1
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Wright CL, Lehtovirta-Morley LE. Nitrification and beyond: metabolic versatility of ammonia oxidising archaea. THE ISME JOURNAL 2023; 17:1358-1368. [PMID: 37452095 PMCID: PMC10432482 DOI: 10.1038/s41396-023-01467-0] [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: 12/20/2022] [Revised: 06/09/2023] [Accepted: 06/21/2023] [Indexed: 07/18/2023]
Abstract
Ammonia oxidising archaea are among the most abundant living organisms on Earth and key microbial players in the global nitrogen cycle. They carry out oxidation of ammonia to nitrite, and their activity is relevant for both food security and climate change. Since their discovery nearly 20 years ago, major insights have been gained into their nitrogen and carbon metabolism, growth preferences and their mechanisms of adaptation to the environment, as well as their diversity, abundance and activity in the environment. Despite significant strides forward through the cultivation of novel organisms and omics-based approaches, there are still many knowledge gaps on their metabolism and the mechanisms which enable them to adapt to the environment. Ammonia oxidising microorganisms are typically considered metabolically streamlined and highly specialised. Here we review the physiology of ammonia oxidising archaea, with focus on aspects of metabolic versatility and regulation, and discuss these traits in the context of nitrifier ecology.
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Affiliation(s)
- Chloe L Wright
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
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2
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Yue Y, Wang F, Pan J, Chen XP, Tang Y, Yang Z, Ma J, Li M, Yang M. Spatiotemporal dynamics, community assembly and functional potential of sedimentary archaea in reservoirs: coaction of stochasticity and nutrient load. FEMS Microbiol Ecol 2022; 98:6701916. [PMID: 36111740 DOI: 10.1093/femsec/fiac109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 08/16/2022] [Accepted: 09/14/2022] [Indexed: 01/21/2023] Open
Abstract
Archaea participate in biogeochemical cycles in aquatic ecosystems, and deciphering their community dynamics and assembly mechanisms is key to understanding their ecological functions. Here, sediments from 12 selected reservoirs from the Wujiang and Pearl River basins in southwest China were investigated using 16S rRNA Illumina sequencing and quantitative PCR for archaeal abundance and richness in all seasons. Generally, archaeal abundance and α-diversity were significantly correlated with temperature; however, β-diversity analysis showed that community structures varied greatly among locations rather than seasons, indicating a distance-decay pattern with geographical variation. The null model revealed the major contribution of stochasticity to archaeal community assembly, which was further confirmed by the neutral community model that could explain 71.7% and 90.2% of the variance in archaeal assembly in the Wujiang and Pearl River basins, respectively. Moreover, sediment total nitrogen and organic carbon levels were significantly correlated with archaeal abundance and α-diversity. Interestingly, these nutrient levels were positively and negatively correlated, respectively, with the abundance of methanogenic and ammonia-oxidized archaea: the dominant sedimentary archaea in these reservoirs. Taken together, this work systematically characterized archaeal community profiles in reservoir sediments and demonstrated the combined action of stochastic processes and nutrient load in shaping archaeal communities in reservoir ecosystems.
