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Nguyen Quoc B, Peng B, De Clippeleir H, Winkler MKH. Case study: Bioaugmenting the comammox dominated biomass from B-stage to enhance nitrification in A-stage at Blue Plains AWWTP. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2024; 96:e11005. [PMID: 38407520 DOI: 10.1002/wer.11005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/27/2024]
Abstract
A comprehensive case study was undertaken at the Blue Plains wastewater treatment plant (WWTP) to explore the bioaugmentation technique of introducing nitrifying sludge into the non-nitrifying stage over the course of two operational years. This innovative approach involved the return of waste activated sludge (WAS) from the biological nutrient removal (BNR) system to enhance the nitrification in the high carbon removal rate system. The complete ammonia oxidizer (comammox) Nitrospira Nitrosa was identified as the main nitrifier in the system. Bioaugmentation was shown to be successful as nitrifiers returned from BNR were able to increase the nitrifying activity of the high carbon removal rate system. There was a positive correlation between returned sludge from the BNR stage and the specific total kjeldahl nitrogen (TKN) removal rate in A stage. The bioaugmentation process resulted in a remarkable threefold increase in the specific TKN removal rate within the A stage. Result suggested that recycling of WAS is a simple technique to bio-augment a low SRT system with nitrifiers and add ammonia oxidation to a previously non-nitrifying stage. The results from this case study hold the potential for applicable implications for other WWTPs that have a similar operational scheme to Blue Plains, allowing them to reuse WAS from the B stage, previously considered waste, to enhance nitrification and thus improving overall nitrogen removal performance. PRACTITIONER POINTS: Comammox identifying as main nitrifier in the B stage. Comammox enriched sludge from B stage successfully bio-augmented the East side of A stage up to threefold. Bioaugmentation of comammox in the West side of A stage was potentially inhibited by the gravity thickened overflow. Sludge returned from B stage to A stage can improve nitrification with a very minor retrofits and short startup times.
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Affiliation(s)
- Bao Nguyen Quoc
- Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA
| | - Bo Peng
- DC Water and Sewer Authority, Washington, District of Columbia, USA
| | | | - Mari-Karoliina H Winkler
- Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA
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Rempfert KR, Nothaft DB, Kraus EA, Asamoto CK, Evans RD, Spear JR, Matter JM, Kopf SH, Templeton AS. Subsurface biogeochemical cycling of nitrogen in the actively serpentinizing Samail Ophiolite, Oman. Front Microbiol 2023; 14:1139633. [PMID: 37152731 PMCID: PMC10160414 DOI: 10.3389/fmicb.2023.1139633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 03/15/2023] [Indexed: 05/09/2023] Open
Abstract
Nitrogen (N) is an essential element for life. N compounds such as ammonium ( NH 4 + ) may act as electron donors, while nitrate ( NO 3 - ) and nitrite ( NO 2 - ) may serve as electron acceptors to support energy metabolism. However, little is known regarding the availability and forms of N in subsurface ecosystems, particularly in serpentinite-hosted settings where hydrogen (H2) generated through water-rock reactions promotes habitable conditions for microbial life. Here, we analyzed N and oxygen (O) isotope composition to investigate the source, abundance, and cycling of N species within the Samail Ophiolite of Oman. The dominant dissolved N species was dependent on the fluid type, with Mg2+- HCO 3 - type fluids comprised mostly of NO 3 - , and Ca2+-OH- fluids comprised primarily of ammonia (NH3). We infer that fixed N is introduced to the serpentinite aquifer as NO 3 - . High concentrations of NO 3 - (>100 μM) with a relict meteoric oxygen isotopic composition (δ18O ~ 22‰, Δ17O ~ 6‰) were observed in shallow aquifer fluids, indicative of NO 3 - sourced from atmospheric deposition (rainwater NO 3 - : δ18O of 53.7‰, Δ17O of 16.8‰) mixed with NO 3 - produced in situ through nitrification (estimated endmember δ18O and Δ17O of ~0‰). Conversely, highly reacted hyperalkaline fluids had high concentrations of NH3 (>100 μM) with little NO 3 - detectable. We interpret that NH3 in hyperalkaline fluids is a product of NO 3 - reduction. The proportionality of the O and N isotope fractionation (18ε / 15ε) measured in Samail Ophiolite NO 3 - was close to unity (18ε / 15ε ~ 1), which is consistent with dissimilatory NO 3 - reduction with a membrane-bound reductase (NarG); however, abiotic reduction processes may also be occurring. The presence of genes commonly involved in N reduction processes (narG, napA, nrfA) in the metagenomes of biomass sourced from aquifer fluids supports potential biological involvement in the consumption of NO 3 - . Production of NH 4 + as the end-product of NO 3 - reduction via dissimilatory nitrate reduction to ammonium (DNRA) could retain N in the subsurface and fuel nitrification in the oxygenated near surface. Elevated bioavailable N in all sampled fluids indicates that N is not likely limiting as a nutrient in serpentinites of the Samail Ophiolite.
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Affiliation(s)
- Kaitlin R. Rempfert
- Department of Geological Sciences, University of Colorado, Boulder, CO, United States
- *Correspondence: Kaitlin R. Rempfert
| | - Daniel B. Nothaft
- Department of Geological Sciences, University of Colorado, Boulder, CO, United States
| | - Emily A. Kraus
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, United States
| | - Ciara K. Asamoto
- Department of Geological Sciences, University of Colorado, Boulder, CO, United States
| | - R. Dave Evans
- School of Biological Sciences, Washington State University, Pullman, WA, United States
| | - John R. Spear
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, United States
- Quantitative Biosciences and Engineering, Colorado School of Mines, Golden, CO, United States
| | - Juerg M. Matter
- National Oceanography Centre, University of Southampton, Southampton, United Kingdom
| | - Sebastian H. Kopf
- Department of Geological Sciences, University of Colorado, Boulder, CO, United States
| | - Alexis S. Templeton
- Department of Geological Sciences, University of Colorado, Boulder, CO, United States
- Alexis S. Templeton
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Wu L, Jia C, Huang S, Yu K, Luo A, Peng Y. Nitrite oxidation in oxygen-deficient conditions during landfill leachate treatment. ENVIRONMENTAL RESEARCH 2022; 214:114090. [PMID: 35970379 DOI: 10.1016/j.envres.2022.114090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 08/06/2022] [Accepted: 08/07/2022] [Indexed: 06/15/2023]
Abstract
Until recently, all known nitrite oxidation occurred in oxygen-rich conditions but now the oxidation of nitrite into nitrate within a low oxygen or anoxic environment has been observed in the ocean. However, this phenomenon is rarely reported in wastewater treatments and its mechanism is unknown. In this study, the partial nitrification and nitrite oxidation were conducted in no enough oxygen in order to remove nitrogen from landfill leachate, save energy, and save money. The results show that the NH4+-N removal efficiency was 99.4%. During phase I of the anaerobic sequential batch reactor (ASBR), no change in Chemical Oxygen Demand (COD) and ammonium were detected. The nitrite concentration decreased from 107 ± 3 mg/L to 0.16 mg/L during 96 h of oxygen- deficiency, while NO3--N increased from 152.5 ± 3 mg/L to 253.65 ± 3 mg/L. The main microorganisms involved in this reaction in the ASBR were Nitrite-Oxidizing Bacteria (NOB), including Nitrospira and Nitrolancea, their relative abundances were 3.56% and 0.13%, respectively. The major NOB (Nitrospira) were confirmed by the further metagenomic binning analysis. This finding shows that nitrite oxidation can occur in oxygen-deficient conditions with specific NOB.
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Affiliation(s)
- Lina Wu
- Key Laboratory of Urban Stormwater System and Water Environment (Ministry of Education), Beijing University of Civil Engineering and Architecture, Beijing, 100044, China.
| | - Chunfang Jia
- Key Laboratory of Urban Stormwater System and Water Environment (Ministry of Education), Beijing University of Civil Engineering and Architecture, Beijing, 100044, China
| | - Shan Huang
- Department of Civil and Environmental Engineering, Princeton University, NJ 08544, USA
| | - Ke Yu
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Anteng Luo
- Key Laboratory of Urban Stormwater System and Water Environment (Ministry of Education), Beijing University of Civil Engineering and Architecture, Beijing, 100044, China
| | - Yongzhen Peng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Centre of Beijing, Beijing University of Technology, Beijing, 100124, China.
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Deterministic Factors Determine the Comammox Community Composition in the Pearl River Estuary Ecosystem. Microbiol Spectr 2022; 10:e0101622. [PMID: 35913204 PMCID: PMC9431512 DOI: 10.1128/spectrum.01016-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Complete ammonia oxidizers (comammox) have been widely detected in riverine and estuarine ecosystems. However, knowledge about the process of comammox community assembly from freshwater to marine environments is still limited. Here, based on deep sequencing, we investigated the community composition of comammox along a salinity gradient in the Pearl River Estuary (PRE), South China. Our results showed that comammox microorganisms in the PRE sediments were extremely diverse and displayed distinct distributional patterns between upstream and downstream habitats. Quantitative PCR demonstrated that comammox was the dominant ammonia-oxidizing microorganism (AOM) in the PRE upstream sediments, and ammonia-oxidizing archaea (AOA) dominated the PRE downstream sediments, while ammonia-oxidizing bacteria (AOB) were not dominant in any section of the PRE. Neutral modeling revealed that stochastic processes explained a limited part of the variation in the comammox community. The majority of beta nearest-taxon index values were higher than 2, indicating that comammox community assembly in the PRE sediments was better explained through a deterministic process than through a stochastic process. Salinity and total nitrogen were the most important contributing factors that shaped the comammox community. This study expanded the current knowledge of the diversity and niche preference of comammox in the estuarine ecosystem, and further enhances our understanding of the assembly of comammox community from freshwater to marine environments. IMPORTANCE Microbial communities are shaped by stochastic (emigration, immigration, birth, death, and genetic drift of species) and deterministic (e.g., environmental factors) processes. However, it remains unknown as to which type of process is more important in influencing the comammox community assembly from freshwater to marine environments. In this study, we compared the relative importance of stochastic and deterministic processes in shaping the assembly of the comammox community, which demonstrated that the deterministic process was more important in determining the community assembly patterns in the PRE ecosystem.
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Zhang SN, Wang JG, Wang DQ, Jiang QY, Quan ZX. Abundance and Niche Differentiation of Comammox in the Sludges of Wastewater Treatment Plants That Use the Anaerobic-Anoxic-Aerobic Process. Life (Basel) 2022; 12:life12070954. [PMID: 35888046 PMCID: PMC9322089 DOI: 10.3390/life12070954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 11/27/2022] Open
Abstract
Complete ammonia oxidizers (comammox), which directly oxidize ammonia to nitrate, were recently identified and found to be ubiquitous in artificial systems. Research on the abundance and niche differentiation of comammox in the sludges of wastewater treatment plants (WWTPs) would be useful for improving the nitrogen removal efficiency of WWTPs. Here, we investigated the relative abundance and diversity of comammox in fifteen sludges of five WWTPs that use the anaerobic−anoxic−aerobic process in Jinan, China, via quantitative polymerase chain reaction and high-throughput sequencing of the 16S rRNA gene and ammonia monooxygenase gene. In the activated sludges in the WWTPs, comammox clade A.1 was widely distributed and mostly comprised Candidatus Nitrospira nitrosa-like comammox (>98% of all comammox). The proportion of this clade was negatively correlated (p < 0.01) with the dissolved oxygen (DO) level (1.7−8 mg/L), and slight pH changes (7.20−7.70) affected the structure of the comammox populations. Nitrospira lineage I frequently coexisted with Nitrosomonas, which generally had a significant positive correlation (p < 0.05) with the DO level. Our study provided an insight into the structure of comammox and other nitrifier populations in WWTPs that use the anaerobic−anoxic−aerobic process, broadening the knowledge about the effects of DO on comammox and other nitrifiers.
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Affiliation(s)
| | | | | | - Qiu-Yue Jiang
- Correspondence: (Q.-Y.J.); (Z.-X.Q.); Tel.: +86-21-3124-0665 (Z.-X.Q.)
| | - Zhe-Xue Quan
- Correspondence: (Q.-Y.J.); (Z.-X.Q.); Tel.: +86-21-3124-0665 (Z.-X.Q.)
