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Xiang Y, Zhou T, Deng S, Shao Z, Liu Y, He Q, Chai H. Nitrite improved nitrification efficiency and enriched ammonia-oxidizing archaea and bacteria in the simultaneous nitrification and denitrification process. WATER RESEARCH X 2023; 21:100204. [PMID: 38098882 PMCID: PMC10719579 DOI: 10.1016/j.wroa.2023.100204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/18/2023] [Accepted: 10/02/2023] [Indexed: 12/17/2023]
Abstract
Simultaneous nitrification and denitrification (SND) is effective and energy-saving for wastewater treatment. As an inevitable intermediate product in the SND process, nitrite affects the efficiency of ammonia oxidation and the composition of nitrifiers. To investigate the impact of nitrite on ammonia oxidation efficiency, two reactors performing SND were respectively operated without nitrite (R1 as control) and with 20 mg N/L nitrite addition (R2 as experimental). The total nitrogen removal efficiency was 74.5% in R1 while 99.0% in R2. With nitrite addition (i.e., 20 mg N/L), the ammonia removal rate in R2 increased to 4.5 times of that in R1. The ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) contributed to respective around 46.9% and 41.8% ammonia removal in R2 based on the results of experiments with specific inhibitors. The number of respective AOA and AOB ammonia monooxygenase gene (amoA) copies increased by 280 and 30 times due to nitrite addition, according to the qPCR results. The high-throughput sequencing results illustrated the increase of dominant AOB species from 0.40% in R1 to 1.59% in R2 and the phylogenetic tree analysis revealed a close link to Nitrosospira multiformis. These results indicated that the ammonia removal efficiency was improved and AOA/AOB were enriched by nitrite addition. The specific nitrite reductases in AOA and AOB boosted the adaptation of nitrite addition. This study demonstrated the positive impacts of nitrite addition on the ammonia removal efficiency and rate in the SND process.
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Affiliation(s)
- Yu Xiang
- School of Architecture and Civil Engineering, Xihua University, Chengdu 610039, China
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Tengzhi Zhou
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Siping Deng
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Zhiyu Shao
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Yiwen Liu
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Qiang He
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Hongxiang Chai
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), College of Environment and Ecology, Chongqing University, Chongqing 400045, China
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Fan Y, Zhang M, Cheng J, Yong D, Ji J, Wu Q, He C. Elucidating nitrifying performance, nitrite accumulation and microbial community in a three-stage plug flow moving bed biofilm reactor (PF - MBBR). CHEMOSPHERE 2022; 297:134087. [PMID: 35216986 DOI: 10.1016/j.chemosphere.2022.134087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 02/13/2022] [Accepted: 02/20/2022] [Indexed: 06/14/2023]
Abstract
A three-stage plug flow moving bed biofilm reactor (PF - MBBR, consisting of three identical chambers of N1, N2 and N3) was proposed for nitrifier enrichment using synthetic wastewater. During the stable operation, the average NH4+-N effluent was 0.67 mg/L and NH4+-N removal was as high as 97.19% with the nitrite accumulation ratio (NAR) of 54.23%, although the biofilm thickness and biomass both presented downward trends from N1 (296 μm, 2280 mg/L), N2 (248 μm, 1850 mg/L) to N3 (198 μm, 1545 mg/L). Particularly, the comparative results of three stages revealed that N2 showed the optimum NH4+-N removal (77.27%) and NAR (75.21%) in the continuous-flow, while NAR of N3 unexpectedly maintained a high level of 65.83% in the batch test, suggesting that ammonia oxidizing bacteria (AOB) accounted for absolute advantage over nitrite oxidizing bacteria (NOB). High-throughput sequencing initially verified different distribution of bacterial community structure, where N2 was far away from N1 and N3 with the lowest community richness and community diversity (operational taxonomic units (OTUs): 454(N2)<527(N3)<621(N1)). Proteobacteria (77.60%-83.09%), Bacteroidetes (1.66%-3.66%), Acidobacteria (2.28%-4.67%), and Planctomycetes (1.19%-6.63%) were the major phyla. At the genus level, AOB (mainly Nitrosomonas) accounted for 5.08% (N1), 20.74% (N2) and 14.24% (N3) while NOB (mainly Nitrospira) increased from 0.14% (N1), 7.06% (N2) to 4.91% (N3) with the total percentages of 5.22%, 27.80% and 19.15%. Finally, the application feasibility of MBBR optimization linked with nitrite (NO2--N) accumulation for deep-level nutrient removal was discussed.
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Affiliation(s)
- Yajun Fan
- College of Hydraulic Science and Engineering, Yangzhou University, Yangzhou, 225100, PR China
| | - Miao Zhang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, PR China.
| | - Jilin Cheng
- College of Hydraulic Science and Engineering, Yangzhou University, Yangzhou, 225100, PR China
| | - Daming Yong
- Yangzhou Polytechnic Institute, Yangzhou, 225127, PR China
| | - Junjie Ji
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, PR China
| | - Qichao Wu
- Yangzhou Polytechnic Institute, Yangzhou, 225127, PR China
| | - Chengda He
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, PR China
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Berrelleza-Valdez F, Parades-Aguilar J, Peña-Limón CE, Certucha-Barragán MT, Gámez-Meza N, Serrano-Palacios D, Medina-Juárez LA, Calderón K. A novel process of the isolation of nitrifying bacteria and their development in two different natural lab-scale packed-bed bioreactors for trichloroethylene bioremediation. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 241:211-218. [PMID: 31004998 DOI: 10.1016/j.jenvman.2019.04.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 03/11/2019] [Accepted: 04/12/2019] [Indexed: 06/09/2023]
Abstract
Trichloroethylene (TCE) is a carcinogenic compound that is commonly present in groundwater and has been detected in drinking water sources for Mexican towns in the Mexico-US border area. Nitrifying bacteria, such as Nitrosomonas europaea, have been shown to be capable of degrading halogenated compounds, including TCE, but it is difficult to obtain high cell concentrations of these bacteria. The aim of the present study was to generate biomass of a nitrifying bacterial consortium from the sludge of an urban wastewater treatment plant (WWTP) and evaluate its capacity to biodegrade TCE in two different natural lab-scaled packed bed bioreactors. The consortium was isolated by a novel method using a continuous stirred-tank bioreactor inoculated with activated sludge from the Domos WWTP located in Cd. Obregón, Sonora, Mexico. The bioreactor was fed with specific media to cultivate ammonia-oxidizing bacteria at a dilution rate near the maximum specific growth rate reported for Nitrosomonas europaea. Optical density and suspended solids measurements were performed to determine the culture biomass production, and the presence of inorganic nitrogen species was determined by spectrophotometry. The presence of nitrifying ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) was confirmed by PCR amplification, and biofilm formation was observed by scanning electron microscopy. Batch-scale experiments confirmed the biodegradative activity of the isolated consortium, which was subsequently fixed in an inorganic carrier as zeolite and a synthetic carrier such as polyurethane to both be used as lab-scale packed-bed bioreactors, with up to 58.63% and 62.7% of TCE biodegradation achieved, respectively, demonstrating a possible alternative for TCE bioremediation in environmental and engineering systems.
