role in the oxidation of ammonia in filtration units of recirculating aquaculture system. The impact of temperature on the abundance of ammonia oxidizing archaea and bacteria, and the expression of ammonia oxidizing gene (amoA) at specific temperature was evaluated. The broken earthen pot pieces used as filter bed materials of recirculating system, showing the presence of microorganisms were introduced in glass containers (5 pieces/5l) filled with synthetic wastewater and exposed to four different temperatures of 10, 20, 30 and 40°C for 40 days. The ammonia oxidation rate was minimum at 10°C. In 20, 30 and 40°C treatments, 99% ammonia was reduced on day-18, 8 and 18, respectively compared to the initial day. Fresh ammonium chloride (2 mM) was added twice to maintain the ammonia concentration in all treatments, except 10°C one. Nitrite-N level was < 1 mg/l at 10°C. The level was highest on day-22 at 20° and 40°C and on day-12 at 30°C. The nitrification was 10 days delayed at 20°C and 40°C compared to 30°C treatment. Concentration of nitrate-N was lowest at 10°C. Highest concentration of nitrate-N was observed on day-40 at 20°C and 40°C and day-26 at 30°C. Highest copy number of bacterial amoA was recorded at 30°C (2.59×107) followed by 20°C (4.08×106), 40°C (1.45×106) and 10°C (5.664×103). Archaeal amoA was highest at 30°C (7.47×103) followed by 40°C (2.98×102) and 20°C (46.8) treatments. Hence it may be concluded that 30°C temperature was optimum for the efficient and faster oxidation of ammonia in the present recirculating system.
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Yang X, Yu X, He Q, Deng T, Guan X, Lian Y, Xu K, Shu L, Wang C, Yan Q, Yang Y, Wu B, He Z. Niche differentiation among comammox ( Nitrospira inopinata) and other metabolically distinct nitrifiers. Front Microbiol 2022; 13:956860. [PMID: 36187961 PMCID: PMC9515657 DOI: 10.3389/fmicb.2022.956860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
Due to global change, increasing nutrient input to ecosystems dramatically affects the nitrogen cycle, especially the nitrification process. Nitrifiers including ammonia-oxidizing archaea (AOAs), ammonia-oxidizing bacteria (AOBs), nitrite-oxidizing bacteria (NOBs), and recently discovered complete ammonia oxidizers (comammoxs) perform nitrification individually or in a community. However, much remains to be learned about their niche differentiation, coexistence, and interactions among those metabolically distinct nitrifiers. Here, we used synthetic microbial ecology approaches to construct synthetic nitrifying communities (SNCs) with different combinations of Nitrospira inopinata as comammox, Nitrososphaera gargensis as AOA, Nitrosomonas communis as AOB, and Nitrospira moscoviensis as NOB. Our results showed that niche differentiation and potential interactions among those metabolically distinct nitrifiers were determined by their kinetic characteristics. The dominant species shifted from N. inopinata to N. communis in the N4 community (with all four types of nitrifiers) as ammonium concentrations increased, which could be well explained by the kinetic difference in ammonia affinity, specific growth rate, and substrate tolerance of nitrifiers in the SNCs. In addition, a conceptual model was developed to infer niche differentiation and possible interactions among the four types of nitrifiers. This study advances our understanding of niche differentiation and provides new strategies to further study their interactions among the four types of nitrifiers.
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Affiliation(s)
- Xueqin Yang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Xiaoli Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Qiang He
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, TN, United States
| | - Ting Deng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Xiaotong Guan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Yingli Lian
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Kui Xu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Yuchun Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
| | - Bo Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
- College of Agronomy, Hunan Agricultural University, Changsha, China
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10
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Tong X, Mohapatra S, Zhang J, Tran NH, You L, He Y, Gin KYH. Source, fate, transport and modelling of selected emerging contaminants in the aquatic environment: Current status and future perspectives. WATER RESEARCH 2022; 217:118418. [PMID: 35417822 DOI: 10.1016/j.watres.2022.118418] [Citation(s) in RCA: 87] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 02/07/2022] [Accepted: 04/04/2022] [Indexed: 06/14/2023]
Abstract
The occurrence of emerging contaminants (ECs), such as pharmaceuticals and personal care products (PPCPs), perfluoroalkyl and polyfluoroalkyl substances (PFASs) and endocrine-disrupting chemicals (EDCs) in aquatic environments represent a major threat to water resources due to their potential risks to the ecosystem and humans even at trace levels. Mathematical modelling can be a useful tool as a comprehensive approach to study their fate and transport in natural waters. However, modelling studies of the occurrence, fate and transport of ECs in aquatic environments have generally received far less attention than the more widespread field and laboratory studies. In this study, we reviewed the current status of modelling ECs based on selected representative ECs, including their sources, fate and various mechanisms as well as their interactions with the surrounding environments in aquatic ecosystems, and explore future development and perspectives in this area. Most importantly, the principles, mathematical derivations, ongoing development and applications of various ECs models in different geographical regions are critically reviewed and discussed. The recommendations for improving data quality, monitoring planning, model development and applications were also suggested. The outcomes of this review can lay down a future framework in developing a comprehensive ECs modelling approach to help researchers and policymakers effectively manage water resources impacted by rising levels of ECs.
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Affiliation(s)
- Xuneng Tong
- Department of Civil & Environmental Engineering, National University of Singapore, 1 Engineering Drive 2, Singapore 117576, Singapore
| | - Sanjeeb Mohapatra
- NUS Environmental Research Institute, National University of Singapore, 1 Create way, Create Tower, #15-02, Singapore 138602, Singapore
| | - Jingjie Zhang
- NUS Environmental Research Institute, National University of Singapore, 1 Create way, Create Tower, #15-02, Singapore 138602, Singapore; Shenzhen Municipal Engineering Lab of Environmental IoT Technologies, Southern University of Science and Technology, Shenzhen, 518055, China; Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
| | - Ngoc Han Tran
- NUS Environmental Research Institute, National University of Singapore, 1 Create way, Create Tower, #15-02, Singapore 138602, Singapore
| | - Luhua You
- NUS Environmental Research Institute, National University of Singapore, 1 Create way, Create Tower, #15-02, Singapore 138602, Singapore
| | - Yiliang He
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Karina Yew-Hoong Gin
- Department of Civil & Environmental Engineering, National University of Singapore, 1 Engineering Drive 2, Singapore 117576, Singapore; NUS Environmental Research Institute, National University of Singapore, 1 Create way, Create Tower, #15-02, Singapore 138602, Singapore.
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11
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Bahram M, Espenberg M, Pärn J, Lehtovirta-Morley L, Anslan S, Kasak K, Kõljalg U, Liira J, Maddison M, Moora M, Niinemets Ü, Öpik M, Pärtel M, Soosaar K, Zobel M, Hildebrand F, Tedersoo L, Mander Ü. Structure and function of the soil microbiome underlying N 2O emissions from global wetlands. Nat Commun 2022; 13:1430. [PMID: 35301304 PMCID: PMC8931052 DOI: 10.1038/s41467-022-29161-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 02/23/2022] [Indexed: 01/16/2023] Open
Abstract
Wetland soils are the greatest source of nitrous oxide (N2O), a critical greenhouse gas and ozone depleter released by microbes. Yet, microbial players and processes underlying the N2O emissions from wetland soils are poorly understood. Using in situ N2O measurements and by determining the structure and potential functional of microbial communities in 645 wetland soil samples globally, we examined the potential role of archaea, bacteria, and fungi in nitrogen (N) cycling and N2O emissions. We show that N2O emissions are higher in drained and warm wetland soils, and are correlated with functional diversity of microbes. We further provide evidence that despite their much lower abundance compared to bacteria, nitrifying archaeal abundance is a key factor explaining N2O emissions from wetland soils globally. Our data suggest that ongoing global warming and intensifying environmental change may boost archaeal nitrifiers, collectively transforming wetland soils to a greater source of N2O.
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Affiliation(s)
- Mohammad Bahram
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia. .,Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | - Mikk Espenberg
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Jaan Pärn
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | | | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Kuno Kasak
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Urmas Kõljalg
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Jaan Liira
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Martin Maddison
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Ülo Niinemets
- Institute of Agricultural & Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Meelis Pärtel
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Kaido Soosaar
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Martin Zobel
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Falk Hildebrand
- Quadram Institute Bioscience, Norwich, Norfolk, UK.,Digital Biology, Earlham Institute, Norwich, Norfolk, UK
| | - Leho Tedersoo
- College of Science, King Saud University, Riyadh, Saudi Arabia.,Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
| | - Ülo Mander
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
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12
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Chen X, Lin H, Dong Y, Li B, Yin T, Liu C. Simultaneous high-efficiency removal of sulfamethoxazole and zinc (II) from livestock and poultry breeding wastewater by a novel dual-functional bacterium, Bacillus sp. SDB4. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:6237-6250. [PMID: 34448142 DOI: 10.1007/s11356-021-15804-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
The complex mixtures of antibiotics and heavy metals are commonly existed in livestock and poultry breeding wastewater. Effective and simultaneous removal of these toxic compounds by microorganisms, especially single strains, remains a considerable challenge. In this study, a novel functional strain SDB4, isolated from duck manure and identified as Bacillus sp., has been shown to possess high removal capabilities for both sulfamethoxazole (SMX) and Zn2+. The maximum removal efficiency achieved 73.97% for SMX and 84.06% for Zn2+ within 48 h in the single pollution system. It has great potential for eliminating SMX along with Zn2+, 78.45% of SMX and 52.91% of Zn2+ were removed in the 20 mg·L-1 SMX and 100 mg·L-1 Zn2+ binary system. Furthermore, the SMX-biotransformation capability of SDB4 was enhanced at low concentrations of Zn2+ (below 100 mg·L-1). The SMX biotransformation and Zn2+ adsorption data fitted well with the pseudo-first-order kinetic model, indicating that the two pollutants were in accordance with the same removal rule. N4-acetyl-SMX was identified as the main stable transformation product during SMX removal. FTIR analyses revealed that OH, NH2, C=O, C-N/N-H, and C-O-C played major roles in the adsorption of Zn2+. Our study of the dually functioning strain SDB4 provides a potential application for the simultaneous biological removal of antibiotics and heavy metals.