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Fan Y, Zhang M, Cheng J, Yong D, Ji J, Wu Q, He C. Elucidating nitrifying performance, nitrite accumulation and microbial community in a three-stage plug flow moving bed biofilm reactor (PF - MBBR). CHEMOSPHERE 2022; 297:134087. [PMID: 35216986 DOI: 10.1016/j.chemosphere.2022.134087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 02/13/2022] [Accepted: 02/20/2022] [Indexed: 06/14/2023]
Abstract
A three-stage plug flow moving bed biofilm reactor (PF - MBBR, consisting of three identical chambers of N1, N2 and N3) was proposed for nitrifier enrichment using synthetic wastewater. During the stable operation, the average NH4+-N effluent was 0.67 mg/L and NH4+-N removal was as high as 97.19% with the nitrite accumulation ratio (NAR) of 54.23%, although the biofilm thickness and biomass both presented downward trends from N1 (296 μm, 2280 mg/L), N2 (248 μm, 1850 mg/L) to N3 (198 μm, 1545 mg/L). Particularly, the comparative results of three stages revealed that N2 showed the optimum NH4+-N removal (77.27%) and NAR (75.21%) in the continuous-flow, while NAR of N3 unexpectedly maintained a high level of 65.83% in the batch test, suggesting that ammonia oxidizing bacteria (AOB) accounted for absolute advantage over nitrite oxidizing bacteria (NOB). High-throughput sequencing initially verified different distribution of bacterial community structure, where N2 was far away from N1 and N3 with the lowest community richness and community diversity (operational taxonomic units (OTUs): 454(N2)<527(N3)<621(N1)). Proteobacteria (77.60%-83.09%), Bacteroidetes (1.66%-3.66%), Acidobacteria (2.28%-4.67%), and Planctomycetes (1.19%-6.63%) were the major phyla. At the genus level, AOB (mainly Nitrosomonas) accounted for 5.08% (N1), 20.74% (N2) and 14.24% (N3) while NOB (mainly Nitrospira) increased from 0.14% (N1), 7.06% (N2) to 4.91% (N3) with the total percentages of 5.22%, 27.80% and 19.15%. Finally, the application feasibility of MBBR optimization linked with nitrite (NO2--N) accumulation for deep-level nutrient removal was discussed.
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Affiliation(s)
- Yajun Fan
- College of Hydraulic Science and Engineering, Yangzhou University, Yangzhou, 225100, PR China
| | - Miao Zhang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, PR China.
| | - Jilin Cheng
- College of Hydraulic Science and Engineering, Yangzhou University, Yangzhou, 225100, PR China
| | - Daming Yong
- Yangzhou Polytechnic Institute, Yangzhou, 225127, PR China
| | - Junjie Ji
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, PR China
| | - Qichao Wu
- Yangzhou Polytechnic Institute, Yangzhou, 225127, PR China
| | - Chengda He
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, PR China
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Complete Genome Sequences of Two Phylogenetically Distinct Nitrospina Strains Isolated from the Atlantic and Pacific Oceans. Microbiol Resour Announc 2022; 11:e0010022. [PMID: 35499332 PMCID: PMC9119035 DOI: 10.1128/mra.00100-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The complete genome sequences of two chemoautotrophic nitrite-oxidizing bacteria of the genus Nitrospina are reported. Nitrospina gracilis strain Nb-211 was isolated from the Atlantic Ocean, and Nitrospina sp. strain Nb-3 was isolated from the Pacific Ocean. We report two highly similar ~3.07-Mbp genome sequences that differ by the presence of ferric iron chelator (siderophore) biosynthesis genes.
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8
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Li S, Peng L, Yang C, Song S, Xu Y. Cometabolic biodegradation of antibiotics by ammonia oxidizing microorganisms during wastewater treatment processes. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 305:114336. [PMID: 34953231 DOI: 10.1016/j.jenvman.2021.114336] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 11/27/2021] [Accepted: 12/16/2021] [Indexed: 05/04/2023]
Abstract
Studies on antibiotic removal during wastewater treatment processes are crucial since their release into the environment could bring potential threats to human health and ecosystem. Cometabolic biodegradation of antibiotics by ammonia oxidizing microorganisms (AOMs) has received special attentions due to the enhanced removal of antibiotics during nitrification processes. However, the interactions between antibiotics and AOMs are less well-elucidated. In this review, the recent research proceedings on cometabolic biodegradation of antibiotics by AOMs were summarized. Ammonia oxidizing bacteria (AOB), ammonia oxidizing archaea (AOA) and complete ammonia oxidizers (comammox) played significant roles in both nitrification and cometabolic biodegradation of antibiotics. Antibiotics at varying concentrations might pose inhibiting or stimulating effect on AOMs, influencing the microbial activity, community abundance and ammonia monooxygenase subunit A gene expression level. AOMs-induced cometabolic biodegradation products were analyzed as well as the corresponding pathways for each type of antibiotics. The effects of ammonium availability, initial antibiotic concentration, sludge retention time and temperature were assessed on the cometabolic biodegradation efficiencies of antibiotics. This work might provide further insights into the fate and removal of antibiotics during nitrification processes.
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Affiliation(s)
- Shengjun Li
- Hubei Key Laboratory of Mineral Resources Processing and Environment, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei, 430070, China; School of Resources and Environmental Engineering, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei, 430070, China
| | - Lai Peng
- Hubei Key Laboratory of Mineral Resources Processing and Environment, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei, 430070, China; School of Resources and Environmental Engineering, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei, 430070, China.
| | - Chenguang Yang
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya Hainan, 572000, China
| | - Shaoxian Song
- Hubei Key Laboratory of Mineral Resources Processing and Environment, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei, 430070, China; School of Resources and Environmental Engineering, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei, 430070, China
| | - Yifeng Xu
- Hubei Key Laboratory of Mineral Resources Processing and Environment, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei, 430070, China; School of Resources and Environmental Engineering, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei, 430070, China.
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Dacal M, García‐Palacios P, Asensio S, Wang J, Singh BK, Maestre FT. Climate change legacies contrastingly affect the resistance and resilience of soil microbial communities and multifunctionality to extreme drought. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14000] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Marina Dacal
- Instituto Multidisciplinar para el Estudio del Medio ‘Ramon Margalef’ Universidad de Alicante San Vicente del Raspeig Spain
- Departamento de Biología y Geología Física y Química Inorgánica Universidad Rey Juan Carlos Móstoles Spain
| | - Pablo García‐Palacios
- Departamento de Biología y Geología Física y Química Inorgánica Universidad Rey Juan Carlos Móstoles Spain
- Instituto de Ciencias Agrarias Consejo Superior de Investigaciones Científicas Madrid Spain
| | - Sergio Asensio
- Instituto Multidisciplinar para el Estudio del Medio ‘Ramon Margalef’ Universidad de Alicante San Vicente del Raspeig Spain
| | - Juntao Wang
- Hawkesbury Institute for the Environment Western Sydney University Penrith NSW Australia
- Global Centre for Land‐Based Innovation Western Sydney University Penrith South DC NSW Australia
| | - Brajesh K. Singh
- Hawkesbury Institute for the Environment Western Sydney University Penrith NSW Australia
- Global Centre for Land‐Based Innovation Western Sydney University Penrith South DC NSW Australia
| | - Fernando T. Maestre
- Instituto Multidisciplinar para el Estudio del Medio ‘Ramon Margalef’ Universidad de Alicante San Vicente del Raspeig Spain
- Departamento de Ecología Universidad de Alicante San Vicente del Raspeig Spain
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Hasan MN, Altaf MM, Khan NA, Khan AH, Khan AA, Ahmed S, Kumar PS, Naushad M, Rajapaksha AU, Iqbal J, Tirth V, Islam S. Recent technologies for nutrient removal and recovery from wastewaters: A review. CHEMOSPHERE 2021; 277:130328. [PMID: 33794428 DOI: 10.1016/j.chemosphere.2021.130328] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
Abstract
Water scarcity and its pollution has become a concern in recent times. The disposal of nutrient-rich (nitrogen and phosphorous) wastewater is also one of the main cause of water pollution through eutrophication, reduced dissolved oxygen that poses threat to aquatic ecosystems. As a result, nutrient removal has become a mandate apart from the removal of organics. However, the removal of nutrients from sewage is a challenging task. Conversely, conventional biological treatment processes provide little relief in nutrient removal. The treated effluents from conventional biological processes do not achieve the stringent nutrient removal disposal standard limits and become primary cause of pollution in the receiving water bodies. This has stressed upon the need for eco-friendly, low-energy and cost-efficient nutrient removal treatment technologies. Various biological treatment combinations or variants are in use for the efficient removal of nutrients. The biological processes in itself or in combination with chemical processes are preferred over technologies based solely on physico-chemical processes for its treatment performance at lower cost. This review summarizes the existing treatment processes and their possible up-gradation with the aim to accomplish the marked effluent standards for the nutrients. The concept of conventional systems and advanced systems for nutrients (nitrogen and phosphorous) removal which are already developed or under development are deeply discussed. Further, the challenges of each treatment systems are abridged. Finally, the possible suggestions for the modification/retrofitting of existing treatment systems for achieving stringent disposal standards are pointed out.
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Affiliation(s)
- Mohd Najibul Hasan
- Department of Civil Engineering, Jamia Millia Islamia (A Central University), New Delhi, 110025, India
| | - Mohd Musheer Altaf
- Department of Life Science, Institute of Information Management and Technology, Aligarh, India
| | - Nadeem A Khan
- Department of Civil Engineering, Jamia Millia Islamia (A Central University), New Delhi, 110025, India
| | - Afzal Husain Khan
- Department of Civil Engineering, Jazan University, 114, Jazan, Saudi Arabia.
| | - Abid Ali Khan
- Department of Civil Engineering, Jamia Millia Islamia (A Central University), New Delhi, 110025, India
| | - Sirajuddin Ahmed
- Department of Civil Engineering, Jamia Millia Islamia (A Central University), New Delhi, 110025, India
| | - P Senthil Kumar
- SSN-Centre for Radiation, Environmental Science and Technology (SSN-CREST), Sri Sivasubramaniya Nadar College of Engineering, Chennai, 603110, Tamil Nadu, India
| | - Mu Naushad
- Advanced Materials Research Chair, Department of Chemistry, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia; Yonsei Frontier Lab, Yonsei University, Seoul, South Korea; International Research Centre of Nanotechnology for Himalayan Sustainability (IRCNHS), Shoolini University, Solan, 173212, Himachal Pradesh, India.
| | - Anushka Upamali Rajapaksha
- Ecosphere Resilience Research Center, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka; Instrument Center, Faculty of Applied Sciences, University of Sri Jayewardenepura, Sri Lanka
| | - Jibran Iqbal
- College of Natural and Health Sciences, Zayed University, P.O. Box 144534, Abu Dhabi, United Arab Emirates
| | - Vineet Tirth
- Mechanical Engineering Department, College of Engineering, King Khalid University, Abha, 61411, Saudi Arabia; Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha, 61413, Asir, Saudi Arabia
| | - Saiful Islam
- Civil Engineering Department, College of Engineering, King Khalid University, Abha, 61411, Saudi Arabia
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Xu H, Deng Y, Li X, Liu Y, Huang S, Yang Y, Wang Z, Hu C. Effect of Increasing C/N Ratio on Performance and Microbial Community Structure in a Membrane Bioreactor with a High Ammonia Load. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:8070. [PMID: 34360363 PMCID: PMC8345800 DOI: 10.3390/ijerph18158070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/25/2021] [Accepted: 07/27/2021] [Indexed: 01/03/2023]
Abstract
Herein, the responses of the operational performance of a membrane bioreactor (MBR) with a high ammonium-nitrogen (NH4+-N) load and microbial community structure to increasing carbon to nitrogen (C/N) ratios were studied. Variation in the influent C/N ratio did not affect the removal efficiencies of chemical oxygen demand (COD) and NH4+-N but gradually abated the ammonia oxidization activity of sludge. The concentration of the sludge in the reactor at the end of the process increased four-fold compared with that of the seed sludge, ensuring the stable removal of NH4+-N. The increasing influent COD concentration resulted in an elevated production of humic acids in soluble microbial product (SMP) and accelerated the rate of membrane fouling. High-throughput sequencing analysis showed that the C/N ratio had selective effects on the microbial community structure. In the genus level, Methyloversatilis, Subsaxibacter, and Pseudomonas were enriched during the operation. However, the relative abundance of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) involved in nitrification declined gradually and were decreased by 86.54 and 90.17%, respectively, with influent COD increasing from 0 to 2000 mg/L. The present study offers a more in-depth insight into the control strategy of the C/N ratio in the operation of an MBR with a high NH4+-N load.
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Affiliation(s)
- Huaihao Xu
- Institute of Environmental Research at Greater Bay, Guangzhou Key Laboratory for Clean Energy and Materials, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China; (H.X.); (Y.D.); (X.L.); (S.H.); (Y.Y.); (C.H.)
| | - Yuepeng Deng
- Institute of Environmental Research at Greater Bay, Guangzhou Key Laboratory for Clean Energy and Materials, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China; (H.X.); (Y.D.); (X.L.); (S.H.); (Y.Y.); (C.H.)
| | - Xiuying Li
- Institute of Environmental Research at Greater Bay, Guangzhou Key Laboratory for Clean Energy and Materials, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China; (H.X.); (Y.D.); (X.L.); (S.H.); (Y.Y.); (C.H.)
| | - Yuxian Liu
- Institute of Environmental Research at Greater Bay, Guangzhou Key Laboratory for Clean Energy and Materials, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China; (H.X.); (Y.D.); (X.L.); (S.H.); (Y.Y.); (C.H.)