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Affiliation(s)
- Fernando Berrelleza-Valdez
- Departamento de Investigaciones Científicas y Tecnológicas, Universidad de Sonora, Blvd. Luis Donaldo Colosio S/N. CP., 83000, Hermosillo, Sonora, Mexico
| | - Jonathan Parades-Aguilar
- Departamento de Investigaciones Científicas y Tecnológicas, Universidad de Sonora, Blvd. Luis Donaldo Colosio S/N. CP., 83000, Hermosillo, Sonora, Mexico
| | - Carlos E Peña-Limón
- Departamento de Investigaciones Científicas y Tecnológicas, Universidad de Sonora, Blvd. Luis Donaldo Colosio S/N. CP., 83000, Hermosillo, Sonora, Mexico.
| | - María Teresa Certucha-Barragán
- Departamento de Ingeniería Química y Metalurgia, Universidad de Sonora, Blvd. Luis Donaldo Colosio S/N. CP., 83000, Hermosillo, Sonora, Mexico
| | - Nohemí Gámez-Meza
- Departamento de Investigaciones Científicas y Tecnológicas, Universidad de Sonora, Blvd. Luis Donaldo Colosio S/N. CP., 83000, Hermosillo, Sonora, Mexico
| | - Denisse Serrano-Palacios
- Departamento de Ciencias del Agua y Medio Ambiente, Instituto Tecnológico de Sonora, Antonio Caso S/N. C.P., 85130, Ciudad Obregón, Sonora, Mexico
| | - Luis Angel Medina-Juárez
- Departamento de Investigaciones Científicas y Tecnológicas, Universidad de Sonora, Blvd. Luis Donaldo Colosio S/N. CP., 83000, Hermosillo, Sonora, Mexico.
| | - Kadiya Calderón
- Departamento de Investigaciones Científicas y Tecnológicas, Universidad de Sonora, Blvd. Luis Donaldo Colosio S/N. CP., 83000, Hermosillo, Sonora, Mexico.
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Jo JH, Kim W, Lim J. Ammonia-oxidizers' diversity in wastewater treatment processes. ENVIRONMENTAL TECHNOLOGY 2018; 39:887-894. [PMID: 28394197 DOI: 10.1080/09593330.2017.1316317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 04/01/2017] [Indexed: 06/07/2023]
Abstract
The diversity of ammonia-oxidizing bacteria (AOB) within the beta-subclass of Proteobacteria was investigated by genus- and family-specific real-time quantitative PCR (qPCR) assays on samples drawn from wastewater treatment systems. The 16S rRNA gene copy numbers ranged from 7.0 × 103 to 6.8 × 106, 1.1 × 107 to 1.8 × 107, and 2.9 × 105 to 1.5 × 107 copies/mL, respectively. Volumetric ammonium load (VAL) in the wastewater treatment systems calculated using the AOB numbers was in the range of 2.1-12.6 mM/d. Distribution patterns of eutrophic (i.e. Nitrosomonas europaea and Nitrosomonas nitrosa clusters) and oligotrophic (i.e. Nitrosomonas cryotolerans cluster) AOB groups were correlated with the VAL values. A high possibility of potential false-positive detection by family-specific qPCR assays was established by evaluating theoretical specificity in in silico and experimental investigations. The specificities of genus-specific qPCR assays were confirmed by amoA PCR, followed by cloning and sequencing. VAL must be the factor influencing the inclusion of AOB species. However, there was no significant correlation between the volatile suspended solid concentration representing chemical oxygen demand and N. europaea's community population, indicating that the degree of ammonia oxidation influenced the community cluster of Nitrosomonas relatively more.
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Affiliation(s)
- Ji Hye Jo
- a Division of Resource Circulation , Korea Environment Institute , Sejong , Republic of Korea
| | - Woong Kim
- b Department of Environmental Engineering , Kyungpook National University , Daegu , Republic of Korea
- c Advanced Institute of Water Industry , Kyungpook National University , Daegu , Republic of Korea
| | - Juntaek Lim
- d Department of Chemical and Biomolecular Engineering , KAIST , Daejeon , Republic of Korea
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Thandar SM, Ushiki N, Fujitani H, Sekiguchi Y, Tsuneda S. Ecophysiology and Comparative Genomics of Nitrosomonas mobilis Ms1 Isolated from Autotrophic Nitrifying Granules of Wastewater Treatment Bioreactor. Front Microbiol 2016; 7:1869. [PMID: 27920767 PMCID: PMC5118430 DOI: 10.3389/fmicb.2016.01869] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 11/07/2016] [Indexed: 01/15/2023] Open
Abstract
Ammonia-oxidizing bacteria (AOB), which oxidize ammonia to nitrite in the first step of nitrification, play an important role in biological wastewater treatment systems. Nitrosomonas mobilis is an important and dominant AOB in various wastewater treatment systems. However, the detailed physiological and genomic properties of N. mobilis have not been thoroughly investigated because of limited success isolating pure cultures. This study investigated the key physiological characteristics of N. mobilis Ms1, which was previously isolated into pure culture from the nitrifying granules of wastewater treatment bioreactor. The pure culture of N. mobilis Ms1 was cultivated in liquid mineral medium with 30 mg-N L-1 (2.14 mM) of ammonium at room temperature under dark conditions. The optimum growth of N. mobilis Ms1 occurred at 27°C and pH 8, with a maximum growth rate of 0.05–0.07 h-1, which corresponded to a generation time of 10–14 h. The half saturation constant for ammonium uptake rate and the maximum ammonium uptake rate of N. mobilis Ms1 were 30.70 ± 0.51 μM NH4+ and 0.01 ± 0.002 pmol NH4+ cells-1 h-1, respectively. N. mobilis Ms1 had higher ammonia oxidation activity than N. europaea in this study. The oxygen uptake activity kinetics of N. mobilis Ms1 were Km(O2) = 21.74 ± 4.01 μM O2 and V max(O2) = 0.06 ± 0.02 pmol O2 cells-1 h-1. Ms1 grew well at ammonium and NaCl concentrations of up to 100 and 500 mM, respectively. The nitrite tolerance of N. mobilis Ms1 was extremely high (up to 300 mM) compared to AOB previously isolated from activated sludge and wastewater treatment plants. The average nucleotide identity between the genomes of N. mobilis Ms1 and other Nitrosomonas species indicated that N. mobilis Ms1 was distantly related to other Nitrosomonas species. The organization of the genes encoding protein inventory involved in ammonia oxidation and nitrifier denitrification processes were different from other Nitrosomonas species. The current study provides a needed physiological and genomic characterization of N. mobilis-like bacteria and a better understanding of their ecophysiological properties, enabling comparison of these bacteria with other AOB in wastewater treatment systems and natural ecosystems.