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Affiliation(s)
- Xi Chen
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- Beijing Key Laboratory on Resource-Oriented Treatment of Industrial Pollutants, Beijing, 100083, China
| | - Hai Lin
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
- Beijing Key Laboratory on Resource-Oriented Treatment of Industrial Pollutants, Beijing, 100083, China.
| | - Yingbo Dong
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
- Beijing Key Laboratory on Resource-Oriented Treatment of Industrial Pollutants, Beijing, 100083, China.
| | - Bing Li
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- Beijing Key Laboratory on Resource-Oriented Treatment of Industrial Pollutants, Beijing, 100083, China
| | - Tingting Yin
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- Beijing Key Laboratory on Resource-Oriented Treatment of Industrial Pollutants, Beijing, 100083, China
| | - Chenjing Liu
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- Beijing Key Laboratory on Resource-Oriented Treatment of Industrial Pollutants, Beijing, 100083, China
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13
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Cai Y, Liang J, Zhang P, Wang Q, Wu Y, Ding Y, Wang H, Fu C, Sun J. Review on strategies of close-to-natural wetland restoration and a brief case plan for a typical wetland in northern China. CHEMOSPHERE 2021; 285:131534. [PMID: 34329151 DOI: 10.1016/j.chemosphere.2021.131534] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 07/03/2021] [Accepted: 07/09/2021] [Indexed: 06/13/2023]
Abstract
Wetlands play an important role in sustaining ecosystems on the earth, which regulate water resources, adjust local climate and produce food for human beings, etc. However, wetlands are facing huge challenges due to human activities and other natural evolution, such as area shrinkage, function weakening and biodiversity decrease, and so on, therefore, some wetlands need to be urgently restored. In this study, the main technology components of close-to-natural restoration of wetlands were summarized. The ecological water requirement and water resource allocation can be optimized for the water balance between social, economy and ecology, which is a key prerequisite for maintaining wetland ecosystem. The pollution of wetland sediments and soils can be assessed by various indicators to provide the scientific basis for natural restoration of wetland base, and suitable strategies should be taken according to the actual conditions of wetland bases. The hydrological connectivity in wetlands and with related water system can be numerically simulated to make the optimal plan for improvement of hydrological connectivity. The ecological restoration of wetlands with the synergetic function of plants, animals and microorganisms was summarized, to improve the quality of wetland water environment and maintain the ecosystem stability. Based on the wetland close-to-natural restoration strategies, a brief ecological restoration plan for a typical wetland, Zaozhadian Wetland, near Xiong'an New Area in the north China was proposed from water resource guarantee, base pollution management, hydrological connectivity improvement and biological restoration. The close-to-natural restoration shows more effective, sustainable and long-lasting and thus a practical prospect.
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Affiliation(s)
- Yajing Cai
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Jinsong Liang
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Panyue Zhang
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China; School of Environmental Chemical Engineering, Chongqing Three Gorges University, Chongqing, 404632, China.
| | - Qingyan Wang
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Yan Wu
- School of Environmental Chemical Engineering, Chongqing Three Gorges University, Chongqing, 404632, China
| | - Yiran Ding
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Hongjie Wang
- Xiong'an Institute of Eco-Environment, Hebei University, Baoding, 071002, China
| | - Chuan Fu
- School of Environmental Chemical Engineering, Chongqing Three Gorges University, Chongqing, 404632, China
| | - Jiajun Sun
- Beijing Engineering Research Center of Process Pollution Control, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing, 100049, China
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14
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Lv J, Yuan R, Wang S. Water diversion induces more changes in bacterial and archaeal communities of river sediments than seasonality. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 293:112876. [PMID: 34098351 DOI: 10.1016/j.jenvman.2021.112876] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 05/01/2021] [Accepted: 05/21/2021] [Indexed: 06/12/2023]
Abstract
Previous studies have demonstrated that seasonal variation is often the most important factor affecting aquatic bacterial assemblages. Whether anthropogenic activities can dominate community dynamics remains unknown. Based on 16S rRNA high-throughput sequencing technology, this study revealed and compared the relative influence of water diversions and seasonality on bacterial and archaeal communities in river sediments from a region with obvious seasonality. The results indicate that the influence of water diversion on bacteria and archaea in water-receiving river sediments exceeded the influence of seasonal variation. Water diversion affected microbes by increasing EC, salinity, water flow rate, and organic matter carbon and nitrogen contents. Seasonal variations affected microbes by altering water temperature. Diversion responders but no season responders were classified by statistical methods in the microbial community. Diversion responder numbers were related to nitrogen concentrations, complex organic carbon contents and EC values, which were mainly affected by water diversion. With the joint impact of water diversion and seasonality, the correlations of bacterial and archaeal numbers with environmental factors were obviously weakened due to the increases in the ecological niche breadths of microorganisms. Natural seasonal changes in bacterial and archaeal communities were totally altered by changes in salinity, nutrients, and hydrological conditions induced by anthropogenic water diversions. These results highlight that human activity may be a stronger driver than natural seasonality in the alteration of bacterial and archaeal communities.
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Affiliation(s)
- Jiali Lv
- College of Environmental and Resource Sciences, Shanxi University, Taiyuan, 030006, China; Shanxi Laboratory for Yellow River, Taiyuan, 030006, China; Key Laboratory of Agricultural Water Resources Research, Innovation Academy for Seed Design, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China; Sino-Danish College of University of Chinese Academy of Sciences, Beijing, 101408, China; Sino-Danish Centre for Education and Research, Beijing, 101408, China
| | - Ruiqiang Yuan
- College of Environmental and Resource Sciences, Shanxi University, Taiyuan, 030006, China; Shanxi Laboratory for Yellow River, Taiyuan, 030006, China.
| | - Shiqin Wang
- Key Laboratory of Agricultural Water Resources Research, Innovation Academy for Seed Design, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China
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15
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Wang H, Li B, Li Y, Chen X, Li X, Xia K, Wang Y. Sludge ratio affects the start-up performance and functional bacteria distribution of a hybrid CANON system. CHEMOSPHERE 2021; 264:128476. [PMID: 33070062 DOI: 10.1016/j.chemosphere.2020.128476] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/13/2020] [Accepted: 09/27/2020] [Indexed: 06/11/2023]
Abstract
To investigate the effect of sludge ratio on the hybrid CANON system, autotrophic nitrogen removal sludge was inoculated with different granule/floc ratios to initiate the CANON system, and maintained the sludge ratio during the operation process. The start-up performances were compared, and the distribution characteristics of functional bacteria were investigated. The results show that the Equivalent system (granules:flocs = 1:1-1:1.5) successfully started-up on day 19, and the nitrogen removal rate (NRR) reached 0.299 kgN m-3·d-1 on day 63. At the same time, it was less affected by the load shock than High-granules and High-flocs systems. Therefore, the Equivalent system had the strongest start-up performance. The activities of the functional bacteria conformed to spatial heterogeneity, unlike the abundance. With the increased floc proportion, the difference in the activity and abundance of anaerobic ammonium-oxidizing bacteria (AAOB) between the granules and flocs increased, while there was a decrease in the difference in aerobic ammonium-oxidizing bacteria (AOB). However, the abundance of Nitrosomonas in the granules was higher than in the flocs when the proportion of flocs was higher than 50%. This study provides new ideas and insights for the fast start-up of the CANON system and can conform to the varying needs of engineering applications.
