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Wu J, Zhan M, Yuan L, Zhu Y, Lin W, Luo J. Sealing solid agar in serum bottles for rapid isolation and long-term preservation of chemoautotrophic ammonia-oxidizing bacteria. WATER RESEARCH 2024; 260:121916. [PMID: 38875857 DOI: 10.1016/j.watres.2024.121916] [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: 02/27/2024] [Revised: 06/06/2024] [Accepted: 06/08/2024] [Indexed: 06/16/2024]
Abstract
Ammonia-oxidizing bacteria (AOB) are ubiquitous on the earth and have broad applications in bioremediation. However, the number of their species with standing in nomenclature and deposited in Microbial Culture Collections still remains low. Moreover, only a few novel species have been reported over the last decades. In this study, we sealed agar in serum bottles to develop a kind of solid agar plate with the oxygen concentration in the headspace maintained at low levels. By using these plates, eight AOB isolates including two novel species were obtained. When AOB cells were grown on the sealed solid agar plates, the time to form visible colonies was largely reduced and the maximum diameter of colonies reached 2 mm, which makes the process of AOB isolation rapid and efficient. Based on five AOB isolates, the headspace oxygen concentration had a significant influence on AOB growth either on solid plate or in liquid culture. Especially, when grown under 21 % O2, the number of colonies formed on solid agar plates was very low and sometimes no visible colony formed. Besides the application on AOB isolation, the sealed solid agar plate was also effective for the enumeration and preservation of AOB cells. When preserved under room temperature for more than ten months, the AOB colonies on the plate could still be recovered. This method provides a feasible way to isolate more novel AOB species from the environment and deposit more species in Microbial Culture Collections.
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Affiliation(s)
- Jiajie Wu
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Manjun Zhan
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Lingling Yuan
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Yueyue Zhu
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Weitie Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China; MOE Joint International Research Laboratory of Synthetic Biology and Medicine, South China University of Technology, Guangzhou 510006, PR China.
| | - Jianfei Luo
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China; MOE Joint International Research Laboratory of Synthetic Biology and Medicine, South China University of Technology, Guangzhou 510006, PR China.
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2
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Pedroza-Camacho LD, Ospina-Sánchez PA, Romero-Perdomo FA, Infante-González NG, Paredes-Céspedes DM, Quevedo-Hidalgo B, Gutiérrez-Romero V, Rivera-Hoyos CM, Pedroza-Rodríguez AM. Wastewater treatment from a science faculty during the COVID-19 pandemic by using ammonium-oxidising and heterotrophic bacteria. 3 Biotech 2024; 14:129. [PMID: 38601881 PMCID: PMC11003938 DOI: 10.1007/s13205-024-03961-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 02/22/2024] [Indexed: 04/12/2024] Open
Abstract
During and after the pandemic caused by the SARS-CoV-2 virus, the use of personal care products and disinfectants increased in universities worldwide. Among these, quaternary ammonium-based products stand out; these compounds and their intermediates caused substantial changes in the chemical composition of the wastewater produced by these institutions. For this reason, improvements and environmentally sustainable biological alternatives were introduced in the existing treatment systems so that these institutions could continue their research and teaching activities. For this reason, the objective of this study was to develop an improved culture medium to cultivate ammonium oxidising bacteria (AOB) to increase the biomass and use them in the treatment of wastewater produced in a faculty of sciences in Bogotá, D.C., Colombia. A Plackett Burman Experimental Design (PBED) and growth curves served for oligotrophic culture medium, and production conditions improved for the AOB. Finally, these bacteria were used with total heterotrophic bacteria (THB) for wastewater treatment in a pilot plant. Modification of base ammonium broth and culture conditions (6607 mg L-1 of (NH4)2SO4, 84 mg L-1 CaCO3, 40 mg L-1 MgSO4·7H2O, 40 mg L-1 CaCl2·2H2O and 200 mg L-1 KH2PO4, 10% (w/v) inoculum, no copper addition, pH 7.0 ± 0.2, 200 r.p.m., 30 days) favoured the growth of Nitrosomonas europea, Nitrosococcus oceani, and Nitrosospira multiformis with values of 8.23 ± 1.9, 7.56 ± 0.7 and 4.2 ± 0.4 Log10 CFU mL-1, respectively. NO2- production was 0.396 ± 0.0264, 0.247 ± 0.013 and 0.185 ± 0.003 mg L-1 for Nitrosomonas europea, Nitrosococcus oceani and Nitrosospira multiformis. After the 5-day wastewater treatment (WW) by co-inoculating the three studied bacteria in the wastewater (with their self-microorganisms), the concentrations of AOB and THB were 5.92 and 9.3 Log10 CFU mL-1, respectively. These values were related to the oxidative decrease of Chemical Oxygen Demand (COD), (39.5 mg L-1), Ammonium ion (NH4+), (6.5 mg L-1) Nitrite (NO2-), (2.0 mg L-1) and Nitrate (NO3-), (1.5 mg L-1), respectively in the five days of treatment. It was concluded, with the improvement of a culture medium and production conditions for three AOB through biotechnological strategies at the laboratory scale, being a promising alternative to bio-augment of the biomass of the studied bacteria under controlled conditions that allow the aerobic removal of COD and nitrogen cycle intermediates present in the studied wastewater. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-03961-4.
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Affiliation(s)
- Lucas D. Pedroza-Camacho
- Laboratorio de Microbiología Ambiental y Suelos, Unidad de Investigaciones Agropecuarias (UNIDIA), Grupo de Biotecnología Ambiental e Industrial (GBAI), Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Carrera 7ma No 43-82, Edifício 50 Lab. 106, P.O. Box 110-23, Bogotá, DC Colombia
| | - Paula A. Ospina-Sánchez
- Laboratorio de Microbiología Ambiental y Suelos, Unidad de Investigaciones Agropecuarias (UNIDIA), Grupo de Biotecnología Ambiental e Industrial (GBAI), Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Carrera 7ma No 43-82, Edifício 50 Lab. 106, P.O. Box 110-23, Bogotá, DC Colombia
| | - Felipe A. Romero-Perdomo
- Laboratorio de Microbiología Ambiental y Suelos, Unidad de Investigaciones Agropecuarias (UNIDIA), Grupo de Biotecnología Ambiental e Industrial (GBAI), Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Carrera 7ma No 43-82, Edifício 50 Lab. 106, P.O. Box 110-23, Bogotá, DC Colombia
| | - Nury G. Infante-González
- Laboratorio de Microbiología Ambiental y Suelos, Unidad de Investigaciones Agropecuarias (UNIDIA), Grupo de Biotecnología Ambiental e Industrial (GBAI), Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Carrera 7ma No 43-82, Edifício 50 Lab. 106, P.O. Box 110-23, Bogotá, DC Colombia
| | - Diana M. Paredes-Céspedes
- Laboratorio de Microbiología Ambiental y Suelos, Unidad de Investigaciones Agropecuarias (UNIDIA), Grupo de Biotecnología Ambiental e Industrial (GBAI), Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Carrera 7ma No 43-82, Edifício 50 Lab. 106, P.O. Box 110-23, Bogotá, DC Colombia
| | - Balkys Quevedo-Hidalgo
- Laboratorio de Biotecnología Aplicada, Grupo de Biotecnología Ambiental e Industrial (GBAI), Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, P.O. Box 110-23, Bogotá, DC Colombia
| | | | - Claudia M. Rivera-Hoyos
- Laboratorio de Biotecnología Molecular, Grupo de Biotecnología Ambiental e Industrial (GBAI), Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, P.O. Box 110-23, Bogotá, DC Colombia
| | - Aura M. Pedroza-Rodríguez
- Laboratorio de Microbiología Ambiental y Suelos, Unidad de Investigaciones Agropecuarias (UNIDIA), Grupo de Biotecnología Ambiental e Industrial (GBAI), Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Carrera 7ma No 43-82, Edifício 50 Lab. 106, P.O. Box 110-23, Bogotá, DC Colombia
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3
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Isshiki R, Fujitani H, Tsuneda S. Variation in growth rates between cultures hinders the cultivation of ammonia-oxidizing bacteria. FEMS Microbiol Lett 2024; 371:fnae013. [PMID: 38400564 DOI: 10.1093/femsle/fnae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/10/2024] [Accepted: 02/22/2024] [Indexed: 02/25/2024] Open
Abstract
Ammonia-oxidizing bacteria, key players in the nitrogen cycle, have been the focus of extensive research. Numerous novel species have been isolated and their growth dynamics were studied. Despite these efforts, controlling their growth to obtain diverse physiological findings remains a challenge. These bacteria often fail to grow, even under optimal conditions. This unpredictable growth pattern could be viewed as a survival strategy. Understanding this heterogeneous behavior could enhance our ability to culture these bacteria. In this study, the variation in the growth rate was quantified for the ammonia-oxidizing bacterium Nitrosomonas mobilis Ms1. Our findings revealed significant growth rate variation under low inoculum conditions. Interestingly, higher cell densities resulted in more stable cultures. A comparative analysis of three Nitrosomonas species showed a correlation between growth rate variation and culture failure. The greater the variation in growth rate, the higher the likelihood of culture failure.
