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Wei Y, Ye M, Chen Y, Li YY. Competitive bio-augmentation overcoming unusual direct inhibitor inefficacy in mainstream nitrite-oxidizing bacteria suppression: Unveiling the underpinnings in microbial and nitrogen metabolism aspects. Sci Total Environ 2024; 926:171900. [PMID: 38527552 DOI: 10.1016/j.scitotenv.2024.171900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/16/2024] [Accepted: 03/20/2024] [Indexed: 03/27/2024]
Abstract
The long-stabilized mainstream partial nitritation/Anammox (PN/A) process continues to encounter significant challenges from nitrite-oxidizing bacteria (NOB). Therefore, this study aimed to determine an efficient, rapid, and easily implementable strategy for inhibiting NOB. A laboratory-scale reactor was operated continuously for 325 days, experiencing NOB outbreak in mainstream and recovery with simulated sidestream support. The results show that direct inhibitory strategies including intermittent aeration and approximately 35 mg/L free ammonia had unusual weak inhibitory effects on NOB activity. Subsequently, the exogenous Anammox from sidestream employed as a competitive bio-augmentation approach rapidly inhibited NOB dynamics. Evidence suggests that the damaged hydroxyapatite granules under low pH conditions might have contributed to NOB dominance by diminishing Anammox bacteria activity, thereby creating a substrate-rich environment favoring NOB survival. In contrast, the introduction of exogenous Candidatus Kuenenia facilitated the nitrogen removal efficiency from 32.5 % to over 80 %. This coincided with a decrease in the relative abundance of Nitrospira from 16.5 % to 2.7 % and NOB activity from 0.34 to 0.07 g N/(g mixed liquor volatile suspended solid)/d. Metagenomic analysis reveals a decrease in the functional potential of most nitrite transport proteins, coupled with a significant increase in eukaryotic-like serine/threonine-protein kinase involved in cellular regulation, during the Anammox activity recovery. This study's findings reveal the feasibility of the bio-augmentation based on substrate competition, wherein sidestream processes support the mainstream PN/A integration, offering significant potential for practical applications.
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Affiliation(s)
- Yanxiao Wei
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Min Ye
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Yujie Chen
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Yu-You Li
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan; Department of Frontier Sciences for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, 6-6-20 Aoba, Aramaki-Aza, Aoba-ku, Sendai, Miyagi 980-8579, Japan.
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2
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Yan Y, Lee J, Han IL, Wang Z, Li G, McCullough K, Klaus S, Kang D, Wang D, Patel A, McQuarrie J, Stinson BM, deBarbadillo C, Dombrowski P, Bott C, Gu AZ. Comammox and unknown ammonia oxidizers contribute to nitrite accumulation in an integrated A-B stage process that incorporates side-stream EBPR (S2EBPR). Water Res 2024; 253:121220. [PMID: 38341969 DOI: 10.1016/j.watres.2024.121220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 11/27/2023] [Accepted: 01/28/2024] [Indexed: 02/13/2024]
Abstract
A novel integrated pilot-scale A-stage high rate activated sludge, B-stage short-cut biological nitrogen removal and side-stream enhanced biological phosphorus removal (A/B-shortcut N-S2EBPR) process for treating municipal wastewater was demonstrated with the aim to achieve simultaneous and carbon- and energy-efficient N and P removal. In this studied period, an average of 7.62 ± 2.17 mg-N/L nitrite accumulation was achieved through atypical partial nitrification without canonical known NOB out-selection. Network analysis confirms the central hub of microbial community as Nitrospira, which was one to two orders of magnitude higher than canonical aerobic oxidizing bacteria (AOB) in a B-stage nitrification tank. The contribution of comammox Nitrospira as AOB was evidenced by the increased amoB/nxr ratio and higher ammonia oxidation activity. Furthermore, oligotyping analysis of Nitrospira revealed two dominant sub-clusters (microdiveristy) within the Nitrospira. The relative abundance of oligotype II, which is phylogenetically close to Nitrospira_midas_s_31566, exhibited a positive correlation with nitrite accumulation in the same operational period, suggesting its role as comammox Nitrospira. Additionally, the phylogenetic investigation suggested that heterotrophic organisms from the family Comamonadacea and the order Rhodocyclaceae embedding ammonia monooxygenase and hydroxylamine oxidase may function as heterotrophic nitrifiers. This is the first study that elucidated the impact of integrating the S2EBPR on nitrifying populations with implications on short-cut N removal. The unique conditions in the side-stream reactor, such as low ORP, favorable VFA concentrations and composition, seemed to exert different selective forces on nitrifying populations from those in conventional biological nutrient removal processes. The results provide new insights for integrating EBPR with short-cut N removal process for mainstream wastewater treatment.
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Affiliation(s)
- Yuan Yan
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY 14850, United States
| | - Jangho Lee
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY 14850, United States
| | - I L Han
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY 14850, United States
| | - Zijian Wang
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY 14850, United States
| | - Guangyu Li
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY 14850, United States
| | - Kester McCullough
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY 14850, United States; Hampton Roads Sanitation District, Virginia Beach, VA 23454, United States; modelEAU, Département de génie civil et de génie des eaux, Université Laval, 1065 av. de la Médecine, Québec, Canada
| | - Stephanie Klaus
- Hampton Roads Sanitation District, Virginia Beach, VA 23454, United States
| | - Da Kang
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY 14850, United States; Department of Environmental Engineering, College of Environmental & Resource Sciences, Zhejiang University, China
| | - Dongqi Wang
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, Shaanxi 710048, China; Department of Civil and Environmental Engineering, Northeastern University, Boston, MA 02115, United States
| | - Anand Patel
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY 14850, United States
| | - Jim McQuarrie
- Denver Metro Wastewater Reclamation District, Denver, CO 80229, United States
| | | | - Christine deBarbadillo
- District of Columbia Water and Sewer Authority, District of Columbia, 5000 Overlook Ave., SW, Washington, DC 20032, United States
| | | | - Charles Bott
- Hampton Roads Sanitation District, Virginia Beach, VA 23454, United States.
| | - April Z Gu
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY 14850, United States.
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3
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Fu K, Zhang X, Fan Y, Bian Y, Qiu F, Cao X. The enrichment characterisation of Nitrospira under high DO conditions. Environ Technol 2024; 45:2156-2170. [PMID: 36601901 DOI: 10.1080/09593330.2023.2165457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 12/31/2022] [Indexed: 06/17/2023]
Abstract
Nitrite-oxidizing bacteria (NOB) are crucial to nitrification and nitrogen elimination in wastewater treatment. Mass reports exist on the links between NOB and other microorganisms, for instance, ammonia-oxidizing bacteria (AOB). However, a few studies exist on the enrichment characterisation of NOB under high dissolved oxygen (DO) conditions. In this study, NOB was designed to be enriched individually under high DO conditions in a continuous aeration sequencing batch reactor (SBR), and the kinetic characterisation of NOB was evaluated. The analysis revealed that the average NO2--N removal rate was steady above 98%, with DO and NO2--N being 3-5 mg L-1 and 50-450 mg L-1, respectively. The NO2--N removal efficiency of the system was significantly enhanced and better than in other studies. The high-throughput sequencing suggested that Parcubacteria_ genera_incertae_sedis was the first dominant genus (21.99%), which often appeared in the NOB biological community with Nitrospira. However, the dominant genus NOB was Nitrospira rather than Nitrobacter (8.49%). This result suggested that Nitrospira was capable of higher NO2--N removal. But lower relative abundance indicated that excessive NO2--N had an adverse effect on the enrichment and activity of Nitrospira. In addition, the nitrite half-saturation constant (KNO2) and the oxygen half-saturation constant (KO) were 1.71 ± 0.19 mg L-1 and 0.95 ± 0.10 mg L-1, respectively. These results showed that the enriched Nitrospira bacteria had different characteristics at the strain level, which can be used as a theoretical basis for wastewater treatment plant design and optimisation.
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Affiliation(s)
- Kunming Fu
- Key Laboratory of Urban Storm Water System and Water Environment Ministry of Education, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
- School of Environment and Energy Engineering, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
| | - Xuemeng Zhang
- School of Environment and Energy Engineering, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
| | - Yang Fan
- School of Environment and Energy Engineering, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
| | - Yihao Bian
- School of Environment and Energy Engineering, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
| | - Fuguo Qiu
- School of Environment and Energy Engineering, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
| | - Xiuqin Cao
- School of Environment and Energy Engineering, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
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4
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Van Tendeloo M, Baptista MC, Van Winckel T, Vlaeminck SE. Recurrent multi-stressor floc treatments with sulphide and free ammonia enabled mainstream partial nitritation/anammox. Sci Total Environ 2024; 912:169449. [PMID: 38123077 DOI: 10.1016/j.scitotenv.2023.169449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/28/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023]
Abstract
Selective suppression of nitrite-oxidising bacteria (NOB) over aerobic and anoxic ammonium-oxidising bacteria (AerAOB and AnAOB) remains a major challenge for mainstream partial nitritation/anammox implementation, a resource-efficient nitrogen removal pathway. A unique multi-stressor floc treatment was therefore designed and validated for the first time under lab-scale conditions while staying true to full-scale design principles. Two hybrid (suspended + biofilm growth) reactors were operated continuously at 20.2 ± 0.6 °C. Recurrent multi-stressor floc treatments were applied, consisting of a sulphide-spiked deoxygenated starvation followed by a free ammonia shock. A good microbial activity balance with high AnAOB (71 ± 21 mg N L-1 d-1) and low NOB (4 ± 17 % of AerAOB) activity was achieved by combining multiple operational strategies: recurrent multi-stressor floc treatments, hybrid sludge (flocs & biofilm), short floc age control, intermittent aeration, and residual ammonium control. The multi-stressor treatment was shown to be the most important control tool and should be continuously applied to maintain this balance. Excessive NOB growth on the biofilm was avoided despite only treating the flocs to safeguard the AnAOB activity on the biofilm. Additionally, no signs of NOB adaptation were observed over 142 days. Elevated effluent ammonium concentrations (25 ± 6 mg N L-1) limited the TN removal efficiency to 39 ± 9 %, complicating a future full-scale implementation. Operating at higher sludge concentrations or reducing the volumetric loading rate could overcome this issue. The obtained results ease the implementation of mainstream PN/A by providing and additional control tool to steer the microbial activity with the multi-stressor treatment, thus advancing the concept of energy neutrality in sewage treatment plants.
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Affiliation(s)
- Michiel Van Tendeloo
- Research Group of Sustainable Energy, Air and Water Technology, Department of Bioscience Engineering, University of Antwerp, 2020 Antwerpen, Belgium
| | - Maria Catarina Baptista
- Research Group of Sustainable Energy, Air and Water Technology, Department of Bioscience Engineering, University of Antwerp, 2020 Antwerpen, Belgium
| | - Tim Van Winckel
- Research Group of Sustainable Energy, Air and Water Technology, Department of Bioscience Engineering, University of Antwerp, 2020 Antwerpen, Belgium
| | - Siegfried E Vlaeminck
- Research Group of Sustainable Energy, Air and Water Technology, Department of Bioscience Engineering, University of Antwerp, 2020 Antwerpen, Belgium.
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5
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Li S, Islam MS, Yang S, Xue Y, Liu Y, Huang X. Potential stimulation of nitrifying bacteria activities and genera by landfill leachate. Sci Total Environ 2024; 912:168620. [PMID: 37977385 DOI: 10.1016/j.scitotenv.2023.168620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/29/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
With the increasing complexity of influent composition in wastewater treatment plants, the potential stimulating effects of refractory organic matter in wastewater on growth characteristics and genera conversion of nitrifying bacteria (ammonium-oxidizing bacteria [AOB] and nitrite-oxidizing bacteria [NOB]) need to be further investigated. In this study, domestic wastewater was co-treated with landfill leachate in the lab-scale reactor, and the competition and co-existence of NOB genera Nitrotoga and Nitrospira were observed. The results demonstrated that the addition of landfill leachate could induce the growth of Nitrotoga, whereas Nitrotoga populations remain less competitive in domestic wastewater operation. In addition, the refractory organic matter in the landfill leachate also would have a potential stimulating effect on the maximum specific growth rate of AOB genus Nitrosomonas (μmax, aob). The μmax, aob of Nitrosomonas in the control group was estimated to be 0.49 d-1 by fitting the ASM model, and the μmax, aob reached 0.66-0.71 d-1 after injection of refractory organic matter in the landfill leachate, while the maximum specific growth rate of NOB (μmax, nob) was always in the range of 1.05-1.13 d-1. These findings have positive significance for the understanding of potential stimulation on nitrification processes and the stable operation of innovative wastewater treatment process.
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Affiliation(s)
- Siqi Li
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Md Sahidul Islam
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Shaolin Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Yu Xue
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Yanchen Liu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
| | - Xia Huang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
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6
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Afroze N, Kim M, Chowdhury MMI, Haroun B, Andalib M, Umble A, Nakhla G. Effect of thermal shock and sustained heat treatment on mainstream partial nitrification and microbial community in sequencing batch reactors. Environ Sci Pollut Res Int 2024; 31:6258-6276. [PMID: 38147251 DOI: 10.1007/s11356-023-31421-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 12/04/2023] [Indexed: 12/27/2023]
Abstract
In order to develop a promising means of achieving mainstream short-cut nitrification, this study evaluated the effect of thermal shock on nitrite accumulation using intermittent offline and continuous inline heat treatment of biomass in sequencing batch reactors (SBRs). The SBRs fed with municipal wastewater were operated at a solid retention time of 7 days and nitrogen loading rate of 0.04 gN/L·d to 0.08 gN/L·d without the application of pre-treatment. Contrary to literature studies that showed suppression of nitrite-oxidizing bacteria at temperature 60 to 80 °C, nitrite accumulation was achieved temporarily when 20% of the biomass was heated for 2 h at 47 °C, as well as in continuously heated SBRs at 37 °C and 42 °C. The continuously heated reactors at 37 °C and 42 °C produced a maximum nitrite accumulation ratio (NAR) of 0.59 and 0.79, respectively, whereas the intermittent offline heating at 47 °C-2 h produced a NAR of 0.37. Although nitrite accumulation was stable only for 10-12 days in all heated reactors, this study demonstrates the achievement of mainstream partial nitrification (PN) at lower temperature (42 °C) than that reported in literature and also highlights the potential for achieving PN by implementing heat treatment of a portion of the return activated sludge (RAS) in biological nitrogen removal (BNR) systems. During the time when full nitrification was achieved, Nitrospira was more dominant than Nitrosomonas in all reactors at ratios of 1.4:1, 2.4:1, 2.4:1, and 3.7:1 for the control SBR (22 °C), 47 °C -2 h offline heating SBR, 37 °C SBR, and 42 °C SBR, respectively, suggesting that it may have played a role as a comammox bacteria capable of degrading ammonia to nitrates at elevated temperature.