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Affiliation(s)
- Heng Wang
- School of Resource and Environmental Engineering, Wuhan University of Technology, Wuhan, Hubei, 430070, China
| | - Bolin Li
- School of Resource and Environmental Engineering, Wuhan University of Technology, Wuhan, Hubei, 430070, China.
| | - Ye Li
- School of Resource and Environmental Engineering, Wuhan University of Technology, Wuhan, Hubei, 430070, China
| | - Xiaoguo Chen
- School of Resource and Environmental Engineering, Wuhan University of Technology, Wuhan, Hubei, 430070, China
| | - Xiang Li
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, Jiangsu, 215009, China
| | - Kai Xia
- School of Resource and Environmental Engineering, Wuhan University of Technology, Wuhan, Hubei, 430070, China
| | - Yue Wang
- School of Resource and Environmental Engineering, Wuhan University of Technology, Wuhan, Hubei, 430070, China
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16
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Li H, Hollstein M, Podder A, Gupta V, Barber M, Goel R. Cyanotoxin impact on microbial-mediated nitrogen transformations at the interface of sediment-water column in surface water bodies. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 266:115283. [PMID: 32805604 DOI: 10.1016/j.envpol.2020.115283] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/23/2020] [Accepted: 07/26/2020] [Indexed: 06/11/2023]
Abstract
Harmful cyanobacterial blooms produce lethal toxins in many aquatic ecosystems experiencing eutrophication. This manuscript presents results on the effects of cyanotoxins on the aerobic microbial communities residing at the interface of sediments and water columns with the ammonia-oxidizing bacteria (AOB) as the model microbial community. Microcystin-LR (MC-LR), a heavily researched cyanotoxin variant, was used as the model cyanotoxin. To measure cyanotoxin influence on the activity of nitrifying microbial communities, an enriched culture of AOBs collected from an ongoing partial nitrification-nitritation reactor was examined for its exposure to 1, 5 and 10 μg/L of MC-LR. The nitritation kinetics experiment demonstrated MC-LR's ability at 1, 5, and 10 μg/L concentrations to prevent ammonium oxidation with statistically significant differences in nitritation rates between the blanks and spiked samples (One-way ANOVA, p < 0.05). Significantly decreased dissolved oxygen (DO) consumption during oxygen update batch tests demonstrated toxin's influence on AOB's oxidizing capabilities when exposed to even lower concentrations of 0.75, 0.5, and 0.25 μg/L of MC-LR in a separate set of experiments. Based on competitive kinetics, the MC-LR inhibition coefficient-the concentration needed to produce half-maximum inhibition of the mixed community AOBs was determined to be 0.083 μg/L. The stress tests proved the recovery of nitritation to some extent at lower MC-LR concentrations (1 and 5 μg/L), but significant irreversible inhibition was recorded when the AOB population was exposed to 10 μg/L MC-LR. The comparisons of amoA gene expressions corresponded well with nitrifying kinetics. All concentrations of MC-LR spiking were determined to produce a discernible impact on the AOB nitritation rate by either destroying the bacterial cell or immediately inhibiting the amoA gene expression.
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Affiliation(s)
- Hanyan Li
- Department of Civil and Environmental Engineering, University of Utah, UT, USA
| | - Marielle Hollstein
- Department of Civil and Environmental Engineering, University of Utah, UT, USA
| | - Aditi Podder
- Department of Civil and Environmental Engineering, University of Utah, UT, USA
| | | | - Michael Barber
- Department of Civil and Environmental Engineering, University of Utah, UT, USA
| | - Ramesh Goel
- Department of Civil and Environmental Engineering, University of Utah, UT, USA.
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17
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Zhang M, Chai L, Huang M, Jia W, Guo J, Huang Y. Deciphering the archaeal communities in tree rhizosphere of the Qinghai-Tibetan plateau. BMC Microbiol 2020; 20:235. [PMID: 32738877 PMCID: PMC7395985 DOI: 10.1186/s12866-020-01913-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 07/19/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The Qinghai-Tibetan Plateau represents one of the most important component of the terrestrial ecosystem and a particularly vulnerable region, which harbouring complex and diverse microbiota. The knowledge about their underground microorganisms have largely been studied, but the characteristics of rhizosphere microbiota, particularly archaeal communities remains unclear. RESULTS High-throughput Illumina sequencing was used to investigate the rhizosphere archaeal communities of two native alpine trees (Picea crassifolia and Populus szechuanica) living on the Qinghai-Tibetan Plateau. The archaeal community structure in rhizospheres significantly differed from that in bulk soil. Thaumarchaeota was the dominant archaeal phylum in all soils tested (92.46-98.01%), while its relative abundance in rhizospheres were significantly higher than that in bulk soil. Ammonium nitrogen, soil organic matter, available phosphorus and pH were significantly correlated with the archaeal community structure, and the deterministic processes dominated the assembly of archaeal communities across all soils. In addition, the network structures of the archaeal community in the rhizosphere were less complex than they were in the bulk soil, and an unclassified archaeal group (Unclassified_k_norank) was identified as the keystone species in all archaeal networks. CONCLUSIONS Overall, the structure, assembly and co-occurrence patterns of archaeal communities are significantly affected by the presence of roots of alpine trees living on the Qinghai-Tibetan Plateau. This study provides new insights into our understanding of archaeal communities in vulnerable ecosystems.
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Affiliation(s)
- Mengjun Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Science and Engineering, Peking University, No.5 Yiheyuan Road Haidian District, Beijing, P.R. China, 10087
| | - Liwei Chai
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Science and Engineering, Peking University, No.5 Yiheyuan Road Haidian District, Beijing, P.R. China, 10087
| | - Muke Huang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Science and Engineering, Peking University, No.5 Yiheyuan Road Haidian District, Beijing, P.R. China, 10087
| | - Weiqian Jia
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Science and Engineering, Peking University, No.5 Yiheyuan Road Haidian District, Beijing, P.R. China, 10087
| | - Jiabao Guo
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Science and Engineering, Peking University, No.5 Yiheyuan Road Haidian District, Beijing, P.R. China, 10087
| | - Yi Huang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Science and Engineering, Peking University, No.5 Yiheyuan Road Haidian District, Beijing, P.R. China, 10087.
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18
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Yan C, Huang J, Cao C, Li R, Ma Y, Wang Y. Effects of PVP-coated silver nanoparticles on enzyme activity, bacterial and archaeal community structure and function in a yellow-brown loam soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:8058-8070. [PMID: 31897981 DOI: 10.1007/s11356-019-07347-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 12/09/2019] [Indexed: 06/10/2023]
Abstract
The undesirable effects of silver nanoparticles (AgNPs) on soil environment have caused much concern. The previous studies, however, focused on sandy soil, with little known on others. In present study, the effects of polyvinylpyrrolidone-coated AgNPs (0, 1, 10, and 100 mg kg- 1 soil) on enzyme activities (urease and dehydrogenase), ammonia-oxidizing bacteria (AOB) and archaea (AOA), bacterial and archaeal communities, and microbial function profile in a yellow-brown loam soil were investigated. The significant dose-response inhibitions of AgNPs on enzyme activities were observed, with dehydrogenase more susceptible to AgNPs. Both of bacterial and archaeal amoA genes were reduced by AgNPs above 10 mg kg- 1, with AOB more susceptible to AgNPs than AOA. AgNPs at 100 mg kg- 1 caused reductions on the dominant Nitrosospira and Nitrosomonas, and even disappearance on Nitrosovibrio, while increase on Nitrososphaera significantly. AgNPs also changed bacterial and archaeal community structure. Exposure to AgNPs at 100 mg kg- 1 caused significant increases by 186.79% and 44.89% for Bacteroidetes and Proteobacteria, while decreases by 47.82%, 44.09%, 43.67%, and 80.44% for Actinobacteria, Chloroflexi, Planctomycetes, and Verrucomicrobia, respectively. Moreover, three dominant archaeal phyla (Thaumarchaeota, Euryarchaeota, and Parvarchaeota) were also reduced in the presence of AgNPs, especially Thaumarchaeota with the significant reduction of 13.71%. PICRUSt prediction revealed that AgNPs indeed had the potential to change soil microbial community's functional contributions. It must be cautious on the interference of AgNPs to soil ecological functions in the future.
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Affiliation(s)
- Chunni Yan
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing, 210096, China
| | - Juan Huang
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing, 210096, China.
| | - Chong Cao
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing, 210096, China
| | - Runqing Li
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing, 210096, China
| | - Yixuan Ma
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing, 210096, China
| | - Yaoyao Wang
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing, 210096, China
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19
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DNA- and RNA-SIP Reveal Nitrospira spp. as Key Drivers of Nitrification in Groundwater-Fed Biofilters. mBio 2019; 10:mBio.01870-19. [PMID: 31690672 PMCID: PMC6831773 DOI: 10.1128/mbio.01870-19] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Nitrification, the oxidative process converting ammonia to nitrite and nitrate, is driven by microbes and plays a central role in the global nitrogen cycle. Our earlier investigations based on 16S rRNA and amoA amplicon analysis, amoA quantitative PCR and metagenomics of groundwater-fed biofilters indicated a consistently high abundance of comammox Nitrospira Here, we hypothesized that these nonclassical nitrifiers drive ammonia-N oxidation. Hence, we used DNA and RNA stable isotope probing (SIP) coupled with 16S rRNA amplicon sequencing to identify the active members in the biofilter community when subjected to a continuous supply of NH4 + or NO2 - in the presence of 13C-HCO3 - (labeled) or 12C-HCO3 - (unlabeled). Allylthiourea (ATU) and sodium chlorate were added to inhibit autotrophic ammonia- and nitrite-oxidizing bacteria, respectively. Our results confirmed that lineage II Nitrospira dominated ammonia oxidation in the biofilter community. A total of 78 (8 by RNA-SIP and 70 by DNA-SIP) and 96 (25 by RNA-SIP and 71 by DNA-SIP) Nitrospira phylotypes (at 99% 16S rRNA sequence similarity) were identified as complete ammonia- and nitrite-oxidizing, respectively. We also detected significant HCO3 - uptake by Acidobacteria subgroup10, Pedomicrobium, Rhizobacter, and Acidovorax under conditions that favored ammonia oxidation. Canonical Nitrospira alone drove nitrite oxidation in the biofilter community, and activity of archaeal ammonia-oxidizing taxa was not detected in the SIP fractions. This study provides the first in situ evidence of ammonia oxidation by comammox Nitrospira in an ecologically relevant complex microbiome.IMPORTANCE With this study we provide the first in situ evidence of ecologically relevant ammonia oxidation by comammox Nitrospira in a complex microbiome and document an unexpectedly high H13CO3 - uptake and growth of proteobacterial and acidobacterial taxa under ammonia selectivity. This finding raises the question of whether comammox Nitrospira is an equally important ammonia oxidizer in other environments.