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Affiliation(s)
- Rino Isshiki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-higashi, Toyohira-ku, Sapporo, Hokkaido 062-8517, Japan
- Comprehensive Research Organization, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hirotsugu Fujitani
- Department of Biological Sciences, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan
- Research Organization for Nano & Life Innovation, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Satoshi Tsuneda
- Comprehensive Research Organization, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
- Research Organization for Nano & Life Innovation, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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4
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Kikuchi S, Fujitani H, Ishii K, Isshiki R, Sekiguchi Y, Tsuneda S. Characterisation of bacteria representing a novel Nitrosomonas clade: Physiology, genomics and distribution of missing ammonia oxidizer. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:404-416. [PMID: 37078228 PMCID: PMC10472526 DOI: 10.1111/1758-2229.13158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/12/2023] [Indexed: 05/03/2023]
Abstract
Members of the genus Nitrosomonas are major ammonia oxidizers that catalyse the first step of nitrification in various ecosystems. To date, six subgenus-level clades have been identified. We have previously isolated novel ammonia oxidizers from an additional clade (unclassified cluster 1) of the genus Nitrosomonas. In this study, we report unique physiological and genomic properties of the strain PY1, compared with representative ammonia-oxidising bacteria (AOB). The apparent half-saturation constant for total ammonia nitrogen and maximum velocity of strain PY1 were 57.9 ± 4.8 μM NH3 + NH4 + and 18.5 ± 1.8 μmol N (mg protein)-1 h-1 , respectively. Phylogenetic analysis based on genomic information revealed that strain PY1 belongs to a novel clade of the Nitrosomonas genus. Although PY1 contained genes to withstand oxidative stress, cell growth of PY1 required catalase to scavenge hydrogen peroxide. Environmental distribution analysis revealed that the novel clade containing PY1-like sequences is predominant in oligotrophic freshwater. Taken together, the strain PY1 had a longer generation time, higher yield and required reactive oxygen species (ROS) scavengers to oxidize ammonia, compared with known AOB. These findings expand our knowledge of the ecophysiology and genomic diversity of ammonia-oxidising Nitrosomonas.
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Affiliation(s)
- Shuta Kikuchi
- Department of Life Science and Medical BioscienceWaseda UniversityTokyoJapan
| | - Hirotsugu Fujitani
- Department of Biological SciencesChuo UniversityTokyoJapan
- Research Organization for Nano & Life InnovationWaseda UniversityTokyoJapan
| | - Kento Ishii
- Department of Life Science and Medical BioscienceWaseda UniversityTokyoJapan
- Research Organization for Nano & Life InnovationWaseda UniversityTokyoJapan
| | - Rino Isshiki
- Department of Life Science and Medical BioscienceWaseda UniversityTokyoJapan
| | - Yuji Sekiguchi
- Biomedical Research InstituteNational Institute of Advanced Industrial Science and Technology (AIST)IbarakiJapan
| | - Satoshi Tsuneda
- Department of Life Science and Medical BioscienceWaseda UniversityTokyoJapan
- Research Organization for Nano & Life InnovationWaseda UniversityTokyoJapan
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5
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Barnum TP, Coates JD. Chlorine redox chemistry is widespread in microbiology. THE ISME JOURNAL 2023; 17:70-83. [PMID: 36202926 PMCID: PMC9751292 DOI: 10.1038/s41396-022-01317-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 11/07/2022]
Abstract
Chlorine is abundant in cells and biomolecules, yet the biology of chlorine oxidation and reduction is poorly understood. Some bacteria encode the enzyme chlorite dismutase (Cld), which detoxifies chlorite (ClO2-) by converting it to chloride (Cl-) and molecular oxygen (O2). Cld is highly specific for chlorite and aside from low hydrogen peroxide activity has no known alternative substrate. Here, we reasoned that because chlorite is an intermediate oxidation state of chlorine, Cld can be used as a biomarker for oxidized chlorine species. Cld was abundant in metagenomes from various terrestrial habitats. About 5% of bacterial and archaeal genera contain a microorganism encoding Cld in its genome, and within some genera Cld is highly conserved. Cld has been subjected to extensive horizontal gene transfer. Genes found to have a genetic association with Cld include known genes for responding to reactive chlorine species and uncharacterized genes for transporters, regulatory elements, and putative oxidoreductases that present targets for future research. Cld was repeatedly co-located in genomes with genes for enzymes that can inadvertently reduce perchlorate (ClO4-) or chlorate (ClO3-), indicating that in situ (per)chlorate reduction does not only occur through specialized anaerobic respiratory metabolisms. The presence of Cld in genomes of obligate aerobes without such enzymes suggested that chlorite, like hypochlorous acid (HOCl), might be formed by oxidative processes within natural habitats. In summary, the comparative genomics of Cld has provided an atlas for a deeper understanding of chlorine oxidation and reduction reactions that are an underrecognized feature of biology.
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Affiliation(s)
- Tyler P Barnum
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - John D Coates
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA.
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6
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Sapsirisuk S, Polburee P, Lorliam W, Limtong S. Discovery of Oleaginous Yeast from Mountain Forest Soil in Thailand. J Fungi (Basel) 2022; 8:1100. [PMID: 36294665 PMCID: PMC9605381 DOI: 10.3390/jof8101100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/14/2022] [Accepted: 10/15/2022] [Indexed: 11/04/2023] Open
Abstract
As an interesting alternative microbial platform for the sustainable synthesis of oleochemical building blocks and biofuels, oleaginous yeasts are increasing in both quantity and diversity. In this study, oleaginous yeast species from northern Thailand were discovered to add to the topology. A total of 127 yeast strains were isolated from 22 forest soil samples collected from mountainous areas. They were identified by an analysis of the D1/D2 domain of the large subunit rRNA (LSU rRNA) gene sequences to be 13 species. The most frequently isolated species were Lipomyces tetrasporus and Lipomyces starkeyi. Based on the cellular lipid content determination, 78 strains of ten yeast species, and two potential new yeast that which accumulated over 20% of dry biomass, were found to be oleaginous yeast strains. Among the oleaginous species detected, Papiliotrema terrestris and Papiliotrema flavescens have never been reported as oleaginous yeast before. In addition, none of the species in the genera Piskurozyma and Hannaella were found to be oleaginous yeast. L. tetrasporus SWU-NGP 2-5 accumulated the highest lipid content of 74.26% dry biomass, whereas Lipomyces mesembrius SWU-NGP 14-6 revealed the highest lipid quantity at 5.20 ± 0.03 g L-1. The fatty acid profiles of the selected oleaginous yeasts varied depending on the strain and suitability for biodiesel production.
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Affiliation(s)
- Sirawich Sapsirisuk
- Department of Microbiology, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand
| | - Pirapan Polburee
- Department of Microbiology, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand
| | - Wanlapa Lorliam
- Department of Microbiology, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand
| | - Savitree Limtong
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Biodiversity Center, Kasetsart University, Bangkok 10900, Thailand
- Academy of Science, The Royal Society of Thailand, Bangkok 10300, Thailand
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7
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Liu B, Lin W, Huang S, Sun Q, Yin H, Luo J. Removal of Mg 2+ inhibition benefited the growth and isolation of ammonia-oxidizing bacteria: An inspiration from bacterial interaction. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:155923. [PMID: 35577082 DOI: 10.1016/j.scitotenv.2022.155923] [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: 04/19/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
Ammonia-oxidizing bacteria (AOB) play an important role in the global nitrogen cycle and have broad applications in the nitrogen removal from wastewater. However, the AOB species are sensitive to environmental factors and usually form tight relationships with other microbes, making the AOB isolation and maintenance are difficult and time-consuming. In this study, the relationship that occurred between AOB and their bacterial partners was found to be able to improve the ammonia oxidation; during the co-cultivation, the magnesium ions (Mg2+) with removal rate as high as 36.7% was removed from culture medium by the concomitant bacterial species, which was regarded as the main reason for improving ammonia oxidation. During the pure cultivation of AOB isolate, when the concentration of Mg2+ reduced to low levels, the ammonia-oxidizing activity was more than 5 times and the amoA gene expression was more than 12 times higher than that grown in the initial culture medium. Based on a newly designed culture medium, the ammonia oxidation of AOB isolate grown in liquid culture was significantly promoted and the visible AOB colonies with much more number and larger diameter were observed to form on agar plates. With the addition of high concentration of calcium carbonate (CaCO3), AOB colonies could be easily and specifically identified by following the hydrolytic zones that formed around AOB colonies. Another AOB isolates were successively obtained from different samples and within a short time, suggesting the feasibility and effectivity of this culture medium and strategy on the AOB isolation from environments.
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Affiliation(s)
- Buchan Liu
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Weitie Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China; MOE Joint International Research Laboratory of Synthetic Biology and Medicine, South China University of Technology, Guangzhou 510006, PR China
| | - Shenxi Huang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Qiuyun Sun
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Hao Yin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Jianfei Luo
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China; MOE Joint International Research Laboratory of Synthetic Biology and Medicine, South China University of Technology, Guangzhou 510006, PR China.