- Linköping University-Guangzhou University Research Center on Urban Sustainable Development, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Shuangqiu Huang
- Institute of Environmental Research at Greater Bay, Guangzhou Key Laboratory for Clean Energy and Materials, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China; (H.X.); (Y.D.); (X.L.); (S.H.); (Y.Y.); (C.H.)
| | - Yunhua Yang
- Institute of Environmental Research at Greater Bay, Guangzhou Key Laboratory for Clean Energy and Materials, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China; (H.X.); (Y.D.); (X.L.); (S.H.); (Y.Y.); (C.H.)
| | - Zhu Wang
- Institute of Environmental Research at Greater Bay, Guangzhou Key Laboratory for Clean Energy and Materials, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China; (H.X.); (Y.D.); (X.L.); (S.H.); (Y.Y.); (C.H.)
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Chun Hu
- Institute of Environmental Research at Greater Bay, Guangzhou Key Laboratory for Clean Energy and Materials, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China; (H.X.); (Y.D.); (X.L.); (S.H.); (Y.Y.); (C.H.)
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12
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Engelen B, Nguyen T, Heyerhoff B, Kalenborn S, Sydow K, Tabai H, Peterson RN, Wegener G, Teske A. Microbial Communities of Hydrothermal Guaymas Basin Surficial Sediment Profiled at 2 Millimeter-Scale Resolution. Front Microbiol 2021; 12:710881. [PMID: 34335545 PMCID: PMC8322767 DOI: 10.3389/fmicb.2021.710881] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 06/22/2021] [Indexed: 01/10/2023] Open
Abstract
The surficial hydrothermal sediments of Guaymas Basin harbor complex microbial communities where oxidative and reductive nitrogen, sulfur, and carbon-cycling populations and processes overlap and coexist. Here, we resolve microbial community profiles in hydrothermal sediment cores of Guaymas Basin on a scale of 2 millimeters, using Denaturing Gradient Gel Electrophoresis (DGGE) to visualize the rapid downcore changes among dominant bacteria and archaea. DGGE analysis of bacterial 16S rRNA gene amplicons identified free-living and syntrophic deltaproteobacterial sulfate-reducing bacteria, fermentative Cytophagales, members of the Chloroflexi (Thermoflexia), Aminicenantes, and uncultured sediment clades. The DGGE pattern indicates a gradually changing downcore community structure where small changes on a 2-millimeter scale accumulate to significantly changing populations within the top 4 cm sediment layer. Functional gene DGGE analyses identified anaerobic methane-oxidizing archaea (ANME) based on methyl-coenzyme M reductase genes, and members of the Betaproteobacteria and Thaumarchaeota based on bacterial and archaeal ammonia monooxygenase genes, respectively. The co-existence and overlapping habitat range of aerobic, nitrifying, sulfate-reducing and fermentative bacteria and archaea, including thermophiles, in the surficial sediments is consistent with dynamic redox and thermal gradients that sustain highly complex microbial communities in the hydrothermal sediments of Guaymas Basin.
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Affiliation(s)
- Bert Engelen
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Tien Nguyen
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Benedikt Heyerhoff
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Saskia Kalenborn
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Katharina Sydow
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Houssem Tabai
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Richard N Peterson
- Department of Coastal and Marine Systems Science, Coastal Carolina University, Conway, SC, United States
| | - Gunter Wegener
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Andreas Teske
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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13
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Liu S, Cai H, Wang J, Wang H, Zheng T, Chen Q, Ni J. In-situ expressions of comammox Nitrospira along the Yangtze River. WATER RESEARCH 2021; 200:117241. [PMID: 34051458 DOI: 10.1016/j.watres.2021.117241] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/07/2021] [Accepted: 05/09/2021] [Indexed: 06/12/2023]
Abstract
The recent discovery of comammox Nitrospira as complete nitrifiers has significantly enriched our understanding on the nitrogen cycle, yet little is known about their metabolic transcripts in natural aquatic ecosystems. Using the genome-centric metatranscriptomics, we provided the first in-situ expression patterns of comammox Nitrospira along the Yangtze River. Our study confirmed widespread expressions of comammox Nitrospira, with the highest transcription accounting for 33.3% and 63.8% of amoA and nxrAB genes expressed in ammonia-oxidizing prokaryotes (AOPs) and Nitrospira sublineages I/II, respectively. Moreover, comammox two clades differed in nitrification, with clade A acting as the dominator to ammonia oxidation in comammox, and clade B contributing more transcripts to nitrite oxidation than to ammonia oxidation. Compared to canonical Nitrospira, comammox community had lower expressions of ammonia/nitrite transporters and nitrogen assimilatory genes, but far higher expressions in urea transport and hydrolysis, facilitating to derivation of ammonia and energy mainly through intracellular ureolytic metabolism. This suggests no need for "reciprocal-feeding" between canonical Nitrospira and AOPs in a natural river. Aerobic mixotrophy of comammox bacteria was suggested by expressions of genes coding for respiratory complexes I-V, oxidative/reductive TCA cycle, oxygen stress defenses, and transport/catabolism of simple carbohydrates and low-biosynthetic-cost amino acids. Intriguingly, significant positive correlations among expressions of ammonia monooxygenases, hydroxylamine dehydrogenase and copper-dependent nitrite reductase indicated that comammox Nitrospira had the potential of converting nitrite to nitric oxide accompanied by ammonia oxidation under low-C/N and aerobic conditions, while gene expressions in this pathway were significantly and positively associated with pH. Overall, this study illustrated novel transcriptional characteristics of comammox Nitrospira, and highlighted the necessity of reassessing their contributions to biogeochemical carbon and nitrogen cycling with perspective of in-situ meta-omics as well as culture experiments.
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Affiliation(s)
- Shufeng Liu
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Peking University, Beijing 100871, China
| | - Hetong Cai
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Peking University, Beijing 100871, China
| | - Jiawen Wang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Peking University, Beijing 100871, China
| | - Haiying Wang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Tong Zheng
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Peking University, Beijing 100871, China; South China Institute of Environmental Sciences, Ministry of Environmental Protection (MEP), Guangzhou 510655, China
| | - Qian Chen
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Peking University, Beijing 100871, China; State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Jinren Ni
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Peking University, Beijing 100871, China; State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China.
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14
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Li X, Wan W, Zheng L, Wang A, Luo X, Huang Q, Chen W. Community assembly mechanisms and co-occurrence patterns of nitrite-oxidizing bacteria communities in saline soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 772:145472. [PMID: 33770900 DOI: 10.1016/j.scitotenv.2021.145472] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 01/16/2021] [Accepted: 01/24/2021] [Indexed: 06/12/2023]
Abstract
Nitrite-oxidizing bacteria (NOB) catalyze the second step of nitrification by oxidizing nitrite to nitrate, which is a key process in the biogeochemical nitrogen cycling. However, little is known about the co-occurrence patterns and assembly processes of NOB communities in agricultural soils with different salinities. Here, we explored the effects of salinity on Nitrobacter and Nitrospira community using high-throughput sequencing and multivariate statistical analyses. Our results showed that high salinity significantly inhibited the nitrite oxidation rates and decreased the abundance of Nitrobacter and Nitrospira. Extreme salty conditions significantly altered the diversity and composition of Nitrospira community but had little effect on Nitrobacter community. Nitrobacter network in high salinity soils was more closely connected while the connectivity of Nitrospira network became weak. Nitrobacter and Nitrospira community exhibited distinct assembly processes at different salinity levels. Stochastic processes were dominant in the Nitrobacter community assembly in both low and high salinity soils. Interestingly, the assembly of Nitrospira community was governed by stochastic and deterministic processes in low and high salinity soils, respectively. To our knowledge, our study provides the first description of the co-occurrence patterns and assembly processes of NOB communities in agricultural soils with different salinities. These results can help us understand the NOB ecological roles and improve the nitrite oxidation activity in a high salinity environment.
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Affiliation(s)
- Xiang Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430010, China
| | - Wenjie Wan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430010, China
| | - Liuxia Zheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430010, China
| | - Achen Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430010, China
| | - Xuesong Luo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430010, China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430010, China; Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430010, China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430010, China.
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15
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Soler-Jofra A, Pérez J, van Loosdrecht MCM. Hydroxylamine and the nitrogen cycle: A review. WATER RESEARCH 2021; 190:116723. [PMID: 33352529 DOI: 10.1016/j.watres.2020.116723] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/21/2020] [Accepted: 12/01/2020] [Indexed: 06/12/2023]
Abstract
Aerobic ammonium oxidizing bacteria were first isolated more than 100 years ago and hydroxylamine is known to be an intermediate. The enzymatic steps involving hydroxylamine conversion to nitrite are still under discussion. For a long time it was assumed that hydroxylamine was directly converted to nitrite by a hydroxylamine oxidoreductase. Recent enzymatic evidences suggest that the actual product of hydroxylamine conversion is NO and a third, yet unknown, enzyme further converts NO to nitrite. More recently, ammonium oxidizing archaea and complete ammonium oxidizing bacteria were isolated and identified. Still the central nitrogen metabolism of these microorganisms presents to researchers the same puzzle: how hydroxylamine is transformed to nitrite. Nitrogen losses in the form of NO and N2O have been identified in all three types of aerobic ammonium oxidizing microorganisms and hydroxylamine is known to play a significant role in the formation. Yet, the pathways and the factors promoting the greenhouse gas emissions are to be fully characterized. Hydroxylamine also plays a yet poorly understood role on anaerobic ammonium oxidizing bacteria and is known to inhibit nitrite oxidizing bacteria. In this review, the role of this elusive intermediate in the metabolism of different key players of the nitrogen cycle is discussed, as well as the putative importance of hydroxylamine as a key nitrogen metabolite for microbial interactions within microbial communities and engineered systems. Overall, for the first time putting together the acquired knowledge about hydroxylamine and the nitrogen cycle over the years in a review, setting potential hypothesis and highlighting possible next steps for research.
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Affiliation(s)
- Aina Soler-Jofra
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Julio Pérez
- Department of Chemical, Biological and Environmental Engineering, Universitat Autonoma de Barcelona, Cerdanyola del Valles, Spain
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands.
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16
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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] [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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17
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Gionfriddo CM, Wymore AM, Jones DS, Wilpiszeski RL, Lynes MM, Christensen GA, Soren A, Gilmour CC, Podar M, Elias DA. An Improved hgcAB Primer Set and Direct High-Throughput Sequencing Expand Hg-Methylator Diversity in Nature. Front Microbiol 2020; 11:541554. [PMID: 33123100 PMCID: PMC7573106 DOI: 10.3389/fmicb.2020.541554] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 08/25/2020] [Indexed: 01/27/2023] Open
Abstract
The gene pair hgcAB is essential for microbial mercury methylation. Our understanding of its abundance and diversity in nature is rapidly evolving. In this study we developed a new broad-range primer set for hgcAB, plus an expanded hgcAB reference library, and used these to characterize Hg-methylating communities from diverse environments. We applied this new Hg-methylator database to assign taxonomy to hgcA sequences from clone, amplicon, and metagenomic datasets. We evaluated potential biases introduced in primer design, sequence length, and classification, and suggest best practices for studying Hg-methylator diversity. Our study confirms the emerging picture of an expanded diversity of HgcAB-encoding microbes in many types of ecosystems, with abundant putative mercury methylators Nitrospirae and Chloroflexi in several new environments including salt marsh and peat soils. Other common microbes encoding HgcAB included Phycisphaerae, Aminicenantes, Spirochaetes, and Elusimicrobia. Combined with high-throughput amplicon specific sequencing, the new primer set also indentified novel hgcAB sequences similar to Lentisphaerae, Bacteroidetes, Atribacteria, and candidate phyla WOR-3 and KSB1 bacteria. Gene abundance data also corroborate the important role of two "classic" groups of methylators (Deltaproteobacteria and Methanomicrobia) in many environments, but generally show a scarcity of hgcAB+ Firmicutes. The new primer set was developed to specifically target hgcAB sequences found in nature, reducing degeneracy and providing increased sensitivity while maintaining broad diversity capture. We evaluated mock communities to confirm primer improvements, including culture spikes to environmental samples with variable DNA extraction and PCR amplification efficiencies. For select sites, this new workflow was combined with direct high-throughput hgcAB sequencing. The hgcAB diversity generated by direct amplicon sequencing confirmed the potential for novel Hg-methylators previously identified using metagenomic screens. A new phylogenetic analysis using sequences from freshwater, saline, and terrestrial environments showed Deltaproteobacteria HgcA sequences generally clustered among themselves, while metagenome-resolved HgcA sequences in other phyla tended to cluster by environment, suggesting horizontal gene transfer into many clades. HgcA from marine metagenomes often formed distinct subtrees from those sequenced from freshwater ecosystems. Overall the majority of HgcA sequences branch from a cluster of HgcAB fused proteins related to Thermococci, Atribacteria (candidate division OP9), Aminicenantes (OP8), and Chloroflexi. The improved primer set and library, combined with direct amplicon sequencing, provide a significantly improved assessment of the abundance and diversity of hgcAB+ microbes in nature.