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Cao L, Zhang J, Zhao R, Deng Y, Liu J, Fu W, Lei Y, Zhang T, Li X, Li B. Genomic characterization, kinetics, and pathways of sulfamethazine biodegradation by Paenarthrobacter sp. A01. ENVIRONMENT INTERNATIONAL 2019; 131:104961. [PMID: 31330364 DOI: 10.1016/j.envint.2019.104961] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 06/02/2019] [Accepted: 06/22/2019] [Indexed: 06/10/2023]
Abstract
Biodegradation is an important route for the removal of sulfamethazine (SMZ), one of the most commonly used sulfonamide antibiotics, in the environment. However, little information is known about the kinetics, products, and pathways of SMZ biodegradation owing to the complexity of its enzyme-based biotransformation processes. In this study, the SMZ-degrading strain A01 belonging to the genus Paenarthrobacter was isolated from SMZ-enriched activated sludge reactors. The bacterial cells were rod-shaped with transient branches 2.50-4.00 μm in length with most forming in a V-shaped arrangement. The genome size of Paenarthrobacter sp. A01 had a total length of 4,885,005 bp with a GC content of 63.5%, and it contained 104 contigs and 55 RNAs. The effects of pH, temperature, initial substrate concentration and additional carbon source on the biodegradation of SMZ were investigated. The results indicated that pH 6.0-7.8, 25 °C and the addition of 0.2 g/L sodium acetate favored the biodegradation, whereas a high concentration of SMZ, 500 mg/L, had an inhibitory effect. The biodegradation kinetics with SMZ as the sole carbon source or 0.2 g/L sodium acetate as the co-substrate fit the modified Gompertz model well with a correlation coefficient (R2) of 0.99. Three biodegradation pathways were proposed involving nine biodegradation products, among which C6H9N3O2S and C12H12N2 were two novel biodegradation products that have not been reported previously. Approximately 90.7% of SMZ was transformed to 2-amino-4, 6-dimethylpyrimidine. Furthermore, sad genes responsible for catabolizing sulfonamides were characterized in A01 with high similarities of 96.0%-100.0%. This study will fill the knowledge gap in the biodegradation of this ubiquitous micropollutant in the aquatic environment.
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Affiliation(s)
- Lijia Cao
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China; School of Environment, Tsinghua University, Beijing, China
| | - Jiayu Zhang
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China; School of Environment, Tsinghua University, Beijing, China
| | - Renxin Zhao
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China; School of Environment, Tsinghua University, Beijing, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Graduate School at Shenzhen, Tsinghua University, China
| | - Yu Deng
- Environmental Biotechnology Laboratory, The University of Hong Kong, Hong Kong, China
| | - Jie Liu
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Wenjie Fu
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China; School of Environment, Tsinghua University, Beijing, China
| | - Yusha Lei
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China; School of Environment, Tsinghua University, Beijing, China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Hong Kong, China
| | - Xiaoyan Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Graduate School at Shenzhen, Tsinghua University, China
| | - Bing Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Graduate School at Shenzhen, Tsinghua University, China.
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Responses of Active Ammonia Oxidizers and Nitrification Activity in Eutrophic Lake Sediments to Nitrogen and Temperature. Appl Environ Microbiol 2019; 85:AEM.00258-19. [PMID: 31253684 DOI: 10.1128/aem.00258-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/19/2019] [Indexed: 01/04/2023] Open
Abstract
Ammonium concentrations and temperature drive the activities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), but their effects on these microbes in eutrophic freshwater sediments are unclear. In this study, surface sediments collected from areas of Taihu Lake (China) with different degrees of eutrophication were incubated under three levels of nitrogen input and temperature, and the autotrophic growth of ammonia oxidizers was assessed using 13C-labeled DNA-based stable-isotope probing (SIP), while communities were characterized using MiSeq sequencing and phylogenetic analysis of 16S rRNA genes. Nitrification rates in sediment microcosms were positively correlated with nitrogen inputs, but there was no marked association with temperature. Incubation of SIP microcosms indicated that AOA and AOB amoA genes were labeled by 13C at 20°C and 30°C in the slightly eutrophic sediment, and AOB amoA genes were labeled to a much greater extent than AOA amoA genes in the moderately eutrophic sediment after 56 days. Phylogenetic analysis of 13C-labeled 16S rRNA genes revealed that the active AOA were mainly affiliated with the Nitrosopumilus cluster, with the Nitrososphaera cluster dominating in the slightly eutrophic sediment at 30°C with low ammonium input (1 mM). Active AOB communities were more sensitive to nitrogen input and temperature than were AOA communities, and they were exclusively dominated by the Nitrosomonas cluster, which tended to be associated with Nitrosomonadaceae-like lineages. Nitrosomonas sp. strain Is79A3 tended to dominate the moderately eutrophic sediment at 10°C with greater ammonium input (2.86 mM). The relative abundance responses of the major active communities to nitrogen input and temperature gradients varied, indicating niche differentiation and differences in the physiological metabolism of ammonia oxidizers that are yet to be described.IMPORTANCE Both archaea and bacteria contribute to ammonia oxidation, which plays a central role in the global cycling of nitrogen and is important for reducing eutrophication in freshwater environments. The abundance and activities of ammonia-oxidizing archaea and bacteria in eutrophic limnic sediments vary with different ammonium concentrations or with seasonal shifts, and how the two factors affect nitrification activity, microbial roles, and active groups in different eutrophic sediments is unclear. The significance of our research is in identifying the archaeal and bacterial responses to anthropogenic activity and climate change, which will greatly enhance our understanding of the physiological metabolic differences of ammonia oxidizers.
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The Role of Pseudomonas in Heterotrophic Nitrification: A Case Study on Shrimp Ponds ( Litopenaeus vannamei) in Soc Trang Province. Microorganisms 2019; 7:microorganisms7060155. [PMID: 31146455 PMCID: PMC6616971 DOI: 10.3390/microorganisms7060155] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 05/22/2019] [Accepted: 05/28/2019] [Indexed: 01/08/2023] Open
Abstract
Based on a total of 6,295,650 sequences from the V3 and V4 regions (16S ribosomal RNA), the composition of the microorganism communities in the water of three Litopenaeus vannamei (Decapoda, Whiteleg shrimp; Soc Trang, Vietnam) ponds were identified. Pseudomonas (10–20.29%), Methylophilus (13.26–24.28%), and Flavobacterium (2.6–19.29%) were the most abundant genera. The total ammonia (TAN) concentration (p = 0.025) and temperature (p = 0.015) were significantly correlated with the relative abundance of Pseudomonas in two bacterial communities (ST1, ST4), whereas the predictive functions of microorganism communities based on 16S rRNA gene data was estimated using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUST), which showed that nitrogen metabolism was significantly negatively correlated (p = 0.049) with TAN concentration. The abundance of Pseudomonas and nitrogen metabolism increased with a decrease in TAN concentration. The correlation between TAN concentration and the abundance of Pseudomonas was followed by the isolation, and heterotrophic nitrifying performance analysis was used to confirm our findings. Six Pseudomonas strains capable of heterotrophic nitrification were isolated from the three water samples and showed a complete reduction of 100 mg/L NH4Cl during a 96-h cultivation. These results indicate the potential of applying Pseudomonas in shrimp ponds for water treatment.
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Newsome L, Lopez Adams R, Downie HF, Moore KL, Lloyd JR. NanoSIMS imaging of extracellular electron transport processes during microbial iron(III) reduction. FEMS Microbiol Ecol 2019; 94:5033680. [PMID: 29878195 PMCID: PMC6041951 DOI: 10.1093/femsec/fiy104] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 06/05/2018] [Indexed: 01/25/2023] Open
Abstract
Microbial iron(III) reduction can have a profound effect on the fate of contaminants in natural and engineered environments. Different mechanisms of extracellular electron transport are used by Geobacter and Shewanella spp. to reduce insoluble Fe(III) minerals. Here we prepared a thin film of iron(III)-(oxyhydr)oxide doped with arsenic, and allowed the mineral coating to be colonised by Geobacter sulfurreducens or Shewanella ANA3 labelled with 13C from organic electron donors. This preserved the spatial relationship between metabolically active Fe(III)-reducing bacteria and the iron(III)-(oxyhydr)oxide that they were respiring. NanoSIMS imaging showed cells of G. sulfurreducens were co-located with the iron(III)-(oxyhydr)oxide surface and were significantly more 13C-enriched compared to cells located away from the mineral, consistent with Geobacter species requiring direct contact with an extracellular electron acceptor to support growth. There was no such intimate relationship between 13C-enriched S. ANA3 and the iron(III)-(oxyhydr)oxide surface, consistent with Shewanella species being able to reduce Fe(III) indirectly using a secreted endogenous mediator. Some differences were observed in the amount of As relative to Fe in the local environment of G. sulfurreducens compared to the bulk mineral, highlighting the usefulness of this type of analysis for probing interactions between microbial cells and Fe-trace metal distributions in biogeochemical experiments.