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Affiliation(s)
- Soe Myat Thandar
- Tsuneda Laboratory, Department of Life Science and Medical Bioscience, Waseda UniversityTokyo, Japan; Department of Biotechnology, Mandalay Technological University, Ministry of EducationMandalay, Myanmar
| | - Norisuke Ushiki
- Tsuneda Laboratory, Department of Life Science and Medical Bioscience, Waseda University Tokyo, Japan
| | - Hirotsugu Fujitani
- Tsuneda Laboratory, Department of Life Science and Medical Bioscience, Waseda University Tokyo, Japan
| | - Yuji Sekiguchi
- Advanced Biomeasurements Research Group, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology Ibaraki, Japan
| | - Satoshi Tsuneda
- Tsuneda Laboratory, Department of Life Science and Medical Bioscience, Waseda University Tokyo, Japan
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Cho K, Shin SG, Lee J, Koo T, Kim W, Hwang S. Nitrification resilience and community dynamics of ammonia-oxidizing bacteria with respect to ammonia loading shock in a nitrification reactor treating steel wastewater. J Biosci Bioeng 2016; 122:196-202. [DOI: 10.1016/j.jbiosc.2016.01.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 01/19/2016] [Accepted: 01/20/2016] [Indexed: 11/29/2022]
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Levén L, Wijnbladh E, Tuvesson M, Kragelund C, Hallin S. Control of Microthrix parvicella and sludge bulking by ozone in a full-scale WWTP. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2016; 73:866-872. [PMID: 26901730 DOI: 10.2166/wst.2015.560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Bulking and rising sludge are common problems in wastewater treatment plants (WWTPs) and are primarily caused by increased growth of filamentous bacteria such as Microthrix parvicella. It has a negative impact on sludge settling properties in activated sludge (AS) process, in addition to being responsible for foam formation. Different methods can be used to control sludge bulking. The aim of this study was to evaluate the dosage of on-site generated ozone in the recycled AS flow in a full-scale WWTP having problems caused by M. parvicella. The evaluation of the experiment was assessed by process data, microscopic analysis and microbial screening on the experimental and control line before, during and after the period of ozone dosage. The ozone treatment resulted in decreased abundance of M. parvicella and improved the settling properties, without impairing the overall process performance. Both chemical oxygen demand (COD)- and N-removal were unaffected and the dominant populations involved in nitrification, as analysed by fluorescent in situ hybridization, remained during the experimental period. When the ozone treatment was terminated, the problems with sludge bulking reappeared, indicating the importance of continuous evaluation of the process.
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Affiliation(s)
- Lotta Levén
- Institute of Agricultural and Environmental Engineering, JTI, PO Box 7033, SE-750 07 Uppsala, Sweden E-mail:
| | - Erik Wijnbladh
- Department of Microbiology, Swedish University of Agricultural Sciences, PO Box 7025, SE-750 07 Uppsala, Sweden
| | | | - Caroline Kragelund
- Department of Biotechnology, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark and Danish Technological Institute, Kongsvang Alle 29, DK-8000, Denmark
| | - Sara Hallin
- Department of Microbiology, Swedish University of Agricultural Sciences, PO Box 7025, SE-750 07 Uppsala, Sweden
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Liu J, Tian Y, Wang D, Lu Y, Zhang J, Zuo W. Quantitative analysis of ammonia-oxidizing bacteria in a combined system of MBR and worm reactors treating synthetic wastewater. BIORESOURCE TECHNOLOGY 2014; 174:294-301. [PMID: 25463811 DOI: 10.1016/j.biortech.2014.09.082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 09/12/2014] [Accepted: 09/17/2014] [Indexed: 06/04/2023]
Abstract
The Static Sequencing Batch Worm Reactor (SSBWR) followed by the MBR (S-MBR) is one of the advanced excess sludge treatments. In this paper, the control MBR (C-MBR) and the SSBWR-MBR were operated in parallel to study the changes of NH3-N removal and ammonia oxidizing bacteria (AOB). The results showed that the capacity of NH3-N removal of the S-MBR was improved by the worm reactors along with the operation. The S-MBR was favorable because it selected for the higher activity of the ammonia oxidization and better cells appearance of the sludge. The five species (Nitrosomonas, Betaproteobacteria, Clostridium, Dechloromonas and Bacteria) were found to be significantly correlate with the ammonia oxidization functions and performance of NH3-N removal in the C-MBR and S-MBR. The Nitrosomonas, Betaproteobacteria and Dechloromonas remained and eventually enriched in the S-MBR played a primary role in the NH3-N removal of the S-MBR.