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Affiliation(s)
- Yihong Yue
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Fushun Wang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, 518060, China.,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Xue-Ping Chen
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Yi Tang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Zhihong Yang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Jing Ma
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, 518060, China.,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Ming Yang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
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3
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Wang D, Wang Y, Liu L, Chen Y, Wang C, Xu X, Yang Y, Wang Y, Zhang T. Niche differentiation and symbiotic association among ammonia/nitrite oxidizers in a full-scale rotating biological contactor. WATER RESEARCH 2022; 225:119137. [PMID: 36198208 DOI: 10.1016/j.watres.2022.119137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/16/2022] [Accepted: 09/18/2022] [Indexed: 06/16/2023]
Abstract
Although the distribution of ammonia/nitrite oxidizers had been profiled in different habitats, current understanding is still limited regarding their niche differentiation in the integrated biofilm reactors, the symbiotic associations of ammonia/nitrite oxidizers, as well as the parasitic interaction between viruses and those functional organisms involved in the nitrogen cycle. Here, the integrated metagenomics and metatranscriptomics are applied to profile the ammonia/nitrite oxidizers communities and transcriptional activities changes along the flowpath of a concatenated full-scale rotating biological contactor (RBC) (frontend Stage-A and backend Stage-B). 19 metagenome-assembled genomes (MAGs) of ammonia/nitrite oxidizers were recovered by using a hybrid assembly approach, including four ammonia-oxidizing bacteria (AOB), two ammonia-oxidizing archaea (AOA), two complete ammonia oxidation bacteria (comammox), eight nitrite-oxidizing bacteria (NOB), and three anaerobic ammonium oxidation bacteria (anammox). Diverse AOB and anammox dominated Stage-A and collectively contributed to nitrogen conversion. With the decline of ammonia concentration along the flowpath, comammox and AOA appeared and increased in relative abundance in Stage-B, accounting for 8.8% of the entire community at the end of this reactor, and their dominating role in nitrogen turnover was indicated by the high transcription activity of their corresponding function genes. Moreover, the variation in the abundance of viruses infecting ammonia and nitrite oxidizers suggests that viruses likely act as a biotic factor mediating ammonia/nitrite oxidizer populations. This study demonstrates that complex factors shaped niche differentiation and symbiotic associations of ammonia/nitrite oxidizers in the RBC and highlights the importance of RBCs as model systems for the investigation of biotic and abiotic factors affecting the composition of microbiomes.
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Affiliation(s)
- Dou Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China
| | - Yulin Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China
| | - Lei Liu
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China
| | - Yiqiang Chen
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China
| | - Chunxiao Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China
| | - Xiaoqing Xu
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China
| | - Yu Yang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China
| | - Yubo Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China; School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China; Shenzhen Bay Laboratory, Shenzhen, China.
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4
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He S, Zhao Z, Tian Z, Xu C, Liu Y, He D, Zhang Y, Zheng M. Comammox bacteria predominate among ammonia-oxidizing microorganisms in municipal but not in refinery wastewater treatment plants. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 316:115271. [PMID: 35594823 DOI: 10.1016/j.jenvman.2022.115271] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 05/03/2022] [Accepted: 05/07/2022] [Indexed: 06/15/2023]
Abstract
Comammox bacteria have proved to be one dominant and significant ammonia-oxidizing microorganisms (AOMs) in municipal wastewater treatment plants (WWTPs), however, it still remains unknown about their abundance and diversity in industrial WWTPs. In this study, activated sludge samples from 8 municipal WWTPs and 6 industrial WWTPs treating refinery wastewater were taken and analyzed using qPCR and amoA gene sequencing. Intriguingly, quantitative real-time PCR (qPCR) results suggested that comammox bacteria had a higher numerical abundance compared with ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in municipal WWTPs but did not in refinery WWTPs. Moreover, comammox amoA sequences obtained from high-throughput sequencing were retrieved from all the 8 municipal samples but only 1 industrial sample. Further phylogenetic analysis revealed that N. nitrosa cluster accounted for as high as 79.56% of the total comammox affiliated sequences, which was the most numerically abundant comammox species in municipal WWTPs. This study provided new insights into the abundance and diversity of comammox bacteria in the biological nitrification process in municipal and refinery wastewater treatment systems.
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Affiliation(s)
- Shishi He
- The Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, Main Building G619, North China Electric Power University, Beijing, 102206, China
| | - Zhirong Zhao
- The Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, Main Building G619, North China Electric Power University, Beijing, 102206, China
| | - Zhichao Tian
- The Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, Main Building G619, North China Electric Power University, Beijing, 102206, China
| | - Chi Xu
- The Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, Main Building G619, North China Electric Power University, Beijing, 102206, China
| | - Yuan Liu
- The Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, Main Building G619, North China Electric Power University, Beijing, 102206, China
| | - Da He
- Key Laboratory of Ecological Impacts of Hydraulic Projects and Restoration of Aquatic Ecosystem of Ministry of Water Resources, Institute of Hydroecology, Ministry of Water Resources & Chinese Academy of Sciences, Wuhan, China
| | - Yinghui Zhang
- Guangxi Huantou Water Group Co. LTD, Nanning, 530015, China
| | - Maosheng Zheng
- The Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, Main Building G619, North China Electric Power University, Beijing, 102206, China.