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Affiliation(s)
- Caitlin M Gionfriddo
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Ann M Wymore
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Daniel S Jones
- BioTechnology Institute, University of Minnesota, St. Paul, MN, United States.,Department of Earth Sciences, Minneapolis, MN, United States
| | - Regina L Wilpiszeski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Mackenzie M Lynes
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Geoff A Christensen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Ally Soren
- Smithsonian Environmental Research Center, Edgewater, MD, United States
| | | | - Mircea Podar
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Dwayne A Elias
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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18
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Liu S, Wang H, Chen L, Wang J, Zheng M, Liu S, Chen Q, Ni J. Comammox Nitrospira within the Yangtze River continuum: community, biogeography, and ecological drivers. THE ISME JOURNAL 2020; 14:2488-2504. [PMID: 32555502 PMCID: PMC7490378 DOI: 10.1038/s41396-020-0701-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 06/02/2020] [Accepted: 06/09/2020] [Indexed: 12/14/2022]
Abstract
The recent discovery of comammox Nitrospira as complete nitrifiers has fundamentally renewed perceptions of nitrogen cycling in natural and engineered systems, yet little is known about the environmental controls on these newly recognized bacteria. Based on improved phylogenetic resolution through successful assembly of ten novel genomes (71-96% completeness), we provided the first biogeographic patterns for planktonic and benthic comammox Nitrospira in the Yangtze River over a 6030 km continuum. Our study revealed the widespread distributions and relative abundance of comammox Nitrospira in this large freshwater system, constituting 30 and 46% of ammonia-oxidizing prokaryotes (AOPs) and displaying 30.4- and 17.9-fold greater abundances than canonical Nitrospira representatives in water and sediments, respectively. Comammox Nitrospira contributed more to nitrifier abundances (34-87% of AOPs) in typical oligotrophic environments with a higher pH and lower temperature, particularly in the plateau (clade B), mountain and foothill (clade A) areas of the upper reach. The dominant position of planktonic comammox Nitrospira was replaced by canonical Nitrospira sublineages I/II and ammonia-oxidizing bacteria from the plateau to downstream plain due to environmental selection, while the dissimilarity of benthic comammox Nitrospira was moderately associated with geographic distance. A substantial decrease (83%) in benthic comammox Nitrospira abundance occurred immediately downstream of the Three Gorges Dam, consistent with a similarly considerable decrease in overall sediment bacterial taxa. Together, this study highlights the previously unrecognized dominance of comammox Nitrospira in major river systems and underlines the importance of revisiting the distributions of and controls on nitrification processes within global freshwater environments.
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Affiliation(s)
- Shufeng Liu
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, 100871, Beijing, China
- Beijing Innovation Center for Engineering Science and Advanced Technology, Peking University, 100871, Beijing, China
| | - Haiying Wang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, 100871, Beijing, China
| | - Liming Chen
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, 100871, Beijing, China
| | - Jiawen Wang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, 100871, Beijing, China
| | - Maosheng Zheng
- Key Laboratory of Regional Energy Systems Optimization, Resources and Environmental Research Academy, North China Electric Power University, 102206, Beijing, China
| | - Sitong Liu
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, 100871, Beijing, China
| | - Qian Chen
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, 100871, Beijing, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, 810016, Xining, China
| | - Jinren Ni
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, 100871, Beijing, China.
- Beijing Innovation Center for Engineering Science and Advanced Technology, Peking University, 100871, Beijing, China.
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, 810016, Xining, China.
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19
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Hernández S, Vives MJ. Phages in Anaerobic Systems. Viruses 2020; 12:E1091. [PMID: 32993161 PMCID: PMC7599459 DOI: 10.3390/v12101091] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 12/21/2022] Open
Abstract
Since the discovery of phages in 1915, these viruses have been studied mostly in aerobic systems, or without considering the availability of oxygen as a variable that may affect the interaction between the virus and its host. However, with such great abundance of anaerobic environments on the planet, the effect that a lack of oxygen can have on the phage-bacteria relationship is an important consideration. There are few studies on obligate anaerobes that investigate the role of anoxia in causing infection. In the case of facultative anaerobes, it is a well-known fact that their shifting from an aerobic environment to an anaerobic one involves metabolic changes in the bacteria. As the phage infection process depends on the metabolic state of the host bacteria, these changes are also expected to affect the phage infection cycle. This review summarizes the available information on phages active on facultative and obligate anaerobes and discusses how anaerobiosis can be an important parameter in phage infection, especially among facultative anaerobes.
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Affiliation(s)
- Santiago Hernández
- Department of Biological Sciences, Universidad de los Andes, Bogotá 111711, Colombia;
| | - Martha J. Vives
- Department of Biological Sciences, Universidad de los Andes, Bogotá 111711, Colombia;
- School of Sciences, Universidad de los Andes, Bogotá 111711, Colombia
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20
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Li P, Zhang Y, Meng Q, Liu Y, Tuyiringire D, Chen Z, Liang S. Trichloroethylene inhibits nitrogen transformation and microbial community structure in Mollisol. ECOTOXICOLOGY (LONDON, ENGLAND) 2020; 29:801-813. [PMID: 32445014 DOI: 10.1007/s10646-020-02230-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/05/2020] [Indexed: 06/11/2023]
Abstract
Trichloroethylene (TCE) is the most ubiquitous halogenated organic pollutant in the environment, it is one of the 129 priority control pollutants. In order to clarify the influence of TCE on microorganisms and nitrogen transformation in Mollisol is the core purpose of this study. Results showed that 10 mg kg-1 TCE is the concentration limit of ammonification in Mollisol. When the concentration of TCE reached 10 mg kg-1 and the effect lasted for over 7 days, the process of ammonia oxidation to nitric acid in Mollisol will be affected. TCE affected the process of nitrate (NO3-) transformation into nitrite (NO2-) by affecting the activity of nitrate reductase, thereby affected the denitrification process in soil. When the concentration of TCE is more than 10 mg kg-1 it reduced the ability of soil microorganisms to obtain nitrogen, thereby affecting soil nitrogen transformation. RDA (Redundancy analysis) showed that the activity of nitrate reductase and the number of nitrifying bacteria and denitrifying bacteria in soil was negatively correlated with the incubation of TCE. In addition, soil nitrate reductase, nitrite reductase, peroxidase activity, ammonifying bacteria, nitrifying bacteria and denitrifying bacteria were negatively correlated with TCE concentration. Beyond that PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) of functional gene structure depend on KEGG (Kyoto Encyclopedia of Genes and Genomes) showed that 20 mg kg-1 TCE significantly inhibited the metabolism of energy and other substances in Mollisol. Based on the above, it is found that TCE significantly affected nitrification and denitrification in Mollisol, thus the nitrogen transformation in Mollisol was affected by TCE contamination.
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Affiliation(s)
- Pengfei Li
- College of Resources and Environment, Northeast Agricultural University, 150030, Harbin, China
- College of Geographical Science, Harbin Normal University, 150025, Harbin, China
| | - Ying Zhang
- College of Resources and Environment, Northeast Agricultural University, 150030, Harbin, China.
| | - Qingjuan Meng
- College of Resources and Environment, Northeast Agricultural University, 150030, Harbin, China
| | - Ying Liu
- College of Resources and Environment, Northeast Agricultural University, 150030, Harbin, China
| | - Diogene Tuyiringire
- College of Resources and Environment, Northeast Agricultural University, 150030, Harbin, China
| | - Zhaobo Chen
- College of Environment and Resources, Dalian Minzu University, 18 Liaohe West Road, 116600, Dalian, China
| | - Shichao Liang
- College of Resources and Environment, Northeast Agricultural University, 150030, Harbin, China
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21
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Shi Y, Jiang Y, Wang S, Wang X, Zhu G. Biogeographic distribution of comammox bacteria in diverse terrestrial habitats. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 717:137257. [PMID: 32065897 DOI: 10.1016/j.scitotenv.2020.137257] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/05/2020] [Accepted: 02/10/2020] [Indexed: 06/10/2023]
Abstract
Comammox, the microbial group capable of completely oxidizing ammonia to nitrate, challenged the traditional two-step nitrification process where ammonia is oxidized by ammonia-oxidizing archaea (AOA) and bacteria (AOB), and nitrite by nitrite-oxidizing bacteria (NOB). However, the distribution of comammox bacteria in various habitats and their potential environmental drivers remain poorly understood. Using qPCR and high-throughput sequencing approach, we analyzed the abundance and community patterns of comammox from 38 samples taken from five different habitat types including paddy fields in Shaoguan and Antu, the wheat fields, river, and grassland in the Qinghai-Tibet Plateau, and the fringe and central riparian zones of Chaohu Lake of China during winter and summer. Comammox bacteria were detected in all samples, with Ca. N. nitrificans dominating the community, followed by Ca. N. nitrosa. Generally, in paddy fields of Shaoguan and Antu, ammonia (NH4+) was the key factor affecting comammox bacteria. However, in wheat fields, river and grassland of the Qinghai-Tibet Plateau, altitude was the strongest factor affecting comammox bacteria. In Chaohu Lake, comammox bacteria showed temporal heterogeneity, being higher in winter than summer, especially in the fringe riparian zone. Our results suggest that comammox is widespread in diverse habitats and exhibit niche partitioning, and can be affected by different environmental factors that may vary by habitat.
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Affiliation(s)
- Yao Shi
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yingying Jiang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Life Science, Shenyang Normal University, Shenyang 110034, China
| | - Shanyun Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Xiaomin Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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22
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Separating and Characterizing Functional Nitrogen Degraders via Magnetic Nanoparticle-Mediated Isolation. J CHEM-NY 2020. [DOI: 10.1155/2020/1841364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Magnetic nanoparticle-mediated isolation (MMI) is a new method for isolating active functional microbes from complex microorganisms without substrate labeling. In this study, the composition and properties of magnetic nanoparticles (MNPs) were characterized by a number of techniques, indicating that MNPs have characteristics such as microinterfaces and can be efficiently fixed on the surface of microbial cells. It also introduced the MMI technology in activated sludge after stable long-term treatment. With further addition of promotor carbon sources, the enrichment of the functional nitrogen degraders in MMI was significantly higher than in samples without MNPs, showing the advantages of MMI in identifying the active degraders. Redundancy analysis (RDA) also showed that the functional nitrogen degraders such as Comamonadaceae_unclassified and Thiobacillus absolutely dominated in situ ammonia degradation, and the change in dominant genera had the same trend as the degradation rate of ammonia nitrogen. In the magnetically functionalized system, the separated functional nitrogen degraders significantly improved ammonia nitrogen degradation efficiency, making it basically stable at more than 80%, up to 91.6%. These results prove that the complex flora created after the addition of MNPs is more adaptable to newly introduced pollutants, and MMI is a powerful tool for studying pollutant-degrading microorganisms under in situ conditions.
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Zhao Y, Tian G, Chen D, Zheng P, Yu J, He J, Mao X, Huang Z, Luo Y, Luo J, Yu B. Dietary protein levels and amino acid supplementation patterns alter the composition and functions of colonic microbiota in pigs. ACTA ACUST UNITED AC 2020; 6:143-151. [PMID: 32542194 PMCID: PMC7283365 DOI: 10.1016/j.aninu.2020.02.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/04/2020] [Accepted: 02/20/2020] [Indexed: 12/11/2022]
Abstract
Different dietary nitrogen (N) patterns may have different effects on gut microbiota. To investigate the effects of different crude protein (CP) levels or essential amino acids (EAA) supplementation patterns on the structure and functions of colonic microbiota, 42 barrows (25 ± 0.39 kg) were randomly assigned to 7 dietary treatments including: diet 1, a high CP diet with balanced 10 EAA; diet 2, a medium CP diet with approximately 2% decreased CP level from diet 1 and balanced 10 EAA; diets 3, 4, 5, 6 and 7, low CP diets with 4% decreased CP level from diet 1. Specifically, diet 3 was only balanced for Lys, Met, Thr and Trp; diets 4, 5 and 6 were further supplemented with Ile, Val and Ile + Val on the basis of diet 3, respectively; and diet 7 was balanced for 10 EAA. Results over a 110-d trial showed that reducing the CP level by 2% or 4% dramatically decreased N intake and excretion (P < 0.05) in the presence of balanced 10 EAA, which was not observed when altering the EAA supplementation patterns in low CP diet (−4%). With balanced 10 EAA, 2% reduction in dietary CP significantly reduced Firmicutes-to-Bacteroidetes (F:B) ratio and significantly elevated the abundance of Prevotellaceae NK3B31 (P < 0.05); whereas 4% reduction evidently increased the abundances of Proteobacteria, Succinivibrio and Lachnospiraceae XPB1014 (P < 0.05). Among the 5 low CP diets (−4%), supplementation with Ile, or Val + Ile, or balanced 10 EAA increased F:B ratio and the abundance of Proteobacteria. In addition, the predicted functions revealed that different CP levels and EAA balanced patterns dramatically altered the mRNA expression profiles of N-metabolizing genes, the “N and energy metabolism” pathways or the metabolism of some small substances, such as amino acids (AA) and vitamins. Our findings suggested that reducing the dietary CP levels by 2% to 4% with balancing 10 EAA, or only further supplementation with Ile or Val + Ile to a low protein diet (−4%) reduced the N contents entering the hindgut to various degrees, altered the abundances of N-metabolizing bacteria, and improved the abilities of N utilization.