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8
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Zulkifli M, Abu Hasan H, Sheikh Abdullah SR, Muhamad MH. A review of ammonia removal using a biofilm-based reactor and its challenges. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 315:115162. [PMID: 35561462 DOI: 10.1016/j.jenvman.2022.115162] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 04/16/2022] [Accepted: 04/22/2022] [Indexed: 06/15/2023]
Abstract
Extensive growth of industries leads to uncontrolled ammonia releases to environment. This can result in significant degradation of the aquatic ecology as well as significant health concerns for humans. Knowing the mechanism of ammonia elimination is the simplest approach to comprehending it. Ammonia has been commonly converted to less hazardous substances either in the form of nitrate or nitrogen gas. Ammonia has been converted into nitrite by ammonia-oxidizing bacteria and further reduced to nitrate by nitrite-oxidizing bacteria in aerobic conditions. Denitrification takes place in an anoxic phase and nitrate is converted into nitrogen gas. It is challenging to remove ammonia by employing technologies that do not incur particularly high costs. Thus, this review paper is focused on biofilm reactors that utilize the nitrification process. Many research publications and patents on biofilm wastewater treatment have been published. However, only a tiny percentage of these projects are for full-scale applications, and the majority of the work was completed within the last few decades. The physicochemical approaches such as ammonia adsorption, coagulation-flocculation, and membrane separation, as well as conventional biological treatments including activated sludge, microalgae, and bacteria biofilm, are briefly addressed in this review paper. The effectiveness of biofilm reactors in removing ammonia was compared, and the microbes that effectively remove ammonia were thoroughly discussed. Overall, biofilm reactors can remove up to 99.7% ammonia from streams with a concentration in range of 16-900 mg/L. As many challenges were identified for ammonia removal using biofilm at a commercial scale, this study offers future perspectives on how to address the most pressing biofilm issues. This review may also improve our understanding of biofilm technologies for the removal of ammonia as well as polishing unit in wastewater treatment plants for the water reuse and recycling, supporting the circular economy concept.
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Affiliation(s)
- Maryam Zulkifli
- Department of Chemical and Process Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor, Malaysia.
| | - Hassimi Abu Hasan
- Department of Chemical and Process Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor, Malaysia; Research Centre for Sustainable Process Technology (CESPRO), Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor, Malaysia.
| | - Siti Rozaimah Sheikh Abdullah
- Department of Chemical and Process Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor, Malaysia; Research Centre for Sustainable Process Technology (CESPRO), Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor, Malaysia.
| | - Mohd Hafizuddin Muhamad
- Department of Chemical and Process Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor, Malaysia.
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9
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A multi-step nitrifying microbial enrichment to remove ammonia and nitrite in brackish aquaculture systems. Biodegradation 2022; 33:373-388. [PMID: 35610494 DOI: 10.1007/s10532-022-09988-9] [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: 08/31/2021] [Accepted: 05/09/2022] [Indexed: 11/02/2022]
Abstract
One of the most important advancements in harnessing the biological nitrification in the field is enrichment solution of nitrifying microbial consortia. In the current study, we developed an improved multi-step enrichment to amplify a targeted microbial consortium from a sediment sample collected in tropical mangrove, Vietnam. The results showed that it took 122 culturing days with five unique continuous enrichment steps, the microbial consortium consumed total 5665 mgN L-1. Relative substrate removal rate increased rapidly from 0.114 mgN L-1 h-1 at the end of the first-step enrichment up to 3.58 mgN L-1 h-1 at the end of the fifth-step enrichment. High-throughput sequencing revealed that Nitrospirae, Proteobacteria and Bacteroidetes were the dominant taxa at the phylum level while Nitrospira, Marinobacter, Denitromonas and Nitrosomonas were the dominant taxa at the genus level in the enriched consortia. A pilot-scale experiment for shrimp cultivation of L. vannamei in 84 day-period proved the efficiency of Total ammonium nitrogen and nitrite removal in the consortium-activated treatment was much higher than the control.
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10
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Sakoula D, Smith GJ, Frank J, Mesman RJ, Kop LFM, Blom P, Jetten MSM, van Kessel MAHJ, Lücker S. Universal activity-based labeling method for ammonia- and alkane-oxidizing bacteria. THE ISME JOURNAL 2022; 16:958-971. [PMID: 34743174 PMCID: PMC8941013 DOI: 10.1038/s41396-021-01144-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 10/13/2021] [Accepted: 10/15/2021] [Indexed: 12/13/2022]
Abstract
The advance of metagenomics in combination with intricate cultivation approaches has facilitated the discovery of novel ammonia-, methane-, and other short-chain alkane-oxidizing microorganisms, indicating that our understanding of the microbial biodiversity within the biogeochemical nitrogen and carbon cycles still is incomplete. The in situ detection and phylogenetic identification of novel ammonia- and alkane-oxidizing bacteria remain challenging due to their naturally low abundances and difficulties in obtaining new isolates from complex samples. Here, we describe an activity-based protein profiling protocol allowing cultivation-independent unveiling of ammonia- and alkane-oxidizing bacteria. In this protocol, 1,7-octadiyne is used as a bifunctional enzyme probe that, in combination with a highly specific alkyne-azide cycloaddition reaction, enables the fluorescent or biotin labeling of cells harboring active ammonia and alkane monooxygenases. Biotinylation of these enzymes in combination with immunogold labeling revealed the subcellular localization of the tagged proteins, which corroborated expected enzyme targets in model strains. In addition, fluorescent labeling of cells harboring active ammonia or alkane monooxygenases provided a direct link of these functional lifestyles to phylogenetic identification when combined with fluorescence in situ hybridization. Furthermore, we show that this activity-based labeling protocol can be successfully coupled with fluorescence-activated cell sorting for the enrichment of nitrifiers and alkane-oxidizing bacteria from complex environmental samples, enabling the recovery of high-quality metagenome-assembled genomes. In conclusion, this study demonstrates a novel, functional tagging technique for the reliable detection, identification, and enrichment of ammonia- and alkane-oxidizing bacteria present in complex microbial communities.
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Affiliation(s)
- Dimitra Sakoula
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands.
- Division of Microbial Ecology, Center for Microbiology and Environmental Systems Science, University of Vienna, Althanstraße 14, 1090, Vienna, Austria.
| | - Garrett J Smith
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Jeroen Frank
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
- Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Rob J Mesman
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Linnea F M Kop
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Pieter Blom
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Mike S M Jetten
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
- Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Maartje A H J van Kessel
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Sebastian Lücker
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands.
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11
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Hossain S, Chow CWK, Cook D, Sawade E, Hewa GA. Review of Nitrification Monitoring and Control Strategies in Drinking Water System. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19074003. [PMID: 35409686 PMCID: PMC8997939 DOI: 10.3390/ijerph19074003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/17/2022] [Accepted: 03/23/2022] [Indexed: 12/29/2022]
Abstract
Nitrification is a major challenge in chloraminated drinking water systems, resulting in undesirable loss of disinfectant residual. Consequently, heterotrophic bacteria growth is increased, which adversely affects the water quality, causing taste, odour, and health issues. Regular monitoring of various water quality parameters at susceptible areas of the water distribution system (WDS) helps to detect nitrification at an earlier stage and allows sufficient time to take corrective actions to control it. Strategies to monitor nitrification in a WDS require conducting various microbiological tests or assessing surrogate parameters that are affected by microbiological activities. Additionally, microbial decay factor (Fm) is used by water utilities to monitor the status of nitrification. In contrast, approaches to manage nitrification in a WDS include controlling various factors that affect monochloramine decay rate and ammonium substrate availability, and that can inhibit nitrification. However, some of these control strategies may increase the regulated disinfection-by-products level, which may be a potential health concern. In this paper, various strategies to monitor and control nitrification in a WDS are critically examined. The key findings are: (i) the applicability of some methods require further validation using real WDS, as the original studies were conducted on laboratory or pilot systems; (ii) there is no linkage/formula found to relate the surrogate parameters to the concentration of nitrifying bacteria, which possibly improve nitrification monitoring performance; (iii) improved methods/monitoring tools are required to detect nitrification at an earlier stage; (iv) further studies are required to understand the effect of soluble microbial products on the change of surrogate parameters. Based on the current review, we recommend that the successful outcome using many of these methods is often site-specific, hence, water utilities should decide based on their regular experiences when considering economic and sustainability aspects.
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Affiliation(s)
- Sharif Hossain
- Scarce Resources and Circular Economy (ScaRCE), UniSA STEM, University of South Australia, Mawson Lakes, SA 5095, Australia; (C.W.K.C.); (G.A.H.)
- Correspondence:
| | - Christopher W. K. Chow
- Scarce Resources and Circular Economy (ScaRCE), UniSA STEM, University of South Australia, Mawson Lakes, SA 5095, Australia; (C.W.K.C.); (G.A.H.)