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Affiliation(s)
- Niema Afroze
- Department of Civil and Environmental Engineering, University of Western Ontario, London, ON, N6A 5B9, Canada.
| | - Mingu Kim
- Department of Chemical and Biochemical Engineering, University of Western Ontario, London, ON, N6A 5B9, Canada
| | - Mohammad M I Chowdhury
- Department of Civil and Environmental Engineering, University of Western Ontario, London, ON, N6A 5B9, Canada
| | - Basem Haroun
- Department of Chemical and Biochemical Engineering, University of Western Ontario, London, ON, N6A 5B9, Canada
| | | | - Arthur Umble
- Stantec Water Institute for Technology & Policy, 1560 Broadway, Suite 1800, Denver, CO, 80202-6000, USA
| | - George Nakhla
- Department of Civil and Environmental Engineering, University of Western Ontario, London, ON, N6A 5B9, Canada
- Department of Chemical and Biochemical Engineering, University of Western Ontario, London, ON, N6A 5B9, Canada
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7
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Martin-Pozas T, Fernandez-Cortes A, Cuezva S, Cañaveras JC, Benavente D, Duarte E, Saiz-Jimenez C, Sanchez-Moral S. New insights into the structure, microbial diversity and ecology of yellow biofilms in a Paleolithic rock art cave (Pindal Cave, Asturias, Spain). Sci Total Environ 2023; 897:165218. [PMID: 37419360 DOI: 10.1016/j.scitotenv.2023.165218] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 06/13/2023] [Accepted: 06/28/2023] [Indexed: 07/09/2023]
Abstract
In the absence of sunlight, caves harbor a great diversity of microbial colonies to extensive biofilms with different sizes and colors visible to the naked eye. One of the most widespread and visible types of biofilm are those with yellow hues that can constitute a serious problem for the conservation of cultural heritage in many caves, such as Pindal Cave (Asturias, Spain). This cave, declared a World Heritage Site by UNESCO for its Paleolithic parietal art, shows a high degree of development of yellow biofilms that represents a real threat to the conservation of painted and engraved figures. This study aims to: 1) identify the microbial structures and the most characteristic taxa composing the yellow biofilms, 2) seek the linked microbiome reservoir primarily contributing to their growth; 3) seed light on the driving vectors that contribute to their formation and determine the subsequent proliferation and spatial distribution. To achieve this goal, we used amplicon-based massive sequencing, in combination with other techniques such as microscopy, in situ hybridization and environmental monitoring, to compare the microbial communities of yellow biofilms with those of drip waters, cave sediments and exterior soil. The results revealed microbial structures related to the phylum Actinomycetota and the most characteristic bacteria in yellow biofilms, represented by the genera wb1-P19, Crossiella, Nitrospira, and Arenimonas. Our findings suggest that sediments serve as potential reservoirs and colonization sites for these bacteria that can develop into biofilms under favorable environmental and substrate conditions, with a particular affinity for speleothems and rugged-surfaced rocks found in condensation-prone areas. This study presents an exhaustive study of microbial communities of yellow biofilms in a cave, which could be used as a procedure for the identification of similar biofilms in other caves and to design effective conservation strategies in caves with valuable cultural heritage.
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Affiliation(s)
- Tamara Martin-Pozas
- Department of Geology, National Museum of Natural Sciences (MNCN-CSIC), 28006 Madrid, Spain.
| | | | - Soledad Cuezva
- Department of Geology, Geography and Environment, University of Alcala, Campus Cientifico-Tecnologico, 28802 Alcala de Henares, Spain.
| | - Juan Carlos Cañaveras
- Department of Environmental and Earth Sciences, University of Alicante, Campus San Vicente del Raspeig, 03690 Alicante, Spain.
| | - David Benavente
- Department of Environmental and Earth Sciences, University of Alicante, Campus San Vicente del Raspeig, 03690 Alicante, Spain.
| | - Elsa Duarte
- Department of History, University of Oviedo, 33011 Oviedo, Spain.
| | - Cesareo Saiz-Jimenez
- Department of Agrochemistry, Environmental Microbiology and Soil and Water Protection, Institute of Natural Resources and Agricultural Biology (IRNAS-CSIC), 41012 Seville, Spain.
| | - Sergio Sanchez-Moral
- Department of Geology, National Museum of Natural Sciences (MNCN-CSIC), 28006 Madrid, Spain.
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Fu K, Bian Y, Yang F, Liao M, Xu J, Qiu F. Influencing factors on the activity of an enriched Nitrospira culture with granular morphology. Environ Technol 2023:1-15. [PMID: 37712531 DOI: 10.1080/09593330.2023.2260122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
Nitrospira is a common genus of nitrite-oxidising bacteria (NOB) found in wastewater treatment plants (WWTPs). To identify the key factors influencing the composition of NOB communities, research was conducted using both sequencing batch reactor (SBR) and continuous flow reactor under different conditions. High-throughput 16S rRNA gene sequencing revealed that Nitrospira (18.79% in R1 and 25.77% in R3) was the dominant NOB under low dissolved oxygen (DO) and low nitrite (NO 2 - -N) concentrations, while Nitrobacter (21.26% in R2) was the dominant NOB under high DO and high NO 2 - -N concentrations. Flocculent and granule sludge were cultivated with Nitrospira as the dominant genus. Compared to Nitrospira flocculent sludge, Nitrospira granule sludge had higher inhibition threshold concentrations for free ammonia (FA) and free nitrous acid (FNA). It was more likely to resist adverse environmental disturbances. Furthermore, the effects of environmental factors such as temperature, pH, and DO on the activity of Nitrospira granular sludge were also studied. The results showed that the optimum temperature and pH for Nitrospira granular sludge were 36°C and 7.0, respectively. Additionally, Nitrospira granular sludge showed a higher dissolved oxygen half-saturation constant (Ko) of 3.67 ± 0.71 mg/L due to its morphological characteristics. However, the majority of WWTPs conditions do not meet the conditions for the Nitrospira granular sludge. Thus, it can be speculated that future development of aerobic partial nitrification granular sludge may automatically eliminate the influence of Nitrospira. This study provides a theoretical basis for a deeper understanding of Nitrospira and the development of future water treatment processes.
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Affiliation(s)
- Kunming Fu
- Key Laboratory of Urban Storm Water System and Water Environment Ministry of Education, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
- Sino-Dutch R&D Centre for Future Wastewater Treatment Technologies/Key Laboratory of Urban Stormwater System and Water Environment, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
| | - Yihao Bian
- Key Laboratory of Urban Storm Water System and Water Environment Ministry of Education, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
- Sino-Dutch R&D Centre for Future Wastewater Treatment Technologies/Key Laboratory of Urban Stormwater System and Water Environment, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
| | - Fan Yang
- Key Laboratory of Urban Storm Water System and Water Environment Ministry of Education, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
- Sino-Dutch R&D Centre for Future Wastewater Treatment Technologies/Key Laboratory of Urban Stormwater System and Water Environment, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
| | - Minhui Liao
- Powerchina Eco-environmental Group Co., Ltd, Shenzhen, China
| | - Jian Xu
- Key Laboratory of Urban Storm Water System and Water Environment Ministry of Education, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
- Sino-Dutch R&D Centre for Future Wastewater Treatment Technologies/Key Laboratory of Urban Stormwater System and Water Environment, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
| | - Fuguo Qiu
- Key Laboratory of Urban Storm Water System and Water Environment Ministry of Education, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
- Sino-Dutch R&D Centre for Future Wastewater Treatment Technologies/Key Laboratory of Urban Stormwater System and Water Environment, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
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9
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Meng S, Liang X, Peng T, Liu Y, Wang H, Huang T, Gu JD, Hu Z. Ecological distribution and function of comammox Nitrospira in the environment. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12557-6. [PMID: 37195422 DOI: 10.1007/s00253-023-12557-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/18/2023]
Abstract
Complete ammonia oxidizers (Comammox) are of great significance for studying nitrification and expanding the understanding of the nitrogen cycle. Moreover, Comammox bacteria are also crucial in natural and engineered environments due to their role in wastewater treatment and maintaining the flux of greenhouse gases to the atmosphere. However, only few studies are there regarding the Comammox bacteria and their role in ammonia and nitrite oxidation in the environment. This review mainly focuses on summarizing the genomes of Nitrospira in the NCBI database. Ecological distribution of Nitrospira was also reviewed and the influence of environmental parameters on genus Nitrospira in different environments has been summarized. Furthermore, the role of Nitrospira in carbon cycle, nitrogen cycle, and sulfur cycle were discussed, especially the comammox Nitrospira. In addition, the overviews of current research and development regarding comammox Nitrospira, were summarized along with the scope of future research. KEY POINTS: • Most of Comammox Nitrospira are widely distributed in both aquatic and terrestrial ecosystems, but it has been studied less frequently in the extreme environments. • Comammox Nitrospira can be involved in different nitrogen transformation process, but rarely involved in nitrogen fixation. • The stable isotope and transcriptome techniques are important methods to study the metabolic function of comammox Nitrospira.
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Affiliation(s)
- Shanshan Meng
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, P.R. China
| | - Xueji Liang
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, P.R. China
| | - Tao Peng
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, P.R. China
| | - Yongjin Liu
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, P.R. China
| | - Hui Wang
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, P.R. China
| | - Tongwang Huang
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, P.R. China
| | - Ji-Dong Gu
- Environmental Science and Engineering Research Group, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, 515063, Guangdong, China
- Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, 515063, Guangdong, China
| | - Zhong Hu
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, P.R. China.
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10
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Mehrani MJ, Kowal P, Sobotka D, Godzieba M, Ciesielski S, Guo J, Makinia J. The coexistence and competition of canonical and comammox nitrite oxidizing bacteria in a nitrifying activated sludge system - Experimental observations and simulation studies. Sci Total Environ 2023; 864:161084. [PMID: 36565884 DOI: 10.1016/j.scitotenv.2022.161084] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
The second step of nitrification can be mediated by nitrite oxidizing bacteria (NOB), i.e. Nitrospira and Nitrobacter, with different characteristics in terms of the r/K theory. In this study, an activated sludge model was developed to account for competition between two groups of canonical NOB and comammox bacteria. Heterotrophic denitrification on soluble microbial products was also incorporated into the model. Four 5-week washout trials were carried out at dissolved oxygen-limited conditions for different temperatures (12 °C vs. 20 °C) and main substrates (NH4+-N vs. NO2--N). Due to the aggressive reduction of solids retention time (from 4 to 1 d), the biomass concentrations were continuously decreased and stabilized after two weeks at a level below 400 mg/L. The collected experimental data (N species, biomass concentrations, and microbiological analyses) were used for model calibration and validation. In addition to the standard predictions (N species and biomass), the newly developed model also accurately predicted two microbiological indicators, including the relative abundance of comammox bacteria as well as nitrifiers to heterotrophs ratio. Sankey diagrams revealed that the relative contributions of specific microbial groups to N conversion pathways were significantly shifted during the trial. The contribution of comammox did not exceed 5 % in the experiments with both NH4+-N and NO2--N substrates. This study contributes to a better understanding of the novel autotrophic N removal processes (e.g. deammonification) with nitrite as a central intermediate product.
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Affiliation(s)
- Mohamad-Javad Mehrani
- Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Narutowicza Street 11/12, 80-233 Gdansk, Poland
| | - Przemyslaw Kowal
- Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Narutowicza Street 11/12, 80-233 Gdansk, Poland
| | - Dominika Sobotka
- Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Narutowicza Street 11/12, 80-233 Gdansk, Poland
| | - Martyna Godzieba
- Department of Environmental Biotechnology, Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, Sloneczna 45G, 10-719 Olsztyn, Poland
| | - Slawomir Ciesielski
- Department of Environmental Biotechnology, Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, Sloneczna 45G, 10-719 Olsztyn, Poland
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Jacek Makinia
- Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Narutowicza Street 11/12, 80-233 Gdansk, Poland.
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11
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Ma B, LaPara TM, Kim T, Hozalski RM. Multi-scale Investigation of Ammonia-Oxidizing Microorganisms in Biofilters Used for Drinking Water Treatment. Environ Sci Technol 2023; 57:3833-3842. [PMID: 36811531 DOI: 10.1021/acs.est.2c06858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Ammonia-oxidizing microorganisms (AOMs) include ammonia-oxidizing bacteria (AOB), archaea (AOA), and Nitrospira spp. sublineage II capable of complete ammonia oxidation (comammox). These organisms can affect water quality not only by oxidizing ammonia to nitrite (or nitrate) but also by cometabolically degrading trace organic contaminants. In this study, the abundance and composition of AOM communities were investigated in full-scale biofilters at 14 facilities across North America and in pilot-scale biofilters operated for 18 months at a full-scale water treatment plant. In general, the relative abundance of AOM in most full-scale biofilters and in the pilot-scale biofilters was as follows: AOB > comammox Nitrospira > AOA. The abundance of AOB in the pilot-scale biofilters increased with increasing influent ammonia concentration and decreasing temperature, whereas AOA and comammox Nitrospira exhibited no correlations with these parameters. The biofilters affected AOM abundance in the water passing through the filters via collecting and shedding but exhibited a minor influence on the composition of AOB and Nitrospira sublineage II communities in the filtrate. Overall, this study highlights the relative importance of AOB and comammox Nitrospira compared to AOA in biofilters and the influence of filter influent water quality on AOM in biofilters and their release into the filtrate.