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5
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Xue Y, Zheng M, Wu S, Liu Y, Huang X. Changes in the Species and Functional Composition of Activated Sludge Communities Revealed Mechanisms of Partial Nitrification Established by Ultrasonication. Front Microbiol 2022; 13:960608. [PMID: 35928152 PMCID: PMC9344063 DOI: 10.3389/fmicb.2022.960608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 06/22/2022] [Indexed: 11/20/2022] Open
Abstract
To achieve energy-efficient shortcut nitrogen removal of wastewater in the future, selective elimination of nitrite-oxidizing bacteria (NOB) while enriching ammonia-oxidizing microorganisms is a crucial step. However, the underlying mechanisms of partial nitrification are still not well understood, especially the newly discovered ultrasound-based partial nitrification. To elucidate this issue, in this study two bioreactors were set up, with one established partial nitrification by ultrasonication while the other didn't. During the operation of both reactors, the taxonomic and functional composition of the microbial community were investigated through metagenomics analysis. The result showed that during ultrasonic partial nitrification, ammonia-oxidizing archaea (AOA), Nitrososphaerales, was enriched more than ammonia-oxidizing bacteria (AOB), Nitrosomonas. The enrichment of microorganisms in the community increased the abundance of genes involved in microbial energy generation from lipid and carbohydrates. On the other hand, the abundance of NOB, Nitrospira and Nitrolancea, and Comammox Nitrospira decreased. Selective inhibition of NOB was highly correlated with genes involved in signal transduction enzymes, such as encoding histidine kinase and serine/threonine kinase. These findings provided deep insight into partial nitrification and contributed to the development of shortcut nitrification in wastewater treatment plants.
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Affiliation(s)
- Yu Xue
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Min Zheng
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St. Lucia, QLD, Australia
| | - Shuang Wu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Yanchen Liu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
- *Correspondence: Yanchen Liu
| | - Xia Huang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
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Al-Ajeel S, Spasov E, Sauder LA, McKnight MM, Neufeld JD. Ammonia-oxidizing archaea and complete ammonia-oxidizing Nitrospira in water treatment systems. WATER RESEARCH X 2022; 15:100131. [PMID: 35402889 PMCID: PMC8990171 DOI: 10.1016/j.wroa.2022.100131] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/07/2022] [Accepted: 03/11/2022] [Indexed: 05/27/2023]
Abstract
Nitrification, the oxidation of ammonia to nitrate via nitrite, is important for many engineered water treatment systems. The sequential steps of this respiratory process are carried out by distinct microbial guilds, including ammonia-oxidizing bacteria (AOB) and archaea (AOA), nitrite-oxidizing bacteria (NOB), and newly discovered members of the genus Nitrospira that conduct complete ammonia oxidation (comammox). Even though all of these nitrifiers have been identified within water treatment systems, their relative contributions to nitrogen cycling are poorly understood. Although AOA contribute to nitrification in many wastewater treatment plants, they are generally outnumbered by AOB. In contrast, AOA and comammox Nitrospira typically dominate relatively low ammonia environments such as drinking water treatment, tertiary wastewater treatment systems, and aquaculture/aquarium filtration. Studies that focus on the abundance of ammonia oxidizers may misconstrue the actual role that distinct nitrifying guilds play in a system. Understanding which ammonia oxidizers are active is useful for further optimization of engineered systems that rely on nitrifiers for ammonia removal. This review highlights known distributions of AOA and comammox Nitrospira in engineered water treatment systems and suggests future research directions that will help assess their contributions to nitrification and identify factors that influence their distributions and activity.