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Affiliation(s)
- Jia Liu
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, China
| | - Yu Tian
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin 150090, China; School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, China.
| | - Dezhen Wang
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, China
| | - Yaobin Lu
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, China
| | - Jun Zhang
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, China
| | - Wei Zuo
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, China
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Abundance and diversity of bacterial nitrifiers and denitrifiers and their functional genes in tannery wastewater treatment plants revealed by high-throughput sequencing. PLoS One 2014; 9:e113603. [PMID: 25420093 PMCID: PMC4242629 DOI: 10.1371/journal.pone.0113603] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 10/26/2014] [Indexed: 11/25/2022] Open
Abstract
Biological nitrification/denitrification is frequently used to remove nitrogen from tannery wastewater containing high concentrations of ammonia. However, information is limited about the bacterial nitrifiers and denitrifiers and their functional genes in tannery wastewater treatment plants (WWTPs) due to the low-throughput of the previously used methods. In this study, 454 pyrosequencing and Illumina high-throughput sequencing, combined with molecular methods, were used to comprehensively characterize structures and functions of nitrification and denitrification bacterial communities in aerobic and anaerobic sludge of two full-scale tannery WWTPs. Pyrosequencing of 16S rRNA genes showed that Proteobacteria and Synergistetes dominated in the aerobic and anaerobic sludge, respectively. Ammonia-oxidizing bacteria (AOB) amoA gene cloning revealed that Nitrosomonas europaea dominated the ammonia-oxidizing community in the WWTPs. Metagenomic analysis showed that the denitrifiers mainly included the genera of Thauera, Paracoccus, Hyphomicrobium, Comamonas and Azoarcus, which may greatly contribute to the nitrogen removal in the two WWTPs. It is interesting that AOB and ammonia-oxidizing archaea had low abundance although both WWTPs demonstrated high ammonium removal efficiency. Good correlation between the qPCR and metagenomic analysis is observed for the quantification of functional genes amoA, nirK, nirS and nosZ, indicating that the metagenomic approach may be a promising method used to comprehensively investigate the abundance of functional genes of nitrifiers and denitrifiers in the environment.
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Srithep P, Khinthong B, Chodanon T, Powtongsook S, Pungrasmi W, Limpiyakorn T. Communities of ammonia-oxidizing bacteria, ammonia-oxidizing archaea and nitrite-oxidizing bacteria in shrimp ponds. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-0858-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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New methods for analysis of spatial distribution and coaggregation of microbial populations in complex biofilms. Appl Environ Microbiol 2013; 79:5978-87. [PMID: 23892743 DOI: 10.1128/aem.01727-13] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In biofilms, microbial activities form gradients of substrates and electron acceptors, creating a complex landscape of microhabitats, often resulting in structured localization of the microbial populations present. To understand the dynamic interplay between and within these populations, quantitative measurements and statistical analysis of their localization patterns within the biofilms are necessary, and adequate automated tools for such analyses are needed. We have designed and applied new methods for fluorescence in situ hybridization (FISH) and digital image analysis of directionally dependent (anisotropic) multispecies biofilms. A sequential-FISH approach allowed multiple populations to be detected in a biofilm sample. This was combined with an automated tool for vertical-distribution analysis by generating in silico biofilm slices and the recently developed Inflate algorithm for coaggregation analysis of microbial populations in anisotropic biofilms. As a proof of principle, we show distinct stratification patterns of the ammonia oxidizers Nitrosomonas oligotropha subclusters I and II and the nitrite oxidizer Nitrospira sublineage I in three different types of wastewater biofilms, suggesting niche differentiation between the N. oligotropha subclusters, which could explain their coexistence in the same biofilms. Coaggregation analysis showed that N. oligotropha subcluster II aggregated closer to Nitrospira than did N. oligotropha subcluster I in a pilot plant nitrifying trickling filter (NTF) and a moving-bed biofilm reactor (MBBR), but not in a full-scale NTF, indicating important ecophysiological differences between these phylogenetically closely related subclusters. By using high-resolution quantitative methods applicable to any multispecies biofilm in general, the ecological interactions of these complex ecosystems can be understood in more detail.
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Limpiyakorn T, Fürhacker M, Haberl R, Chodanon T, Srithep P, Sonthiphand P. amoA-encoding archaea in wastewater treatment plants: a review. Appl Microbiol Biotechnol 2013; 97:1425-39. [DOI: 10.1007/s00253-012-4650-7] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 12/09/2012] [Accepted: 12/11/2012] [Indexed: 02/01/2023]
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Yasuda T, Waki M, Kuroda K, Hanajima D, Fukumoto Y, Yamagishi T, Suwa Y, Suzuki K. Responses of community structure of amoA
-encoding archaea and ammonia-oxidizing bacteria in ammonia biofilter with rockwool mixtures to the gradual increases in ammonium and nitrate. J Appl Microbiol 2012. [DOI: 10.1111/jam.12091] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- T. Yasuda
- Institute of Livestock and Grassland Science; National Agriculture and Food Research Organization; Tsukuba Ibaraki Japan
| | - M. Waki
- Institute of Livestock and Grassland Science; National Agriculture and Food Research Organization; Tsukuba Ibaraki Japan
| | - K. Kuroda
- Kyushu Okinawa Agricultural Research Center; National Agriculture and Food Research Organization; Koshi Kumamoto Japan
| | - D. Hanajima
- Agricultural Research Center for Hokkaido Region; National Agriculture and Food Research Organization; Sapporo Hokkaido Japan
| | - Y. Fukumoto
- Institute of Livestock and Grassland Science; National Agriculture and Food Research Organization; Tsukuba Ibaraki Japan
| | - T. Yamagishi
- Institute of Environmental Management Technology; National Institute of Advanced Industrial Science and Technology; Tsukuba Ibaraki Japan
| | - Y. Suwa
- Department of Biological Sciences; Chuo University; Tokyo Japan
| | - K. Suzuki
- Institute of Livestock and Grassland Science; National Agriculture and Food Research Organization; Tsukuba Ibaraki Japan
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Yamamoto N, Oishi R, Suyama Y, Tada C, Nakai Y. Ammonia-oxidizing bacteria rather than ammonia-oxidizing archaea were widely distributed in animal manure composts from field-scale facilities. Microbes Environ 2012; 27:519-24. [PMID: 22972386 PMCID: PMC4103565 DOI: 10.1264/jsme2.me12053] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The distribution of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in cattle, swine, and chicken manure compost was analyzed. PCR-denaturing gradient gel electrophoresis (DGGE) showed that a Candidatus Nitrososphaera gargensis-like sequence dominated in cattle manure compost, while few AOA were detected in other composts. In the case of AOB, Nitrosomonas-like sequences were detected with higher diversity in cattle and swine manure composts. The relative abundance of ammonia oxidizers by real-time PCR revealed that more AOB was present in compost except in one swine manure compost. Our results indicated that AOB rather than AOA are widely distributed in animal manure compost.