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Affiliation(s)
- Ben Ma
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, 500 Pillsbury Dr. SE, Minneapolis, Minnesota 55455, United States
| | - Timothy M LaPara
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, 500 Pillsbury Dr. SE, Minneapolis, Minnesota 55455, United States
- Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
| | - Taegyu Kim
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, 500 Pillsbury Dr. SE, Minneapolis, Minnesota 55455, United States
| | - Raymond M Hozalski
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, 500 Pillsbury Dr. SE, Minneapolis, Minnesota 55455, United States
- Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
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12
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Ghimire-Kafle S, Weaver ME Jr, Bollmann A. Ecophysiological and Genomic Characterization of the Freshwater Complete Ammonia Oxidizer Nitrospira sp. Strain BO4. Appl Environ Microbiol 2023; 89:e0196522. [PMID: 36719237 DOI: 10.1128/aem.01965-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Complete ammonia oxidizers (comammox) are a group of ubiquitous chemolithoautotrophic bacteria capable of deriving energy from the oxidation of ammonia to nitrate via nitrite. Here, we present a study characterizing the comammox strain Nitrospira sp. BO4 using a combination of cultivation-dependent and molecular methods. The enrichment culture BO4 was obtained from the sediment of Lake Burr Oak, a mesotrophic lake in eastern Ohio. The metagenome of the enrichment culture was sequenced, and a metagenome-assembled genome (MAG) was constructed for Nitrospira sp. BO4. The closest characterized relative of Nitrospira sp. BO4 was "Candidatus Nitrospira kreftii." All genes for ammonia and nitrite oxidation, reductive tricarboxylic acid (TCA) cycle, and other pathways of the central metabolism were detected. Nitrospira sp. BO4 used ammonia and oxidized it to nitrate with nitrite as the intermediate. The culture grew on initial ammonium concentrations between 0.01 and 3 mM with the highest rates observed at the lowest ammonium concentrations. Blue light completely inhibited the growth of Nitrospira sp. BO4, while white light reduced the growth and red light had no effect on the growth. Nitrospira sp. BO4 did not grow on nitrite as its sole substrate. When supplied with ammonium and nitrite, the culture utilized nitrite after most of the ammonium was consumed. In summary, the genomic information of Nitrospira sp. BO4 coupled with the growth experiments shows that Nitrospira sp. BO4 is a freshwater comammox species. Future research will focus on further characterization of the niches of comammox in freshwater environments. IMPORTANCE Nitrification is a key process in the global nitrogen cycle. Complete ammonia oxidizers (comammox) were discovered recently, and only three enrichment cultures and one pure culture have been characterized with respect to activity and growth under different conditions. The cultivated comammox strains were obtained from engineered systems such as a recirculating aquaculture system and hot water pipes. Here, we present the first study characterizing a comammox strain obtained from a mesotrophic freshwater lake. In freshwater environments, comammox coexist with ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Our results will help elucidate physiological characteristics of comammox and the distribution and niche differentiation of different ammonia oxidizers in freshwater environments.
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13
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Kowal P, Mehrani MJ, Sobotka D, Ciesielski S, Mąkinia J. Rearrangements of the nitrifiers population in an activated sludge system under decreasing solids retention times. Environ Res 2022; 214:113753. [PMID: 35772505 DOI: 10.1016/j.envres.2022.113753] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 06/17/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Due to the key role of nitrite in novel nitrogen removal systems, nitrite oxidizing bacteria (NOB) have been receiving increasing attention. In this study, the coexistence and interactions of nitrifying bacteria were explored at decreasing solids retention times (SRTs). Four 5-week washout experiments were carried out in laboratory-scale (V = 10 L) sequencing batch reactors (SBRs) with mixed liquor from two full-scale activated sludge systems (continuous flow vs SBR). During the experiments, the SRT was gradually reduced from the initial value of 4.0 d to approximately 1.0 d. The reactors were operated under limited dissolved oxygen conditions (set point of 0.6 mg O2/L) and two process temperatures: 12 °C (winter) and 20 °C (summer). At both temperatures, the progressive SRT reduction was inefficient for the out-selection of both canonical NOB and comammox Nitrospira. However, the dominant NOB switched from Nitrospira to Ca. Nitrotoga, whereas the dominant AOB was always Nitrosomonas. The results of this study are important for optimizing NOB suppression strategies in the novel N removal processes, which are based on nitrite accumulation.
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Affiliation(s)
- Przemyslaw Kowal
- Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Narutowicza Street 11/12, 80-233, Gdansk, Poland.
| | - Mohamad-Javad Mehrani
- Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Narutowicza Street 11/12, 80-233, Gdansk, Poland
| | - Dominika Sobotka
- Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Narutowicza Street 11/12, 80-233, Gdansk, Poland
| | - Sławomir Ciesielski
- Department of Environmental Biotechnology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Ul. Sloneczna 45G, 10-709, Olsztyn, Poland
| | - Jacek Mąkinia
- Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Narutowicza Street 11/12, 80-233, Gdansk, Poland
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Huang T, Xia J, Liu T, Su Z, Guan Y, Guo J, Wang C, Zheng M. Comammox Nitrospira Bacteria Are Dominant Ammonia Oxidizers in Mainstream Nitrification Bioreactors Emended with Sponge Carriers. Environ Sci Technol 2022; 56:12584-12591. [PMID: 35973026 DOI: 10.1021/acs.est.2c03641] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Complete ammonia oxidation (i.e., comammox) is a newly discovered microbial process performed by a subset of the Nitrospira genus, and this unique microbial process has been ubiquitously detected in various wastewater treatment units. However, the operational conditions favoring comammox prevalence remain unclear. In this study, the dominance of comammox Nitrospira in four sponge biofilm reactors fed with low-strength ammonium (NH4+ = 23 ± 3 mg N/L) wastewater was proved by coupling 16S rRNA gene amplicon sequencing, quantitative polymerase chain reaction (qPCR), and metagenomic sequencing. The results showed that comammox Nitrospira dominated in the nitrifying guild over canonical ammonia-oxidizing bacteria (AOB) constantly, despite the significant variation in the residual ammonium concentration (0.01-15 mg N/L) under different sets of operating conditions. This result indicates that sponge biofilms greatly favor retaining comammox Nitrospira in wastewater treatment and highlights an essential role of biomass retention in the comammox prevalence. Moreover, analyses of the assembled metagenomic sequences revealed that the retrieved amoA gene sequences affiliated with comammox Nitrospira (53.9-66.0% read counts of total amoA gene reads) were always higher than those (28.4-43.4%) related to β-proteobacterial AOB taxa. The comammox Nitrospira bacteria detected in the present biofilm systems were close to clade A Candidatus Nitrospira nitrosa.
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Affiliation(s)
- Tuo Huang
- School of Environment, Tsinghua University, Beijing 100084, China
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Jun Xia
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Tao Liu
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Zicheng Su
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Yuntao Guan
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Chengwen Wang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Min Zheng
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
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15
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Sampara P, Luo Y, Lin X, Ziels RM. Integrating Genome-Resolved Metagenomics with Trait-Based Process Modeling to Determine Biokinetics of Distinct Nitrifying Communities within Activated Sludge. Environ Sci Technol 2022; 56:11670-11682. [PMID: 35929783 PMCID: PMC9387530 DOI: 10.1021/acs.est.2c02081] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Conventional bioprocess models for wastewater treatment are based on aggregated bulk biomass concentrations and do not incorporate microbial physiological diversity. Such a broad aggregation of microbial functional groups can fail to predict ecosystem dynamics when high levels of physiological diversity exist within trophic guilds. For instance, functional diversity among nitrite-oxidizing bacteria (NOB) can obfuscate engineering strategies for their out-selection in activated sludge (AS), which is desirable to promote energy-efficient nitrogen removal. Here, we hypothesized that different NOB populations within AS can have different physiological traits that drive process performance, which we tested by estimating biokinetic growth parameters using a combination of highly replicated respirometry, genome-resolved metagenomics, and process modeling. A lab-scale AS reactor subjected to a selective pressure for over 90 days experienced resilience of NOB activity. We recovered three coexisting Nitrospira population genomes belonging to two sublineages, which exhibited distinct growth strategies and underwent a compositional shift following the selective pressure. A trait-based process model calibrated at the NOB genus level better predicted nitrite accumulation than a conventional process model calibrated at the NOB guild level. This work demonstrates that trait-based modeling can be leveraged to improve our prediction, control, and design of functionally diverse microbiomes driving key environmental biotechnologies.
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16
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Al-Ajeel S, Spasov E, Sauder LA, McKnight MM, Neufeld JD. Ammonia-oxidizing archaea and complete ammonia-oxidizing Nitrospira in water treatment systems. Water Res X 2022; 15:100131. [PMID: 35402889 PMCID: PMC8990171 DOI: 10.1016/j.wroa.2022.100131] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/07/2022] [Accepted: 03/11/2022] [Indexed: 05/27/2023]
Abstract
Nitrification, the oxidation of ammonia to nitrate via nitrite, is important for many engineered water treatment systems. The sequential steps of this respiratory process are carried out by distinct microbial guilds, including ammonia-oxidizing bacteria (AOB) and archaea (AOA), nitrite-oxidizing bacteria (NOB), and newly discovered members of the genus Nitrospira that conduct complete ammonia oxidation (comammox). Even though all of these nitrifiers have been identified within water treatment systems, their relative contributions to nitrogen cycling are poorly understood. Although AOA contribute to nitrification in many wastewater treatment plants, they are generally outnumbered by AOB. In contrast, AOA and comammox Nitrospira typically dominate relatively low ammonia environments such as drinking water treatment, tertiary wastewater treatment systems, and aquaculture/aquarium filtration. Studies that focus on the abundance of ammonia oxidizers may misconstrue the actual role that distinct nitrifying guilds play in a system. Understanding which ammonia oxidizers are active is useful for further optimization of engineered systems that rely on nitrifiers for ammonia removal. This review highlights known distributions of AOA and comammox Nitrospira in engineered water treatment systems and suggests future research directions that will help assess their contributions to nitrification and identify factors that influence their distributions and activity.
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17
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Van Tendeloo M, Xie Y, Van Beeck W, Zhu W, Lebeer S, Vlaeminck SE. Oxygen control and stressor treatments for complete and long-term suppression of nitrite-oxidizing bacteria in biofilm-based partial nitritation/anammox. Bioresour Technol 2021; 342:125996. [PMID: 34598074 DOI: 10.1016/j.biortech.2021.125996] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/15/2021] [Accepted: 09/19/2021] [Indexed: 06/13/2023]
Abstract
Mainstream nitrogen removal by partial nitritation/anammox (PN/A) can realize energy and cost savings for sewage treatment. Selective suppression of nitrite oxidizing bacteria (NOB) remains a key bottleneck for PN/A implementation. A rotating biological contactor was studied with an overhead cover and controlled air/N2 inflow to regulate oxygen availability at 20 °C. Biofilm exposure to dissolved oxygen concentrations < 0.51 ± 0.04 mg O2 L-1 when submerged in the water and < 1.41 ± 0.31 mg O2 L-1 when emerged in the headspace (estimated), resulted in complete and long-term NOB suppression with a low relative nitrate production ratio of 10 ± 4%. Additionally, weekly biofilm stressor treatments with free ammonia (FA) (29 ± 1 mg NH3-N L-1 for 3 h) could improve the NOB suppression while free nitrous acid treatments had insufficient effect. This study demonstrated the potential of managing NOB suppression in biofilm-based systems by oxygen control and recurrent FA exposure, opening opportunities for resource efficient nitrogen removal.
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Affiliation(s)
- Michiel Van Tendeloo
- Research Group of Sustainable Energy, Air and Water Technology, Department of Bioscience Engineering, University of Antwerp, 2020 Antwerpen, Belgium
| | - Yankai Xie
- Research Group of Sustainable Energy, Air and Water Technology, Department of Bioscience Engineering, University of Antwerp, 2020 Antwerpen, Belgium
| | - Wannes Van Beeck
- Research Group Environmental Ecology and Applied Microbiology (ENdEMIC), Department of Bioscience Engineering, University of Antwerp, 2020 Antwerpen, Belgium
| | - Weiqiang Zhu
- Research Group of Sustainable Energy, Air and Water Technology, Department of Bioscience Engineering, University of Antwerp, 2020 Antwerpen, Belgium
| | - Sarah Lebeer
- Research Group Environmental Ecology and Applied Microbiology (ENdEMIC), Department of Bioscience Engineering, University of Antwerp, 2020 Antwerpen, Belgium
| | - Siegfried E Vlaeminck
- Research Group of Sustainable Energy, Air and Water Technology, Department of Bioscience Engineering, University of Antwerp, 2020 Antwerpen, Belgium.
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18
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Lu J, Hong Y, Wei Y, Gu JD, Wu J, Wang Y, Ye F, Lin JG. Nitrification mainly driven by ammonia-oxidizing bacteria and nitrite-oxidizing bacteria in an anammox-inoculated wastewater treatment system. AMB Express 2021; 11:158. [PMID: 34837527 PMCID: PMC8627542 DOI: 10.1186/s13568-021-01321-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 11/16/2021] [Indexed: 11/26/2022] Open
Abstract
Anaerobic ammonium oxidation (anammox) process has been acknowledged as an environmentally friendly and time-saving technique capable of achieving efficient nitrogen removal. However, the community of nitrification process in anammox-inoculated wastewater treatment plants (WWTPs) has not been elucidated. In this study, ammonia oxidation (AO) and nitrite oxidation (NO) rates were analyzed with the incubation of activated sludge from Xinfeng WWTPs (Taiwan, China), and the community composition of nitrification communities were investigated by high-throughput sequencing. Results showed that both AO and NO had strong activity in the activated sludge. The average rates of AO and NO in sample A were 6.51 µmol L−1 h−1 and 6.52 µmol L−1 h−1, respectively, while the rates in sample B were 14.48 µmol L−1 h−1 and 14.59 µmol L−1 h−1, respectively. The abundance of the nitrite-oxidizing bacteria (NOB) Nitrospira was 0.89–4.95 × 1011 copies/g in both samples A and B, the abundance of ammonia-oxidizing bacteria (AOB) was 1.01–9.74 × 109 copies/g. In contrast, the abundance of ammonia-oxidizing archaea (AOA) was much lower than AOB, only with 1.28–1.53 × 105 copies/g in samples A and B. The AOA community was dominated by Nitrosotenuis, Nitrosocosmicus, and Nitrososphaera, while the AOB community mainly consisted of Nitrosomonas and Nitrosococcus. The dominant species of Nitrospira were Candidatus Nitrospira defluvii, Candidatus Nitrospira Ecomare2 and Nitrospira inopinata. In summary, the strong nitrification activity was mainly catalyzed by AOB and Nitrospira, maintaining high efficiency in nitrogen removal in the anammox-inoculated WWTPs by providing the substrates required for denitrification and anammox processes.