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Affiliation(s)
- Yumei Zhao
- Key Laboratory of Animal Disease-Resistance Nutrition, Animal Nutrition Institute, Sichuan Agricultural University, Ya'an 625014, China
| | - Gang Tian
- Key Laboratory of Animal Disease-Resistance Nutrition, Animal Nutrition Institute, Sichuan Agricultural University, Ya'an 625014, China
| | - Daiwen Chen
- Key Laboratory of Animal Disease-Resistance Nutrition, Animal Nutrition Institute, Sichuan Agricultural University, Ya'an 625014, China
| | - Ping Zheng
- Key Laboratory of Animal Disease-Resistance Nutrition, Animal Nutrition Institute, Sichuan Agricultural University, Ya'an 625014, China
| | - Jie Yu
- Key Laboratory of Animal Disease-Resistance Nutrition, Animal Nutrition Institute, Sichuan Agricultural University, Ya'an 625014, China
| | - Jun He
- Key Laboratory of Animal Disease-Resistance Nutrition, Animal Nutrition Institute, Sichuan Agricultural University, Ya'an 625014, China
| | - Xiangbing Mao
- Key Laboratory of Animal Disease-Resistance Nutrition, Animal Nutrition Institute, Sichuan Agricultural University, Ya'an 625014, China
| | - Zhiqing Huang
- Key Laboratory of Animal Disease-Resistance Nutrition, Animal Nutrition Institute, Sichuan Agricultural University, Ya'an 625014, China
| | - Yuheng Luo
- Key Laboratory of Animal Disease-Resistance Nutrition, Animal Nutrition Institute, Sichuan Agricultural University, Ya'an 625014, China
| | - Junqiu Luo
- Key Laboratory of Animal Disease-Resistance Nutrition, Animal Nutrition Institute, Sichuan Agricultural University, Ya'an 625014, China
| | - Bing Yu
- Key Laboratory of Animal Disease-Resistance Nutrition, Animal Nutrition Institute, Sichuan Agricultural University, Ya'an 625014, China
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Abstract
Nitrification is a major issue that utilities must address if they utilize chloramines as a secondary disinfectant. Nitrification is the oxidation of free ammonia to nitrite which is then further oxidized to nitrate. Free ammonia is found in drinking water systems as a result of overfeeding at the water treatment plant (WTP) or as a result of the decomposition of monochloramine. Premise plumbing systems (i.e., the plumbing systems within buildings and homes) are characterized by irregular usage patterns, high water age, high temperature, and high surface-to-volume ratios. These characteristics create ideal conditions for increased chloramine decay, bacterial growth, and nitrification. This review discusses factors within premise plumbing that are likely to influence nitrification, and vice versa. Factors influencing, or influenced by, nitrification include the rate at which chloramine residual decays, microbial regrowth, corrosion of pipe materials, and water conservation practices. From a regulatory standpoint, the greatest impact of nitrification within premise plumbing is likely to be a result of increased lead levels during Lead and Copper Rule (LCR) sampling. Other drinking water regulations related to nitrifying parameters are monitored in a manner to reduce premise plumbing impacts. One way to potentially control nitrification in premise plumbing systems is through the development of building management plans.
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C. Alzate Marin J, H. Caravelli A, E. Zaritzky N. Performance of Anoxic-Oxic Sequencing Batch Reactor for Nitrification and Aerobic Denitrification. Biotechnol Bioeng 2019. [DOI: 10.5772/intechopen.84775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Wang W, Su Y, Wang B, Wang Y, Zhuang L, Zhu G. Spatiotemporal shifts of ammonia-oxidizing archaea abundance and structure during the restoration of a multiple pond and plant-bed/ditch wetland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 684:629-640. [PMID: 31170597 DOI: 10.1016/j.scitotenv.2019.04.415] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/23/2019] [Accepted: 04/27/2019] [Indexed: 06/09/2023]
Abstract
Ammonia-oxidizing archaea (AOA) microorganisms have been increasingly found in aquatic and terrestrial environments. These microorganisms make vital contributions to ammonia oxidation in such systems. However, their community succession characteristics in man-made wetland ecosystems have scarcely been reported. We assessed the AOA's spatiotemporal shifts in the sediments of a constructed wetland (CW) - the Shijiuyang constructed wetland (SJY-CW) - in China from the third year (2011) to the fifth year (2013) of the CW operation. The SJY-CW is composed of a pretreatment pond, a multiple plant-bed/ditch system, and a post-treatment pond. Results showed that AOA abundance in the pre- and post-treatment ponds remained invariant through 2011-2012 and decreased in 2013, while the abundance in the plant-bed/ditch system decreased gradually with wetland operation. The AOA abundance in 2013 was one order of magnitude lower than that through 2011-2012, and the AOA abundance in the plant-bed/ditch system was generally higher than that in the pre- and post-treatment ponds from 2011 to 2013. AOA diversity showed little temporal differentiation with a slightly decreasing trend for community richness index Chao1 and diversity index Shannon H' from 2011 to 2013. The AOA community was dominated by the Nitrososphaera cluster accompanied by an increasing Nitrosopumilus cluster and Nitrososphaera sister cluster within the wetland operation. Hierarchical clustering and redundancy analysis verified the horizontal shifts of AOA communities. The shifts occurred preferentially in the central plant-bed/ditch system. The operational duration of the wetland became a key factor influencing AOA abundance and community shift in SJY-CW sediments.
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Affiliation(s)
- Weidong Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Yu Su
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Baoling Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Yu Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Linjie Zhuang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; College of Environmental Science and Engineering, Donghua University, Shanghai 201620, PR China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China.
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27
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Nsenga Kumwimba M, Meng F. Roles of ammonia-oxidizing bacteria in improving metabolism and cometabolism of trace organic chemicals in biological wastewater treatment processes: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 659:419-441. [PMID: 31096373 DOI: 10.1016/j.scitotenv.2018.12.236] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 11/20/2018] [Accepted: 12/15/2018] [Indexed: 05/27/2023]
Abstract
While there has been a significant recent improvement in the removal of pollutants in natural and engineered systems, trace organic chemicals (TrOCs) are posing a major threat to aquatic environments and human health. There is a critical need for developing potential strategies that aim at enhancing metabolism and/or cometabolism of these compounds. Recently, knowledge regarding biodegradation of TrOCs by ammonia-oxidizing bacteria (AOB) has been widely developed. This review aims to delineate an up-to-date version of the ecophysiology of AOB and outline current knowledge related to biodegradation efficiencies of the frequently reported TrOCs by AOB. The paper also provides an insight into biodegradation pathways by AOB and transformation products of these compounds and makes recommendations for future research of AOB. In brief, nitrifying WWTFs (wastewater treatment facilities) were superior in degrading most TrOCs than non-nitrifying WWTFs due to cometabolic biodegradation by the AOB. To fully understand and/or enhance the cometabolic biodegradation of TrOCs by AOB, recent molecular research has focused on numerous crucial factors including availability of the compounds to AOB, presence of growth substrate (NH4-N), redox potentials, microorganism diversity (AOB and heterotrophs), physicochemical properties and operational parameters of the WWTFs, molecular structure of target TrOCs and membrane-based technologies, may all significantly impact the cometabolic biodegradation of TrOCs. Still, further exploration is required to elucidate the mechanisms involved in biodegradation of TrOCs by AOB and the toxicity levels of formed products.
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Affiliation(s)
- Mathieu Nsenga Kumwimba
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China; Faculty of Agronomy, Department of Natural Resources and Environmental Management, University of Lubumbashi, Democratic Republic of the Congo
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China.
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Salinity stresses make a difference in the start-up of membrane bioreactor: performance, microbial community and membrane fouling. Bioprocess Biosyst Eng 2018; 42:445-454. [DOI: 10.1007/s00449-018-2048-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 11/19/2018] [Indexed: 10/27/2022]
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29
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Bourgeois FR, Monette F, Cyr DG. Operational modifications for the development of nitrifying bacteria in a large-scale biological aerated filter and its impact on wastewater treatment. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2018; 78:1704-1714. [PMID: 30500794 DOI: 10.2166/wst.2018.447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
To develop a better understanding for fixed biomass processes, the development of a nitrifying bacterial biofilm, as well as the performance of treatment during modifications to operational conditions of a full-scale submerged biological filter were examined. The development of the nitrifying biofilm was investigated at four depth levels (1, 2, 4 and 5 feet). The result of bacterial subpopulations analyzed by qPCR relative to the physico-chemical parameters of the wastewater during the various tests (sustained aeration, modified backwash parameters and inflow restriction) revealed an increase of the relative presence of nitrifying microorganisms throughout the biofilm (especially for nitrite oxidizing bacteria (NOB)), but this was not necessarily accompanied by a better nitrification rate. The highest observed nitrification rate was 49% of removal in the test cell during backwashing conditions, whereas the relative ammonia oxidizing bacteria (AOB) population was 0.032% and NOB was 0.008% of the total biomass collected. The highest percentage of nitrifying bacteria observed (0.034% AOB and 0.18% NOB) resulted in a nitrification rate of 21%. The treatment of organic matter determined by measuring the chemical and biochemical oxygen demand (COD, CBOD5) was improved.
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Affiliation(s)
- François-René Bourgeois
- Département de génie de la construction. STEPPE - Station Expérimentale des Procédés Pilotes en Environnement, École de technologie supérieure - Université du Québec, 1100 Notre-Dame Street West, Montréal, Québec H3C 1K3, Canada E-mail:
| | - Frédéric Monette
- Département de génie de la construction. STEPPE - Station Expérimentale des Procédés Pilotes en Environnement, École de technologie supérieure - Université du Québec, 1100 Notre-Dame Street West, Montréal, Québec H3C 1K3, Canada E-mail:
| | - Daniel G Cyr
- Laboratoire de toxicologie environnementale, INRS-Institut Armand-Frappier - Université du Québec, 531, boulevard des Prairies, Laval, Québec H7V 1B7, Canada
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30
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Jeong D, Cho K, Lee CH, Lee S, Bae H. Effects of salinity on nitrification efficiency and bacterial community structure in a nitrifying osmotic membrane bioreactor. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.08.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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31
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Dai L, Liu C, Yu L, Song C, Peng L, Li X, Tao L, Li G. Organic Matter Regulates Ammonia-Oxidizing Bacterial and Archaeal Communities in the Surface Sediments of Ctenopharyngodon idellus Aquaculture Ponds. Front Microbiol 2018; 9:2290. [PMID: 30319588 PMCID: PMC6165866 DOI: 10.3389/fmicb.2018.02290] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 09/07/2018] [Indexed: 01/28/2023] Open
Abstract
Ammonia-oxidizing bacteria (AOB) and archaea (AOA) play important roles in nitrogen removal in aquaculture ponds, but their distribution and the environmental factors that drive their distribution are largely unknown. In this study, we collected surface sediment samples from Ctenopharyngodon idellus ponds in three different areas in China that practice aquaculture. The community structure of AOB and AOA and physicochemical characteristics in the ponds were investigated. The results showed that AOA were more abundant than AOB in all sampling ponds except one, but sediment AOB and AOA numbers varied greatly between ponds. Correlation analyses indicated a significant correlation between the abundance of AOB and arylsulfatase, as well as the abundance of AOA and total nitrogen (TN) and arylsulfatase. In addition, AOB/AOA ratio was found to be significantly correlated with the microbial biomass carbon. AOB were grouped into seven clusters affiliated to Nitrosospira and Nitrosomonas, and AOA were grouped into six clusters affiliated to Nitrososphaera, Nitrososphaera sister group, and Nitrosopumilus. AOB/AOA diversity in the surface sediments of aquaculture ponds varied according to the levels of total organic carbon (TOC), and AOB and AOA diversity was significantly correlated with arylsulfatase and β-glucosidase, respectively. The compositions of the AOB communities were also found to be significantly influenced by sediment eutrophic status (TOC and TN levels), and pH. In addition, concentrations of acid phosphatase and arylsulfatase in surface sediments were significantly correlated with the prominent bacterial amoA genotypes, and concentrations of TOC and urease were found to be significantly correlated with the prominent archaeal amoA genotype compositions. Taken together, our results indicated that AOB and AOA communities in the surface sediments of Ctenopharyngodon idellus aquaculture ponds are regulated by organic matter and its availability to the microorganisms.