- Future Industries Institute, University of South Australia, Mawson Lakes, SA 5095, Australia
| | - David Cook
- South Australian Water Corporation, Adelaide, SA 5000, Australia; (D.C.); (E.S.)
| | - Emma Sawade
- South Australian Water Corporation, Adelaide, SA 5000, Australia; (D.C.); (E.S.)
| | - Guna A. Hewa
- Scarce Resources and Circular Economy (ScaRCE), UniSA STEM, University of South Australia, Mawson Lakes, SA 5095, Australia; (C.W.K.C.); (G.A.H.)
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12
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Ayiti OE, Babalola OO. Sustainable Intensification of Maize in the Industrial Revolution: Potential of Nitrifying Bacteria and Archaea. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.827477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Sustainable intensification is a means that proffer a solution to the increasing demand for food without degrading agricultural land. Maize is one of the most important crops in the industrial revolution era, there is a need for its sustainable intensification. This review discusses the role of maize in the industrial revolution, progress toward sustainable production, and the potential of nitrifying bacteria and archaea to achieve sustainable intensification. The era of the industrial revolution (IR) uses biotechnology which has proven to be the most environmentally friendly choice to improve crop yield and nutrients. Scientific research and the global economy have benefited from maize and maize products which are vast. Research on plant growth-promoting microorganisms is on the increase. One of the ways they carry out their function is by assisting in the cycling of geochemical, thus making nutrients available for plant growth. Nitrifying bacteria and archaea are the engineers of the nitrification process that produce nitrogen in forms accessible to plants. They have been identified in the rhizosphere of many crops, including maize, and have been used as biofertilizers. This study's findings could help in the development of microbial inoculum, which could be used to replace synthetic fertilizer and achieve sustainable intensification of maize production during the industrial revolution.
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13
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Lin YP, Ansari A, Wunderlich RF, Lur HS, Ngoc-Dan Cao T, Mukhtar H. Assessing the influence of environmental niche segregation in ammonia oxidizers on N 2O fluxes from soil and sediments. CHEMOSPHERE 2022; 289:133049. [PMID: 34838835 DOI: 10.1016/j.chemosphere.2021.133049] [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: 07/21/2021] [Revised: 10/18/2021] [Accepted: 11/22/2021] [Indexed: 06/13/2023]
Abstract
Understanding the environmental niche segregation of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and its impact on their relative contributions to nitrification and nitrous oxide (N2O) production is essential for predicting N2O dynamics within an ecosystem. Here, we used ammonia oxidizer-specific inhibitors to measure the differential contributions of AOA and AOB to potential ammonia oxidization (PAO) and N2O fluxes over pH (4.0-9.0) and temperature (10-45 °C) gradients in five soils and three wetland sediments. AOA and AOB activities were differentiated using PTIO (2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide), 1-octyne, and acetylene. We used square root growth (SQRT) and macromolecular rate theory (MMRT) models to estimate cardinal temperatures and thermodynamic characteristics for AOA- and AOB-dominated PAO and N2O fluxes. We found that AOA and AOB occupied different niches for PAO, and soil temperature was the major determinant of niche specialization. SQRT and MMRT models predicted a higher optimum temperature for AOA-dominated PAO and N2O fluxes compared with those of AOB. Additionally, PAO was dominated by AOA in acidic conditions, whereas both AOA- and AOB-dominated N2O fluxes decreased with increasing pH. Consequently, net N2O fluxes (AOA and AOB) under acidic conditions were approximately one to three-fold higher than those observed in alkaline conditions. Moreover, structural equation and linear regression modeling confirmed a significant positive correlation (R2 = 0.45, p < 0.01) between PAO and N2O fluxes. Collectively, these results show the influence of ammonia oxidizer responses to temperature and pH on nitrification-driven N2O fluxes, highlighting the potential for mitigating N2O emissions via pH manipulation.
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Affiliation(s)
- Yu-Pin Lin
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taiwan
| | - Andrianto Ansari
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taiwan
| | | | - Huu-Sheng Lur
- Department of Agronomy, National Taiwan University, Taiwan
| | - Thanh Ngoc-Dan Cao
- Graduate Institute of Environmental Engineering, National Taiwan University, Taiwan
| | - Hussnain Mukhtar
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taiwan.
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14
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Wu J, Kong Z, Luo Z, Qin Y, Rong C, Wang T, Hanaoka T, Sakemi S, Ito M, Kobayashi S, Kobayashi M, Xu KQ, Kobayashi T, Kubota K, Li YY. A successful start-up of an anaerobic membrane bioreactor (AnMBR) coupled mainstream partial nitritation-anammox (PN/A) system: A pilot-scale study on in-situ NOB elimination, AnAOB growth kinetics, and mainstream treatment performance. WATER RESEARCH 2021; 207:117783. [PMID: 34768103 DOI: 10.1016/j.watres.2021.117783] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 10/04/2021] [Accepted: 10/14/2021] [Indexed: 05/06/2023]
Abstract
In this pilot-scale study, an innovative mainstream treatment process that couples the anaerobic membrane reactor (AnMBR) with a one-stage PN/A system was proposed for advancing the concept of carbon neutrality in the municipal wastewater treatment plant. This work demonstrates the start-up procedure of a pilot-scale one-stage PN/A system for mainstream treatment. The 255-day start-up of the one-stage PN/A system involved the cultivation of ammonium-oxidizing bacteria (AOB) from the activated sludge, suppression of nitrite-oxidizing bacteria (NOB), investigation of in-situ growth kinetics of anammox bacteria (AnAOB), and the 50-day operation of the pilot-scale AnMBR-PN/A process for natural mainstream treatment. It is verified in the pilot-scale system for the first time that the in-situ free ammonia (FA) and free nitrous acid (FNA) exposure could effectively eliminate the Nitrospira (the NOB genus) while retaining the Nitosonomas (the AOB genus) community in the suspended sludge. NOB community rebounding was not detected even at the mainstream conditions with low nitrogen concentrations (Influent ammonium concentration=38±6 mg-NH4+-N/L) by intermittent aeration to control the system dissolved oxygen (DO) below 0.5 mg/L. The results of the mainstream treatment showed that the average effluent total nitrogen (TN) in the coupled process was generally lower than 10 mg-N/L, which meets the discharge limits of most prefectures in Japan. The investigated results of the in-situ anammox bacteria (AnAOB) growth kinetics suggested that the promoted start-up strategy of taking advantage of the warm months with higher mainstream temperature to achieve the rapid in-situ growth of the AnAOB is applicable in the investigated regions. From the perspective of the removal performance of the TN and organic substance, the AnMBR-PN/A process has great potential as the layouts of the carbon-neutral mainstream wastewater treatment plants.
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Affiliation(s)
- Jiang Wu
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi 980-8579, Japan; Center for Material Cycles and Waste Management Research, National Institute for Environmental Studies, Tsukuba 305-8506, Japan.
| | - Zhe Kong
- Research Center for Environmental Bio-technology, School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Zibin Luo
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi 980-8579, Japan
| | - Yu Qin
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi 980-8579, Japan
| | - Chao Rong
- Graduate School of Environmental Studies, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi 980-8579, Japan
| | - Tianjie Wang
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi 980-8579, Japan
| | - Taira Hanaoka
- Solution Engineering Group, Environmental Engineering Department, Mitsubishi Kakoki Kaisha, Ltd., 1-2 Miyamae-Cho, Kawasaki-Ku, Kawasaki, Kanagawa 210-0012, Japan
| | - Shinichi Sakemi
- Solution Engineering Group, Environmental Engineering Department, Mitsubishi Kakoki Kaisha, Ltd., 1-2 Miyamae-Cho, Kawasaki-Ku, Kawasaki, Kanagawa 210-0012, Japan
| | - Masami Ito
- Global Water Recycling and Reuse System Association, Japan, 5-1, Soto-Kanda 1-15 Chome, Chiyoda-Ku, Tokyo 101-0021, Japan
| | - Shigeki Kobayashi
- Global Water Recycling and Reuse System Association, Japan, 5-1, Soto-Kanda 1-15 Chome, Chiyoda-Ku, Tokyo 101-0021, Japan
| | - Masumi Kobayashi
- Separation and Aqua Chemicals Department, Mitsubishi Chemical Corporation, Gate City Osaki East Tower, 11-2 Osaki 1-chome, Shinagawa-Ku, Tokyo 141-0032, Japan
| | - Kai-Qin Xu
- Center for Material Cycles and Waste Management Research, National Institute for Environmental Studies, Tsukuba 305-8506, Japan
| | - Takuro Kobayashi
- Center for Material Cycles and Waste Management Research, National Institute for Environmental Studies, Tsukuba 305-8506, Japan
| | - Kengo Kubota
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi 980-8579, Japan; Graduate School of Environmental Studies, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi 980-8579, Japan
| | - Yu-You Li
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi 980-8579, Japan; Graduate School of Environmental Studies, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi 980-8579, Japan.