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19
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Zhao M, Tang X, Sun D, Hou L, Liu M, Zhao Q, Klümper U, Quan Z, Gu JD, Han P. Salinity gradients shape the nitrifier community composition in Nanliu River Estuary sediments and the ecophysiology of comammox Nitrospira inopinata. Sci Total Environ 2021; 795:148768. [PMID: 34247082 DOI: 10.1016/j.scitotenv.2021.148768] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/24/2021] [Accepted: 06/27/2021] [Indexed: 06/13/2023]
Abstract
The recent discovery of complete ammonia oxidizers (comammox), which convert ammonia to nitrate in a single organism, revolutionized the conventional understanding that two types of nitrifying microorganisms have to be involved in the nitrification process for more than 100 years. However, how different types of nitrifiers in response to salinity change remains largely unclear. This study not only investigated nitrifier community (including ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), comammox and nitrite-oxidizing Nitrospira) in the Nanliu estuary to find the ecological relationship between salinity and functional communities and also studied the physiology of a typical comammox Nitrospira inopinata in response to a salinity gradient. Based on sequences retrieved with four sets of functional gene primes, comammox Nitrospira was in general, mainly composed of clade A, with a clear separation of clade A1 subgroup in all samples and clade A2 subgroup in low salinity ones. As expected, group I.1b and group I.1a AOA dominated the AOA community in low- and high-salinity samples, respectively. Nitrosomonas-AOB were detected in all samples while Nitrosospira-AOB were mainly found in relatively high-salinity samples. Regarding general Nitrospira, lineages II and IV were the major groups in most of the samples, while lineage I Nitrospira was only detected in low-salinity samples. Furthermore, the comammox pure culture of N. inopinata showed an optimal salinity at 0.5‰ and ceased to grow at 12.8‰ for ammonia oxidation, but remained active for nitrite oxidation. These results show new evidence regarding niche specificity of different nitrifying microorganisms modulated mainly by salinity, and also a clear response by comammox N. inopinata to a wide range of simulated salinity levels.
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Affiliation(s)
- Mengyue Zhao
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xiufeng Tang
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Dongyao Sun
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Institute of Eco-Chongming, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China
| | - Qiang Zhao
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Uli Klümper
- Institute for Hydrobiology, Technische Universität Dresden, 01062 Dresden, Germany
| | - Zhexue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ji-Dong Gu
- Environmental Engineering, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, China
| | - Ping Han
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Institute of Eco-Chongming, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China.
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20
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Sun D, Tang X, Zhao M, Zhang Z, Hou L, Liu M, Wang B, Klümper U, Han P. Corrigendum: Distribution and Diversity of Comammox Nitrospira in Coastal Wetlands of China. Front Microbiol 2021; 12:731921. [PMID: 34512610 PMCID: PMC8429277 DOI: 10.3389/fmicb.2021.731921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 07/31/2021] [Indexed: 11/19/2022] Open
Affiliation(s)
- Dongyao Sun
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, Shanghai, China
| | - Xiufeng Tang
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, Shanghai, China
| | - Mengyue Zhao
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, Shanghai, China
| | - Zongxiao Zhang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Min Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, Shanghai, China.,Institute of Eco-Chongming, East China Normal University, Shanghai, China
| | - Baozhan Wang
- Key Laboratory of Microbiology for Agricultural Environment (Ministry of Agriculture), College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Uli Klümper
- Institute for Hydrobiology, Technische Universität Dresden, Dresden, Germany
| | - Ping Han
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, Shanghai, China.,State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China.,Institute of Eco-Chongming, East China Normal University, Shanghai, China
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21
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Gao FY, Li YY, Yao HY. [Research progress on primers and molecular ecology of comammox Nitrospira]. Ying Yong Sheng Tai Xue Bao 2021; 31:2831-2840. [PMID: 34494806 DOI: 10.13287/j.1001-9332.202008.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Nitrification is a key process in nitrogen cycling, which has received considerable attention in the research field of soil biochemistry. In 2015, the discovery of complete ammonia oxidizers (Comammox) challenged conventional two-step nitrification perspective, which represented a paradigm shift in the understanding of soil nitrogen cycling. Comammox are a group of microorganisms capable of conducting both steps of nitrification. In this review, we summarized current understan-ding of the molecular ecology of comammox, including specific molecular biomarkers for comammox, phylogenetic and genomic surveys of comammox and particularly the distribution, diversity and ecological significance of comammox in soil. Further studies should focus on: 1) designing specific molecular biomarkers to examine the distribution and diversity of comammox; 2) optimizing cultivation techniques to isolate/enrich comammox cultures and expending our insights into physiological traits of comammox; 3) characterizing their distribution and in situ activities to elucidate the contribution of comammox processes to soil nitrification and their ecological features, which may assist in unco-vering the mechanisms of nitrogen cycling and promote the environmental protection of soil ecosystem.
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Affiliation(s)
- Fu-Yun Gao
- Wuhan Institute of Technology, Wuhan 430205, China.,Institite of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, Fujian, China
| | - Ya-Ying Li
- Wuhan Institute of Technology, Wuhan 430205, China.,Institite of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, Fujian, China
| | - Huai-Ying Yao
- Wuhan Institute of Technology, Wuhan 430205, China.,Institite of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, Fujian, China
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22
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Liang F, Wen Y, Dong X, Wang Y, Pan G, Jiang F, Luo H, Jin W, Wang J, Song H. Response of activity and community composition of nitrite-oxidizing bacteria to partial substitution of chemical fertilizer by organic fertilizer. Environ Sci Pollut Res Int 2021; 28:29332-29343. [PMID: 33559074 DOI: 10.1007/s11356-020-12038-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 12/08/2020] [Indexed: 06/12/2023]
Abstract
Nitrite oxidation as the second step of nitrification can become the determining step in disturbed soil systems. As a beneficial fertilization practice to maintain high crop yield and soil fertility, partial substitution of chemical fertilizer (CF) by organic fertilizer (OF) may exert a notable disturbance to soil systems. However, how nitrite oxidation responds to different proportions of CF to OF is still unclear. We sampled soils from a 4-year field experiment subject to a gradient of increasing proportions of OF to CF application. Activity, size, and structure of Nitrospira-like and Nitrobacter-like nitrite-oxidizing bacteria (NOB) community were measured. The results revealed that with increasing proportion of OF to CF application, potential nitrite oxidation activity (PNO) showed a marked decreasing trend. PNO was significantly correlated with the abundance of Nitrobacter-like but not Nitrospira-like NOB. The abundance of Nitrobacter-like was significantly influenced by soil organic matter, organic nitrogen (N), and available N. In addition, PNO was also affected by the structure of Nitrobacter-like NOB. The relative abundance of Nitrobacter hamburgensis, alkalicus, winogradskyi, and vulgaris responded differently to the proportions of OF to CF application. Organic N, organic matter, and available N were the main factor shaping their community structure. Overall, Nitrobacter-like NOB is more sensitive and plays a more important role than Nitrospira-like NOB in responding to different proportions of OF to CF application.
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Affiliation(s)
- Fei Liang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Yongkang Wen
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Xiao Dong
- School of Engineering, Anhui Agricultural University, Hefei, 230036, China
| | - Yiyao Wang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Guangyuan Pan
- Anhui General Station for Agricultural Technology Extension, Hefei, 230001, China
| | - Fangying Jiang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Huaying Luo
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Wenjun Jin
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Jun Wang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - He Song
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China.
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23
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Zhao X, Jiang J, Zhou Z, Zheng Y, Shao Y, Zuo Y, Ren Y, An Y. Responses of microbial structures, functions and metabolic pathways for nitrogen removal to different hydraulic retention times in anaerobic side-stream reactor coupled membrane bioreactors. Bioresour Technol 2021; 329:124903. [PMID: 33662853 DOI: 10.1016/j.biortech.2021.124903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/20/2021] [Accepted: 02/20/2021] [Indexed: 06/12/2023]
Abstract
Synchronous sludge reduction and nitrogen removal have attracted increasing attention, while the underlying mechanisms of diverse nitrogen metabolism within the complicated processes remain unclear. Four anoxic/oxic membrane bioreactors, three of which were upgraded by anaerobic side-stream reactors (ASSR) and carriers (APSSR-MBRs), were operated to determine effects of hydraulic retention time of ASSRs. APSSR-MBRs achieved more significant nitrogen removal and higher nitrate uptake rate because of more denitrifying bacteria and the supernumerary release of secondary substrates. Ammonia uptake rate showed the diverse Nitrospira preceded over anaerobic decay and sulfide inhibition in the ASSR, and made the reactor exhibit higher nitrification capacity. Metagenomic analysis indicated that APSSR-MBRs showed higher abundances of genes related to nitrogen consumption processes, and higher abundances on the carriers, confirming their pivotal roles in nitrogen metabolism. This study provided novel perspectives to build a bridge between process model and nitrogen metabolism in the sludge reduction system..
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Affiliation(s)
- Xiaodan Zhao
- Shanghai Engineering Research Center of Energy - Saving in Heat Exchange Systems, Shanghai University of Electric Power, Shanghai 200090, China
| | - Jie Jiang
- Shanghai Engineering Research Center of Energy - Saving in Heat Exchange Systems, Shanghai University of Electric Power, Shanghai 200090, China
| | - Zhen Zhou
- Shanghai Engineering Research Center of Energy - Saving in Heat Exchange Systems, Shanghai University of Electric Power, Shanghai 200090, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China.
| | - Yue Zheng
- Shanghai Engineering Research Center of Energy - Saving in Heat Exchange Systems, Shanghai University of Electric Power, Shanghai 200090, China
| | - Yanjun Shao
- Shanghai Engineering Research Center of Energy - Saving in Heat Exchange Systems, Shanghai University of Electric Power, Shanghai 200090, China
| | - Yi Zuo
- Shanghai Engineering Research Center of Energy - Saving in Heat Exchange Systems, Shanghai University of Electric Power, Shanghai 200090, China
| | - Yuqing Ren
- Shanghai Engineering Research Center of Energy - Saving in Heat Exchange Systems, Shanghai University of Electric Power, Shanghai 200090, China
| | - Ying An
- Shanghai Engineering Research Center of Energy - Saving in Heat Exchange Systems, Shanghai University of Electric Power, Shanghai 200090, China
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24
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Agrawal S, Weissbrodt DG, Annavajhala M, Jensen MM, Arroyo JMC, Wells G, Chandran K, Vlaeminck SE, Terada A, Smets BF, Lackner S. Time to act-assessing variations in qPCR analyses in biological nitrogen removal with examples from partial nitritation/anammox systems. Water Res 2021; 190:116604. [PMID: 33279744 DOI: 10.1016/j.watres.2020.116604] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 10/31/2020] [Accepted: 11/03/2020] [Indexed: 06/12/2023]
Abstract
Quantitative PCR (qPCR) is broadly used as the gold standard to quantify microbial community fractions in environmental microbiology and biotechnology. Benchmarking efforts to ensure the comparability of qPCR data for environmental bioprocesses are still scarce. Also, for partial nitritation/anammox (PN/A) systems systematic investigations are still missing, rendering meta-analysis of reported trends and generic insights potentially precarious. We report a baseline investigation of the variability of qPCR-based analyses for microbial communities applied to PN/A systems. Round-robin testing was performed for three PN/A biomass samples in six laboratories, using the respective in-house DNA extraction and qPCR protocols. The concentration of extracted DNA was significantly different between labs, ranged between 2.7 and 328 ng mg-1 wet biomass. The variability among the qPCR abundance data of different labs was very high (1-7 log fold) but differed for different target microbial guilds. DNA extraction caused maximum variation (3-7 log fold), followed by the primers (1-3 log fold). These insights will guide environmental scientists and engineers as well as treatment plant operators in the interpretation of qPCR data.
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Affiliation(s)
- Shelesh Agrawal
- Department of Civil and Environmental Engineering Sciences, Institute IWAR, Chair of Wastewater Engineering, Technical University of Darmstadt, Franziska-Braun-Straße 7, 64287 Darmstadt, Germany.
| | - David G Weissbrodt
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Medini Annavajhala
- Department of Earth and Environmental Engineering, Columbia University, New York, USA
| | - Marlene Mark Jensen
- Department of Environmental Engineering, Microbial Ecology & Technology Laboratory, Technical University of Denmark, Bygningtorvet, Bldg 115, DK-2800, Lyngby, Denmark
| | | | - George Wells
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, USA
| | - Kartik Chandran
- Department of Earth and Environmental Engineering, Columbia University, New York, USA
| | - Siegfried E Vlaeminck
- Department of Bioscience Engineering, Research Group of Sustainable Energy, Air and Water Technology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium
| | - Akihiko Terada
- Institute of Global Innovation Research and Department of Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka, Koganei, Tokyo 184-8588, Japan
| | - Barth F Smets
- Department of Environmental Engineering, Microbial Ecology & Technology Laboratory, Technical University of Denmark, Bygningtorvet, Bldg 115, DK-2800, Lyngby, Denmark
| | - Susanne Lackner
- Department of Civil and Environmental Engineering Sciences, Institute IWAR, Chair of Wastewater Engineering, Technical University of Darmstadt, Franziska-Braun-Straße 7, 64287 Darmstadt, Germany
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25
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Fujitani H, Nomachi M, Takahashi Y, Hasebe Y, Eguchi M, Tsuneda S. Successful enrichment of low-abundant comammox Nitrospira from nitrifying granules under ammonia-limited conditions. FEMS Microbiol Lett 2021; 367:5731803. [PMID: 32037440 DOI: 10.1093/femsle/fnaa025] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 02/08/2020] [Indexed: 12/25/2022] Open
Abstract
In artificial engineered systems, nitrification is a key reaction that accounts for the removal of biological nitrogen. Recently, a single microbe capable of oxidizing ammonia to nitrate, known as a complete ammonia oxidizer (comammox), has been discovered. Although the abundance and diversity of comammox Nitrospira in engineered systems have been identified through molecular-based approaches, the enrichment and isolation of comammox Nitrospira remains a challenge. Therefore, the aim of this study was to enrich comammox Nitrospira from nitrifying granules, which were used to increase the efficiency of biological nitrogen removal in wastewater treatment plants. We sought to accomplish this through the use of a fixed-bed continuous feeding bioreactor. Fluorescence in situ hybridization, 16S rRNA gene amplicon sequencing and qPCR of functional genes were utilized to monitor the growth of nitrifiers including comammox Nitrospira. Cloning of comammox amoA genes identified amoA phylogeny of enriched comammox Nitrospira. This work is an example demonstrating that continuous supply of low ammonium concentrations alongside biomass carriers is effective in cultivating comammox Nitrospira from engineered systems.