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Affiliation(s)
- Nozomi Yamamoto
- Laboratory of Sustainable Environmental Biology, Graduate School of Agricultural Science, Tohoku University, 232–3 Yomogida, Naruko-onsen, Osaki, Miyagi 989–6711, Japan
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Real-time PCR quantification of the population dynamics of ammonia-oxidizing bacteria in a pilot-scale wastewater treatment plant. Biochem Eng J 2012. [DOI: 10.1016/j.bej.2012.04.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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16
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Wang X, Wen X, Xia Y, Hu M, Zhao F, Ding K. Ammonia oxidizing bacteria community dynamics in a pilot-scale wastewater treatment plant. PLoS One 2012; 7:e36272. [PMID: 22558415 PMCID: PMC3338686 DOI: 10.1371/journal.pone.0036272] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2011] [Accepted: 04/03/2012] [Indexed: 11/19/2022] Open
Abstract
Background Chemoautotrophic ammonia oxidizing bacteria (AOB) have the metabolic ability to oxidize ammonia to nitrite aerobically. This metabolic feature has been widely used, in combination with denitrification, to remove nitrogen from wastewater in wastewater treatment plants (WWTPs). However, the relative influence of specific deterministic environmental factors to AOB community dynamics in WWTP is uncertain. The ecological principles underlying AOB community dynamics and nitrification stability and how they are related are also poorly understood. Methodology/Principal Findings The community dynamics of ammonia oxidizing bacteria (AOB) in a pilot-scale WWTP were monitored over a one-year period by Terminal Restriction Fragment Length Polymorphism (T-RFLP). During the study period, the effluent ammonia concentrations were almost below 2 mg/L, except for the first 60 days, indicting stable nitrification. T-RFLP results showed that, during the test period with stable nitrification, the AOB community structures were not stable, and the average change rate (every 15 days) of AOB community structures was 10%±8%. The correlations between T-RFLP profiles and 10 operational and environmental parameters were tested by Canonical Correlation Analysis (CCA) and Mantel test. The results indicated that the dynamics of AOB community correlated most strongly with Dissolved Oxygen (DO), effluent ammonia, effluent Biochemical Oxygen Demand (BOD) and temperature. Conclusions/Significance This study suggests that nitrification stability is not necessarily accompanied by a stable AOB community, and provides insight into parameters controlling the AOB community dynamics within bioreactors with stable nitrification.
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Affiliation(s)
- Xiaohui Wang
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing, China
| | - Xianghua Wen
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing, China
- * E-mail:
| | - Yu Xia
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing, China
| | - Ma Hu
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing, China
| | - Fang Zhao
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing, China
| | - Kun Ding
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing, China
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Almstrand R, Lydmark P, Lindgren PE, Sörensson F, Hermansson M. Dynamics of specific ammonia-oxidizing bacterial populations and nitrification in response to controlled shifts of ammonium concentrations in wastewater. Appl Microbiol Biotechnol 2012; 97:2183-91. [DOI: 10.1007/s00253-012-4047-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 03/16/2012] [Accepted: 03/19/2012] [Indexed: 12/01/2022]
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Kim JG, Jung MY, Park SJ, Rijpstra WIC, Sinninghe Damsté JS, Madsen EL, Min D, Kim JS, Kim GJ, Rhee SK. Cultivation of a highly enriched ammonia-oxidizing archaeon of thaumarchaeotal group I.1b from an agricultural soil. Environ Microbiol 2012; 14:1528-43. [PMID: 22515152 DOI: 10.1111/j.1462-2920.2012.02740.x] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nitrification of excess ammonia in soil causes eutrophication of water resources and emission of atmospheric N(2) O gas. The first step of nitrification, ammonia oxidation, is mediated by Archaea as well as Bacteria. The physiological reactions mediated by ammonia-oxidizing archaea (AOA) and their contribution to soil nitrification are still unclear. Results of non-culture-based studies have shown the thaumarchaeotal group I.1b lineage of AOA to be dominant over both AOA of group I.1a and ammonia-oxidizing bacteria in various soils. We obtained from an agricultural soil a highly enriched ammonia-oxidizing culture dominated by a single archaeal population [c. 90% of total cells, as determined microscopically (by fluorescence in situ hybridization) and by quantitative PCR of its 16S rRNA gene]. The archaeon (termed 'strain JG1') fell within thaumarchaeotal group I.1b and was related to the moderately thermophilic archaeon, Candidatus Nitrososphaera gargensis, and the mesophilic archaeon, Ca. Nitrososphaera viennensis with 97.0% and 99.1% 16S rRNA gene sequence similarity respectively. Strain JG1 was neutrophilic (growth range pH 6.0-8.0) and mesophilic (growth range temperature 25-40°C). The optimum temperature of strain JG1 (35-40°C) is > 10°C higher than that of ammonia-oxidizing bacteria (AOB). Membrane analysis showed that strain JG1 contained a glycerol dialkyl glycerol tetraether, GDGT-4, and its regioisomer as major core lipids; this crenarchaeol regioisomer was previously detected in similar abundance in the thermophile, Ca. N. gargensis and has been frequently observed in tropical soils. Substrate uptake assays showed that the affinity of strain JG1 for ammonia and oxygen was much higher than those of AOB. These traits may give a competitive advantage to AOA related to strain JG1 in oligotrophic environments. (13) C-bicarbonate incorporation into archaeal lipids of strain JG1 established its ability to grow autotrophically. Strain JG1 produced a significant amount of N(2) O gas - implicating AOA as a possible source of N(2) O emission from soils. Sequences of archaeal amoA and 16S rRNA genes closely related to those of strain JG1 have been retrieved from various terrestrial environments in which lineage of strain JG1 is likely engaged in autotrophic nitrification.