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15
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Lin YP, Ansari A, Cheng LC, Lin CM, Wunderlich RF, Cao TND, Mukhtar H. Measuring Responses of Dicyandiamide-, 3,4-Dimethylpyrazole Phosphate-, and Allylthiourea-Induced Nitrification Inhibition to Soil Abiotic and Biotic Factors. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:7130. [PMID: 34281066 PMCID: PMC8297033 DOI: 10.3390/ijerph18137130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/25/2021] [Accepted: 06/28/2021] [Indexed: 11/16/2022]
Abstract
Nitrification inhibitors (NIs) such as dicyandiamide (DCD), 3,4-dimethylpyrazole phosphate (DMPP), and allylthiourea (AT) are commonly used to suppress ammonia oxidization at different time scales varying from a few hours to several months. Although the responses of NIs to edaphic and temperature conditions have been studied, the influence of the aforementioned factors on their inhibitory effect remains unknown. In this study, laboratory-scale experiments were conducted to assess the short-term (24 h) influence of eight abiotic and biotic factors on the inhibitory effects of DCD, DMPP, and AT across six cropped and non-cropped soils at two temperature conditions with three covariates of soil texture. Simultaneously, the dominant contributions of ammonia-oxidizing archaea (AOA) and bacteria (AOB) to potential ammonia oxidization (PAO) were distinguished using the specific inhibitor 2 phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO). Our results revealed that AT demonstrated a considerably greater inhibitory effect (up to 94.9% for an application rate of 75 mg of NI/kg of dry soil) than DCD and DMPP. The inhibitory effect of AT was considerably affected by the relative proportions of silt, sand, and clay in the soil and total PAO. In contrast to previous studies, the inhibitory effects of all three NIs remained largely unaffected by the landcover type and temperature conditions for the incubation period of 24 h. Furthermore, the efficacy of all three tested NIs was not affected by the differential contributions of AOA and AOB to PAO. Collectively, our results suggested a limited influence of temperature on the inhibitory effects of all three NIs but a moderate dependence of AT on the soil texture and PAO. Our findings can enhance the estimation of the inhibitory effect in soil, and pure cultures targeting the AOA and AOB supported ammonia oxidization and, hence, nitrogen dynamics under NI applications.
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Affiliation(s)
- Yu-Pin Lin
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei 10617, Taiwan; (Y.-P.L.); (A.A.); (L.-C.C.); (C.-M.L.); (R.-F.W.)
| | - Andrianto Ansari
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei 10617, Taiwan; (Y.-P.L.); (A.A.); (L.-C.C.); (C.-M.L.); (R.-F.W.)
- Department of Agronomy, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Lien-Chieh Cheng
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei 10617, Taiwan; (Y.-P.L.); (A.A.); (L.-C.C.); (C.-M.L.); (R.-F.W.)
| | - Chiao-Ming Lin
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei 10617, Taiwan; (Y.-P.L.); (A.A.); (L.-C.C.); (C.-M.L.); (R.-F.W.)
| | - Rainer-Ferdinand Wunderlich
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei 10617, Taiwan; (Y.-P.L.); (A.A.); (L.-C.C.); (C.-M.L.); (R.-F.W.)
| | - Thanh-Ngoc-Dan Cao
- Graduate Institute of Environmental Engineering, National Taiwan University, Taipei 10617, Taiwan;
| | - Hussnain Mukhtar
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei 10617, Taiwan; (Y.-P.L.); (A.A.); (L.-C.C.); (C.-M.L.); (R.-F.W.)
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16
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Xing XY, Tang YF, Xu HF, Qin HL, Liu Y, Zhang WZ, Chen AL, Zhu BL. Warming Shapes nirS- and nosZ-Type Denitrifier Communities and Stimulates N 2O Emission in Acidic Paddy Soil. Appl Environ Microbiol 2021; 87:e0296520. [PMID: 33837014 PMCID: PMC8174758 DOI: 10.1128/aem.02965-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/13/2021] [Indexed: 11/20/2022] Open
Abstract
Warming strongly stimulates soil nitrous oxide (N2O) emission, contributing to the global warming trend. Submerged paddy soils exhibit huge N2O emission potential; however, the N2O emission pathway and underlying mechanisms for warming are not clearly understood. We conducted an incubation experiment using 15N to investigate the dynamics of N2O emission at controlled temperatures (5, 15, 25, and 35°C) in 125% water-filled pore space. The community structures of nitrifiers and denitrifiers were determined via high-throughput sequencing of functional genes. Our results showed that elevated temperature sharply enhanced soil N2O emission from submerged paddy soil. Denitrification was the main contributor, accounting for more than 90% of total N2O emission at all treatment temperatures. N2O flux was coordinatively regulated by nirK-, nirS-, and nosZ-containing denitrifiers but not ammonia-oxidizing archaea or ammonia-oxidizing bacteria. The nirS-containing denitrifiers were more sensitive to temperature shifts, especially at a lower temperature range (5 to 25°C), and showed a stronger correlation with N2O flux than that of nirK-containing denitrifiers. In contrast, nosZ-containing denitrifiers exhibited substantial variation at higher temperatures (15 to 35°C), thereby playing an important role in N2O consumption. Certain taxa of nirS- and nosZ-containing denitrifiers regulated N2O flux, including nirS-containing denitrifiers affiliated with Rhodanobacter and Cupriavidus as well as nosZ-containing denitrifiers affiliated with Azoarcus and Azospirillum. Together, these findings suggest that elevated temperature can significantly increase N2O emission from denitrification in submerged paddy soils by shifting the overall community structures and enriching some indigenous taxa of nirS- and nosZ-containing denitrifiers. IMPORTANCE The interdependence between global warming and greenhouse gas N2O has always been the hot spot. However, information on factors contributing to N2O and temperature-dependent community structure changes is scarce. This study demonstrated high-temperature-induced N2O emission from submerged paddy soils, mainly via stimulating denitrification. Further, we speculate that key functional denitrifiers drive N2O emission. This study showed that denitrifiers were more sensitive to temperature rise than nitrifiers, and the temperature sensitivity differed among denitrifier communities. N2O-consuming denitrifiers (nosZ-containing denitrifiers) were more sensitive at a higher temperature range than N2O-producing denitrifiers (nirS-containing denitrifiers). This study's findings help predict N2O fluxes under different degrees of warming and develop strategies to mitigate N2O emissions from paddy fields based on microbial community regulation.
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Affiliation(s)
- Xiao-Yi Xing
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Taoyuan Agroecosystem Research Station, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- Urban Construction College, Shaoyang University, Shaoyang, China
| | - Ya-Fang Tang
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, College of Life Science and Technology, Hubei Engineering University, Xiaogan, China
| | - Hui-Fang Xu
- School of Agricultural Sciences, Jiangxi Agricultural University, Nanchang, China
| | - Hong-Ling Qin
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Taoyuan Agroecosystem Research Station, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Yi Liu
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Taoyuan Agroecosystem Research Station, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Wen-Zhao Zhang
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Taoyuan Agroecosystem Research Station, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - An-Lei Chen
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Taoyuan Agroecosystem Research Station, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Bao-Li Zhu
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Taoyuan Agroecosystem Research Station, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
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17
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Sakoula D, Koch H, Frank J, Jetten MSM, van Kessel MAHJ, Lücker S. Enrichment and physiological characterization of a novel comammox Nitrospira indicates ammonium inhibition of complete nitrification. THE ISME JOURNAL 2021; 15:1010-1024. [PMID: 33188298 PMCID: PMC8115096 DOI: 10.1038/s41396-020-00827-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 10/27/2020] [Accepted: 10/30/2020] [Indexed: 01/29/2023]
Abstract
The recent discovery of bacteria within the genus Nitrospira capable of complete ammonia oxidation (comammox) demonstrated that the sequential oxidation of ammonia to nitrate via nitrite can also be performed within a single bacterial cell. Although comammox Nitrospira exhibit a wide distribution in natural and engineered ecosystems, information on their physiological properties is scarce due to the limited number of cultured representatives. Additionally, most available genomic information is derived from metagenomic sequencing and high-quality genomes of Nitrospira in general are limited. In this study, we obtained a high (90%) enrichment of a novel comammox species, tentatively named "Candidatus Nitrospira kreftii", and performed a detailed genomic and physiological characterization. The complete genome of "Ca. N. kreftii" allowed reconstruction of its basic metabolic traits. Similar to Nitrospira inopinata, the enrichment culture exhibited a very high ammonia affinity (Km(app)_NH3 ≈ 0.040 ± 0.01 µM), but a higher nitrite affinity (Km(app)_NO2- = 12.5 ± 4.0 µM), indicating an adaptation to highly oligotrophic environments. Furthermore, we observed partial inhibition of ammonia oxidation at ammonium concentrations as low as 25 µM. This inhibition of "Ca. N. kreftii" indicates that differences in ammonium tolerance rather than affinity could potentially be a niche determining factor for different comammox Nitrospira.