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Affiliation(s)
- Hirotsugu Fujitani
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Central 6, Higashi 1-1-1, Tsukuba, 305-8566, Japan.,Research Organization for Nano & Life Innovation, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Manami Nomachi
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Yu Takahashi
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Yoshiaki Hasebe
- Organo Corp. R&D Center, Nishioonuma 4-4-1, Minami-ku, Sagamihara, 252-0332, Japan
| | - Masahiro Eguchi
- Organo Corp. R&D Center, Nishioonuma 4-4-1, Minami-ku, Sagamihara, 252-0332, Japan
| | - Satoshi Tsuneda
- 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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26
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Vijayan A, Vattiringal Jayadradhan RK, Pillai D, Prasannan Geetha P, Joseph V, Isaac Sarojini BS. Nitrospira as versatile nitrifiers: Taxonomy, ecophysiology, genome characteristics, growth, and metabolic diversity. J Basic Microbiol 2021; 61:88-109. [PMID: 33448079 DOI: 10.1002/jobm.202000485] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/30/2020] [Accepted: 12/28/2020] [Indexed: 12/14/2022]
Abstract
The global nitrogen cycle is of paramount significance as it affects important processes like primary productivity and decomposition. Nitrification, the oxidation of ammonia to nitrate via nitrite, is a key process in the nitrogen cycle. The knowledge about nitrification has been challenged during the last few decades with inventions like anaerobic ammonia oxidation, ammonia-oxidizing archaea, and recently the complete ammonia oxidation (comammox). The discovery of comammox Nitrospira has made a paradigm shift in nitrification, before which it was considered as a two-step process, mediated by chemolithoautotrophic ammonia oxidizers and nitrite oxidizers. The genome of comammox Nitrospira equipped with molecular machineries for both ammonia and nitrite oxidation. The genus Nitrospira is ubiquitous, comes under phylum Nitrospirae, which comprises six sublineages consisting of canonical nitrite oxidizers and comammox. The single-step nitrification is energetically more feasible; furthermore, the existence of diverse metabolic pathways in Nitrospira is critical for its establishment in various habitats. The present review discusses the taxonomy, ecophysiology, isolation, identification, growth, and metabolic diversity of the genus Nitrospira; compares the genomes of canonical nitrite-oxidizing Nitrospira and comammox Nitrospira, and analyses the differences of Nitrospira with other nitrifying bacteria.
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Affiliation(s)
- Ardhra Vijayan
- Department of Aquatic Animal Health Management, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
| | - Rejish Kumar Vattiringal Jayadradhan
- Department of Aquatic Animal Health Management, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India.,Department of Aquaculture, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
| | - Devika Pillai
- Department of Aquatic Animal Health Management, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
| | - Preena Prasannan Geetha
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Kochi, Kerala, India
| | - Valsamma Joseph
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Kochi, Kerala, India
| | - Bright Singh Isaac Sarojini
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Kochi, Kerala, India
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27
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Coutinho FH, Cabello-Yeves PJ, Gonzalez-Serrano R, Rosselli R, López-Pérez M, Zemskaya TI, Zakharenko AS, Ivanov VG, Rodriguez-Valera F. New viral biogeochemical roles revealed through metagenomic analysis of Lake Baikal. Microbiome 2020; 8:163. [PMID: 33213521 PMCID: PMC7678222 DOI: 10.1186/s40168-020-00936-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 10/12/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Lake Baikal is the largest body of liquid freshwater on Earth. Previous studies have described the microbial composition of this habitat, but the viral communities from this ecosystem have not been characterized in detail. RESULTS Here, we describe the viral diversity of this habitat across depth and seasonal gradients. We discovered 19,475 bona fide viral sequences, which are derived from viruses predicted to infect abundant and ecologically important taxa that reside in Lake Baikal, such as Nitrospirota, Methylophilaceae, and Crenarchaeota. Diversity analysis revealed significant changes in viral community composition between epipelagic and bathypelagic zones. Analysis of the gene content of individual viral populations allowed us to describe one of the first bacteriophages that infect Nitrospirota, and their extensive repertoire of auxiliary metabolic genes that might enhance carbon fixation through the reductive TCA cycle. We also described bacteriophages of methylotrophic bacteria with the potential to enhance methanol oxidation and the S-adenosyl-L-methionine cycle. CONCLUSIONS These findings unraveled new ways by which viruses influence the carbon cycle in freshwater ecosystems, namely, by using auxiliary metabolic genes that act upon metabolisms of dark carbon fixation and methylotrophy. Therefore, our results shed light on the processes through which viruses can impact biogeochemical cycles of major ecological relevance. Video Abstract.
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Affiliation(s)
- F H Coutinho
- Evolutionary Genomics Group, Dpto. Producción Vegetal y Microbiología, Universidad Miguel Hernández, Aptdo. 18., Ctra. Alicante-Valencia N-332, s/n, San Juan de Alicante, 03550, Alicante, Spain.
| | - P J Cabello-Yeves
- Evolutionary Genomics Group, Dpto. Producción Vegetal y Microbiología, Universidad Miguel Hernández, Aptdo. 18., Ctra. Alicante-Valencia N-332, s/n, San Juan de Alicante, 03550, Alicante, Spain
| | - R Gonzalez-Serrano
- Evolutionary Genomics Group, Dpto. Producción Vegetal y Microbiología, Universidad Miguel Hernández, Aptdo. 18., Ctra. Alicante-Valencia N-332, s/n, San Juan de Alicante, 03550, Alicante, Spain
| | - R Rosselli
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands
- Utrecht University, Utrecht, The Netherlands
| | - M López-Pérez
- Evolutionary Genomics Group, Dpto. Producción Vegetal y Microbiología, Universidad Miguel Hernández, Aptdo. 18., Ctra. Alicante-Valencia N-332, s/n, San Juan de Alicante, 03550, Alicante, Spain
| | - T I Zemskaya
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - A S Zakharenko
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - V G Ivanov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - F Rodriguez-Valera
- Evolutionary Genomics Group, Dpto. Producción Vegetal y Microbiología, Universidad Miguel Hernández, Aptdo. 18., Ctra. Alicante-Valencia N-332, s/n, San Juan de Alicante, 03550, Alicante, Spain
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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28
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Park S, Seungdae O. Inhibitory mechanisms and fate of the analgesic drug acetaminophen in nitrifying activated sludge. J Hazard Mater 2020; 399:123104. [PMID: 32544770 DOI: 10.1016/j.jhazmat.2020.123104] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/15/2020] [Accepted: 05/29/2020] [Indexed: 06/11/2023]
Abstract
This work investigated the inhibitory effects and fate of acetaminophen (N-acetyl-p-aminophenol, APAP) on activated sludge (AS) under nitrifying and aerobic conditions. APAP disrupted the two-step biological nitrification process in a dose-dependent manner. 100 mg/L APAP inhibited ammonia oxidation (the first step of nitrification) accompanied by a significant reduction (> 80 %) of Nitrosomonas oligotropha in relative abundance. 50 mg/L of APAP had no significant effects on ammonia oxidation but interrupted nitrite oxidation (the second step of nitrification) with more than 90 % reduction of Candidatus Nitrospira defluvii. APAP was removed in nitrifying activated sludge via largely the biotransformation route. Both nitrifiers and heterotrophic microorganisms contributed to overall APAP removal. An AS bioreactor was acclimated to 100 mg/L APAP as the sole source of carbon, nitrogen, and energy to enrich the microbial community with APAP-metabolizing heterotrophs. During acclimation, dynamic changes in community phenotypes occurred with significant reduction in species richness and diversity. Community acclimation significantly increased APAP biotransformation rates. 16S rRNA gene-based community profiling showed selective enrichment for Pseudomonas and Sphingomonas, both with demonstrated APAP metabolic capacity.
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Affiliation(s)
- Sangeun Park
- Department of Civil Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Oh Seungdae
- Department of Civil Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do, Republic of Korea.
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29
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How SW, Nittami T, Ngoh GC, Curtis TP, Chua ASM. An efficient oxic-anoxic process for treating low COD/N tropical wastewater: Startup, optimization and nitrifying community structure. Chemosphere 2020; 259:127444. [PMID: 32640378 DOI: 10.1016/j.chemosphere.2020.127444] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/08/2020] [Accepted: 06/15/2020] [Indexed: 05/26/2023]
Abstract
In this study, we assessed and optimized a low-dissolved-oxygen oxic-anoxic (low-DO OA) process to achieve a low-cost and sustainable solution for wastewater treatment systems in the developing tropical countries treating low chemical oxygen demand-to-nitrogen ratio (COD/N) wastewater. The low-DO OA process attained complete ammonia removal and the effluent nitrate nitrogen (NO3-N) was below 0.3 mg/L. The recommended hydraulic retention time and sludge retention time (SRT) were 16 h and 20 days, respectively. The 16S rRNA sequencing data revealed that long SRT (20 days) encouraged the growth of nitrite-oxidizing bacteria (NOB) affiliated with "Candidatus Nitrospira defluvii". Comammox made up 10-20% of the Nitrospira community. NOB and comammox related to Nitrospira were enriched at long SRT (20 days) to achieve good low-DO nitrification performance. The low-DO OA process was efficient and has simpler design than conventional processes, which are keys for sustainable wastewater treatment systems in the developing countries treating low COD/N wastewater.
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Affiliation(s)
- Seow Wah How
- Department of Chemical Engineering, Faculty of Engineering, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Tadashi Nittami
- Division of Materials Science and Chemical Engineering, Faculty of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama, 240-8501, Japan
| | - Gek Cheng Ngoh
- Department of Chemical Engineering, Faculty of Engineering, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Thomas P Curtis
- School of Engineering, Newcastle University, Newcastle Upon Tyne, NE1 7RU, United Kingdom
| | - Adeline Seak May Chua
- Department of Chemical Engineering, Faculty of Engineering, University of Malaya, 50603, Kuala Lumpur, Malaysia.
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30
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Park SJ, Andrei AŞ, Bulzu PA, Kavagutti VS, Ghai R, Mosier AC. Expanded Diversity and Metabolic Versatility of Marine Nitrite-Oxidizing Bacteria Revealed by Cultivation- and Genomics-Based Approaches. Appl Environ Microbiol 2020; 86:e01667-20. [PMID: 32917751 PMCID: PMC7642081 DOI: 10.1128/aem.01667-20] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/03/2020] [Indexed: 12/30/2022] Open
Abstract
Nitrite-oxidizing bacteria (NOB) are ubiquitous and abundant microorganisms that play key roles in global nitrogen and carbon biogeochemical cycling. Despite recent advances in understanding NOB physiology and taxonomy, currently very few cultured NOB or representative NOB genome sequences from marine environments exist. In this study, we employed enrichment culturing and genomic approaches to shed light on the phylogeny and metabolic capacity of marine NOB. We successfully enriched two marine NOB (designated MSP and DJ) and obtained a high-quality metagenome-assembled genome (MAG) from each organism. The maximum nitrite oxidation rates of the MSP and DJ enrichment cultures were 13.8 and 30.0 μM nitrite per day, respectively, with these optimum rates occurring at 0.1 mM and 0.3 mM nitrite, respectively. Each enrichment culture exhibited a different tolerance to various nitrite and salt concentrations. Based on phylogenomic position and overall genome relatedness indices, both NOB MAGs were proposed as novel taxa within the Nitrospinota and Nitrospirota phyla. Functional predictions indicated that both NOB MAGs shared many highly conserved metabolic features with other NOB. Both NOB MAGs encoded proteins for hydrogen and organic compound metabolism and defense mechanisms for oxidative stress. Additionally, these organisms may have the genetic potential to produce cobalamin (an essential enzyme cofactor that is limiting in many environments) and, thus, may play an important role in recycling cobalamin in marine sediment. Overall, this study appreciably expands our understanding of the Nitrospinota and Nitrospirota phyla and suggests that these NOB play important biogeochemical roles in marine habitats.IMPORTANCE Nitrification is a key process in the biogeochemical and global nitrogen cycle. Nitrite-oxidizing bacteria (NOB) perform the second step of aerobic nitrification (converting nitrite to nitrate), which is critical for transferring nitrogen to other organisms for assimilation or energy. Despite their ecological importance, there are few cultured or genomic representatives from marine systems. Here, we obtained two NOB (designated MSP and DJ) enriched from marine sediments and estimated the physiological and genomic traits of these marine microbes. Both NOB enrichment cultures exhibit distinct responses to various nitrite and salt concentrations. Genomic analyses suggest that these NOB are metabolically flexible (similar to other previously described NOB) yet also have individual genomic differences that likely support distinct niche distribution. In conclusion, this study provides more insights into the ecological roles of NOB in marine environments.