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Affiliation(s)
- Jong-Geol Kim
- Department of Microbiology, Chungbuk National University, 12 Gaeshin-dong, Heungduk-gu, Cheongju, Korea
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OISHI R, HIROOKA K, OTAWA K, TADA C, NAKAI Y. Ammonia-oxidizing Archaea in laboratory-scale activated sludge systems for wastewater of low- or high-ammonium concentration. Anim Sci J 2011; 83:571-6. [DOI: 10.1111/j.1740-0929.2011.00995.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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20
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Characterization of the Microbial Community in a Partial Nitrifying Sequencing Batch Biofilm Reactor. Curr Microbiol 2011; 63:543-50. [DOI: 10.1007/s00284-011-0019-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 09/12/2011] [Indexed: 10/17/2022]
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21
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Wang X, Wen X, Yan H, Ding K, Hu M. Community dynamics of ammonia oxidizing bacteria in a full-scale wastewater treatment system with nitrification stability. ACTA ACUST UNITED AC 2010. [DOI: 10.1007/s11783-010-0254-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2022]
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22
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Yamamoto N, Otawa K, Nakai Y. Diversity and abundance of ammonia-oxidizing bacteria and ammonia-oxidizing archaea during cattle manure composting. MICROBIAL ECOLOGY 2010; 60:807-815. [PMID: 20607531 DOI: 10.1007/s00248-010-9714-6] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Accepted: 06/20/2010] [Indexed: 05/29/2023]
Abstract
Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) play important roles in nitrification in various environments. They may also be key communities for ammonia oxidation in composting systems, although few studies have discussed their presence. We investigated the relative diversity and abundance of AOB and AOA using cloning procedures, denaturing gradient gel electrophoresis analysis, and real-time PCR during several stages in the process of cattle manure composting. Our results revealed that the AOB community structure changed during the process. At the high-temperature stage (>60°C), a member of the Nitrosomonas europaea/eutropha cluster dominated while the uncultured Nitrosomonas spp. cluster appeared after the temperature decreased. Additionally, our analysis indicated that AOA sequences, which were classified into a soil/sediment cluster, were present after the temperature decreased during the composting process. At these stages, the number of the archaeal amoA gene copies (3.2 or 3.9 × 10(7) copies per gram freeze-dried compost) was significantly higher than that of bacterial amoA gene copies (2.2-7.2 × 10(6) copies per gram freeze-dried compost). Our results suggest that both AOB and AOA are actively involved in nitrification of composting systems.
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Affiliation(s)
- Nozomi Yamamoto
- Laboratory of Sustainable Environmental Biology, Graduate School of Agricultural Science, Tohoku University, Osaki, Miyagi, Japan
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Sonthiphand P, Limpiyakorn T. Change in ammonia-oxidizing microorganisms in enriched nitrifying activated sludge. Appl Microbiol Biotechnol 2010; 89:843-53. [PMID: 20922378 DOI: 10.1007/s00253-010-2902-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Revised: 09/17/2010] [Accepted: 09/18/2010] [Indexed: 11/27/2022]
Abstract
In this study, sludge was taken from a municipal wastewater treatment plant that contained a nearly equal number of archaeal amoA genes (5.70 × 10⁶ ± 3.30 × 10⁵ copies mg sludge⁻¹) to bacterial amoA genes (8.60 × 10⁶ ± 7.64 × 10⁵ copies mg sludge⁻¹) and enriched in three continuous-flow reactors receiving an inorganic medium containing different ammonium concentrations: 2, 10, and 30 mM NH (4) (+) -N (28, 140, and 420 mg N l⁻¹). The abundance and communities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in enriched nitrifying activated sludge (NAS) were monitored at days 60 and 360 of the operation. Early on, between day 0 and day 60 of reactor operation, comparative abundance of AOA amoA genes to AOB amoA genes varied among the reactors depending on the ammonium levels found in the reactors. As compared to the seed sludge, the number of AOA amoA genes was unchanged in the reactor with lower ammonium level (0.06 ± 0.04 mgN l⁻¹), while in the reactors with higher ammonium levels (0.51 ± 0.33 and 0.25 ± 0.10 mgN l⁻¹), the numbers of AOA amoA genes were deteriorated. By day 360, AOA disappeared from the ammonia-oxidizing consortiums in all reactors. The majority of the AOA sequences from all NASs at each sampling period fell into a single AOA cluster, however, suggesting that the ammonium did not affect the AOA communities under this operational condition. This result is contradictory to the case of AOB, where the communities varied significantly among the NASs. AOB with a high affinity for ammonia were present in the reactors with lower ammonium levels, whereas AOB with a low affinity to ammonia existed in the reactors with higher ammonium levels.
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Characterization and quantification of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in a nitrogen-removing reactor using T-RFLP and qPCR. Appl Microbiol Biotechnol 2010; 87:1167-76. [PMID: 20405121 PMCID: PMC2886134 DOI: 10.1007/s00253-010-2595-2] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Revised: 03/29/2010] [Accepted: 03/31/2010] [Indexed: 11/16/2022]
Abstract
Using ammonia monooxygenase α-subunit (amoA) gene and 16S rRNA gene, the community structure and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in a nitrogen-removing reactor, which was operated for five phases, were characterized and quantified by cloning, terminal restriction fragment length polymorphism (T-RFLP), and quantitative polymerase chain reaction (qPCR). The results suggested that the dominant AOB in the reactor fell to the genus Nitrosomonas, while the dominant AOA belonged to Crenarchaeotal Group I.1a in phylum Crenarchaeota. Real-time PCR results demonstrated that the levels of AOB amoA varied from 2.9 × 103 to 2.3 × 105 copies per nanogram DNA, greatly (about 60 times) higher than those of AOA, which ranged from 1.7 × 102 to 3.8 × 103 copies per nanogram DNA. This indicated the possible leading role of AOB in the nitrification process in this study. T-RFLP results showed that the AOB community structure significantly shifted in different phases while AOA only showed one major peak for all the phases. The analyses also suggested that the AOB community was more sensitive than that of AOA to operational conditions, such as ammonia loading and dissolved oxygen.
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25
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Relationship between respirometric activity and community of entrapped nitrifying bacteria: Implications for partial nitrification. Enzyme Microb Technol 2010. [DOI: 10.1016/j.enzmictec.2009.10.014] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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26
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Allen JG, Beutel MW, Call DR, Fischer AM. Effects of oxygenation on ammonia oxidation potential and microbial diversity in sediment from surface-flow wetland mesocosms. BIORESOURCE TECHNOLOGY 2010; 101:1389-1392. [PMID: 19815408 DOI: 10.1016/j.biortech.2009.09.050] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Revised: 09/10/2009] [Accepted: 09/16/2009] [Indexed: 05/28/2023]
Abstract
Addition of oxygen to surface-flow wetland mesocosms treating synthetic secondary effluent resulted in a significant increase in ammonia oxidation potential in sediment compared to non-oxygenated controls. Ammonia oxidation potential in oxygenated wetland sediment (1.2-3.5 mg N g dw(-1) d(-1)) was 2-3 orders of magnitude higher than those measured in sediment and soil systems reported in the literature. Phylogenic analysis of sediment from the two treatments revealed substantial differences in microbial diversity including the presence of ammonia-oxidizing bacteria (Nitrosomonas oligotropha) and denitrifying bacteria only in oxygenated sediment, and an increase in the diversity of aerobic phototrophs and methanotrophs in control sediment. These observations supported the contention by Palmer et al. (2009) that oxygenation 'activated' nitrifying bacteria in wetland sediment leading to high rates of biological ammonia oxidation.