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Affiliation(s)
- Laura Newsome
- Williamson Research Centre, School of Earth and Environmental Sciences, University of Manchester, Manchester, M13 9PL, UK
| | - Rebeca Lopez Adams
- Williamson Research Centre, School of Earth and Environmental Sciences, University of Manchester, Manchester, M13 9PL, UK
| | - Helen F Downie
- Williamson Research Centre, School of Earth and Environmental Sciences, University of Manchester, Manchester, M13 9PL, UK
| | - Katie L Moore
- School of Materials, University of Manchester, Manchester, M13 9PL, UK.,Photon Science Institute, University of Manchester, Manchester, M13 9PL, UK
| | - Jonathan R Lloyd
- Williamson Research Centre, School of Earth and Environmental Sciences, University of Manchester, Manchester, M13 9PL, UK
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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: 60] [Impact Index Per Article: 12.0] [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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Pan KL, Gao JF, Fan XY, Li DC, Dai HH. The more important role of archaea than bacteria in nitrification of wastewater treatment plants in cold season despite their numerical relationships. WATER RESEARCH 2018; 145:552-561. [PMID: 30199800 DOI: 10.1016/j.watres.2018.08.066] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/24/2018] [Accepted: 08/30/2018] [Indexed: 05/04/2023]
Abstract
Nitrification failure of wastewater treatment plants (WWTPs) in cold season calls into investigations of the functional ammonia-oxidizing microorganisms (AOMs). In this study, we report the abundance of ammonia-oxidizing archaea (AOA), bacteria (AOB) and complete ammonia-oxidizing (comammox) Nitrospira in 23 municipal WWTPs in cold season, and explore the correlations between AOMs abundance and their relative contribution to nitrification. The copy numbers of AOA and AOB amoA gene ranged from 2.42 × 107 to 2.47 × 109 and 5.54 × 106 to 3.31 × 109 copies/g sludge, respectively. The abundance of amoA gene of Candidatus Nitrospira inopinata, an important strain of comammox Nitrospira, was stable with averaged abundance of 8.47 × 106 copies/g sludge. DNA-based stable isotope probing (DNA-SIP) assays were conducted with three typical WWTPs in which the abundance of AOA was lower than, similar to and higher than that of AOB, respectively. The results showed that considerable 13C-assimilation by AOA was detected during active nitrification in all WWTPs, whereas just a much lesser extent of 13C-incorporation by AOB and comammox Nitrospira was found in one WWTP. High-throughput sequencing with 13C-labeled DNA also showed the higher reads abundance of AOA than AOB and comammox Nitrospira. Nitrososphaera viennensis was the dominant active AOA, while Nitrosomonas oligotropha and Nitrosomonas europaea were identified as active AOB. The results obtained suggest that AOA, rather than AOB and comammox Nitrospira, dominate ammonia oxidation in WWTPs in cold season despite the numerical relationships of AOMs.
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Affiliation(s)
- Kai-Ling Pan
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing, 100124, China
| | - Jing-Feng Gao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing, 100124, China.
| | - Xiao-Yan Fan
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing, 100124, China
| | - Ding-Chang Li
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing, 100124, China
| | - Hui-Hui Dai
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing, 100124, China
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Incorporation of 13C-HCO 3- by ammonia-oxidizing archaea and bacteria during ammonia oxidation of sludge from a municipal wastewater treatment plant. Appl Microbiol Biotechnol 2018; 102:10767-10777. [PMID: 30343425 DOI: 10.1007/s00253-018-9436-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 09/23/2018] [Accepted: 10/07/2018] [Indexed: 10/28/2022]
Abstract
Ammonia-oxidizing archaea (AOA) have recently been proposed as potential players for ammonia removal in wastewater treatment plants (WWTPs). However, there is little evidence directly showing the contribution of AOA to ammonia oxidation in these engineered systems. In this study, DNA-stable isotope probing (DNA-SIP) with labeled 13C-HCO3- was introduced to sludge from a municipal WWTP. Quantitative PCR demonstrated that AOA amoA genes outnumbered AOB amoA genes in this WWTP sludge. AOA amoA gene sequence analysis revealed that AOA present in this WWTP were specific to one subcluster within the group 1.1b Thaumarchaeota. When ammonia was supplied to DNA-SIP incubation, the DNA-SIP profiles demonstrated the incorporation of the 13C into AOA and AOB. However, the 13C was not found to be assimilated into both microorganisms in the incubation without ammonia. Specific primers were designed to target amoA genes of AOA belonging to the subcluster found in this WWTP. Applying the primers to DNA-SIP experiment revealed that AOA of this subcluter most likely utilized inorganic carbon during ammonia oxidation under the studied conditions.
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Pan KL, Gao JF, Li HY, Fan XY, Li DC, Jiang H. Ammonia-oxidizing bacteria dominate ammonia oxidation in a full-scale wastewater treatment plant revealed by DNA-based stable isotope probing. BIORESOURCE TECHNOLOGY 2018; 256:152-159. [PMID: 29438915 DOI: 10.1016/j.biortech.2018.02.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 01/31/2018] [Accepted: 02/02/2018] [Indexed: 05/04/2023]
Abstract
A full-scale wastewater treatment plant (WWTP) with three separate treatment processes was selected to investigate the effects of seasonality and treatment process on the community structures of ammonia-oxidizing archaea (AOA) and bacteria (AOB). And then DNA-based stable isotope probing (DNA-SIP) was applied to explore the active ammonia oxidizers. The results of high-throughput sequencing indicated that treatment processes varied AOB communities rather than AOA communities. AOA slightly outnumbered AOB in most of the samples, whose abundance was significantly correlated with temperature. DNA-SIP results showed that the majority of AOB amoA gene was labeled by 13C-substrate, while just a small amount of AOA amoA gene was labeled. As revealed by high-throughput sequencing of heavy DNA, Nitrosomonadaceae-like AOB, Nitrosomonas sp. NP1, Nitrosomonas oligotropha and Nitrosomonas marina were the active AOB, and Nitrososphaera viennensis dominated the active AOA. The results indicated that AOB, not AOA, dominated active ammonia oxidation in the test WWTP.
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Affiliation(s)
- Kai-Ling Pan
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing 100124, China
| | - Jing-Feng Gao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing 100124, China.
| | - Hong-Yu Li
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing 100124, China
| | - Xiao-Yan Fan
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing 100124, China
| | - Ding-Chang Li
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing 100124, China
| | - Hao Jiang
- Research Department of Microbiology, Allwegene Technology Co., Ltd, Beijing 102209, China
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Espenberg M, Truu M, Mander Ü, Kasak K, Nõlvak H, Ligi T, Oopkaup K, Maddison M, Truu J. Differences in microbial community structure and nitrogen cycling in natural and drained tropical peatland soils. Sci Rep 2018; 8:4742. [PMID: 29549345 PMCID: PMC5856767 DOI: 10.1038/s41598-018-23032-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 03/06/2018] [Indexed: 01/02/2023] Open
Abstract
Tropical peatlands, which play a crucial role in the maintenance of different ecosystem services, are increasingly drained for agriculture, forestry, peat extraction and human settlement purposes. The present study investigated the differences between natural and drained sites of a tropical peatland in the community structure of soil bacteria and archaea and their potential to perform nitrogen transformation processes. The results indicate significant dissimilarities in the structure of soil bacterial and archaeal communities as well as nirK, nirS, nosZ, nifH and archaeal amoA gene-possessing microbial communities. The reduced denitrification and N2-fixing potential was detected in the drained tropical peatland soil. In undisturbed peatland soil, the N2O emission was primarily related to nirS-type denitrifiers and dissimilatory nitrate reduction to ammonium, while the conversion of N2O to N2 was controlled by microbes possessing nosZ clade I genes. The denitrifying microbial community of the drained site differed significantly from the natural site community. The main reducers of N2O were microbes harbouring nosZ clade II genes in the drained site. Additionally, the importance of DNRA process as one of the controlling mechanisms of N2O fluxes in the natural peatlands of the tropics revealed from the results of the study.
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Affiliation(s)
- Mikk Espenberg
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, 46 Vanemuise Street, 51014, Tartu, Estonia.
| | - Marika Truu
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, 46 Vanemuise Street, 51014, Tartu, Estonia
| | - Ülo Mander
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, 46 Vanemuise Street, 51014, Tartu, Estonia
| | - Kuno Kasak
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, 46 Vanemuise Street, 51014, Tartu, Estonia
| | - Hiie Nõlvak
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, 46 Vanemuise Street, 51014, Tartu, Estonia
| | - Teele Ligi
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, 46 Vanemuise Street, 51014, Tartu, Estonia
| | - Kristjan Oopkaup
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, 46 Vanemuise Street, 51014, Tartu, Estonia
| | - Martin Maddison
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, 46 Vanemuise Street, 51014, Tartu, Estonia
| | - Jaak Truu
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, 46 Vanemuise Street, 51014, Tartu, Estonia
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Cai M, Ng SK, Lim CK, Lu H, Jia Y, Lee PKH. Physiological and Metagenomic Characterizations of the Synergistic Relationships between Ammonia- and Nitrite-Oxidizing Bacteria in Freshwater Nitrification. Front Microbiol 2018. [PMID: 29535685 PMCID: PMC5835065 DOI: 10.3389/fmicb.2018.00280] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Nitrification plays a crucial role in global nitrogen cycling and treatment processes. However, the relationships between the nitrifier guilds of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) are still poorly understood, especially in freshwater habitats. This study examined the physiological interactions between the AOB and NOB present in a freshwater aquarium biofilter by culturing them, either together or separately, in a synthetic medium. Metagenomic and 16S rRNA gene sequencing revealed the presence and the draft genomes of Nitrosomonas-like AOB as well as Nitrobacter-like NOB in the cultures, including the first draft genome of Nitrobacter vulgaris. The nitrifiers exhibited different growth rates with different ammonium (NH4+) or nitrite concentrations (50-1,500 μM) and the growth rates were elevated under a high bicarbonate (HCO3-) concentration. The half-saturation constant (Ks for NH4+), the maximum growth rate (μmax), and the lag duration indicated a strong dependence on the synergistic relationships between the two guilds. Overall, the ecophysiological and metagenomic results in this study provided insights into the phylogeny of the key nitrifying players in a freshwater biofilter and showed that interactions between the two nitrifying guilds in a microbial community enhanced nitrification.