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Farooq MS, Uzair M, Maqbool Z, Fiaz S, Yousuf M, Yang SH, Khan MR. Improving Nitrogen Use Efficiency in Aerobic Rice Based on Insights Into the Ecophysiology of Archaeal and Bacterial Ammonia Oxidizers. FRONTIERS IN PLANT SCIENCE 2022; 13:913204. [PMID: 35769304 PMCID: PMC9234532 DOI: 10.3389/fpls.2022.913204] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/16/2022] [Indexed: 05/22/2023]
Abstract
The abundance and structural composition of nitrogen (N) transformation-related microbial communities under certain environmental conditions provide sufficient information about N cycle under different soil conditions. This study aims to explore the major challenge of low N use efficiency (NUE) and N dynamics in aerobic rice systems and reveal the agronomic-adjustive measures to increase NUE through insights into the ecophysiology of ammonia oxidizers. Water-saving practices, like alternate wetting and drying (AWD), dry direct seeded rice (DDSR), wet direct seeding, and saturated soil culture (SSC), have been evaluated in lowland rice; however, only few studies have been conducted on N dynamics in aerobic rice systems. Biological ammonia oxidation is majorly conducted by two types of microorganisms, ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). This review focuses on how diversified are ammonia oxidizers (AOA and AOB), whose factors affect their activities and abundance under different soil conditions. It summarizes findings on pathways of N cycle, rationalize recent research on ammonia oxidizers in N-cycle, and thereby suggests adjustive agronomic measures to reduce N losses. This review also suggests that variations in soil properties significantly impact the structural composition and abundance of ammonia oxidizers. Nitrification inhibitors (NIs) especially nitrapyrin, reduce the nitrification rate and inhibit the abundance of bacterial amoA without impacting archaeal amoA. In contrast, some NIs confine the hydrolysis of synthetic N and, therefore, keep low NH4 +-N concentrations that exhibit no or very slight impact on ammonia oxidizers. Variations in soil properties are more influential in the community structure and abundance of ammonia oxidizers than application of synthetic N fertilizers and NIs. Biological nitrification inhibitors (BNIs) are natural bioactive compounds released from roots of certain plant species, such as sorghum, and could be commercialized to suppress the capacity of nitrifying soil microbes. Mixed application of synthetic and organic N fertilizers enhances NUE and plant N-uptake by reducing ammonia N losses. High salt concentration promotes community abundance while limiting the diversity of AOB and vice versa for AOA, whereas AOA have lower rate for potential nitrification than AOB, and denitrification accounts for higher N2 production. Archaeal abundance, diversity, and structural composition change along an elevation gradient and mainly depend on various soil factors, such as soil saturation, availability of NH4 +, and organic matter contents. Microbial abundance and structural analyses revealed that the structural composition of AOA was not highly responsive to changes in soil conditions or N amendment. Further studies are suggested to cultivate AOA and AOB in controlled-environment experiments to understand the mechanisms of AOA and AOB under different conditions. Together, this evaluation will better facilitate the projections and interpretations of ammonia oxidizer community structural composition with provision of a strong basis to establish robust testable hypotheses on the competitiveness between AOB and AOA. Moreover, after this evaluation, managing soils agronomically for potential utilization of metabolic functions of ammonia oxidizers would be easier.