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Affiliation(s)
- Lili Dai
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China.,College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Chengqing Liu
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China.,College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Liqin Yu
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Chaofeng Song
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Liang Peng
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Xiaoli Li
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Ling Tao
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Gu Li
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
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Ammonia oxidizers in the sea-surface microlayer of a coastal marine inlet. PLoS One 2018; 13:e0202636. [PMID: 30125317 PMCID: PMC6101417 DOI: 10.1371/journal.pone.0202636] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 08/07/2018] [Indexed: 11/19/2022] Open
Abstract
Planktonic archaea are thought to play an important role in ammonia oxidation in marine environments. Data on the distribution, abundance, and diversity of ammonia oxidizers in the coastal sea-surface microlayer (SML) are lacking, despite previous reports of high abundance of Thaumarchaeota in the SML of estuaries and freshwater lakes. Here, we failed to detect the presence of ammonia-oxidizing bacteria in any of our samples taken from a semi-enclosed marine inlet in Japan. Therefore, we shifted our focus to examine the archaeal community composition as well as the Thaumarchaeota marine group I (MG-I) and ammonia monooxygenase subunit A (amoA) gene copy numbers and composition in the SML and corresponding underlying water (UW, 20 cm). amoA gene copy numbers obtained by quantitative PCR were consistent with the typical values observed in the surface waters of oceanic and coastal environments where nitrification activity has been detected, but the copy numbers were two- to three-fold less than those reported from the surface layers and UW of high mountain lakes. Both amoA and MG-I 16S rRNA gene copy numbers were significantly negatively correlated with chlorophyll-a and transparent exopolymer particle concentrations in the SML. Communities of archaea and ammonia-oxidizing archaea in SML samples collected during low wind conditions (≤5 m s–1) differed the most from those in UW samples, whereas the communities in SML samples collected during high wind conditions were similar to the UW communities. In the SML, low ratios of amoA to MG-I 16S rRNA genes were observed, implying that most of the SML Thaumarchaeota lacked amoA. To our knowledge, our results provide the first comparison of ammonia-oxidizing communities in the coastal SML with those in the UW.
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Jung MY, Islam MA, Gwak JH, Kim JG, Rhee SK. Nitrosarchaeum koreense gen. nov., sp. nov., an aerobic and mesophilic, ammonia-oxidizing archaeon member of the phylum Thaumarchaeota isolated from agricultural soil. Int J Syst Evol Microbiol 2018; 68:3084-3095. [PMID: 30124400 DOI: 10.1099/ijsem.0.002926] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A mesophilic, chemolithoautotrophic, neutrophilic and aerobic ammonia-oxidizing archaeon, designated strain MY1T, was isolated from agricultural soil. Microscopic observation revealed short, rod-shaped cells with a diameter of 0.3-0.5 µm and length of 0.6-1.0 µm. The isolate had no flagella and pili, and possessed no genes associated with archaeal flagella synthesis. The major membrane lipids consisted mainly of the glycerol dibiphytanyl glycerol tetraether (GDGT) lipids GDGT-0 to GDGT-4 and crenarchaeol. The major intact polar lipids (IPLs) were determined as hexose plus phosphohexose IPL and dihexose IPL. Strain MY1T obtains energy by aerobically oxidizing ammonia and carbon by fixing CO2. An optimal growth was observed at 25 °C, at pH 7 and with 0.2-0.4 % (w/v) salinity that corresponds with its terrestrial habitat. The addition of α-keto acids was necessary to stimulate growth. The strain tolerated ammonium and nitrite concentrations up to 10 and 5 mM, respectively. The MY1T genome has a DNA G+C content of 32.7 mol%. Phylogenetic analysis based on the 16S rRNA gene showed that strain MY1T belongs to the family Nitrosopumilaceaeof the phylum Thaumarchaeota, sharing the highest 16S rRNA gene sequence similarity (96.6-97.1 %) with marine isolates of the genus Nitrosopumilus. The average nucleotide identity was 78 % between strain MY1T and Nitrosopumilus maritimus SCM1T, indicating distant relatedness. Based on the phenotypic, phylogenetic and genomic analyses, it was concluded that strain MY1T belongs to the novel genus Nitrosarchaeum, under which the name Nitrosarchaeum koreense sp. nov. is proposed as the type species. The type strain is MY1T (=JCM 31640T=KCTC 4249T).
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Affiliation(s)
- Man-Young Jung
- 1Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 28644, Republic of Korea.,2Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria
| | - Md Arafat Islam
- 1Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 28644, Republic of Korea
| | - Joo-Han Gwak
- 1Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 28644, Republic of Korea
| | - Jong-Geol Kim
- 1Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 28644, Republic of Korea
| | - Sung-Keun Rhee
- 1Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 28644, Republic of Korea
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Kitzinger K, Koch H, Lücker S, Sedlacek CJ, Herbold C, Schwarz J, Daebeler A, Mueller AJ, Lukumbuzya M, Romano S, Leisch N, Karst SM, Kirkegaard R, Albertsen M, Nielsen PH, Wagner M, Daims H. Characterization of the First " Candidatus Nitrotoga" Isolate Reveals Metabolic Versatility and Separate Evolution of Widespread Nitrite-Oxidizing Bacteria. mBio 2018; 9:e01186-18. [PMID: 29991589 PMCID: PMC6050957 DOI: 10.1128/mbio.01186-18] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 06/14/2018] [Indexed: 11/30/2022] Open
Abstract
Nitrification is a key process of the biogeochemical nitrogen cycle and of biological wastewater treatment. The second step, nitrite oxidation to nitrate, is catalyzed by phylogenetically diverse, chemolithoautotrophic nitrite-oxidizing bacteria (NOB). Uncultured NOB from the genus "Candidatus Nitrotoga" are widespread in natural and engineered ecosystems. Knowledge about their biology is sparse, because no genomic information and no pure "Ca Nitrotoga" culture was available. Here we obtained the first "Ca Nitrotoga" isolate from activated sludge. This organism, "Candidatus Nitrotoga fabula," prefers higher temperatures (>20°C; optimum, 24 to 28°C) than previous "Ca Nitrotoga" enrichments, which were described as cold-adapted NOB. "Ca Nitrotoga fabula" also showed an unusually high tolerance to nitrite (activity at 30 mM NO2-) and nitrate (up to 25 mM NO3-). Nitrite oxidation followed Michaelis-Menten kinetics, with an apparent Km (Km(app)) of ~89 µM nitrite and a Vmax of ~28 µmol of nitrite per mg of protein per h. Key metabolic pathways of "Ca Nitrotoga fabula" were reconstructed from the closed genome. "Ca Nitrotoga fabula" possesses a new type of periplasmic nitrite oxidoreductase belonging to a lineage of mostly uncharacterized proteins. This novel enzyme indicates (i) separate evolution of nitrite oxidation in "Ca Nitrotoga" and other NOB, (ii) the possible existence of phylogenetically diverse, unrecognized NOB, and (iii) together with new metagenomic data, the potential existence of nitrite-oxidizing archaea. For carbon fixation, "Ca Nitrotoga fabula" uses the Calvin-Benson-Bassham cycle. It also carries genes encoding complete pathways for hydrogen and sulfite oxidation, suggesting that alternative energy metabolisms enable "Ca Nitrotoga fabula" to survive nitrite depletion and colonize new niches.IMPORTANCE Nitrite-oxidizing bacteria (NOB) are major players in the biogeochemical nitrogen cycle and critical for wastewater treatment. However, most NOB remain uncultured, and their biology is poorly understood. Here, we obtained the first isolate from the environmentally widespread NOB genus "Candidatus Nitrotoga" and performed a detailed physiological and genomic characterization of this organism ("Candidatus Nitrotoga fabula"). Differences between key phenotypic properties of "Ca Nitrotoga fabula" and those of previously enriched "Ca Nitrotoga" members reveal an unexpectedly broad range of physiological adaptations in this genus. Moreover, genes encoding components of energy metabolisms outside nitrification suggest that "Ca Nitrotoga" are ecologically more flexible than previously anticipated. The identification of a novel nitrite-oxidizing enzyme in "Ca Nitrotoga fabula" expands our picture of the evolutionary history of nitrification and might lead to discoveries of novel nitrite oxidizers. Altogether, this study provides urgently needed insights into the biology of understudied but environmentally and biotechnologically important microorganisms.
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Affiliation(s)
- Katharina Kitzinger
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network "Chemistry meets Microbiology," University of Vienna, Vienna, Austria
- Max-Planck-Institute for Marine Microbiology, Bremen, Germany
| | - Hanna Koch
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network "Chemistry meets Microbiology," University of Vienna, Vienna, Austria
| | - Sebastian Lücker
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Christopher J Sedlacek
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network "Chemistry meets Microbiology," University of Vienna, Vienna, Austria
| | - Craig Herbold
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network "Chemistry meets Microbiology," University of Vienna, Vienna, Austria
| | - Jasmin Schwarz
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network "Chemistry meets Microbiology," University of Vienna, Vienna, Austria
| | - Anne Daebeler
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network "Chemistry meets Microbiology," University of Vienna, Vienna, Austria
| | - Anna J Mueller
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network "Chemistry meets Microbiology," University of Vienna, Vienna, Austria
| | - Michael Lukumbuzya
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network "Chemistry meets Microbiology," University of Vienna, Vienna, Austria
| | - Stefano Romano
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network "Chemistry meets Microbiology," University of Vienna, Vienna, Austria
| | - Nikolaus Leisch
- Max-Planck-Institute for Marine Microbiology, Bremen, Germany
| | - Søren Michael Karst
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Rasmus Kirkegaard
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Mads Albertsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Michael Wagner
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network "Chemistry meets Microbiology," University of Vienna, Vienna, Austria
| | - Holger Daims
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network "Chemistry meets Microbiology," University of Vienna, Vienna, Austria
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Distinct distribution patterns of ammonia-oxidizing archaea and bacteria in sediment and water column of the Yellow River estuary. Sci Rep 2018; 8:1584. [PMID: 29371667 PMCID: PMC5785527 DOI: 10.1038/s41598-018-20044-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 01/12/2018] [Indexed: 11/20/2022] Open
Abstract
Ammonia oxidation is a critical process of estuarine nitrogen cycling involving ammonia-oxidizing archaea (AOA) and bacteria (AOB). However, the distribution patterns of ammonia-oxidizing microorganisms (AOMs) between different habitats in the same area remain unclear. The present study investigated the AOMs’ abundance and community compositions in both sediment and water habitats of the Yellow River estuary. Quantitative PCR (qPCR) revealed that AOA showed significant higher abundance than AOB both in sediment and water samples. AOA and AOB abundance distribution trends were consistent in sediment but distinct in water along the sampling sites. Clone library-based analyses showed that AOA sequences were affiliated with Nitrososphaera, Nitrosopumilus and Nitrosotalea clusters. Generally, Nitrososphaera was predominant in sediment, while Nitrosopumilus and Nitrosotalea dominated in water column. AOB sequences were classified into genera Nitrosospira and Nitrosomonas, and Nitrosospira dominated in both habitats. Principal coordinate analysis (PCoA) also indicated AOA community structures exhibited significant differences between two habitats, while AOB were not. Ammonium and carbon contents were the potential key factors to influence AOMs’ abundance and compositions in sediment, while no measured variables were determined to have major influences on communities in water habitat. These findings increase the understanding of the AOMs’ distribution patterns in estuarine ecosystems.
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Ham B, Choi BY, Chae GT, Kirk MF, Kwon MJ. Geochemical Influence on Microbial Communities at CO 2-Leakage Analog Sites. Front Microbiol 2017; 8:2203. [PMID: 29170659 PMCID: PMC5684959 DOI: 10.3389/fmicb.2017.02203] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 10/26/2017] [Indexed: 01/22/2023] Open
Abstract
Microorganisms influence the chemical and physical properties of subsurface environments and thus represent an important control on the fate and environmental impact of CO2 that leaks into aquifers from deep storage reservoirs. How leakage will influence microbial populations over long time scales is largely unknown. This study uses natural analog sites to investigate the long-term impact of CO2 leakage from underground storage sites on subsurface biogeochemistry. We considered two sites with elevated CO2 levels (sample groups I and II) and one control site with low CO2 content (group III). Samples from sites with elevated CO2 had pH ranging from 6.2 to 4.5 and samples from the low-CO2 control group had pH ranging from 7.3 to 6.2. Solute concentrations were relatively low for samples from the control group and group I but high for samples from group II, reflecting varying degrees of water-rock interaction. Microbial communities were analyzed through clone library and MiSeq sequencing. Each 16S rRNA analysis identified various bacteria, methane-producing archaea, and ammonia-oxidizing archaea. Both bacterial and archaeal diversities were low in groundwater with high CO2 content and community compositions between the groups were also clearly different. In group II samples, sequences classified in groups capable of methanogenesis, metal reduction, and nitrate reduction had higher relative abundance in samples with relative high methane, iron, and manganese concentrations and low nitrate levels. Sequences close to Comamonadaceae were abundant in group I, while the taxa related to methanogens, Nitrospirae, and Anaerolineaceae were predominant in group II. Our findings provide insight into subsurface biogeochemical reactions that influence the carbon budget of the system including carbon fixation, carbon trapping, and CO2 conversion to methane. The results also suggest that monitoring groundwater microbial community can be a potential tool for tracking CO2 leakage from geologic storage sites.