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Affiliation(s)
- Soo-Je Park
- Department of Biology, Jeju National University, Jeju, Republic of Korea
| | - Adrian-Ştefan Andrei
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - Paul-Adrian Bulzu
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - Vinicius S Kavagutti
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Rohit Ghai
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - Annika C Mosier
- Department of Integrative Biology, University of Colorado Denver, Denver, Colorado, USA
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31
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Sun D, Tang X, Zhao M, Zhang Z, Hou L, Liu M, Wang B, Klümper U, Han P. Distribution and Diversity of Comammox Nitrospira in Coastal Wetlands of China. Front Microbiol 2020; 11:589268. [PMID: 33123118 PMCID: PMC7573150 DOI: 10.3389/fmicb.2020.589268] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/15/2020] [Indexed: 12/17/2022] Open
Abstract
Complete ammonia oxidizers (comammox), able to individually oxidize ammonia to nitrate, are considered to play a significant role in the global nitrogen cycle. However, the distribution of comammox Nitrospira in estuarine tidal flat wetland and the environmental drivers affecting their abundance and diversity remain unknown. Here, we present a large-scale investigation on the geographical distribution of comammox Nitrospira along the estuarine tidal flat wetlands of China, where comammox Nitrospira were successfully detected in 9 of the 16 sampling sites. The abundance of comammox Nitrospira ranged from 4.15 × 105 to 6.67 × 106 copies/g, 2.21- to 5.44-folds lower than canonical ammonia oxidizers: ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Phylogenetic analysis based on the alpha subunit of the ammonia monooxygenase encoding gene (amoA) revealed that comammox Nitrospira Clade A, mainly originating from upstream river inputs, accounts for more than 80% of the detected comammox Nitrospira, whereas comammox Nitrospira clade B were rarely detected. Comammox Nitrospira abundance and dominant comammox Nitrospira OTUs varied within the estuarine samples, showing a geographical pattern. Salinity and pH were the most important environmental drivers affecting the distribution of comammox Nitrospira in estuarine tidal flat wetlands. The abundance of comammox Nitrospira was further negatively correlated with high ammonia and nitrite concentrations. Altogether, this study revealed the existence, abundance and distribution of comammox Nitrospira and the driving environmental factors in estuarine ecosystems, thus providing insights into the ecological niches of this recently discovered nitrifying consortium and their contributions to nitrification in global estuarine environments.
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Affiliation(s)
- Dongyao Sun
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, Shanghai, China
| | - Xiufeng Tang
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, Shanghai, China
| | - Mengyue Zhao
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, Shanghai, China
| | - Zongxiao Zhang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Min Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, Shanghai, China.,Institute of Eco-Chongming, East China Normal University, Shanghai, China
| | - Baozhan Wang
- Key Laboratory of Microbiology for Agricultural Environment (Ministry of Agriculture), College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Uli Klümper
- Institute for Hydrobiology, Technische Universität Dresden, Dresden, Germany
| | - Ping Han
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, Shanghai, China.,State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China.,Institute of Eco-Chongming, East China Normal University, Shanghai, China
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32
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Seuntjens D, Carvajal Arroyo JM, Van Tendeloo M, Chatzigiannidou I, Molina J, Nop S, Boon N, Vlaeminck SE. Mainstream partial nitritation/anammox with integrated fixed-film activated sludge: Combined aeration and floc retention time control strategies limit nitrate production. Bioresour Technol 2020; 314:123711. [PMID: 32622275 DOI: 10.1016/j.biortech.2020.123711] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 05/26/2023]
Abstract
Implementation of mainstream partial nitritation/anammox (PN/A) can lead to more sustainable and cost-effective sewage treatment. For mainstream PN/A reactor, an integrated fixed-film activated sludge (IFAS) was operated (26 °C). The effects of floccular aerobic sludge retention time (AerSRTfloc), a novel aeration strategy, and N-loading rate were tested to optimize the operational strategy. The best performance was observed with a low, but sufficient AerSRTfloc (~7d) and continuous aeration with two alternating dissolved oxygen setpoints: 10 min at 0.07-0.13 mg O2 L-1 and 5 min at 0.27-0.43 mg O2 L-1. Nitrogen removal rates were 122 ± 23 mg N L-1 d-1, and removal efficiencies 73 ± 13%. These conditions enabled flocs to act as nitrite sources while the carriers were nitrite sinks, with low abundance of nitrite oxidizing bacteria. The operational strategies in the source-sink framework can serve as a guideline for successful operation of mainstream PN/A reactors.
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Affiliation(s)
- Dries Seuntjens
- CMET - Center for Microbial Ecology and Technology, Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Jose M Carvajal Arroyo
- CMET - Center for Microbial Ecology and Technology, Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Michiel Van Tendeloo
- Research Group of Sustainable Energy, Air and Water Technology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium
| | - Ioanna Chatzigiannidou
- CMET - Center for Microbial Ecology and Technology, Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Janet Molina
- CMET - Center for Microbial Ecology and Technology, Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Samnang Nop
- Imec, ELIS - IDLab, Ghent University, Belgium
| | - Nico Boon
- CMET - Center for Microbial Ecology and Technology, Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Siegfried E Vlaeminck
- Research Group of Sustainable Energy, Air and Water Technology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium.
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33
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Ouyang Y, Norton JM. Nitrite Oxidizer Activity and Community Are More Responsive Than Their Abundance to Ammonium-Based Fertilizer in an Agricultural Soil. Front Microbiol 2020; 11:1736. [PMID: 32849372 PMCID: PMC7417772 DOI: 10.3389/fmicb.2020.01736] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/02/2020] [Indexed: 01/01/2023] Open
Abstract
Autotrophic nitrification is mediated by ammonia oxidizing bacteria (AOB) or ammonia oxidizing archaea (AOA) and nitrite oxidizing bacteria (NOB). Mounting studies have examined the impact of nitrogen (N) fertilization on the dynamic and diversity of AOA and AOB, while we have limited information on the response of the activity, abundance, and diversity of NOB to N fertilization. We investigated the influence of organic and inorganic N fertilizers on soil NOB in silage corn field plots that received contrasting nitrogen (N) treatments: control (no additional N), ammonium sulfate (AS 100 and 200 kg N ha-1), and compost (200 kg N ha-1). Nitrifying community was examined using a universal marker (16S rRNA gene), functional gene markers (AOB amoA and Nitrospira nxrB), and metagenomics. The overall nitrifying community was not altered after the first fertilization but was significantly shifted by 4-year repeated application of ammonium fertilizers. Nitrospira were the dominant NOB (>99.7%) in our agricultural soil. Both community compositions of AOB and Nitrospira were significantly changed by ammonium fertilizers but not by compost after 4 years of repeated applications. All nitrifiers, including comammox, were recovered in soil metagenomes based on a gene-targeted assembly, but their sequence counts were very low. Although N treatment did not affect the abundance of Nitrospira nxrB determined by real-time quantitative PCR, ammonium fertilizers significantly promoted rates of potential nitrite oxidation determined at 0.15 mM nitrite in soil slurries. Understanding the response of both ammonia oxidizers and nitrite oxidizers to N fertilization may initiate or improve strategies for mitigating potential environmental impacts of nitrate production in agricultural ecosystems.
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Affiliation(s)
- Yang Ouyang
- Department of Plants, Soils and Climate, Utah State University, Logan, UT, United States
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
| | - Jeanette M. Norton
- Department of Plants, Soils and Climate, Utah State University, Logan, UT, United States
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35
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Takahashi Y, Fujitani H, Hirono Y, Tago K, Wang Y, Hayatsu M, Tsuneda S. Enrichment of Comammox and Nitrite-Oxidizing Nitrospira From Acidic Soils. Front Microbiol 2020; 11:1737. [PMID: 32849373 PMCID: PMC7396549 DOI: 10.3389/fmicb.2020.01737] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/02/2020] [Indexed: 12/02/2022] Open
Abstract
In agricultural soils fertilized with a high amount of ammonium nitrogen, the pH decreases because of the oxidation of ammonia by nitrifiers. Molecular-based analyses have revealed that members of the genus Nitrospira dominate over other nitrifiers in some acidic soils. However, terrestrial Nitrospira are rarely cultivated and little is known about their ecophysiology. In addition, recent studies discovered a single microbe with the potential to oxidize both ammonia and nitrite (complete ammonia oxidizer; comammox) within Nitrospira, which had been previously recognized as a nitrite oxidizer. Despite their broad distribution, there are no enrichment samples of comammox from terrestrial or acidic environments. Here, we report the selective enrichment of both comammox and nitrite-oxidizing Nitrospira from the acidic soil of a heavily fertilized tea field. Long-term enrichment was performed with two individual continuous-feeding bioreactors capable of controlling ammonia or nitrite concentration and pH. We found that excessive ammonium supply was a key factor to enhance the growth of comammox Nitrospira under acidic conditions. Additionally, a low concentration of nitrite was fed to prevent the accumulation of free nitrous acid and inhibition of cell growth under low pH, resulting in the selective enrichment of nitrite-oxidizing Nitrospira. Based on 16S rRNA gene analysis, Nitrospira accounting for only 1.2% in an initial soil increased to approximately 80% of the total microorganisms in both ammonia- and nitrite-fed bioreactors. Furthermore, amoA amplicon sequencing revealed that two phylotypes belonging to comammox clade A were enriched in an ammonia-fed bioreactor. One group was closely related to previously cultivated strains, and the other was classified into a different cluster consisting of only uncultivated representatives. These two groups coexisted in the bioreactor controlled at pH 6.0, but the latter became dominant after the pH decreased to 5.5. Additionally, a physiological experiment revealed that the enrichment sample oxidizes ammonia at pH <4, which is in accordance with the strongly acidic tea field soil; this value is lower than the active pH range of isolated acid-adapted nitrifiers. In conclusion, we successfully enriched multiple phylotypes of comammox and nitrite-oxidizing Nitrospira and revealed that the pH and concentrations of protonated N-compounds were potential niche determinants.
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Affiliation(s)
- Yu Takahashi
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Hirotsugu Fujitani
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Tokyo, Japan
| | - Yuhei Hirono
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), Shimada, Japan
| | - Kanako Tago
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Yong Wang
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Masahito Hayatsu
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
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36
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Wang S, Liu C, Wang X, Yuan D, Zhu G. Dissimilatory nitrate reduction to ammonium (DNRA) in traditional municipal wastewater treatment plants in China: Widespread but low contribution. Water Res 2020; 179:115877. [PMID: 32402861 DOI: 10.1016/j.watres.2020.115877] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 04/17/2020] [Accepted: 04/22/2020] [Indexed: 06/11/2023]
Abstract
Recent reports on the occurrence and contribution of dissimilatory nitrate reduction to ammonium (DNRA) in marine, inland water, and soil systems have greatly improved our understanding of the global nitrogen (N) cycle. This also promoted the investigation of the role and ecological features of DNRA in anthropogenic ecosystems. However, so far, the use of DNRA in municipal wastewater treatment plants (WWTPs), which are one of the most common and largest biotechnologically artificial water ecosystems, has not been investigated. Accordingly, this study focused on the abundance, activity, community structure, and diversity of DNRA bacteria in full-scale WWTPs. DNRA bacteria were detected in all treatment units in six tested municipal WWTPs, even in aerobic zones (dissolved oxygen > 2 mg L-1). Although the relative abundance of DNRA bacteria (0.2-4.0%) was less than that of denitrifying bacteria (0.7-10.1%) among all investigated samples, the abundance of DNRA bacteria still reaches 109 gene copies g-1. However, 15N-isotope tracing indicated that the potential DNRA rates were significantly lower (0.4-2.1 nmol N g-1 h-1) than those of denitrification (9.5-15.7 nmol N g-1 h-1), but higher than anammox rate (0.3-1.3 nmol N g-1 h-1). The DNRA bacterial community structure was primarily affected by temperature gradient despite the treatment process. High-throughput sequencing analysis targeting the DNRA nrfA gene showed that Nitrospira accounted for the largest proportion of nrfA genes among all samples (6.2-36.3%), followed by Brocadia (5.9-22.1%). Network analysis further indicated that Nitrospira played an important role in both the DNRA bacterial community and entire bacterial community in municipal WWTPs. These results suggest that the ecological habitats of DNRA bacteria in anthropogenic ecosystems were far more abundant than previously assumed. However, the contribution to N transformation by the widespread DNRA was not significant in traditional municipal WWTPs.
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Affiliation(s)
- Shanyun Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Chunlei Liu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Xiaoxia Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Dongdan Yuan
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.
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37
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Shen C, Zhang SJ, Peng YZ. [Effect of Free Hydroxylamine on the Activity of Two Typical Nitrite-oxidizing Bacteria]. Huan Jing Ke Xue 2020; 41:2805-2811. [PMID: 32608797 DOI: 10.13227/j.hjkx.201911110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The sludge from enrichment of Nitrobacter and Nitrospira was used as a research object and batch tests were performed. The inhibitory effects of hydroxylamine on Nitrobacter and Nitrospira under the same pH and different hydroxylamine concentration gradients, the same hydroxylamine concentration, and different pH gradients were investigated. The results showed that under the same pH condition, the activity of Nitrobacter decreased with increasing hydroxylamine concentration. Under the same hydroxylamine concentration (HA=5 mg·L-1) at a higher pH environment (pH ≥ 7.5), hydroxylamine produced more free hydroxylamine (FHA) and the inhibitory effect on Nitrobacter was improved. At a low pH environment (pH≤7), ionic hydroxylamine promoted the activity of Nitrobacter. The inhibitory effect of hydroxylamine on Nitrospira was limited. When pH=7.5 and hydroxylamine concentration was 45 mg·L-1, the relative activity of Nitrospira was 82%. The NOB growth rate kinetics model and the non-substrate inhibition linear equation were used to describe the effect of FHA on Nitrobacter and Nitrospira activity. The coefficient of determination R2 was 0.90 and 0.94, respectively. FHA may be the main reason for inhibiting the activity of Nitrobacter and Nitrospira.