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Affiliation(s)
- Jennifer G Allen
- Washington State University, Department of Civil and Environmental Engineering, Ecological Engineering Group, Pullman, WA 99164, USA
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Matsumoto S, Ishikawa D, Saeki G, Aoi Y, Tsuneda S. Microbial Population Dynamics and Community Structure during the Formation of Nitrifying Granules to Treat Ammonia-Rich Inorganic Wastewater. Microbes Environ 2010; 25:164-70. [DOI: 10.1264/jsme2.me10107] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Shinya Matsumoto
- Department of Life Science and Medical Bioscience, Waseda University
| | - Daisuke Ishikawa
- Department of Life Science and Medical Bioscience, Waseda University
| | - Goro Saeki
- Department of Life Science and Medical Bioscience, Waseda University
| | - Yoshiteru Aoi
- Waseda Institute for Advanced Study, Waseda University
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, Waseda University
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Qiu S, Chen G, Zhou Y. Abundance and diversity of ammonia-oxidizing bacteria in relation to ammonium in a chinese shallow eutrophic urban lake. Braz J Microbiol 2010; 41:218-26. [PMID: 24031484 PMCID: PMC3768599 DOI: 10.1590/s1517-838220100001000031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2009] [Revised: 05/01/2009] [Accepted: 07/24/2009] [Indexed: 11/21/2022] Open
Abstract
The measures of most-probable-number and restriction fragment length polymorphism analysis were used to analyze the abundance and diversity of ammonia-oxidizing bacteria in sediment of a Chinese shallow eutrophic urban lake (Lake Yuehu). Among the 5 sampling sites, ammonia concentration in interstitial water was positively proportional not only to the content of organic matter, but also to ammonia-oxidizing bacteria numbers (at a magnitude of 105 cells g-1 dry weight) in sediment significantly. Furthermore, the diversity of ammonia-oxidizing bacteria were determined by means of PCR primers targeting the amoA gene with five gene libraries created and restriction pattern analysis. The 13 restriction patterns were recorded with 4 ones being common among all sampling sites. The 8 restriction patterns including 4 unique ones were found at the site with the highest NH4+ concentrations in interstitial water, while, there were only common patterns without unique ones at the site with the lowest NH4+ concentrations in interstitial water. Phylogenetic analysis showed that the amoA fragments retrieved belong to Nitrosomonas oligotropha & ureae lineage, N. europaea lineage, N. communis lineage and Nitrosospira lineage, most of which were affiliated with the genus Nitrosomonas. The N. oligotropha & ureae-like bacteria were the dominant species. Thus, the abundance and diversity of sediment AOB is closely linked to ammonium status in eutrophic lakes.
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Affiliation(s)
- Shanlian Qiu
- Institute of Hydrobiology, Chinese Academy of Sciences , 7 Donghu Nan Road, Wuhan, Hubei 430072 , China ; Graduate School of the Chinese Academy of Sciences , 19 Yuquan Road, Beijing 100049 , China
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29
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Wang X, Wen X, Criddle C, Wells G, Zhang J, Zhao Y. Community analysis of ammonia-oxidizing bacteria in activated sludge of eight wastewater treatment systems. J Environ Sci (China) 2010; 22:627-634. [PMID: 20617742 DOI: 10.1016/s1001-0742(09)60155-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
We investigated the communities of ammonia-oxidizing bacteria (AOB) in activated sludge collected from eight wastewater treatment systems using polymerase chain reaction (PCR) followed by terminal restriction fragment length polymorphism (T-RFLP), cloning, and sequencing of the alpha-subunit of the ammonia monooxygenase gene (amoA). The T-RFLP fingerprint analyses showed that different wastewater treatment systems harbored distinct AOB communities. However, there was no remarkable difference among the AOB T-RFLP profiles from different parts of the same system. The T-RFLP fingerprints showed that a full-scale wastewater treatment plant (WWTP) contained a larger number of dominant AOB species than a pilot-scale reactor. The source of influent affected the AOB community, and the WWTPs treating domestic wastewater contained a higher AOB diversity than those receiving mixed domestic and industrial wastewater. However, the AOB community structure was little affected by the treatment process in this study. Phylogenetic analysis of the cloned amoA genes clearly indicated that all the dominant AOB in the systems was closely related to Nitrosomonas spp. not to Nitrosospira spp. Members of the Nitrosomonas oligotropha and Nitrosomonas communis clusters were found in all samples, while members of Nitrosomonas europaea cluster occurred in some systems.
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Affiliation(s)
- Xiaohui Wang
- Department of Environmental Science and Engineering, Tsinghua University, Beijing 100084, China.