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Affiliation(s)
- Dimitra Sakoula
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands ,grid.10420.370000 0001 2286 1424Present Address: Division of Microbial Ecology, Center for Microbiology and Environmental Systems Science, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Hanna Koch
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Jeroen Frank
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands ,grid.5590.90000000122931605Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Mike S. M. Jetten
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands ,grid.5590.90000000122931605Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Maartje A. H. J. van Kessel
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Sebastian Lücker
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
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18
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Nardi P, Laanbroek HJ, Nicol GW, Renella G, Cardinale M, Pietramellara G, Weckwerth W, Trinchera A, Ghatak A, Nannipieri P. Biological nitrification inhibition in the rhizosphere: determining interactions and impact on microbially mediated processes and potential applications. FEMS Microbiol Rev 2021; 44:874-908. [PMID: 32785584 DOI: 10.1093/femsre/fuaa037] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 08/10/2020] [Indexed: 12/11/2022] Open
Abstract
Nitrification is the microbial conversion of reduced forms of nitrogen (N) to nitrate (NO3-), and in fertilized soils it can lead to substantial N losses via NO3- leaching or nitrous oxide (N2O) production. To limit such problems, synthetic nitrification inhibitors have been applied but their performance differs between soils. In recent years, there has been an increasing interest in the occurrence of biological nitrification inhibition (BNI), a natural phenomenon according to which certain plants can inhibit nitrification through the release of active compounds in root exudates. Here, we synthesize the current state of research but also unravel knowledge gaps in the field. The nitrification process is discussed considering recent discoveries in genomics, biochemistry and ecology of nitrifiers. Secondly, we focus on the 'where' and 'how' of BNI. The N transformations and their interconnections as they occur in, and are affected by, the rhizosphere, are also discussed. The NH4+ and NO3- retention pathways alternative to BNI are reviewed as well. We also provide hypotheses on how plant compounds with putative BNI ability can reach their targets inside the cell and inhibit ammonia oxidation. Finally, we discuss a set of techniques that can be successfully applied to solve unresearched questions in BNI studies.
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Affiliation(s)
- Pierfrancesco Nardi
- Consiglio per la ricerca e l'analisi dell'economia agraria - Research Centre for Agriculture and Environment (CREA-AA), Via della Navicella 2-4, Rome 00184, Italy
| | - Hendrikus J Laanbroek
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands; Ecology and Biodiversity Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Graeme W Nicol
- Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Ecully, 69134, France
| | - Giancarlo Renella
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Viale dell'Università 16, 35020 Legnaro, Italy
| | - Massimiliano Cardinale
- Department of Biological and Environmental Sciences and Technologies - DiSTeBA, University of Salento, Centro Ecotekne - via Provinciale Lecce-Monteroni, I-73100, Lecce, Italy
| | - Giacomo Pietramellara
- Department of Agriculture, Food, Environment and Forestry, University of Firenze, P.le delle Cascine 28, Firenze 50144, Italy
| | - Wolfram Weckwerth
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria; Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
| | - Alessandra Trinchera
- Consiglio per la ricerca e l'analisi dell'economia agraria - Research Centre for Agriculture and Environment (CREA-AA), Via della Navicella 2-4, Rome 00184, Italy
| | - Arindam Ghatak
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
| | - Paolo Nannipieri
- Department of Agriculture, Food, Environment and Forestry, University of Firenze, P.le delle Cascine 28, Firenze 50144, Italy
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19
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Mueller AJ, Jung MY, Strachan CR, Herbold CW, Kirkegaard RH, Wagner M, Daims H. Genomic and kinetic analysis of novel Nitrospinae enriched by cell sorting. THE ISME JOURNAL 2021; 15:732-745. [PMID: 33067588 PMCID: PMC8026999 DOI: 10.1038/s41396-020-00809-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 09/23/2020] [Accepted: 10/05/2020] [Indexed: 12/18/2022]
Abstract
Chemolithoautotrophic nitrite-oxidizing bacteria (NOB) are key players in global nitrogen and carbon cycling. Members of the phylum Nitrospinae are the most abundant, known NOB in the oceans. To date, only two closely affiliated Nitrospinae species have been isolated, which are only distantly related to the environmentally abundant uncultured Nitrospinae clades. Here, we applied live cell sorting, activity screening, and subcultivation on marine nitrite-oxidizing enrichments to obtain novel marine Nitrospinae. Two binary cultures were obtained, each containing one Nitrospinae strain and one alphaproteobacterial heterotroph. The Nitrospinae strains represent two new genera, and one strain is more closely related to environmentally abundant Nitrospinae than previously cultured NOB. With an apparent half-saturation constant of 8.7 ± 2.5 µM, this strain has the highest affinity for nitrite among characterized marine NOB, while the other strain (16.2 ± 1.6 µM) and Nitrospina gracilis (20.1 ± 2.1 µM) displayed slightly lower nitrite affinities. The new strains and N. gracilis share core metabolic pathways for nitrite oxidation and CO2 fixation but differ remarkably in their genomic repertoires of terminal oxidases, use of organic N sources, alternative energy metabolisms, osmotic stress and phage defense. The new strains, tentatively named "Candidatus Nitrohelix vancouverensis" and "Candidatus Nitronauta litoralis", shed light on the niche differentiation and potential ecological roles of Nitrospinae.
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Affiliation(s)
- Anna J Mueller
- University of Vienna, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, Althanstrasse 14, 1090, Vienna, Austria
| | - Man-Young Jung
- University of Vienna, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, Althanstrasse 14, 1090, Vienna, Austria
- Department of Science Education, Jeju National University, 102 Jejudaehak-ro, Jeju, 63243, Republic of Korea
| | - Cameron R Strachan
- Department for Farm Animals and Public Health, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210, Vienna, Austria
- FFoQSI GmbH, Technopark 1C, 3430, Tulln, Austria
| | - Craig W Herbold
- University of Vienna, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, Althanstrasse 14, 1090, Vienna, Austria
| | - Rasmus H Kirkegaard
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Michael Wagner
- University of Vienna, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, Althanstrasse 14, 1090, Vienna, Austria
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
- University of Vienna, The Comammox Research Platform, Vienna, Austria
| | - Holger Daims
- University of Vienna, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, Althanstrasse 14, 1090, Vienna, Austria.
- University of Vienna, The Comammox Research Platform, Vienna, Austria.
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20
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Liang Q, Yamashita T, Koike K, Matsuura N, Honda R, Hara-Yamamura H, Yokoyama H, Yamamoto-Ikemoto R. A bioelectrochemical-system-based trickling filter reactor for wastewater treatment. BIORESOURCE TECHNOLOGY 2020; 315:123798. [PMID: 32707501 DOI: 10.1016/j.biortech.2020.123798] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/02/2020] [Accepted: 07/04/2020] [Indexed: 05/10/2023]
Abstract
A bioelectrochemical system (BES)-based trickling filter (TF) reactor was utilized for wastewater treatment. At a COD load of 1.0 g-COD/L/day, effluent chemical oxygen demand (COD) and total nitrogen (TN) were 115 and 108 mg/L, respectively, which were allowed for discharge. Superior performance was achieved at 0.5 g-COD/L/day with a circulation rate of 8 L/h, and both COD and TN removal were >98%. Coulombic efficiency was 11% at 1.0 g-COD/L/day and at most 16% at 0.5 g-COD/L/day. COD removal decreased when the BES was removed, demonstrating that BES improved COD removal capability. In anodic biofilms, exoelectrogenic, facultative, nitrifying, and sulfate-reducing bacteria could coexist. Geobacter for current generation grew inside the biofilm, and bacteria in the middle and outer layers consumed oxygen and degraded organic matter and nitrogen. This BES-based TF reactor may be used for efficient and cost-effective COD and TN removal at high loads without excess sludge removal.
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Affiliation(s)
- Qiaochu Liang
- Graduate School of Natural Science & Technology, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Takahiro Yamashita
- Division of Animal Environment and Waste Management Research, Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization (NARO), 2 Ikenodai, Tsukuba 305-0901, Japan
| | - Kazuyoshi Koike
- Graduate School of Natural Science & Technology, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Norihisa Matsuura
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Ryo Honda
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Hiroe Hara-Yamamura
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Hiroshi Yokoyama
- Division of Animal Environment and Waste Management Research, Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization (NARO), 2 Ikenodai, Tsukuba 305-0901, Japan
| | - Ryoko Yamamoto-Ikemoto
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan.
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21
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Lukumbuzya M, Kristensen JM, Kitzinger K, Pommerening-Röser A, Nielsen PH, Wagner M, Daims H, Pjevac P. A refined set of rRNA-targeted oligonucleotide probes for in situ detection and quantification of ammonia-oxidizing bacteria. WATER RESEARCH 2020; 186:116372. [PMID: 32916620 DOI: 10.1016/j.watres.2020.116372] [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: 05/26/2020] [Revised: 08/12/2020] [Accepted: 08/31/2020] [Indexed: 06/11/2023]
Abstract
Ammonia-oxidizing bacteria (AOB) of the betaproteobacterial genera Nitrosomonas and Nitrosospira are key nitrifying microorganisms in many natural and engineered ecosystems. Since many AOB remain uncultured, fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes has been one of the most widely used approaches to study the community composition, abundance, and other features of AOB directly in environmental samples. However, the established and widely used AOB-specific 16S rRNA-targeted FISH probes were designed up to two decades ago, based on much smaller rRNA gene sequence datasets than available today. Several of these probes cover their target AOB lineages incompletely and suffer from a weak target specificity, which causes cross-hybridization of probes that should detect different AOB lineages. Here, a set of new highly specific 16S rRNA-targeted oligonucleotide probes was developed and experimentally evaluated that complements the existing probes and enables the specific detection and differentiation of the known, major phylogenetic clusters of betaproteobacterial AOB. The new probes were successfully applied to visualize and quantify AOB in activated sludge and biofilm samples from seven pilot- and full-scale wastewater treatment systems. Based on its improved target group coverage and specificity, the refined probe set will facilitate future in situ analyses of AOB.