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Affiliation(s)
- Chen Shen
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Shu-Jun Zhang
- Research and Development Center of Beijing Drainage Group Corporation, Beijing 100022, China
| | - Yong-Zhen Peng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
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38
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Mehrani MJ, Sobotka D, Kowal P, Ciesielski S, Makinia J. The occurrence and role of Nitrospira in nitrogen removal systems. Bioresour Technol 2020; 303:122936. [PMID: 32059161 DOI: 10.1016/j.biortech.2020.122936] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/27/2020] [Accepted: 01/29/2020] [Indexed: 05/04/2023]
Abstract
Application of the modern microbial techniques changed the paradigm about the microorganisms performing nitrification. Numerous investigations recognized representatives of the genus Nitrospira as a key and predominant nitrite-oxidizing bacteria in biological nutrient removal systems, especially under low dissolved oxygen and substrate conditions. The recent discovery of Nitrospira capable of performing complete ammonia oxidation (comammox) raised a fundamental question about the actual role of Nitrospira in both nitrification steps. This review summarizes the current knowledge about morphological, physiological and genetic characteristics of the canonical and comammox Nitrospira. Potential implications of comammox for the functional aspects of nitrogen removal have been highlighted. The complex meta-analysis of literature data was applied to identify specific individual variables and their combined interactions on the Nitrospira abundance. In addition to dissolved oxygen and influent nitrogen concentrations, temperature and pH may play an important role in enhancing or suppressing the Nitrospira activity.
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Affiliation(s)
- Mohamad-Javad Mehrani
- Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Narutowicza Street 11/12, 80-233 Gdansk, Poland
| | - Dominika Sobotka
- Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Narutowicza Street 11/12, 80-233 Gdansk, Poland
| | - Przemyslaw Kowal
- Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Narutowicza Street 11/12, 80-233 Gdansk, Poland
| | - Sławomir Ciesielski
- Department of Environmental Biotechnology, Faculty of Environmental Sciences, University of Warmia and Mazury in Olsztyn, ul. Sloneczna 45G, 10-709 Olsztyn, Poland
| | - Jacek Makinia
- Faculty of Civil and Environmental Engineering, Gdansk University of Technology, Narutowicza Street 11/12, 80-233 Gdansk, Poland.
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Aoi R, Miyamoto T, Yokota A, Ota Y, Fujitani H, Tsuneda S, Noda N. MazF Endoribonucleolytic Toxin Conserved in Nitrospira Specifically Cleaves the AACU, AACG, and AAUU Motifs. Toxins (Basel) 2020; 12:E287. [PMID: 32365819 DOI: 10.3390/toxins12050287] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/28/2020] [Accepted: 04/28/2020] [Indexed: 11/27/2022] Open
Abstract
MazF is an endoribonucleolytic toxin that cleaves intracellular RNAs in sequence-specific manners. It is liberated in bacterial cells in response to environmental changes and is suggested to contribute to bacterial survival by inducing translational regulation. Thus, determining the cleavage specificity provides insights into the physiological functions of MazF orthologues. Nitrospira, detected in a wide range of environments, is thought to have evolved the ability to cope with their surroundings. To investigate the molecular mechanism of its environmental adaption, a MazF module from Nitrospira strain ND1, which was isolated from the activated sludge of a wastewater treatment plant, is examined in this study. By combining a massive parallel sequencing method and fluorometric assay, we detected that this functional RNA-cleaving toxin specifically recognizes the AACU, AACG, and AAUU motifs. Additionally, statistical analysis suggested that this enzyme regulates various specific functions in order to resist environmental stresses.
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40
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Hong Y, Jiao L, Wu J. New primers, taxonomic database and cut-off value for processing nxrB gene high-throughput sequencing data by MOTHUR. J Microbiol Methods 2020; 173:105939. [PMID: 32360381 DOI: 10.1016/j.mimet.2020.105939] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/28/2020] [Accepted: 04/28/2020] [Indexed: 11/24/2022]
Abstract
To analyse the diversity of Nitrospira with functional nxrB genes, we designed and optimized a new primer set, Nxr-f27/Nxr-r617, and constructed a database for taxonomic classification. We also propose a cut-off value for processing the high-throughput sequencing data with MOTHUR.
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41
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Vergara E, Neira G, González C, Cortez D, Dopson M, Holmes DS. Evolution of Predicted Acid Resistance Mechanisms in the Extremely Acidophilic Leptospirillum Genus. Genes (Basel) 2020; 11:E389. [PMID: 32260256 DOI: 10.3390/genes11040389] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/02/2020] [Accepted: 03/04/2020] [Indexed: 02/01/2023] Open
Abstract
Organisms that thrive in extremely acidic environments (≤pH 3.5) are of widespread importance in industrial applications, environmental issues, and evolutionary studies. Leptospirillum spp. constitute the only extremely acidophilic microbes in the phylogenetically deep-rooted bacterial phylum Nitrospirae. Leptospirilli are Gram-negative, obligatory chemolithoautotrophic, aerobic, ferrous iron oxidizers. This paper predicts genes that Leptospirilli use to survive at low pH and infers their evolutionary trajectory. Phylogenetic and other bioinformatic approaches suggest that these genes can be classified into (i) "first line of defense", involved in the prevention of the entry of protons into the cell, and (ii) neutralization or expulsion of protons that enter the cell. The first line of defense includes potassium transporters, predicted to form an inside positive membrane potential, spermidines, hopanoids, and Slps (starvation-inducible outer membrane proteins). The "second line of defense" includes proton pumps and enzymes that consume protons. Maximum parsimony, clustering methods, and gene alignments are used to infer the evolutionary trajectory that potentially enabled the ancestral Leptospirillum to transition from a postulated circum-neutral pH environment to an extremely acidic one. The hypothesized trajectory includes gene gains/loss events driven extensively by horizontal gene transfer, gene duplications, gene mutations, and genomic rearrangements.
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Cui B, Yang Q, Liu X, Huang S, Yang Y, Liu Z. The effect of dissolved oxygen concentration on long-term stability of partial nitrification process. J Environ Sci (China) 2020; 90:343-351. [PMID: 32081330 DOI: 10.1016/j.jes.2019.12.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 12/08/2019] [Accepted: 12/17/2019] [Indexed: 06/10/2023]
Abstract
Dissolved oxygen (DO) concentration is regarded as one of the crucial factors to influence partial nitrification process. However, achieving and keeping stable partial nitrification under different DO concentrations were widely reported. The mechanism of DO concentration influencing partial nitrification is still unclear. Therefore, in this study two same sequencing batch reactors (SBRs) cultivated same seeding sludge were built up with real-time control strategy. Different DO concentrations were controlled in SBRs to explore the effect of DO concentration on the long-term stability of partial nitrification process at room temperature. It was discovered that ammonium oxidation rate (AOR) was inhibited when DO concentration decreased from 2.5 to 0.5 mg/L. The abundance of Nitrospira increased from 1011.5 to 1013.7 copies/g DNA, and its relative percentage increased from 0.056% to 3.2% during 190 operational cycles, causing partial nitrification gradually turning into complete nitrification process. However, when DO was 2.5 mg/L the abundance of Nitrospira was stable and AOB was always kept at 1010.7 copies/g DNA. High AOR was maintained, and stable partial nitrification process was kept. Ammonia oxidizing bacteria (AOB) activity was significantly higher than nitrite oxidizing bacteria (NOB) activity at DO of 2.5 mg/L, which was crucial to maintain excellent nitrite accumulation performance.
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Affiliation(s)
- Bin Cui
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Qing Yang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China.
| | - Xiuhong Liu
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Siting Huang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Yubing Yang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Zhibin Liu
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
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Luo Y, Yao J, Wang X, Zheng M, Guo D, Chen Y. Efficient municipal wastewater treatment by oxidation ditch process at low temperature: Bacterial community structure in activated sludge. Sci Total Environ 2020; 703:135031. [PMID: 31726299 DOI: 10.1016/j.scitotenv.2019.135031] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/10/2019] [Accepted: 10/16/2019] [Indexed: 06/10/2023]
Abstract
Temperature is a key element affecting the activity of microorganisms in activated sludge. Low water temperature generally leads to decreasing wastewater treatment efficiency and destroying sludge settleability. In this study, activated sludge samples from a municipal wastewater treatment plant (WWTP) implementing oxidation ditch process was used to investigate the bacterial community characteristics of a system that operates well in a cold region (Xinjiang, China) by high-throughput 16S rRNA gene sequencing. The results showed that the influent temperature was 7-12 °C in winter and 13-17 °C in summer, while the sludge volume index (SVI) of samples was between 51 and 74 mL/g. The average removal efficiencies for chemical oxygen demand (COD), biochemical oxygen demand (BOD5), suspended solid (SS), ammonia nitrogen (NH4+-N), total nitrogen (TN), and total phosphorus (TP) were 94%, 95%, 95%, 91%, 73% and 89%, respectively. The bacteria were distributed in 32 phyla and 559 genera. The dominant phyla were Proteobacteria (28.85-48.45%), Bacteroidetes (20.00-31.22%), Chloroflexi (3.59-12.23%), Actinobacteria (1.58-15.54%) and Firmicutes (1.38-10.49%). The dominant genera were Saprospiraceae_norank (4.41-12.23%), Comamonadaceae_unclassified (3.82-8.83%), Anaerolineaceae_norank (1.39-9.35%), Dokdonella (1.13-11.26%), Candidatus_Microthrix (0.26-7.50%), Flavobacterium (0.32-8.14%), Ferribacterium (0.36-5.19%) and Nitrospira (0.084-5.37%), which were different from those found in warm-region WWTPs. Contrary to previous studies, the relative abundance of ammonia-oxidizing bacteria (AOB; Nitrosomonas and Nitrosomonadaceae) and nitrite-oxidizing bacteria (NOB; Nitrospira) increased when the temperature decreased. The successful operation of this WWTP suggests that cold-region WWTPs can achieve good pollutants removal efficiency by simultaneously maintaining an ultra-low sludge load and high dissolved oxygen concentration in the oxidation ditch. The findings of this study provide fundamental knowledge required for an efficient and stable operation of WWTPs in cold regions.
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Affiliation(s)
- Yuanshuang Luo
- College of Resources and Environmental Science, Xinjiang University, Urumqi, Xinjiang, China
| | - Junqin Yao
- College of Resources and Environmental Science, Xinjiang University, Urumqi, Xinjiang, China.
| | - Xiyuan Wang
- College of Resources and Environmental Science, Xinjiang University, Urumqi, Xinjiang, China
| | - Meiying Zheng
- Altay Sewage Purification and Management Institute, Altay, Xinjiang, China
| | - Deyong Guo
- Altay Sewage Purification and Management Institute, Altay, Xinjiang, China
| | - Yinguang Chen
- College of Resources and Environmental Science, Xinjiang University, Urumqi, Xinjiang, China; College of Environmental Science and Engineering, Tongji University, Shanghai, China
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How SW, Chua ASM, Ngoh GC, Nittami T, Curtis TP. Enhanced nitrogen removal in an anoxic-oxic-anoxic process treating low COD/N tropical wastewater: Low-dissolved oxygen nitrification and utilization of slowly-biodegradable COD for denitrification. Sci Total Environ 2019; 693:133526. [PMID: 31376760 DOI: 10.1016/j.scitotenv.2019.07.332] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/17/2019] [Accepted: 07/20/2019] [Indexed: 06/10/2023]
Abstract
Many wastewater treatment plants (WWTPs) operating in biological nitrogen removal activated sludge process in the tropics are facing the pressure of increasingly stringent effluent standards while seeking solutions to reduce the plants' energy consumption and operating cost. This study investigated the feasibility of applying low-dissolved oxygen (low-DO) nitrification and utilizing slowly-biodegradable chemical oxygen demand (sbCOD) for denitrification, which helps to reduce energy usage and operating cost in treating low soluble COD-to-nitrogen tropical wastewater. The tropical wastewater was first characterized using wastewater fractionation and respirometry batch tests. Then, a lab-scale sequencing batch reactor (SBR) was operated to evaluate the long-term stability of low-DO nitrification and utilizing sbCOD for denitrification in an anoxic-oxic (AO) process treating tropical wastewater. The wastewater fractionation experiment revealed that particulate settleable solids (PSS) in the wastewater provided slowly-biodegradable COD (sbCOD), which made up the major part (51 ± 10%) of the total COD. The PSS hydrolysis rate constant at tropical temperature (30 °C) was 2.5 times higher than that at 20 °C, suggesting that sbCOD may be utilized for denitrification. During the SBR operation, high nitrification efficiency (93 ± 6%) was attained at low-DO condition (0.9 ± 0.1 mg O2/L). Utilizing sbCOD for post-anoxic denitrification in the SBR reduced the effluent nitrate concentration. Quantitative polymerase chain reaction, 16S rRNA amplicon sequencing and fluorescence in-situ hybridization revealed that the genus Nitrospira was a dominant nitrifier. 16S rRNA amplicon sequencing result suggested that 50% of the Nitrospira-related operational taxonomic units were affiliated with comammox, which may imply that the low-DO condition and the warm wastewater promoted their growth. The nitrogen removal in a tropical AO process was enhanced by incorporating low-DO nitrification and utilizing sbCOD for post-anoxic denitrification, which contributes to an improved energy sustainability of WWTPs.
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Affiliation(s)
- Seow Wah How
- Department of Chemical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Adeline Seak May Chua
- Department of Chemical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Gek Cheng Ngoh
- Department of Chemical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Tadashi Nittami
- Division of Materials Science and Chemical Engineering, Faculty of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Thomas P Curtis
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
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Gülay A, Fowler SJ, Tatari K, Thamdrup B, Albrechtsen HJ, Al-Soud WA, Sørensen SJ, Smets BF. DNA- and RNA-SIP Reveal Nitrospira spp. as Key Drivers of Nitrification in Groundwater-Fed Biofilters. mBio 2019; 10:e01870-19. [PMID: 31690672 DOI: 10.1128/mBio.01870-19] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Nitrification, the oxidative process converting ammonia to nitrite and nitrate, is driven by microbes and plays a central role in the global nitrogen cycle. Our earlier investigations based on 16S rRNA and amoA amplicon analysis, amoA quantitative PCR and metagenomics of groundwater-fed biofilters indicated a consistently high abundance of comammox Nitrospira Here, we hypothesized that these nonclassical nitrifiers drive ammonia-N oxidation. Hence, we used DNA and RNA stable isotope probing (SIP) coupled with 16S rRNA amplicon sequencing to identify the active members in the biofilter community when subjected to a continuous supply of NH4 + or NO2 - in the presence of 13C-HCO3 - (labeled) or 12C-HCO3 - (unlabeled). Allylthiourea (ATU) and sodium chlorate were added to inhibit autotrophic ammonia- and nitrite-oxidizing bacteria, respectively. Our results confirmed that lineage II Nitrospira dominated ammonia oxidation in the biofilter community. A total of 78 (8 by RNA-SIP and 70 by DNA-SIP) and 96 (25 by RNA-SIP and 71 by DNA-SIP) Nitrospira phylotypes (at 99% 16S rRNA sequence similarity) were identified as complete ammonia- and nitrite-oxidizing, respectively. We also detected significant HCO3 - uptake by Acidobacteria subgroup10, Pedomicrobium, Rhizobacter, and Acidovorax under conditions that favored ammonia oxidation. Canonical Nitrospira alone drove nitrite oxidation in the biofilter community, and activity of archaeal ammonia-oxidizing taxa was not detected in the SIP fractions. This study provides the first in situ evidence of ammonia oxidation by comammox Nitrospira in an ecologically relevant complex microbiome.IMPORTANCE With this study we provide the first in situ evidence of ecologically relevant ammonia oxidation by comammox Nitrospira in a complex microbiome and document an unexpectedly high H13CO3 - uptake and growth of proteobacterial and acidobacterial taxa under ammonia selectivity. This finding raises the question of whether comammox Nitrospira is an equally important ammonia oxidizer in other environments.