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Wells GF, Park HD, Yeung CH, Eggleston B, Francis CA, Criddle CS. Ammonia-oxidizing communities in a highly aerated full-scale activated sludge bioreactor: betaproteobacterial dynamics and low relative abundance of Crenarchaea. Environ Microbiol 2009; 11:2310-28. [DOI: 10.1111/j.1462-2920.2009.01958.x] [Citation(s) in RCA: 210] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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31
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Fortunato CS, Carlini DB, Ewers E, Bushaw-Newton KL. Nitrifier and denitrifier molecular operational taxonomic unit compositions from sites of a freshwater estuary of Chesapeake Bay. Can J Microbiol 2009; 55:333-46. [PMID: 19370077 DOI: 10.1139/w08-124] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Temporal and spatial changes in the molecular operational taxonomic unit (OTU) compositions of bacteria harboring genes for nitrification and denitrification were assessed using denaturing gradient gel electrophoresis (DGGE), clone-based DNA sequencing of selected PCR products, and analyses of ammonium and organic matter concentrations. Sediment, overlying water, and pore-water samples were taken from different vegetated sites of Jug Bay National Estuarine Research Reserve, Maryland, during spring, summer, and fall 2006. OTU richness and the diversities of nitrifiers and denitrifiers were assessed by the presence of bands on DGGE gels, both ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) were seasonally dependent. AOB OTU richness was highest in the summer when NOB richness was decreased, whereas NOB richness was highest in the spring when AOB richness was decreased. The OTU diversities of nitrifiers did not correlate with ammonium concentrations, organic matter concentrations, or the presence of vegetation. The OTU diversities of denitrifiers possessing either the nirK or nosZ genes were not seasonally dependent but were positively correlated with organic matter content (p = 0.0015, r2 = 0.27; p < 0.0001, r2 = 0.39, respectively). Additionally, the presence of vegetation significantly enhanced nosZ species richness (Wilcoxon/Kruskal-Wallis test, p < 0.008), but this trend was not seen for nirK OTU richness. Banding patterns for nirK OTUs were more similar within sites for each season compared with any of the other genes. Over all seasons, nirK OTU richness was highest and AOB and nosZ OTU richness were lowest (Wilcoxon/Kruskal-Wallis test, p < 0.0001). High levels of sequence divergence among cloned nirK PCR products indicate a broad diversity of nirK homologs in this freshwater estuary.
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Affiliation(s)
- Caroline S Fortunato
- Department of Biology, American University, 4400 Massachusetts Avenue NW, Washington, D.C. 20016, USA
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Cabezas A, Draper P, Etchebehere C. Fluctuation of microbial activities after influent load variations in a full-scale SBR: recovery of the biomass after starvation. Appl Microbiol Biotechnol 2009; 84:1191-202. [DOI: 10.1007/s00253-009-2138-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Revised: 07/07/2009] [Accepted: 07/09/2009] [Indexed: 10/20/2022]
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Life without light: microbial diversity and evidence of sulfur- and ammonium-based chemolithotrophy in Movile Cave. ISME JOURNAL 2009; 3:1093-104. [PMID: 19474813 DOI: 10.1038/ismej.2009.57] [Citation(s) in RCA: 142] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Microbial diversity in Movile Cave (Romania) was studied using bacterial and archaeal 16S rRNA gene sequence and functional gene analyses, including ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), soxB (sulfate thioesterase/thiohydrolase) and amoA (ammonia monooxygenase). Sulfur oxidizers from both Gammaproteobacteria and Betaproteobacteria were detected in 16S rRNA, soxB and RuBisCO gene libraries. DNA-based stable-isotope probing analyses using 13C-bicarbonate showed that Thiobacillus spp. were most active in assimilating CO2 and also implied that ammonia and nitrite oxidizers were active during incubations. Nitrosomonas spp. were detected in both 16S rRNA and amoA gene libraries from the 'heavy' DNA and sequences related to nitrite-oxidizing bacteria Nitrospira and Candidatus 'Nitrotoga' were also detected in the 'heavy' DNA, which suggests that ammonia/nitrite oxidation may be another major primary production process in this unique ecosystem. A significant number of sequences associated with known methylotrophs from the Betaproteobacteria were obtained, including Methylotenera, Methylophilus and Methylovorus, supporting the view that cycling of one-carbon compounds may be an important process within Movile Cave. Other sequences detected in the bacterial 16S rRNA clone library included Verrucomicrobia, Firmicutes, Bacteroidetes, alphaproteobacterial Rhodobacterales and gammaproteobacterial Xanthomonadales. Archaeal 16S rRNA sequences retrieved were restricted within two groups, namely the Deep-sea Hydrothermal Vent Euryarchaeota group and the Miscellaneous Crenarchaeotic group. No sequences related to known sulfur-oxidizing archaea, ammonia-oxidizing archaea, methanogens or anaerobic methane-oxidizing archaea were detected in this clone library. The results provided molecular biological evidence to support the hypothesis that Movile Cave is driven by chemolithoautotrophy, mainly through sulfur oxidation by sulfur-oxidizing bacteria and reveal that ammonia- and nitrite-oxidizing bacteria may also be major primary producers in Movile Cave.
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Zhang XW, Qin YY, Ren HQ, Li DT, Yang H. Seasonal variation in communities of ammonia-oxidizing bacteria based on polymerase chain reaction – denaturing gradient gel electrophoresis in a biofilm reactor for drinking water pretreatment. Can J Microbiol 2008; 54:358-65. [DOI: 10.1139/w08-011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The diversity and variation of total and active ammonia-oxidizing bacteria in a full-scale aerated submerged biofilm reactor for drinking water pretreatment were characterized by clone libraries and denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA and its gene during a whole year. Sequences obtained from clone libraries affiliated with the Nitrosomonas oligotropha lineage and the Nitrosomonas communis lineage. An uncultured subgroup of Nitrosomonas communis lineage was also detected. Seasonal variations in both total and active ammonia-oxidizing bacteria communities were observed in the DGGE profiles, but an RNA-based analysis reflected more obvious dynamic changes in ammonia-oxidizer community than a DNA-based approach. Statistical study based on canonical correspondence analysis showed that a community shift of active ammonia oxidizers was significantly influenced by temperature and pH, but no significant correlation was found between environmental variables and total ammonia-oxidizer community shift.
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Affiliation(s)
- Xiao-Wen Zhang
- Key Laboratory of Microbial Metabolism (Shanghai Jiaotong University), Ministry of Education, School of Life Science and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China
- School of the Environment, Nanjing University, Nanjing 210093, China
| | - Ying-Ying Qin
- Key Laboratory of Microbial Metabolism (Shanghai Jiaotong University), Ministry of Education, School of Life Science and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China
- School of the Environment, Nanjing University, Nanjing 210093, China
| | - Hong-Qiang Ren
- Key Laboratory of Microbial Metabolism (Shanghai Jiaotong University), Ministry of Education, School of Life Science and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China
- School of the Environment, Nanjing University, Nanjing 210093, China
| | - Dao-Tang Li
- Key Laboratory of Microbial Metabolism (Shanghai Jiaotong University), Ministry of Education, School of Life Science and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China
- School of the Environment, Nanjing University, Nanjing 210093, China
| | - Hong Yang
- Key Laboratory of Microbial Metabolism (Shanghai Jiaotong University), Ministry of Education, School of Life Science and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China
- School of the Environment, Nanjing University, Nanjing 210093, China
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