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Affiliation(s)
- Mingwei Cai
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong
| | - Siu-Kin Ng
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong
| | - Chee Kent Lim
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong
| | - Hongyuan Lu
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong
| | - Yangyang Jia
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong
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Roy D, McEvoy J, Blonigen M, Amundson M, Khan E. Seasonal variation and ex-situ nitrification activity of ammonia oxidizing archaea in biofilm based wastewater treatment processes. BIORESOURCE TECHNOLOGY 2017; 244:850-859. [PMID: 28841790 DOI: 10.1016/j.biortech.2017.08.060] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 08/09/2017] [Accepted: 08/10/2017] [Indexed: 05/04/2023]
Abstract
The abundance of ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) was investigated in full-scale two-stage trickling filters (TF) and moving bed bioreactor (MBBR) treating municipal wastewater. Biofilm samples were collected for 17months from nitrifying TF (NTF), biochemical oxygen demand TF (BTF), and MBBR media. The abundance of AOA and AOB was determined using a quantitative PCR approach targeting the ammonia monooxygenase subunit A gene of archaea and bacteria. AOA were dominant in the NTF and MBBR, while AOB dominated in the BTF. AOA and AOB were more abundant during warmer months, and AOA were detected in the BTF only during warmer months. In laboratory nitrification activity experiments, ammonia oxidation to nitrite decreased when AOA populations from the NTF and MBBR were inhibited, demonstrating that AOA contributed to nitrification. This study has shown that AOA outnumber AOB and contribute to ammonia oxidation in full-scale nitrifying biofilm processes.
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Affiliation(s)
- Dhritikshama Roy
- Environmental and Conservation Sciences Program (#2820), North Dakota State University, Fargo, ND 58108-6050, USA; Department of Civil and Environmental Engineering (#2470), North Dakota State University, Fargo, ND 58108-6050, USA
| | - John McEvoy
- Department of Veterinary and Microbiological Science (#7690), North Dakota State University, Fargo, ND 58108-6050, USA
| | - Mark Blonigen
- City of Fargo, 3400 North Broadway, Fargo, ND 58102, USA
| | - Maria Amundson
- City of Moorhead, 2121 28th Street N, Moorhead, MN 56560, USA
| | - Eakalak Khan
- Department of Civil and Environmental Engineering (#2470), North Dakota State University, Fargo, ND 58108-6050, USA.
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32
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Bai Z, Xie H, Kao-Kniffin J, Chen B, Shao P, Liang C. Shifts in microbial trophic strategy explain different temperature sensitivity of CO2 flux under constant and diurnally varying temperature regimes. FEMS Microbiol Ecol 2017; 93:3814241. [PMID: 28499007 DOI: 10.1093/femsec/fix063] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 05/09/2017] [Indexed: 12/31/2022] Open
Abstract
Understanding soil CO2 flux temperature sensitivity (Q10) is critical for predicting ecosystem-level responses to climate change. Yet, the effects of warming on microbial CO2 respiration still remain poorly understood under current Earth system models, partly as a result of thermal acclimation of organic matter decomposition. We conducted a 117-day incubation experiment under constant and diurnally varying temperature treatments based on four forest soils varying in vegetation stand and soil horizon. Our results showed that Q10 was greater under varying than constant temperature regimes. This distinction was most likely attributed to differences in the depletion of available carbon between constant high and varying high-temperature treatments, resulting in significantly higher rates of heterotrophic respiration in the varying high-temperature regime. Based on 16S rRNA gene sequencing data using Illumina, the varying high-temperature regime harbored higher prokaryotic alpha-diversity, was more dominated by the copiotrophic strategists and sustained a distinct community composition, in comparison to the constant-high treatment. We found a tightly coupled relationship between Q10 and microbial trophic guilds: the copiotrophic prokaryotes responded positively with high Q10 values, while the oligotrophs showed a negative response. Effects of vegetation stand and soil horizon consistently supported that the copiotrophic vs oligotrophic strategists determine the thermal sensitivity of CO2 flux. Our observations suggest that incorporating prokaryotic functional traits, such as shifts between copiotrophy and oligotrophy, is fundamental to our understanding of thermal acclimation of microbially mediated soil organic carbon cycling. Inclusion of microbial functional shifts may provide the potential to improve our projections of responses in microbial community and CO2 efflux to a changing environment in forest ecosystems.
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Affiliation(s)
- Zhen Bai
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Hongtu Xie
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Jenny Kao-Kniffin
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Baodong Chen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pengshuai Shao
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Chao Liang
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
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Modeling of soil nitrification responses to temperature reveals thermodynamic differences between ammonia-oxidizing activity of archaea and bacteria. ISME JOURNAL 2016; 11:896-908. [PMID: 27996979 DOI: 10.1038/ismej.2016.179] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 10/25/2016] [Accepted: 11/04/2016] [Indexed: 11/08/2022]
Abstract
Soil nitrification potential (NP) activities of ammonia-oxidizing archaea and bacteria (AOA and AOB, respectively) were evaluated across a temperature gradient (4-42 °C) imposed upon eight soils from four different sites in Oregon and modeled with both the macromolecular rate theory and the square root growth models to quantify the thermodynamic responses. There were significant differences in response by the dominant AOA and AOB contributing to the NPs. The optimal temperatures (Topt) for AOA- and AOB-supported NPs were significantly different (P<0.001), with AOA having Topt>12 °C greater than AOB. The change in heat capacity associated with the temperature dependence of nitrification (ΔCP‡) was correlated with Topt across the eight soils, and the ΔCP‡ of AOB activity was significantly more negative than that of AOA activity (P<0.01). Model results predicted, and confirmatory experiments showed, a significantly lower minimum temperature (Tmin) and different, albeit very similar, maximum temperature (Tmax) values for AOB than for AOA activity. The results also suggested that there may be different forms of AOA AMO that are active over different temperature ranges with different Tmin, but no evidence of multiple Tmin values within the AOB. Fundamental differences in temperature-influenced properties of nitrification driven by AOA and AOB provides support for the idea that the biochemical processes associated with NH3 oxidation in AOA and AOB differ thermodynamically from each other, and that also might account for the difficulties encountered in attempting to model the response of nitrification to temperature change in soil environments.
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Shi Y, Adams JM, Ni Y, Yang T, Jing X, Chen L, He JS, Chu H. The biogeography of soil archaeal communities on the eastern Tibetan Plateau. Sci Rep 2016; 6:38893. [PMID: 27958324 PMCID: PMC5153633 DOI: 10.1038/srep38893] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 11/14/2016] [Indexed: 12/13/2022] Open
Abstract
The biogeographical distribution of soil bacterial communities has been widely investigated. However, there has been little study of the biogeography of soil archaeal communities on a regional scale. Here, using high-throughput sequencing, we characterized the archaeal communities of 94 soil samples across the eastern Tibetan Plateau. Thaumarchaeota was the predominant archael phylum in all the soils, and Halobacteria was dominant only in dry soils. Archaeal community composition was significantly correlated with soil moisture content and C:N ratio, and archaeal phylotype richness was negatively correlated with soil moisture content (r = −0.47, P < 0.01). Spatial distance, a potential measure of the legacy effect of evolutionary and dispersal factors, was less important than measured environmental factors in determining the broad scale archaeal community pattern. These results indicate that soil moisture and C:N ratio are the key factors structuring soil archaeal communities on the eastern Tibetan Plateau. Our findings suggest that archaeal communities have adjusted their distributions rapidly enough to reach range equilibrium in relation to past environmental changes e.g. in water availability and soil nutrient status. This responsiveness may allow better prediction of future responses of soil archaea to environmental change in these sensitive ecosystems.
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Affiliation(s)
- Yu Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing 210008, China
| | - Jonathan M Adams
- Department of Biological Sciences, Seoul National University, Gwanak, Seoul 151, Republic of Korea
| | - Yingying Ni
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing 210008, China
| | - Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing 210008, China
| | - Xin Jing
- Department of Ecology, College of Urban and Environmental Sciences and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, 5 Yiheyuan Road, Beijing 100871, China
| | - Litong Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 23 Xinning Road, Xining 810008, China
| | - Jin-Sheng He
- Department of Ecology, College of Urban and Environmental Sciences and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, 5 Yiheyuan Road, Beijing 100871, China.,Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 23 Xinning Road, Xining 810008, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing 210008, China
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35
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Bacterial abundance and diversity in pond water supplied with different feeds. Sci Rep 2016; 6:35232. [PMID: 27759010 PMCID: PMC5069485 DOI: 10.1038/srep35232] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 09/22/2016] [Indexed: 01/17/2023] Open
Abstract
The abundance and diversity of bacteria in two types of ponds were investigated by quantitative PCR and Illumina MiSeq sequencing. The results revealed that the abundance of bacterial 16S rRNA genes in D ponds (with grass carp fed sudan grass) was significantly lower than that in E ponds (with grass carp fed commercial feed). The microbial communities were dominated by Proteobacteria, Cyanobacteria, Bacteroidetes, and Actinobacteria in both E and D ponds, while the abundance of some genera was significantly different between the two types of ponds. Specifically, some potential pathogens such as Acinetobacter and Aeromonas were found to be significantly decreased, while some probiotics such as Comamonadaceae unclassified and Bacillales unclassified were significantly increased in D ponds. In addition, water quality of D ponds was better than that of E ponds. Temperature, dissolved oxygen and nutrients had significant influence on bacterial communities. The differences in bacterial community compositions between the two types of ponds could be partially explained by the different water conditions.