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Affiliation(s)
- Michael Lukumbuzya
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Jannie Munk Kristensen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Katharina Kitzinger
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria; Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Andreas Pommerening-Röser
- University of Hamburg, Institute of Plant Science and Microbiology, Microbiology and Biotechnology, Hamburg, Germany
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Michael Wagner
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria; Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark; Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria; University of Vienna, The Comammox Research Platform, Vienna, Austria
| | - Holger Daims
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria; University of Vienna, The Comammox Research Platform, Vienna, Austria.
| | - Petra Pjevac
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria; Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
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22
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Fujitani H, Momiuchi K, Ishii K, Nomachi M, Kikuchi S, Ushiki N, Sekiguchi Y, Tsuneda S. Genomic and Physiological Characteristics of a Novel Nitrite-Oxidizing Nitrospira Strain Isolated From a Drinking Water Treatment Plant. Front Microbiol 2020; 11:545190. [PMID: 33042056 PMCID: PMC7522533 DOI: 10.3389/fmicb.2020.545190] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 08/24/2020] [Indexed: 11/13/2022] Open
Abstract
Nitrite-oxidizing bacteria (NOB) catalyze the second step of nitrification, which is an important process of the biogeochemical nitrogen cycle and is exploited extensively as a biological nitrogen removal process. Members of the genus Nitrospira are often identified as the dominant NOB in a diverse range of natural and artificial environments. Additionally, a number of studies examining the distribution, abundance, and characterization of complete ammonia oxidation (comammox) Nitrospira support the ecological importance of the genus Nitrospira. However, niche differentiation between nitrite-oxidizing Nitrospira and comammox Nitrospira remains unknown due to a lack of pure cultures. In this study, we report the isolation, physiology, and genome of a novel nitrite-oxidizing Nitrospira strain isolated from a fixed-bed column at a drinking water treatment plant. Continuous feeding of ammonia led to the enrichment of Nitrospira-like cells, as well as members of ammonia-oxidizing genus Nitrosomonas. Subsequently, a microcolony sorting technique was used to isolate a novel nitrite-oxidizing Nitrospira strain. Sequences of strains showing the growth of microcolonies in microtiter plates were checked. Consequently, the most abundant operational taxonomic unit (OTU) exhibited high sequence similarity with Nitrospira japonica (98%) at the 16S rRNA gene level. The two other Nitrospira OTUs shared over 99% sequence similarities with N. japonica and Nitrospira sp. strain GC86. Only one strain identified as Nitrospira was successfully subcultivated and designated as Nitrospira sp. strain KM1 with high sequence similarity with N. japonica (98%). The half saturation constant for nitrite and the maximum nitrite oxidation rate of strain KM1 were orders of magnitude lower than the published data of other known Nitrospira strains; moreover, strain KM1 was more sensitive to free ammonia compared with previously isolated Nitrospira strains. Therefore, the new Nitrospira strain appears to be better adapted to oligotrophic environments compared with other known non-marine nitrite oxidizers. The complete genome of strain KM1 was 4,509,223 bp in length and contained 4,318 predicted coding sequences. Average nucleotide identities between strain KM1 and known cultured Nitrospira genome sequences are 76.7-78.4%, suggesting at least species-level novelty of the strain in the Nitrospira lineage II. These findings broaden knowledge of the ecophysiological diversity of nitrite-oxidizing Nitrospira.
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Affiliation(s)
- Hirotsugu Fujitani
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.,Research Organization for Nano & Life Innovation, Waseda University, Tokyo, Japan
| | - Kengo Momiuchi
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Kento Ishii
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Manami Nomachi
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Shuta Kikuchi
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Norisuke Ushiki
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Yuji Sekiguchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Satoshi Tsuneda
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo, Japan.,Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
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23
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Ishii K, Fujitani H, Sekiguchi Y, Tsuneda S. Physiological and genomic characterization of a new 'Candidatus Nitrotoga' isolate. Environ Microbiol 2020; 22:2365-2382. [PMID: 32285573 DOI: 10.1111/1462-2920.15015] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 04/01/2020] [Accepted: 04/07/2020] [Indexed: 11/28/2022]
Abstract
Oxidation of nitrite to nitrate is an important process in the global nitrogen cycle. Recent molecular biology-based studies have revealed that the widespread nitrite-oxidizing bacteria (NOB) belonging to the genus 'Candidatus Nitrotoga' may be highly important for the environment. However, the insufficient availability of pure Nitrotoga cultures has limited our understanding of their physiological and genomic characteristics. Here, we isolated the 'Ca. Nitrotoga' sp. strain AM1P, from a previously enriched Nitrotoga culture, using an improved isolation strategy. Although 'Ca. Nitrotoga' have been recognized as cold-adapted NOB, the strain AM1P had a slightly higher optimum growth temperature at 23°C. Strain AM1P showed a pH optimum of 8.3 and was not inhibited even at high nitrite concentrations (20 mM). We obtained the complete genome of the strain and compared the genome profile to five previously sequenced 'Ca. Nitrotoga' strains. Comparative genomics suggested that lactate dehydrogenase may be only encoded in the strain AM1P and closely related genomes. While the growth yield of AM1P did not change, we observed faster growth in the presence of lactate in comparison to purely chemolithoautotrophic growth. The characterization of the new strain AM1P sheds light on the physiological adaptation of this environmentally important, but understudied genus 'Ca. Nitrotoga'.
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Affiliation(s)
- Kento Ishii
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, Japan
| | - Hirotsugu Fujitani
- Research Organization for Nano and Life Innovation, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, Japan.,Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, Japan
| | - Yuji Sekiguchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, Japan
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, Japan.,Research Organization for Nano and Life Innovation, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, Japan
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24
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Isshiki R, Fujitani H, Tsuneda S. Transcriptome Analysis of the Ammonia-Oxidizing Bacterium Nitrosomonas mobilis Ms1 Reveals Division of Labor between Aggregates and Free-living Cells. Microbes Environ 2020; 35. [PMID: 32115437 PMCID: PMC7308568 DOI: 10.1264/jsme2.me19148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Bacteria change their metabolic states to increase survival by forming aggregates. Ammonia-oxidizing bacteria also form aggregates in response to environmental stresses. Nitrosomonas mobilis, an ammonia-oxidizing bacterium with high stress tolerance, often forms aggregates mainly in wastewater treatment systems. Despite the high frequency of aggregate formation by N. mobilis, its relationship with survival currently remains unclear. In the present study, aggregates were formed in the late stage of culture with the accumulation of nitrite as a growth inhibitor. To clarify the significance of aggregate formation in N. mobilis Ms1, a transcriptome analysis was performed. Comparisons of the early and late stages of culture revealed that the expression of stress response genes (chaperones and proteases) increased in the early stage. Aggregate formation may lead to stress avoidance because stress response genes were not up-regulated in the late stage of culture during which aggregates formed. Furthermore, comparisons of free-living cells with aggregates in the early stage of culture showed differences in gene expression related to biosynthesis (ATP synthase and ribosomal proteins) and motility and adhesion (flagella, pilus, and chemotaxis). Biosynthesis genes for growth were up-regulated in free-living cells, while motility and adhesion genes for adaptation were up-regulated in aggregates. These results indicate that N. mobilis Ms1 cells adapt to an unfavorable environment and grow through the division of labor between aggregates and free-living cells.