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Affiliation(s)
- Baknoon Ham
- KU-KIST Green School, Korea University, Seoul, South Korea
| | - Byoung-Young Choi
- Korea Institute of Geoscience and Mineral Resources, Daejeon, South Korea
| | - Gi-Tak Chae
- Korea Institute of Geoscience and Mineral Resources, Daejeon, South Korea
| | - Matthew F Kirk
- Department of Geology, Kansas State University, Manhattan, KS, United States
| | - Man Jae Kwon
- KU-KIST Green School, Korea University, Seoul, South Korea.,Department of Earth and Environmental Sciences, Korea University, Seoul, South Korea
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Bacteria alone establish the chemical basis of the wood-fall chemosynthetic ecosystem in the deep-sea. ISME JOURNAL 2017; 12:367-379. [PMID: 28984846 PMCID: PMC5776450 DOI: 10.1038/ismej.2017.163] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 06/29/2017] [Accepted: 08/24/2017] [Indexed: 01/05/2023]
Abstract
Wood-fall ecosystems host chemosynthetic bacteria that use hydrogen sulfide as an electron donor. The production of hydrogen sulfide from decaying wood in the deep-sea has long been suspected to rely on the activity of wood-boring bivalves, Xylophaga spp. However, recent mesocosm experiments have shown hydrogen sulfide production in the absence of wood borers. Here, we combined in situ chemical measurements, amplicon sequencing and metagenomics to test whether the presence of Xylophaga spp.-affected hydrogen sulfide production and wood microbial community assemblages. During a short-term experiment conducted in a deep-sea canyon, we found that wood-fall microbial communities could produce hydrogen sulfide in the absence of Xylophaga spp. The presence of wood borers had a strong impact on the microbial community composition on the wood surface but not in the wood centre, where communities were observed to be homogeneous among different samples. When wood borers were excluded, the wood centre community did not have the genetic potential to degrade cellulose or hemicellulose but could use shorter carbohydrates such as sucrose. We conclude that wood centre communities produce fermentation products that can be used by the sulfate-reducing bacteria detected near the wood surface. We thus demonstrate that microorganisms alone could establish the chemical basis essential for the recruitment of chemolithotrophic organisms in deep-sea wood falls.
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Wang Y, Ma L, Mao Y, Jiang X, Xia Y, Yu K, Li B, Zhang T. Comammox in drinking water systems. WATER RESEARCH 2017; 116:332-341. [PMID: 28390307 DOI: 10.1016/j.watres.2017.03.042] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Revised: 03/18/2017] [Accepted: 03/18/2017] [Indexed: 05/04/2023]
Abstract
The discovery of complete ammonia oxidizer (comammox) has fundamentally upended our perception of the global nitrogen cycle. Here, we reported four metagenome assembled genomes (MAGs) of comammox Nitrospira that were retrieved from metagenome datasets of tap water in Singapore (SG-bin1 and SG-bin2), Hainan province, China (HN-bin3) and Stanford, CA, USA (ST-bin4). Genes of phylogenetically distinct ammonia monooxygenase subunit A (amoA) and hydroxylamine dehydrogenase (hao) were identified in these four MAGs. Phylogenetic analysis based on ribosomal proteins, AmoA, hao and nitrite oxidoreductase (subunits nxrA and nxrB) sequences indicated their close relationships with published comammox Nitrospira. Canonical ammonia-oxidizing microbes (AOM) were also identified in the three tap water samples, ammonia-oxidizing bacteria (AOB) in Singapore's and Stanford's samples and ammonia-oxidizing archaea (AOA) in Hainan's sample. The comammox amoA-like sequences were also detected from some other drinking water systems, and even outnumbered the AOA and AOB amoA-like sequences. The findings of MAGs and the occurrences of AOM in different drinking water systems provided a significant clue that comammox are widely distributed in drinking water systems.
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Affiliation(s)
- Yulin Wang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Liping Ma
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Yanping Mao
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Xiaotao Jiang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Yu Xia
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Ke Yu
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Bing Li
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Tong Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong.
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Sobotka D, Tuszynska A, Kowal P, Ciesielski S, Czerwionka K, Makinia J. Long-term performance and microbial characteristics of the anammox-enriched granular sludge cultivated in a bench-scale sequencing batch reactor. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2017.01.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Reyes C, Schneider D, Lipka M, Thürmer A, Böttcher ME, Friedrich MW. Nitrogen Metabolism Genes from Temperate Marine Sediments. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2017; 19:175-190. [PMID: 28283802 PMCID: PMC5405112 DOI: 10.1007/s10126-017-9741-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 02/05/2017] [Indexed: 05/26/2023]
Abstract
In this study, we analysed metagenomes along with biogeochemical profiles from Skagerrak (SK) and Bothnian Bay (BB) sediments, to trace the prevailing nitrogen pathways. NO3- was present in the top 5 cm below the sediment-water interface at both sites. NH4+ increased with depth below 5 cm where it overlapped with the NO3- zone. Steady-state modelling of NO3- and NH4+ porewater profiles indicates zones of net nitrogen species transformations. Bacterial protease and hydratase genes appeared to make up the bulk of total ammonification genes. Genes involved in ammonia oxidation (amo, hao), denitrification (nir, nor), dissimilatory NO3- reduction to NH4+ (nfr and otr) and in both of the latter two pathways (nar, nap) were also present. Results show ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) are similarly abundant in both sediments. Also, denitrification genes appeared more abundant than DNRA genes. 16S rRNA gene analysis showed that the relative abundance of the nitrifying group Nitrosopumilales and other groups involved in nitrification and denitrification (Nitrobacter, Nitrosomonas, Nitrospira, Nitrosococcus and Nitrosomonas) appeared less abundant in SK sediments compared to BB sediments. Beggiatoa and Thiothrix 16S rRNA genes were also present, suggesting chemolithoautotrophic NO3- reduction to NO2- or NH4+ as a possible pathway. Our results show the metabolic potential for ammonification, nitrification, DNRA and denitrification activities in North Sea and Baltic Sea sediments.
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Affiliation(s)
- Carolina Reyes
- Microbial Ecophysiology, University of Bremen, Leobener Strasse, D-28359, Bremen, Germany.
- Department of Environmental Geosciences, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
| | - Dominik Schneider
- Department of Genomic and Applied Microbiology, University of Göttingen, Grisebachstrasse 8, D-37077, Göttingen, Germany
| | - Marko Lipka
- Geochemistry and Stable Isotope Biogeochemistry Group, Leibniz Institute for Baltic Sea Research (IOW), Seestrasse 15, D-18119, Warnemünde, Germany
| | - Andrea Thürmer
- Department of Genomic and Applied Microbiology, University of Göttingen, Grisebachstrasse 8, D-37077, Göttingen, Germany
| | - Michael E Böttcher
- Geochemistry and Stable Isotope Biogeochemistry Group, Leibniz Institute for Baltic Sea Research (IOW), Seestrasse 15, D-18119, Warnemünde, Germany
| | - Michael W Friedrich
- Microbial Ecophysiology, University of Bremen, Leobener Strasse, D-28359, Bremen, Germany
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Wang Z, Luo G, Li J, Chen SY, Li Y, Li WT, Li AM. Response of performance and ammonia oxidizing bacteria community to high salinity stress in membrane bioreactor with elevated ammonia loading. BIORESOURCE TECHNOLOGY 2016; 216:714-721. [PMID: 27290667 DOI: 10.1016/j.biortech.2016.05.123] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 05/25/2016] [Accepted: 05/26/2016] [Indexed: 06/06/2023]
Abstract
Effect of elevated ammonia loading rate (ALR) and increasing salinity on the operation of membrane bioreactor (MBR) and the response of microbial community were investigated. Results showed that MBR started up with 1% NaCl stress achieved amazing nitrification performance at high salinity up to 4% when treating wastewater containing 1000mg/L NH(+)4-N. Further increasing salinity to 7% led to failure of MBR unrecoverably. Steep decline of sludge activity contributed to the extremely worse performance. High-throughput sequencing analysis showed that both ALR and salinity had selective effects on the microbial community structure. In genus level, Methyloversatilis and Maribacter were enriched during the operation. Survival of salt-resistant microbes contributed to the rising of richness and diversity at 2% and 4% NaCl stress. Analysis of amoA-gene-based cloning revealed Nitrosomonas marina are chiefly responsible for catalyzing ammonia oxidation in high ALR at high salinity stress.
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Affiliation(s)
- Zhu Wang
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, China; School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Gan Luo
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Jun Li
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Shi-Yu Chen
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Yan Li
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
| | - Wen-Tao Li
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Ai-Min Li
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
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Genomics of a phototrophic nitrite oxidizer: insights into the evolution of photosynthesis and nitrification. ISME JOURNAL 2016; 10:2669-2678. [PMID: 27093047 DOI: 10.1038/ismej.2016.56] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 02/24/2016] [Accepted: 03/04/2016] [Indexed: 11/09/2022]
Abstract
Oxygenic photosynthesis evolved from anoxygenic ancestors before the rise of oxygen ~2.32 billion years ago; however, little is known about this transition. A high redox potential reaction center is a prerequisite for the evolution of the water-oxidizing complex of photosystem II. Therefore, it is likely that high-potential phototrophy originally evolved to oxidize alternative electron donors that utilized simpler redox chemistry, such as nitrite or Mn. To determine whether nitrite could have had a role in the transition to high-potential phototrophy, we sequenced and analyzed the genome of Thiocapsa KS1, a Gammaproteobacteria capable of anoxygenic phototrophic nitrite oxidation. The genome revealed a high metabolic flexibility, which likely allows Thiocapsa KS1 to colonize a great variety of habitats and to persist under fluctuating environmental conditions. We demonstrate that Thiocapsa KS1 does not utilize a high-potential reaction center for phototrophic nitrite oxidation, which suggests that this type of phototrophic nitrite oxidation did not drive the evolution of high-potential phototrophy. In addition, phylogenetic and biochemical analyses of the nitrite oxidoreductase (NXR) from Thiocapsa KS1 illuminate a complex evolutionary history of nitrite oxidation. Our results indicate that the NXR in Thiocapsa originates from a different nitrate reductase clade than the NXRs in chemolithotrophic nitrite oxidizers, suggesting that multiple evolutionary trajectories led to modern nitrite-oxidizing bacteria.
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Lee DE, Lee J, Kim YM, Myeong JI, Kim KH. Uncultured bacterial diversity in a seawater recirculating aquaculture system revealed by 16S rRNA gene amplicon sequencing. J Microbiol 2016; 54:296-304. [PMID: 27033205 DOI: 10.1007/s12275-016-5571-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 03/07/2016] [Accepted: 03/14/2016] [Indexed: 01/21/2023]
Abstract
Bacterial diversity in a seawater recirculating aquaculture system (RAS) was investigated using 16S rRNA amplicon sequencing to understand the roles of bacterial communities in the system. The RAS was operated at nine different combinations of temperature (15°C, 20°C, and 25°C) and salinity (20‰, 25‰, and 32.5‰). Samples were collected from five or six RAS tanks (biofilters) for each condition. Fifty samples were analyzed. Proteobacteria and Bacteroidetes were most common (sum of both phyla: 67.2% to 99.4%) and were inversely proportional to each other. Bacteria that were present at an average of ≥ 1% included Actinobacteria (2.9%) Planctomycetes (2.0%), Nitrospirae (1.5%), and Acidobacteria (1.0%); they were preferentially present in packed bed biofilters, mesh biofilters, and maturation biofilters. The three biofilters showed higher diversity than other RAS tanks (aerated biofilters, floating bed biofilters, and fish tanks) from phylum to operational taxonomic unit (OTU) level. Samples were clustered into several groups based on the bacterial communities. Major taxonomic groups related to family Rhodobacteraceae and Flavobacteriaceae were distributed widely in the samples. Several taxonomic groups like [Saprospiraceae], Cytophagaceae, Octadecabacter, and Marivita showed a cluster-oriented distribution. Phaeobacter and Sediminicola-related reads were detected frequently and abundantly at low temperature. Nitrifying bacteria were detected frequently and abundantly in the three biofilters. Phylogenetic analysis of the nitrifying bacteria showed several similar OTUs were observed widely through the biofilters. The diverse bacterial communities and the minor taxonomic groups, except for Proteobacteria and Bacteroidetes, seemed to play important roles and seemed necessary for nitrifying activity in the RAS, especially in packed bed biofilters, mesh biofilters, and maturation biofilters.
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Affiliation(s)
- Da-Eun Lee
- Department of Microbiology, Pukyong National University, Busan, 48513, Republic of Korea
| | - Jinhwan Lee
- Aquaculture Research Division, National Institute of Fisheries Science, Busan, 46083, Republic of Korea
| | - Young-Mog Kim
- Department of Food Science and Technology, Pukyong National University, Busan, 48513, Republic of Korea
| | - Jeong-In Myeong
- Aquaculture Research Division, National Institute of Fisheries Science, Busan, 46083, Republic of Korea
| | - Kyoung-Ho Kim
- Department of Microbiology, Pukyong National University, Busan, 48513, Republic of Korea.