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Shan J, Ji R, Yu Y, Xie Z, Yan X. Biochar, activated carbon, and carbon nanotubes have different effects on fate of (14)C-catechol and microbial community in soil. Sci Rep 2015; 5:16000. [PMID: 26515132 PMCID: PMC4626844 DOI: 10.1038/srep16000] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 10/07/2015] [Indexed: 12/02/2022] Open
Abstract
This study investigated the effects of biochar, activated carbon (AC)-, and single-walled and multi-walled carbon nanotubes (SWCNTs and MWCNTs) in various concentrations (0, 0.2, 20, and 2,000 mg/kg dry soil) on the fate of 14C-catechol and microbial community in soil. The results showed that biochar had no effect on the mineralization of 14C-catechol, whereas AC at all amendment rates and SWCNTs at 2,000 mg/kg significantly reduced mineralization. Particularly, MWCNTs at 0.2 mg/kg significantly stimulated mineralization compared with the control soil. The inhibitory effects of AC and SWCNTs on the mineralization were attributed to the inhibited soil microbial activities and the shifts in microbial communities, as suggested by the reduced microbial biomass C and the separated phylogenetic distance. In contrast, the stimulatory effects of MWCNTs on the mineralization were attributed to the selective stimulation of specific catechol-degraders by MWCNTs at 0.2 mg/kg. Only MWCNTs amendments and AC at 2,000 mg/kg significantly changed the distribution of 14C residues within the fractions of humic substances. Our findings suggest biochar, AC, SWCNTs and MWCNTs have different effects on the fate of 14C-catechol and microbial community in soil.
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Affiliation(s)
- Jun Shan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.,Changshu Agro-ecological Experimental Station, Chinese Academy of Sciences, Changshu 215555, China
| | - Rong Ji
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Yongjie Yu
- College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Zubin Xie
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xiaoyuan Yan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.,Changshu Agro-ecological Experimental Station, Chinese Academy of Sciences, Changshu 215555, China
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37
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Li J, Zhang J, Liu L, Fan Y, Li L, Yang Y, Lu Z, Zhang X. Annual periodicity in planktonic bacterial and archaeal community composition of eutrophic Lake Taihu. Sci Rep 2015; 5:15488. [PMID: 26503553 PMCID: PMC4621408 DOI: 10.1038/srep15488] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 09/28/2015] [Indexed: 02/06/2023] Open
Abstract
Bacterioplankton plays a key role in nutrient cycling and is closely related to water eutrophication and algal bloom. We used high-throughput 16S rRNA gene sequencing to profile archaeal and bacterial community compositions in the surface water of Lake Taihu. It is one of the largest lakes in China and has suffered from recurring cyanobacterial bloom. A total of 81 water samples were collected from 9 different sites in 9 different months of 2012. We found that temporal variation of the microbial community was significantly greater than spatial variation (adonis, n = 9999, P < 1e−4). The composition of bacterial community in December was similar to that in January, and so was the archaeal community, suggesting potential annual periodicity. Unsupervised K-means clustering was used to identify the synchrony of abundance variations between different taxa. We found that the cluster consisting mostly of ACK-M1, C111 (members of acIV), Pelagibacteraceae (alfV-A) and Synechococcaceae showed relatively higher abundance in autumn. On the contrary, the cluster of Comamonadaceae and Methylophilaceae (members of lineage betI and betIV) had higher abundance in spring. The co-occurrence relationships between taxa were greatly altered during the cyanobacterial bloom according to our further network module analysis.
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Affiliation(s)
- Junfeng Li
- MOE Key Lab of Bioinformatics; Bioinformatics Division/Center for Synthetic and Systems Biology, TNLIST and Department of Automation, Tsinghua University, Beijing, China
| | - Junyi Zhang
- State Key Lab for Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.,Wuxi Environmental Monitoring Centre, Wuxi, China
| | - Liyang Liu
- MOE Key Lab of Bioinformatics; Bioinformatics Division/Center for Synthetic and Systems Biology, TNLIST and Department of Automation, Tsinghua University, Beijing, China
| | - Yucai Fan
- State Key Lab for Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Lianshuo Li
- MOE Key Lab of Bioinformatics; Bioinformatics Division/Center for Synthetic and Systems Biology, TNLIST and Department of Automation, Tsinghua University, Beijing, China
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Zuhong Lu
- State Key Lab for Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.,Department of Biomedical Engineering, Peking University, Beijing, China
| | - Xuegong Zhang
- MOE Key Lab of Bioinformatics; Bioinformatics Division/Center for Synthetic and Systems Biology, TNLIST and Department of Automation, Tsinghua University, Beijing, China
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38
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Zhang HH, Huang TL, Chen SN, Yang X, Lv K, Sekar R. Abundance and diversity of bacteria in oxygen minimum drinking water reservoir sediments studied by quantitative PCR and pyrosequencing. MICROBIAL ECOLOGY 2015; 69:618-629. [PMID: 25502074 DOI: 10.1007/s00248-014-0539-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 11/19/2014] [Indexed: 06/04/2023]
Abstract
Reservoir sediment is one of the most stressful environments for microorganisms due to periodically oxygen minimum conditions. In this study, the abundance and composition of bacteria associated with sediments from three drinking water reservoirs (Zhoucun, ZCR; Shibianyu, SBYR; and Jinpen, JPR) were investigated by quantitative polymerase chain reaction and 16S rRNA-based 454 pyrosequencing. The results of physico-chemical analysis of sediments showed that the organic matter and total nitrogen were significantly higher in ZCR as compared to JPR (P < 0.01). The bacterial abundance was 9.13 × 10(6), 1.14 × 10(7), and 6.35 × 10(6) copies/ng DNA in sediments of SBYR, ZCR, and JPR, respectively (P < 0.01). The pyrosequencing revealed a total of 9,673 operational taxonomic units, which were affiliated with 17 phyla. The dominant phylum was Firmicutes (56.83%) in JPR; whereas, the dominance of Proteobacteria was observed in SBYR with 40.38% and ZCR with 39.56%. The Shannon-Wiener diversity (H') was high in ZCR; whereas, Chao 1 richness was high in SBYR. The dominant genera were Clostridium with 42.15% and Bacillus with 20.44% in JPR. Meanwhile, Dechloromonas with 14.80% and Smithella with 7.20% were dominated in ZCR, and Bacillus with 45.45% and Acinetobacter with 5.15% in SBYR. The heat map profiles and redundancy analysis indicated substantial differences in sediment bacterial community composition among three reservoirs. Moreover, it appears from the results that physico-chemical variables of sediments including pH, organic matter, total nitrogen, and available phosphorous played key roles in shaping the bacterial community diversity. The results obtained from this study will broaden our understanding on the bacterial community structure of sediments in oxygen minimum and stressful freshwater environments.
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Affiliation(s)
- Hai-han Zhang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, Shaanxi Province, China
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39
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Wu Y, Tan L, Liu W, Wang B, Wang J, Cai Y, Lin X. Profiling bacterial diversity in a limestone cave of the western Loess Plateau of China. Front Microbiol 2015; 6:244. [PMID: 25870592 PMCID: PMC4378288 DOI: 10.3389/fmicb.2015.00244] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/12/2015] [Indexed: 11/25/2022] Open
Abstract
Bacteria and archaea sustain subsurface cave ecosystems by dominating primary production and fueling biogeochemical cyclings, despite the permanent darkness and shortage of nutrients. However, the heterogeneity and underlying mechanism of microbial diversity in caves, in particular those well connect to surface environment are largely unexplored. In this study, we examined the bacterial abundance and composition in Jinjia Cave, a small and shallow limestone cave located on the western Loess Plateau of China, by enumerating and pyrosequencing small subunit rRNA genes. The results clearly reveal the contrasting bacterial community compositions in relation to cave habitat types, i.e., rock wall deposit, aquatic sediment, and sinkhole soil, which are differentially connected to the surface environment. The deposits on the cave walls were dominated by putative cave-specific bacterial lineages within the γ-Proteobacteria or Actinobacteria that are routinely found on cave rocks around the world. In addition, sequence identity with known functional groups suggests enrichments of chemolithotrophic bacteria potentially involved in autotrophic C fixation and inorganic N transformation on rock surfaces. By contrast, bacterial communities in aquatic sediments were more closely related to those in the overlying soils. This is consistent with the similarity in elemental composition between the cave sediment and the overlying soil, implicating the influence of mineral chemistry on cave microhabitat and bacterial composition. These findings provide compelling molecular evidence of the bacterial community heterogeneity in an East Asian cave, which might be controlled by both subsurface and surface environments.