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Affiliation(s)
- Rino Isshiki
- Department of Life Science and Medical Bioscience, Waseda University
| | - Hirotsugu Fujitani
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology.,Research Organization for Nano & Life Innovation, Waseda University
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, Waseda University.,Research Organization for Nano & Life Innovation, Waseda University
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25
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Ginawi A, Wang L, Wang H, Yu B, Yunjun Y. Effects of environmental variables on abundance of ammonia-oxidizing communities in sediments of Luotian River, China. PeerJ 2020; 8:e8256. [PMID: 31934502 PMCID: PMC6951284 DOI: 10.7717/peerj.8256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 11/20/2019] [Indexed: 12/14/2022] Open
Abstract
Ammonia-oxidizing communities play important functional roles in the nitrification. However, environmental stresses can significantly affect this process by controlling the abundant communities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities. In this study, we examined the abundance variations of ammonia-oxidizing communities using quantitative polymerase chain reaction (qPCR) and terminal-restriction fragment length polymorphism (T-RFLP) in a typical subtropical river, Luotian County, South Dabie Mountains, China. Clone libraries were conducted to evaluate the community structure and abundance of AOA and AOB in sediments. Results showed that Nitrososphaera sp and Nitrosopumilus sp were the most dominant AOA. The abundance of the AOA and AOB amoA gene ranged from 5.28 × 108 gene copies (g-soil−1) to 2.23 × 108 gene copies (g-soil−1) and 5.45 × 108 gene copies (g-soil−1) to 3.30 × 107 gene copies (g-soil−1), respectively. Five environmental variables, namely, ORP, DO, NO\documentclass[12pt]{minimal}
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}{}${}_{4}^{+}$\end{document}4+ were played a major function in microbial communities of AOA and AOB in sediments. The T-RFLP profiles of AOA showed that 488 and 116 bp T-RFs were dominated. Overall, the results of this study showed that anthropogenic activities andenvironmental stress in rivers can alter the structure and function of microbes in their variable environment.
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Affiliation(s)
- Amjed Ginawi
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Faculty of Marine Science and Fisheries, Red Sea University, Port Sudan, Red Sea State, Sudan
| | - Lixiao Wang
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Huading Wang
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Bingbing Yu
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yan Yunjun
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
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26
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Holmes DE, Dang Y, Smith JA. Nitrogen cycling during wastewater treatment. ADVANCES IN APPLIED MICROBIOLOGY 2019; 106:113-192. [PMID: 30798802 DOI: 10.1016/bs.aambs.2018.10.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Many wastewater treatment plants in the world do not remove reactive nitrogen from wastewater prior to release into the environment. Excess reactive nitrogen not only has a negative impact on human health, it also contributes to air and water pollution, and can cause complex ecosystems to collapse. In order to avoid the deleterious effects of excess reactive nitrogen in the environment, tertiary wastewater treatment practices that ensure the removal of reactive nitrogen species need to be implemented. Many wastewater treatment facilities rely on chemicals for tertiary treatment, however, biological nitrogen removal practices are much more environmentally friendly and cost effective. Therefore, interest in biological treatment is increasing. Biological approaches take advantage of specific groups of microorganisms involved in nitrogen cycling to remove reactive nitrogen from reactor systems by converting ammonia to nitrogen gas. Organisms known to be involved in this process include autotrophic ammonia-oxidizing bacteria, heterotrophic ammonia-oxidizing bacteria, ammonia-oxidizing archaea, anaerobic ammonia oxidizing bacteria (anammox), nitrite-oxidizing bacteria, complete ammonia oxidizers, and dissimilatory nitrate reducing microorganisms. For example, in nitrifying-denitrifying reactors, ammonia- and nitrite-oxidizing bacteria convert ammonia to nitrate and then denitrifying microorganisms reduce nitrate to nonreactive dinitrogen gas. Other nitrogen removal systems (anammox reactors) take advantage of anammox bacteria to convert ammonia to nitrogen gas using NO as an oxidant. A number of promising new biological treatment technologies are emerging and it is hoped that as the cost of these practices goes down more wastewater treatment plants will start to include a tertiary treatment step.
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27
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Chen J, Nie Y, Liu W, Wang Z, Shen W. Ammonia-Oxidizing Archaea Are More Resistant Than Denitrifiers to Seasonal Precipitation Changes in an Acidic Subtropical Forest Soil. Front Microbiol 2017; 8:1384. [PMID: 28790990 PMCID: PMC5522861 DOI: 10.3389/fmicb.2017.01384] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 07/10/2017] [Indexed: 12/02/2022] Open
Abstract
Seasonal precipitation changes are increasingly severe in subtropical areas. However, the responses of soil nitrogen (N) cycle and its associated functional microorganisms to such precipitation changes remain unclear. In this study, two projected precipitation patterns were manipulated: intensifying the dry-season drought (DD) and extending the dry-season duration (ED) but increasing the wet-season storms following the DD and ED treatment period. The effects of these two contrasting precipitation patterns on soil net N transformation rates and functional gene abundances were quantitatively assessed through a resistance index. Results showed that the resistance index of functional microbial abundance (-0.03 ± 0.08) was much lower than that of the net N transformation rate (0.55 ± 0.02) throughout the experiment, indicating that microbial abundance was more responsive to precipitation changes compared with the N transformation rate. Spring drought under the ED treatment significantly increased the abundances of both nitrifying (amoA) and denitrifying genes (nirK, nirS, and nosZ), while changes in these gene abundances overlapped largely with control treatment during droughts in the dry season. Interestingly, the resistance index of the ammonia-oxidizing archaea (AOA) amoA abundance was significantly higher than that of the denitrifying gene abundances, suggesting that AOA were more resistant to the precipitation changes. This was attributed to the stronger environmental adaptability and higher resource utilization efficiency of the AOA community, as indicated by the lack of correlations between AOA gene abundance and environmental factors [i.e., soil water content, ammonium (NH4+) and dissolved organic carbon concentrations] during the experiment.
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Affiliation(s)
- Jie Chen
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China.,College of Life Science, University of Chinese Academy of SciencesBeijing, China.,Department of Soil Science of Temperate Ecosystems, University of GöttingenGöttingen, Germany
| | - Yanxia Nie
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Wei Liu
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Zhengfeng Wang
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Weijun Shen
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
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28
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Enrichment and Physiological Characterization of a Cold-Adapted Nitrite-Oxidizing Nitrotoga sp. from an Eelgrass Sediment. Appl Environ Microbiol 2017; 83:AEM.00549-17. [PMID: 28500038 DOI: 10.1128/aem.00549-17] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/02/2017] [Indexed: 12/26/2022] Open
Abstract
Nitrite-oxidizing bacteria (NOB) are responsible for the second step of nitrification in natural and engineered ecosystems. The recently discovered genus Nitrotoga belongs to the Betaproteobacteria and potentially has high environmental importance. Although environmental clones affiliated with Nitrotoga are widely distributed, the limited number of cultivated Nitrotoga spp. results in a poor understanding of their ecophysiological features. In this study, we successfully enriched the nonmarine cold-adapted Nitrotoga sp. strain AM1 from coastal sand in an eelgrass zone and investigated its physiological characteristics. Multistep-enrichment approaches led to an increase in the abundance of AM1 to approximately 80% of the total bacterial population. AM1 was the only detectable NOB in the bacterial community. The 16S rRNA gene sequence of AM1 was 99.6% identical to that of "Candidatus Nitrotoga arctica," which was enriched from permafrost-affected soil. The highest nitrogen oxidation rate of AM1 was observed at 16°C. The half-saturation constant (Km ) and the generation time were determined to be 25 μM NO2- and 54 h, respectively. The nitrite oxidation rate of AM1 was stimulated at concentrations of <30 mM NH4Cl but completely inhibited at 50 mM NH4Cl. AM1 can grow well under specific environmental conditions, such as low temperature and in the presence of a relatively high concentration of free ammonia. These results help improve our comprehension of the functional importance of NitrotogaIMPORTANCE Nitrite-oxidizing bacteria (NOB) are key players in the second step of nitrification, which is an important process of the nitrogen cycle. Recent studies have suggested that the organisms of the novel NOB genus Nitrotoga were widely distributed and played a functional role in natural and engineered ecosystems. However, only a few Nitrotoga enrichments have been obtained, and little is known about their ecology and physiology. In this study, we successfully enriched a Nitrotoga sp. from sand in a shallow coastal marine ecosystem and undertook a physiological characterization. The laboratory experiments showed that the Nitrotoga enrichment culture could adapt not only to low temperature but also to relatively high concentrations of free ammonia. The determination of as-yet-unknown unique characteristics of Nitrotoga contributes to the improvement of our insights into the microbiology of nitrification.
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Abe T, Ushiki N, Fujitani H, Tsuneda S. A rapid collection of yet unknown ammonia oxidizers in pure culture from activated sludge. WATER RESEARCH 2017; 108:169-178. [PMID: 27836171 DOI: 10.1016/j.watres.2016.10.070] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 10/25/2016] [Accepted: 10/27/2016] [Indexed: 06/06/2023]
Abstract
Nitrification is an important reaction in the biological nitrogen removal process in wastewater treatment plants (WWTPs). As ammonia-oxidizing microbes are slow-growing and sensitive to environmental factors such as free ammonia, pure strains are hard to obtain, preventing our understanding of their physiological characteristics. To conquer this hurdle, we report a high-throughput isolation technique based on scattering signatures, which exploits the tendency of many ammonia-oxidizing bacteria (AOB) to form microcolonies in activated sludge. The AOB microcolonies were directly sorted from the activated sludge without long incubation and enrichment bias, and were sequentially inoculated into 96-well microtiter plates containing growth medium. Phylogenetic analysis of the pure strains isolated in this study revealed a deeply branching and unrecognized lineage and diversity within the genus Nitrosomonas, beyond our expectation.
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Affiliation(s)
- Takuma Abe
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Norisuke Ushiki
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hirotsugu Fujitani
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
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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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