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Affiliation(s)
- Muhammad Shahbaz Farooq
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
| | - Zubaira Maqbool
- Institute of Soil Science, Pir Mehr Ali Shah-Arid Agriculture University, Rawalpindi, Pakistan
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | | | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu, South Korea
- *Correspondence: Seung Hwan Yang,
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
- Muhammad Ramzan Khan,
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8
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Duan H, Zhao Y, Koch K, Wells GF, Zheng M, Yuan Z, Ye L. Insights into Nitrous Oxide Mitigation Strategies in Wastewater Treatment and Challenges for Wider Implementation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:7208-7224. [PMID: 33975433 DOI: 10.1021/acs.est.1c00840] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Nitrous oxide (N2O) emissions account for the majority of the carbon footprint of wastewater treatment plants (WWTPs). Many N2O mitigation strategies have since been developed while a holistic view is still missing. This article reviews the state-of-the-art of N2O mitigation studies in wastewater treatment. Through analyzing existing studies, this article presents the essential knowledge to guide N2O mitigations, and the logics behind mitigation strategies. In practice, mitigations are mainly carried out by aeration control, feed scheme optimization, and process optimization. Despite increasingly more studies, real implementation remains rare, which is a combined result of unclear climate change policies/incentives, as well as technical challenges. Five critical technical challenges, as well as opportunities, of N2O mitigations were identified. It is proposed that (i) quantification methods for overall N2O emissions and pathway contributions need improvement; (ii) a reliable while straightforward mathematical model is required to quantify benefits and compare mitigation strategies; (iii) tailored risk assessment needs to be conducted for WWTPs, in which more long-term full-scale trials of N2O mitigation are urgently needed to enable robust assessments of the resulting operational costs and impact on nutrient removal performance; (iv) current mitigation strategies focus on centralized WWTPs, more investigations are warranted for decentralised systems, especially decentralized activated sludge WWTPs; and (v) N2O may be mitigated by adopting novel strategies promoting N2O reduction denitrification or microorganisms that emit less N2O. Overall, we conclude N2O mitigation research is reaching a maturity while challenges still exist for a wider implementation, especially in relation to the reliability of N2O mitigation strategies and potential risks to nutrient removal performances of WWTPs.
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Affiliation(s)
- Haoran Duan
- School of Chemical Engineering, the University of Queensland, St. Lucia, Queensland 4072, Australia
- Advanced Water Management Centre (AWMC), the University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Yingfen Zhao
- School of Chemical Engineering, the University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Konrad Koch
- Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, 85748 Garching, Germany
| | - George F Wells
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Min Zheng
- Advanced Water Management Centre (AWMC), the University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Zhiguo Yuan
- Advanced Water Management Centre (AWMC), the University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Liu Ye
- School of Chemical Engineering, the University of Queensland, St. Lucia, Queensland 4072, Australia
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9
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Zhao W, Vermace RR, Mattes TE, Just C. Impacts of ammonia loading and biofilm age on the prevalence of nitrogen-cycling microorganisms in a full-scale submerged attached-growth reactor. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2021; 93:787-796. [PMID: 33124148 DOI: 10.1002/wer.1471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 10/04/2020] [Accepted: 10/11/2020] [Indexed: 06/11/2023]
Abstract
This study reports the impacts of seasonal ammonia load changes and biofilm age on the quantity of biomass and on the prevalence of ammonia- and nitrite-metabolizing organisms within a submerged attached-growth reactor (SAGR™) following lagoon treatment. Ammonia (NH3 ) loadings (0.12-3.17 kg/d) in the primary SAGR were measured over 223 days from May to December in 2017. Adjustment of the wastewater flow path on September 1 successfully increased NH3 loading to the primary SAGR, which subsequently caused reactor biomass to increase. The NH3 removal rate in October (0.5 kg/d) was greater than rates in June and July (0.3 and 0.2 kg/d) despite a water temperature decrease from >24 to 15.6°C. This elevated removal rate in October, and the sustained removal rate in December (0.4 kg/d, 5.3°C) were associated with a measured increase in microbial biomass. The relative abundance of the anammox organism C. Brocadia was 5 times greater in the mature biofilm after 686 days of growth, and the genus Pseudomonas increased sevenfold. The presence of Pseudomonas, which contains denitrifying species, and anammox suggests a high potential for removal of total nitrogen in SAGRs. PRACTITIONER POINTS: Pseudomonas prevalence and the presence of anammox suggest a high potential for total nitrogen removal in mature SAGR biofilms. The abundance of the anammox microorganism C. Brocadia was greater after 686 days of biofilm growth compared with 33 days. Simple operational changes can increase biomass in the SAGR to maintain, or even increase, NH3 transformation rates during cold weather.