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Affiliation(s)
- Yucheng Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science - Chinese Academy of Sciences, Nanjing China
| | - Liangcheng Tan
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment - Chinese Academy of Sciences, Xi'an China ; State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment - Chinese Academy of Sciences, Xi'an China
| | - Wuxing Liu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science - Chinese Academy of Sciences, Nanjing China
| | - Baozhan Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science - Chinese Academy of Sciences, Nanjing China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology - Chinese Academy of Sciences, Nanjing China
| | - Yanjun Cai
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment - Chinese Academy of Sciences, Xi'an China
| | - Xiangui Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science - Chinese Academy of Sciences, Nanjing China
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40
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Mosier AC, Li Z, Thomas BC, Hettich RL, Pan C, Banfield JF. Elevated temperature alters proteomic responses of individual organisms within a biofilm community. ISME JOURNAL 2014; 9:180-94. [PMID: 25050524 DOI: 10.1038/ismej.2014.113] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 06/01/2014] [Accepted: 06/03/2014] [Indexed: 01/08/2023]
Abstract
Microbial communities that underpin global biogeochemical cycles will likely be influenced by elevated temperature associated with environmental change. Here, we test an approach to measure how elevated temperature impacts the physiology of individual microbial groups in a community context, using a model microbial-based ecosystem. The study is the first application of tandem mass tag (TMT)-based proteomics to a microbial community. We accurately, precisely and reproducibly quantified thousands of proteins in biofilms growing at 40, 43 and 46 °C. Elevated temperature led to upregulation of proteins involved in amino-acid metabolism at the level of individual organisms and the entire community. Proteins from related organisms differed in their relative abundance and functional responses to temperature. Elevated temperature repressed carbon fixation proteins from two Leptospirillum genotypes, whereas carbon fixation proteins were significantly upregulated at higher temperature by a third member of this genus. Leptospirillum group III bacteria may have been subject to viral stress at elevated temperature, which could lead to greater carbon turnover in the microbial food web through the release of viral lysate. Overall, these findings highlight the utility of proteomics-enabled community-based physiology studies, and provide a methodological framework for possible extension to additional mixed culture and environmental sample analyses.
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Affiliation(s)
- Annika C Mosier
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Zhou Li
- 1] Oak Ridge National Laboratory, Oak Ridge, TN, USA [2] Graduate School of Genome Science and Technology, University of Tennessee-Oak Ridge National Laboratory, Knoxville, TN, USA
| | - Brian C Thomas
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | | | - Chongle Pan
- Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jillian F Banfield
- 1] Department of Earth and Planetary Science, University of California, Berkeley, CA, USA [2] Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA
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41
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Zeng J, Zhao D, Yu Z, Huang R, Wu QL. Temperature responses of ammonia-oxidizing prokaryotes in freshwater sediment microcosms. PLoS One 2014; 9:e100653. [PMID: 24959960 PMCID: PMC4069112 DOI: 10.1371/journal.pone.0100653] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 05/27/2014] [Indexed: 12/03/2022] Open
Abstract
In order to investigate the effects of temperature on the abundances and community compositions of ammonia-oxidizing archaea (AOA) and bacteria (AOB), lake microcosms were constructed and incubated at 15°C, 25°C and 35°C for 40 days, respectively. Temperature exhibited different effects on the abundance and diversity of archaeal and bacterial amoA gene. The elevated temperature increased the abundance of archaeal amoA gene, whereas the abundance of bacterial amoA gene decreased. The highest diversity of bacterial amoA gene was found in the 25°C treatment sample. However, the 25°C treatment sample maintained the lowest diversity of archaeal amoA gene. Most of the archaeal amoA sequences obtained in this study affiliated with the Nitrosopumilus cluster. Two sequences obtained from the 15°C treatment samples were affiliated with the Nitrosotalea cluster. N. oligotropha lineage was the most dominant bacterial amoA gene group. Several sequences affiliated to Nitrosospira and undefined N. europaea/NC. mobilis like lineage were found in the pre-incubation and 25°C treatment groups.
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Affiliation(s)
- Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
- * E-mail:
| | - Dayong Zhao
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China
- College of Hydrology and Water Resources, Hohai University, Nanjing, China
| | - Zhongbo Yu
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China
- College of Hydrology and Water Resources, Hohai University, Nanjing, China
| | - Rui Huang
- College of Hydrology and Water Resources, Hohai University, Nanjing, China
| | - Qinglong L. Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
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42
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Wu Y, Conrad R. Ammonia oxidation-dependent growth of group I.1b Thaumarchaeota in acidic red soil microcosms. FEMS Microbiol Ecol 2014; 89:127-34. [PMID: 24724989 DOI: 10.1111/1574-6941.12340] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 02/17/2014] [Accepted: 04/03/2014] [Indexed: 11/28/2022] Open
Abstract
Accumulating evidence suggests that Thaumarchaeota may control nitrification in acidic soils. However, the composition of the thaumarchaeotal communities and their functioning is not well known. Therefore, we studied nitrification activity in relation to abundance and composition of Thaumarchaeota in an acidic red soil from China, using microcosms incubated with and without cellulose amendment. Cellulose was selected to simulate the input of crop residues used to increase soil fertility by local farming. Accumulation of NO3-(-N) was correlated with the growth of Thaumarchaeota as determined by qPCR of 16S rRNA and ammonia monooxygenase (amoA) genes. Both nitrification activity and thaumarchaeotal growth were inhibited by acetylene. They were also inhibited by cellulose amendment, possibly due to the depletion of ammonium by enhanced heterotrophic assimilation. These results indicated that growth of Thaumarchaeota was dependent on ammonia oxidation. The thaumarchaeotal 16S rRNA gene sequences in the red soil were dominated by a clade related to soil fosmid clone 29i4 within the group I.1b, which is widely distributed but so far uncultured. The archaeal amoA sequences were mainly related to the Nitrososphaera sister cluster. These observations suggest that fosmid clone 29i4 and Nitrososphaera sister cluster represent the same group of Thaumarchaeota and dominate ammonia oxidation in acidic red soil.
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Affiliation(s)
- Yucheng Wu
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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Crenarchaeal heterotrophy in salt marsh sediments. ISME JOURNAL 2014; 8:1534-43. [PMID: 24553469 DOI: 10.1038/ismej.2014.15] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 12/21/2013] [Accepted: 01/06/2014] [Indexed: 11/08/2022]
Abstract
Mesophilic Crenarchaeota (also known as Thaumarchaeota) are ubiquitous and abundant in marine habitats. However, very little is known about their metabolic function in situ. In this study, salt marsh sediments from New Jersey were screened via stable isotope probing (SIP) for heterotrophy by amending with a single (13)C-labeled compound (acetate, glycine or urea) or a complex (13)C-biopolymer (lipids, proteins or growth medium (ISOGRO)). SIP incubations were done at two substrate concentrations (30-150 μM; 2-10 mg ml(-1)), and (13)C-labeled DNA was analyzed by terminal restriction fragment length polymorphism (TRFLP) analysis of 16S rRNA genes. To test for autotrophy, an amendment with (13)C-bicarbonate was also performed. Our SIP analyses indicate salt marsh crenarchaea are heterotrophic, double within 2-3 days and often compete with heterotrophic bacteria for the same organic substrates. A clone library of (13)C-amplicons was screened to find matches to the (13)C-TRFLP peaks, with seven members of the Miscellaneous Crenarchaeal Group and seven members from the Marine Group 1.a Crenarchaeota being discerned. Some of these crenarchaea displayed a preference for particular carbon sources, whereas others incorporated nearly every (13)C-substrate provided. The data suggest salt marshes may be an excellent model system for studying crenarchaeal metabolic capabilities and can provide information on the competition between crenarchaea and other microbial groups to improve our understanding of microbial ecology.
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Tran NH, Urase T, Ngo HH, Hu J, Ong SL. Insight into metabolic and cometabolic activities of autotrophic and heterotrophic microorganisms in the biodegradation of emerging trace organic contaminants. BIORESOURCE TECHNOLOGY 2013; 146:721-731. [PMID: 23948223 DOI: 10.1016/j.biortech.2013.07.083] [Citation(s) in RCA: 244] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Revised: 07/17/2013] [Accepted: 07/19/2013] [Indexed: 05/06/2023]
Abstract
Many efforts have been made to understand the biodegradation of emerging trace organic contaminants (EOCs) in the natural and engineered systems. This review summarizes the current knowledge on the biodegradation of EOCs while having in-depth discussion on metabolism and cometabolism of EOCs. Biodegradation of EOCs is mainly attributed to cometabolic activities of both heterotrophic and autotrophic microorganisms. Metabolism of EOCs can only be observed by heterotrophic microbes. Autotrophic ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaeal (AOA) cometabolize a variety of EOCs via the non-specific enzymes, such as ammonia monooxygenase (AMO). Higher biodegradation of EOCs is often noted under nitrification at high ammonia loading rate. The presence of a growth substrate promotes cometabolic biodegradation of EOCs. Potential strategies for enhancing the biodegradation of EOCs were also proposed in this review.
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Affiliation(s)
- Ngoc Han Tran
- Department of Civil and Environmental Engineering, Faculty of Engineering, National University of Singapore, 1 Engineering Drive 2, Singapore 117576, Singapore.
| | - Taro Urase
- School of Bioscience and Biotechnology, Tokyo University of Technology, Katakura 1404-1, Hachioji, Tokyo 1920982, Japan
| | - Huu Hao Ngo
- School of Civil and Environmental Engineering, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia.
| | - Jiangyong Hu
- Department of Civil and Environmental Engineering, Faculty of Engineering, National University of Singapore, 1 Engineering Drive 2, Singapore 117576, Singapore
| | - Say Leong Ong
- Department of Civil and Environmental Engineering, Faculty of Engineering, National University of Singapore, 1 Engineering Drive 2, Singapore 117576, Singapore
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