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Bartelme RP, Smith MC, Sepulveda-Villet OJ, Newton RJ. Component Microenvironments and System Biogeography Structure Microorganism Distributions in Recirculating Aquaculture and Aquaponic Systems. mSphere 2019; 4:e00143-19. [PMID: 31270175 DOI: 10.1128/mSphere.00143-19] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Recirculating aquaculture systems (RAS) are agroecosystems for intensive on-land cultivation of products of fisheries. Practitioners that incorporate edible plant production into RAS refer to these facilities as aquaponic systems (AP). RAS have the potential to offset declining production levels of wild global fisheries while reducing waste and product distance to market, but system optimization is needed to reduce costs. Both RAS and AP rely on microbial consortia for maintaining water quality and promoting fish/plant health, but little is known about the microorganisms actually present. This lack of knowledge prevents optimization of designs and operational controls to target the growth of beneficial microbial species or consortia. The significance of our research is in identifying the common microorganisms that inhabit production RAS and AP and the operational factors that influence which microorganisms colonize and become abundant. Identifying these organisms is a first step toward advanced control of microbial activities that improve reproducibility and reduce costs. Flowthrough and pond aquaculture system microbiome management practices aim to mitigate fish disease and stress. However, the operational success of recirculating aquaculture systems (RAS) depends directly on system microbial community activities. In RAS, each component environment is engineered for a specific microbial niche for waste management, as the water continuously flowing through the system must be processed before returning to the rearing tank. In this study, we compared waste management component microbiomes (rearing tank water, pH correction tank, solid-waste clarifier, biofilter, and degassing tower) within a commercial-scale freshwater RAS by high-throughput 16S rRNA gene sequencing. To assess consistency among freshwater RAS microbiomes, we also compared the microbial community compositions of six aquaculture and aquaponic farms. Community assemblages reflected site and source water relationships, and the presence of a hydroponic subsystem was a major community determinant. In contrast to the facility-specific community composition, some sequence variants, mainly classified into Flavobacterium, Cetobacterium, the family Sphingomonadaceae, and nitrifying guilds of ammonia-oxidizing archaea and Nitrospira, were common across all facilities. The findings of this study suggest that, independently of system design, core taxa exist across RAS rearing similar fish species but that system design informs the individual aquatic microbiome assemblages. Future RAS design would benefit from understanding the roles of these core taxa and then capitalizing on their activities to further reduce system waste/added operational controls. IMPORTANCE Recirculating aquaculture systems (RAS) are agroecosystems for intensive on-land cultivation of products of fisheries. Practitioners that incorporate edible plant production into RAS refer to these facilities as aquaponic systems (AP). RAS have the potential to offset declining production levels of wild global fisheries while reducing waste and product distance to market, but system optimization is needed to reduce costs. Both RAS and AP rely on microbial consortia for maintaining water quality and promoting fish/plant health, but little is known about the microorganisms actually present. This lack of knowledge prevents optimization of designs and operational controls to target the growth of beneficial microbial species or consortia. The significance of our research is in identifying the common microorganisms that inhabit production RAS and AP and the operational factors that influence which microorganisms colonize and become abundant. Identifying these organisms is a first step toward advanced control of microbial activities that improve reproducibility and reduce costs.
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Mundinger AB, Lawson CE, Jetten MSM, Koch H, Lücker S. Cultivation and Transcriptional Analysis of a Canonical Nitrospira Under Stable Growth Conditions. Front Microbiol 2019; 10:1325. [PMID: 31333593 PMCID: PMC6606698 DOI: 10.3389/fmicb.2019.01325] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 05/28/2019] [Indexed: 12/20/2022] Open
Abstract
Nitrite-oxidizing bacteria (NOB) are vital players in the global nitrogen cycle that convert nitrite to nitrate during the second step of nitrification. Within this functional guild, members of the genus Nitrospira are most widespread, phylogenetically diverse, and physiologically versatile, and they drive nitrite oxidation in many natural and engineered ecosystems. Despite their ecological and biotechnological importance, our understanding of their energy metabolism is still limited. A major bottleneck for a detailed biochemical characterization of Nitrospira is biomass production, since they are slow-growing and fastidious microorganisms. In this study, we cultivated Nitrospira moscoviensis under nitrite-oxidizing conditions in a continuous stirred tank reactor (CSTR) system. This cultivation setup enabled accurate control of physicochemical parameters and avoided fluctuating levels of their energy substrate nitrite, thus ensuring constant growth conditions and furthermore allowing continuous biomass harvesting. Transcriptomic analyses under these conditions supported the predicted core metabolism of N. moscoviensis, including expression of all proteins required for carbon fixation via the reductive tricarboxylic acid cycle, assimilatory nitrite reduction, and the complete respiratory chain. Here, simultaneous expression of multiple copies of respiratory complexes I and III suggested functional differentiation. The transcriptome also indicated that the previously assumed membrane-bound nitrite oxidoreductase (NXR), the enzyme catalyzing nitrite oxidation, is formed by three soluble subunits. Overall, the transcriptomic data greatly refined our understanding of the metabolism of Nitrospira. Moreover, the application of a CSTR to cultivate Nitrospira is an important foundation for future proteomic and biochemical characterizations, which are crucial for a better understanding of these fascinating microorganisms.
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Affiliation(s)
- Aniela B Mundinger
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Christopher E Lawson
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, United States
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Hanna Koch
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Sebastian Lücker
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
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Vandekerckhove TGL, Kerckhof FM, De Mulder C, Vlaeminck SE, Boon N. Determining stoichiometry and kinetics of two thermophilic nitrifying communities as a crucial step in the development of thermophilic nitrogen removal. Water Res 2019; 156:34-45. [PMID: 30904709 DOI: 10.1016/j.watres.2019.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/08/2019] [Accepted: 03/09/2019] [Indexed: 06/09/2023]
Abstract
Nitrification and denitrification, the key biological processes for thermophilic nitrogen removal, have separately been established in bioreactors at 50 °C. A well-characterized set of kinetic parameters is essential to integrate these processes while safeguarding the autotrophs performing nitrification. Knowledge on thermophilic nitrifying kinetics is restricted to isolated or highly enriched batch cultures, which do not represent bioreactor conditions. This study characterized the stoichiometry and kinetics of two thermophilic (50 °C) nitrifying communities. The most abundant ammonia oxidizing archaea (AOA) were related to the Nitrososphaera genus, clustering relatively far from known species Nitrososphaera gargensis (95.5% 16S rRNA gene sequence identity). The most abundant nitrite oxidizing bacteria (NOB) were related to Nitrospira calida (97% 16S rRNA gene sequence identity). The nitrification biomass yield was 0.20-0.24 g VSS g-1 N, resulting mainly from a high AOA yield (0.16-0.20 g VSS g-1 N), which was reflected in a high AOA abundance in the community (57-76%) compared to NOB (5-11%). Batch-wise determination of decay rates (AOA: 0.23-0.29 d-1; NOB: 0.32-0.43 d-1) rendered an overestimation compared to in situ estimations of overall decay rate (0.026-0.078 d-1). Possibly, the inactivation rate rather than the actual decay rate was determined in batch experiments. Maximum growth rates of AOA and NOB were 0.12-0.15 d-1 and 0.13-0.33 d-1 respectively. NOB were susceptible to nitrite, opening up opportunities for shortcut nitrogen removal. However, NOB had a similar growth rate and oxygen affinity (0.15-0.55 mg O2 L-1) as AOA and were resilient towards free ammonia (IC50 > 16 mg NH3-N L-1). This might complicate NOB outselection using common practices to establish shortcut nitrogen removal (SRT control; aeration control; free ammonia shocks). Overall, the obtained insights can assist in integrating thermophilic conversions and facilitate single-sludge nitrification/denitrification.
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Affiliation(s)
- Tom G L Vandekerckhove
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Gent, Belgium
| | - Frederiek-Maarten Kerckhof
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Gent, Belgium
| | - Chaïm De Mulder
- BIOMATH, Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, 9000, Gent, Belgium
| | - Siegfried E Vlaeminck
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Gent, Belgium; Research Group of Sustainable Energy, Air and Water Technology, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerpen, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Gent, Belgium.
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Aburto-Medina A, Shahsavari E, Salzman SA, Kramer A, Ball AS, Allinson G. Elucidation of the microbial diversity in rivers in south-west Victoria, Australia impacted by rural agricultural contamination (dairy farming). Ecotoxicol Environ Saf 2019; 172:356-363. [PMID: 30731266 DOI: 10.1016/j.ecoenv.2019.01.112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 01/24/2019] [Accepted: 01/31/2019] [Indexed: 06/09/2023]
Abstract
We assessed the water quality of south-west Victorian rivers impacted by the dairy industry using traditional water quality assessment together with culture-dependent (colilert/enterolert) and also culture-independent (next generation sequencing) microbial methods. The aim of the study was to identify relationships/associations between dairy farming intensity and water contamination. Water samples with high total and faecal coliforms (>1000 MPN cfu/100 ml), and with high nitrogen levels (TN) were observed in zones with a high proportion of dairy farming. Members of the genus Nitrospira, Rhodobacter and Rhodoplanes were predominant in such high cattle density zones. Samples from sites in zones with lower dairy farming activities registered faecal coliform numbers within the permissible limits (<1000 MPN cfu/100 ml) and showed the presence of a wide variety of microorganisms. However, no bacterial pathogens were found in the river waters regardless of the proportion of cattle. The data suggests that using the spatially weighted proportion of land used for dairy farming is a useful way to target at-risk sub-catchments across south west Victoria; further work is required to confirm that this approach is applicable in other regions.
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Affiliation(s)
- Arturo Aburto-Medina
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, Victoria 3083, Australia.
| | - Esmaeil Shahsavari
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, Victoria 3083, Australia
| | - Scott A Salzman
- Department of Information Systems and Business Analytics, Deakin University, Warrnambool, Victoria 3280 Australia
| | - Andrew Kramer
- Environment Protection Authority Victoria, Centre for Applied Sciences, Ernest Jones Drive, Macleod, Victoria 3085 Australia; Waikato Regional Council, Private Bag 3038, Waikato Mail Centre, Hamilton 3240, New Zealand
| | - Andrew S Ball
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, Victoria 3083, Australia
| | - Graeme Allinson
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Melbourne, Victoria 3001, Australia
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Wegen S, Nowka B, Spieck E. Low Temperature and Neutral pH Define " Candidatus Nitrotoga sp." as a Competitive Nitrite Oxidizer in Coculture with Nitrospira defluvii. Appl Environ Microbiol 2019; 85:e02569-18. [PMID: 30824434 DOI: 10.1128/AEM.02569-18] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 02/07/2019] [Indexed: 11/20/2022] Open
Abstract
Nitrification is an essential process for N removal in activated sludge to avoid toxicity of ammonium and nitrite. Besides Nitrospira, "Candidatus Nitrotoga" has been identified as a key nitrite-oxidizing bacterium (NOB) performing the second step of nitrification, nitrite oxidation to nitrate, in wastewater treatment plants (WWTPs). However, the driving forces for the dominance of Nitrotoga in certain plants have often remained unclear and could not be explained solely by temperature effects. In this study, we characterized the physiology of the ammonium-dependent Nitrotoga sp. BS with regard to temperature and pH variations and evaluated its competitiveness against Nitrospira defluvii Both NOB originated from the same WWTP and shared a comparable pH optimum of 7.3. Based on these results, coculturing experiments with these NOB were performed in batch reactors operated at either 17°C or 22°C to compare their abundances under optimal (pH 7.4) or suboptimal (pH 6.4) conditions using 1 mM nitrite. As revealed by quantitative PCR (qPCR), fluorescence in situ hybridization (FISH), and 16S amplicon sequencing, Nitrotoga sp. BS was clearly favored by its optimal growth parameters and dominated over Ns. defluvii at pH 7.4 and 17°C, whereas a pH of 6.4 was more selective for Ns. defluvii Our synthetic communities revealed that niche differentiation of NOB is influenced by a complex interaction of environmental parameters and has to be evaluated for single species.IMPORTANCE "Ca. Nitrotoga" is a NOB of high environmental relevance, but physiological data exist for only a few representatives. Initially, it was detected in specialized niches of low temperature and low nitrite concentrations, but later on, its ubiquitous distribution revealed its critical role for N removal in engineered systems like WWTPs. In this study, we analyzed the competition between Nitrotoga and Nitrospira in bioreactors and identified conditions where the K strategist Ns. defluvii was almost replaced by Nitrotoga sp. BS. We show that the pH value is an important factor that regulates the composition of the nitrite-oxidizing enrichment with a dominance of Nitrotoga sp. BS versus Ns. defluvii at a neutral pH of 7.4 in combination with a temperature of 17°C. The physiological diversity of novel Nitrotoga cultures improves our knowledge about niche differentiation of NOB with regard to functional nitrification under suboptimal conditions.
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