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Tangkitjawisut W, Limpiyakorn T, Powtongsook S, Pornkulwat P, Suwannasilp BB. Differences in nitrite-oxidizing communities and kinetics in a brackish environment after enrichment at low and high nitrite concentrations. J Environ Sci (China) 2016; 42:41-49. [PMID: 27090693 DOI: 10.1016/j.jes.2015.07.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 07/17/2015] [Accepted: 08/05/2015] [Indexed: 06/05/2023]
Abstract
Nitrite accumulation in shrimp ponds can pose serious adverse effects to shrimp production and the environment. This study aims to develop an effective process for the enrichment of ready-to-use nitrite-oxidizing bacteria (NOB) inocula that would be appropriate for nitrite removal in brackish shrimp ponds. To achieve this objective, the effects of nitrite concentrations on NOB communities and nitrite oxidation kinetics in a brackish environment were investigated. Moving-bed biofilm sequencing batch reactors and continuous moving-bed biofilm reactors were used for the enrichment of NOB at various nitrite concentrations, using sediment from brackish shrimp ponds as seed inoculum. The results from NOB population analysis with quantitative polymerase chain reaction (qPCR) show that only Nitrospira were detected in the sediment from the shrimp ponds. After the enrichment, both Nitrospira and Nitrobacter coexisted in the reactors controlling effluent nitrite at 0.1 and 0.5 mg-NO2(-)-N/L. On the other hand, in the reactors controlling effluent nitrite at 3, 20, and 100 mg-NO2(-)-N/L, Nitrobacter outcompeted Nitrospira in many orders of magnitude. The half saturation coefficients (Ks) for nitrite oxidation of the enrichments at low nitrite concentrations (0.1 and 0.5 mg-NO2(-)-N/L) were in the range of 0.71-0.98 mg-NO2(-)-N/L. In contrast, the K(s) values of NOB enriched at high nitrite concentrations (3, 20, and 100 mg-NO2(-)-N/L) were much higher (8.36-12.20 mg-NO2(-)-N/L). The results suggest that the selection of nitrite concentrations for the enrichment of NOB inocula can significantly influence NOB populations and kinetics, which could affect the effectiveness of their applications in brackish shrimp ponds.
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Affiliation(s)
- Wipasanee Tangkitjawisut
- Department of Environmental Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok 10330, Thailand
| | - Tawan Limpiyakorn
- Department of Environmental Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok 10330, Thailand; Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, Bangkok 10330, Thailand
| | - Sorawit Powtongsook
- Center of Excellence for Marine Biotechnology, Department of Marine Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Preeyaporn Pornkulwat
- Department of Environmental Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok 10330, Thailand
| | - Benjaporn Boonchayaanant Suwannasilp
- Department of Environmental Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok 10330, Thailand; Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, Bangkok 10330, Thailand.
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Metagenomic Evidence for the Presence of Comammox Nitrospira-Like Bacteria in a Drinking Water System. mSphere 2015; 1:mSphere00054-15. [PMID: 27303675 PMCID: PMC4863621 DOI: 10.1128/msphere.00054-15] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 12/08/2015] [Indexed: 11/23/2022] Open
Abstract
Nitrification plays an important role in regulating the concentrations of inorganic nitrogen species in a range of environments, from drinking water and wastewater treatment plants to the oceans. Until recently, aerobic nitrification was considered to be a two-step process involving ammonia-oxidizing bacteria or archaea and nitrite-oxidizing bacteria. This process requires close cooperation between these two functional guilds for complete conversion of ammonia to nitrate, without the accumulation of nitrite or other intermediates, such as nitrous oxide, a potent greenhouse gas. The discovery of a single organism with the potential to oxidize both ammonia and nitrite adds a new dimension to the current understanding of aerobic nitrification, while presenting opportunities to rethink nitrogen management in engineered systems. We report metagenomic evidence for the presence of a Nitrospira-like organism with the metabolic potential to perform the complete oxidation of ammonia to nitrate (i.e., it is a complete ammonia oxidizer [comammox]) in a drinking water system. This metagenome bin was discovered through shotgun DNA sequencing of samples from biologically active filters at the drinking water treatment plant in Ann Arbor, MI. Ribosomal proteins, 16S rRNA, and nxrA gene analyses confirmed that this genome is related to Nitrospira-like nitrite-oxidizing bacteria. The presence of the full suite of ammonia oxidation genes, including ammonia monooxygenase and hydroxylamine dehydrogenase, on a single ungapped scaffold within this metagenome bin suggests the presence of recently discovered comammox potential. Evaluations based on coverage and k-mer frequency distribution, use of two different genome-binning approaches, and nucleic acid and protein similarity analyses support the presence of this scaffold within the Nitrospira metagenome bin. The amoA gene found in this metagenome bin is divergent from those of canonical ammonia and methane oxidizers and clusters closely with the unusual amoA gene of comammox Nitrospira. This finding suggests that previously reported imbalances in abundances of nitrite- and ammonia-oxidizing bacteria/archaea may likely be explained by the capacity of Nitrospira-like organisms to completely oxidize ammonia. This finding might have significant implications for our understanding of microbially mediated nitrogen transformations in engineered and natural systems. IMPORTANCE Nitrification plays an important role in regulating the concentrations of inorganic nitrogen species in a range of environments, from drinking water and wastewater treatment plants to the oceans. Until recently, aerobic nitrification was considered to be a two-step process involving ammonia-oxidizing bacteria or archaea and nitrite-oxidizing bacteria. This process requires close cooperation between these two functional guilds for complete conversion of ammonia to nitrate, without the accumulation of nitrite or other intermediates, such as nitrous oxide, a potent greenhouse gas. The discovery of a single organism with the potential to oxidize both ammonia and nitrite adds a new dimension to the current understanding of aerobic nitrification, while presenting opportunities to rethink nitrogen management in engineered systems.
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The Crystal Structure of Nitrosomonas europaea Sucrose Synthase Reveals Critical Conformational Changes and Insights into Sucrose Metabolism in Prokaryotes. J Bacteriol 2015; 197:2734-46. [PMID: 26013491 DOI: 10.1128/jb.00110-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 05/19/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED In this paper we report the first crystal structure of a prokaryotic sucrose synthase from the nonphotosynthetic bacterium Nitrosomonas europaea. The obtained structure was in an open form, whereas the only other available structure, from the plant Arabidopsis thaliana, was in a closed conformation. Comparative structural analysis revealed a "hinge-latch" combination, which is critical to transition between the open and closed forms of the enzyme. The N. europaea sucrose synthase shares the same fold as the GT-B family of the retaining glycosyltransferases. In addition, a triad of conserved homologous catalytic residues in the family was shown to be functionally critical in the N. europaea sucrose synthase (Arg567, Lys572, and Glu663). This implies that sucrose synthase shares not only a common origin with the GT-B family but also a similar catalytic mechanism. The enzyme preferred transferring glucose from ADP-glucose rather than UDP-glucose like the eukaryotic counterparts. This predicts that these prokaryotic organisms have a different sucrose metabolic scenario from plants. Nucleotide preference determines where the glucose moiety is targeted after sucrose is degraded. IMPORTANCE We obtained biochemical and structural evidence of sucrose metabolism in nonphotosynthetic bacteria. Until now, only sucrose synthases from photosynthetic organisms have been characterized. Here, we provide the crystal structure of the sucrose synthase from the chemolithoautotroph N. europaea. The structure supported that the enzyme functions with an open/close induced fit mechanism. The enzyme prefers as the substrate adenine-based nucleotides rather than uridine-based like the eukaryotic counterparts, implying a strong connection between sucrose and glycogen metabolism in these bacteria. Mutagenesis data showed that the catalytic mechanism must be conserved not only in sucrose synthases but also in all other retaining GT-B glycosyltransferases.
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Size-fraction partitioning of community gene transcription and nitrogen metabolism in a marine oxygen minimum zone. ISME JOURNAL 2015; 9:2682-96. [PMID: 25848875 DOI: 10.1038/ismej.2015.44] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 02/11/2015] [Accepted: 02/26/2015] [Indexed: 02/01/2023]
Abstract
The genetic composition of marine microbial communities varies at the microscale between particle-associated (PA; >1.6 μm) and free-living (FL; 0.2-1.6 μm) niches. It remains unclear, however, how metabolic activities differ between PA and FL fractions. We combined rate measurements with metatranscriptomics to quantify PA and FL microbial activity in the oxygen minimum zone (OMZ) of the Eastern Tropical North Pacific, focusing on dissimilatory processes of the nitrogen (N) cycle. Bacterial gene counts were 8- to 15-fold higher in the FL compared with the PA fraction. However, rates of all measured N cycle processes, excluding ammonia oxidation, declined significantly following particle (>1.6 μm) removal. Without particles, rates of nitrate reduction to nitrite (1.5-9.4nMNd(-1)) fell to zero and N2 production by denitrification (0.5-1.7nMNd(-1)) and anammox (0.3-1.9nMNd(-1)) declined by 53-85%. The proportional representation of major microbial taxa and N cycle gene transcripts in metatranscriptomes followed fraction-specific trends. Transcripts encoding nitrate reductase were uniform among PA and FL fractions, whereas anammox-associated transcripts were proportionately enriched up to 15-fold in the FL fraction. In contrast, transcripts encoding enzymes for N2O and N2 production by denitrification were enriched up to 28-fold in PA samples. These patterns suggest that the majority of N cycle activity, excluding N2O and N2 production by denitrification, is confined to a FL majority that is critically dependent on access to particles, likely as a source of organic carbon and inorganic N. Variable particle distributions may drive heterogeneity in N cycle activity and gene expression in OMZs.
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Li B, Huang W, Zhang C, Feng S, Zhang Z, Lei Z, Sugiura N. Effect of TiO2 nanoparticles on aerobic granulation of algal-bacterial symbiosis system and nutrients removal from synthetic wastewater. BIORESOURCE TECHNOLOGY 2015; 187:214-220. [PMID: 25855527 DOI: 10.1016/j.biortech.2015.03.118] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 03/19/2015] [Accepted: 03/25/2015] [Indexed: 06/04/2023]
Abstract
The influence of TiO2 nanoparticles (TiO2-NPs) (10-50mg/L) on aerobic granulation of algal-bacterial symbiosis system was investigated by using two identical sequencing batch reactors (SBRs). Although little adverse effect was observed on their nitritation efficiency (98-100% in both reactors), algal-bacterial granules in the control SBR (Rc) gradually lost stability mainly brought about by algae growth. TiO2-NPs addition to RT was found to enhance the granulation process achieving stable and compact algal-bacterial granules with remarkably improved nitratation thus little nitrite accumulation in RT when influent TiO2-NPs⩾30mg/L. Despite almost similar organics and phosphorus removals obtained in both reactors, the stably high nitratation efficiency in addition to much stable granular structure in RT suggests that TiO2-NPs addition might be a promising remedy for the long-term operation of algal-bacterial granular system, most probably attributable to the stimulated excretion of extracellular polymeric substances and less filamentous TM7.
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Affiliation(s)
- Bing Li
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Wenli Huang
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Chao Zhang
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Sisi Feng
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Zhenya Zhang
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Zhongfang Lei
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan.
| | - Norio Sugiura
- Malaysia-Japan International Institute of Technology (MJIIT), Universiti Teknologi Malaysia, Jalan Semarak, Kuala Lumpur 54100, Malaysia; Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
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Flood M, Frabutt D, Floyd D, Powers A, Ezegwe U, Devol A, Tiquia-Arashiro SM. Ammonia-oxidizing bacteria and archaea in sediments of the Gulf of Mexico. ENVIRONMENTAL TECHNOLOGY 2015; 36:124-135. [PMID: 25409591 DOI: 10.1080/09593330.2014.942385] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The diversity (richness and community composition) of ammonia-oxidizing archaea (AOA) and bacteria (AOB) within sediments of the Gulf of Mexico was examined. Using polymerase chain reaction primers designed to specifically target the archaeal ammonia monooxygenase-subunit (amoA) gene and bacterial amoA gene, we found AOA and AOB to be present in all three sampling sites. Archaeal amoA libraries were dominated by a few widely distributed Nitrosopumilus-like sequence types, whereas AOB diversity showed significant variation in both richness and community composition. Majority of the bacterial amoA sequences recovered belong to Betaproteobacteria and very few belong to Gammaproteobacteria. Results suggest that water depth and nutrient availability were identified as potential drivers that affected the selection of the AOA and AOB communities. Besides influencing the abundance of individual taxa, these environmental factors also had an impact on the overall richness of the overall AOA and AOB communities. The richness and diversity of AOA and AOB genes were higher at the shallowest sediments (100 m depth) and the deepest sediments (1300 m depth). The reduced diversity in the deepest sediments could be explained by much lower nutrient availability.
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Affiliation(s)
- Matthew Flood
- a Department of Natural Sciences , The University of Michigan , 115F Science Building, Dearborn , MI 48128 , USA
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