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Affiliation(s)
- Weilun Zhao
- Civil & Environmental Engineering, University of Iowa, Iowa City, IA, USA
| | - Rebecca R Vermace
- Civil & Environmental Engineering, University of Iowa, Iowa City, IA, USA
| | - Timothy E Mattes
- Civil & Environmental Engineering, University of Iowa, Iowa City, IA, USA
| | - Craig Just
- Civil & Environmental Engineering, University of Iowa, Iowa City, IA, USA
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10
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Rose A, Padovan A, Christian K, van de Kamp J, Kaestli M, Tsoukalis S, Bodrossy L, Gibb K. The Diversity of Nitrogen-Cycling Microbial Genes in a Waste Stabilization Pond Reveals Changes over Space and Time that Is Uncoupled to Changing Nitrogen Chemistry. MICROBIAL ECOLOGY 2021; 81:1029-1041. [PMID: 33170351 PMCID: PMC8062326 DOI: 10.1007/s00248-020-01639-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 11/04/2020] [Indexed: 05/26/2023]
Abstract
Nitrogen removal is an important process for wastewater ponds prior to effluent release. Bacteria and archaea can drive nitrogen removal if they possess the genes required to metabolize nitrogen. In the tropical savanna of northern Australia, we identified the previously unresolved microbial communities responsible for nitrogen cycling in a multi-pond wastewater stabilization system by measuring genomic DNA and cDNA for the following: nifH (nitrogen fixation); nosZ (denitrification); hzsA (anammox); archaeal AamoA and bacterial BamoA (ammonia oxidation); nxrB (nitrite oxidation); and nrfA (dissimilatory NO3 reduction to NH3). By collecting 160 DNA and 40 cDNA wastewater samples and measuring nitrogen (N)-cycling genes using a functional gene array, we found that genes from all steps of the N cycle were present and, except for nxrB, were also expressed. As expected, N-cycling communities showed daily, seasonal, and yearly shifts. However, contrary to our prediction, probes from most functional groups, excluding nosZ and AamoA, were different between ponds. Further, different genes that perform the same N-cycling role sometimes had different trends over space and time, resulting in only weak correlations between the different functional communities. Although N-cycling communities were correlated with wastewater nitrogen levels and physico-chemistry, the relationship was not strong enough to reliably predict the presence or diversity of N-cycling microbes. The complex and dynamic response of these genes to other functional groups and the changing physico-chemical environment provides insight into why altering wastewater pond conditions can result an abundance of some gene variants while others are lost.
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Affiliation(s)
- A Rose
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, 0909, Australia.
| | - A Padovan
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, 0909, Australia
| | - K Christian
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, 0909, Australia
| | - J van de Kamp
- CSIRO Oceans and Atmosphere, Hobart, Tasmania, 7004, Australia
| | - M Kaestli
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, 0909, Australia
| | - S Tsoukalis
- PowerWater Corporation, Darwin, Northern Territory, 0820, Australia
| | - L Bodrossy
- CSIRO Oceans and Atmosphere, Hobart, Tasmania, 7004, Australia
| | - K Gibb
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, 0909, Australia
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11
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Yang Y, Herbold CW, Jung MY, Qin W, Cai M, Du H, Lin JG, Li X, Li M, Gu JD. Survival strategies of ammonia-oxidizing archaea (AOA) in a full-scale WWTP treating mixed landfill leachate containing copper ions and operating at low-intensity of aeration. WATER RESEARCH 2021; 191:116798. [PMID: 33444853 DOI: 10.1016/j.watres.2020.116798] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/22/2020] [Accepted: 12/28/2020] [Indexed: 05/04/2023]
Abstract
Recent studies indicate that ammonia-oxidizing archaea (AOA) may play an important role in nitrogen removal by wastewater treatment plants (WWTPs). However, our knowledge of the mechanisms employed by AOA for growth and survival in full-scale WWTPs is still limited. Here, metagenomic and metatranscriptomic analyses combined with a laboratory cultivation experiment revealed that three active AOAs (WS9, WS192, and WS208) belonging to family Nitrososphaeraceae were active in the deep oxidation ditch (DOD) of a full-scale WWTP treating landfill leachate, which is configured with three continuous aerobic-anoxic (OA) modules with low-intensity aeration (≤ 1.5 mg/L). AOA coexisted with AOB and complete ammonia oxidizers (Comammox), while the ammonia-oxidizing microbial (AOM) community was unexpectedly dominated by the novel AOA strain WS9. The low aeration, long retention time, and relatively high inputs of ammonium and copper might be responsible for the survival of AOA over AOB and Comammox, while the dominance of WS9, specifically may be enhanced by substrate preference and uniquely encoded retention strategies. The urease-negative WS9 is specifically adapted for ammonia acquisition as evidenced by the high expression of an ammonium transporter, whereas two metabolically versatile urease-positive AOA strains (WS192 and WS208) can likely supplement ammonia needs with urea. This study provides important information for the survival and application of the eutrophic Nitrososphaeraceae AOA and advances our understanding of archaea-dominated ammonia oxidation in a full-scale wastewater treatment system.
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Affiliation(s)
- Yuchun Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou 510275, China
| | - Craig W Herbold
- University of Vienna, Center for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Althanstrasse 14, 1090 Vienna, Austria
| | - Man-Young Jung
- Division of Biology Education, Department of Science Education, Jeju National University, 102 Jejudaehak-ro, Jeju 63243, South Korea; Interdisciplinary Graduate Programme in Advance Convergence Technology and Science, Faculty of Science Education, Jeju National University, Jeju 6324, South Korea
| | - Wei Qin
- School of Oceanography, University of Washington, Seattle, Washington, United States; Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Mingwei Cai
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Huan Du
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Jih-Gaw Lin
- Institute of Environmental Engineering, National Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan
| | - Xiaoyan Li
- Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China.
| | - Ji-Dong Gu
- Environmental Engineering, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, China; Southern Laboratory of Ocean Science and Engineering, Zhuhai, Guangdong, China.
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12
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Wang Y, Qin W, Jiang X, Ju F, Mao Y, Zhang A, Stahl DA, Zhang T. Seasonal Prevalence of Ammonia-Oxidizing Archaea in a Full-Scale Municipal Wastewater Treatment Plant Treating Saline Wastewater Revealed by a 6-Year Time-Series Analysis. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:2662-2673. [PMID: 33539079 DOI: 10.1021/acs.est.0c07703] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Although several molecular-based studies have demonstrated the involvement of ammonia-oxidizing archaea (AOA) in ammonia oxidation in wastewater treatment plants (WWTPs), factors affecting the persistence and growth of AOA in these engineered systems have not been resolved. Here, we show a seasonal prevalence of AOA in a full-scale WWTP (Shatin, Hong Kong SAR) over a 6-year period of observation, even outnumbering ammonia-oxidizing bacteria in the seasonal peaks in 3 years, which may be due to the high bioavailable copper concentrations. Comparative analysis of three metagenome-assembled genomes of group I.1a AOA obtained from the activated sludge and 16S rRNA gene sequences recovered from marine sediments suggested that the seawater used for toilet flushing was the primary source of the WWTP AOA. A rare AOA population in the estuarine source water became transiently abundant in the WWTP with a metagenome-based relative abundance of up to 1.3% over three seasons of observation. Correlation-based network analysis revealed a robust co-occurrence relationship between these AOA and organisms potentially active in nitrite oxidation. Moreover, a strong correlation between the dominant AOA and an abundant proteobacterial organism suggested that capacity for extracellular polymeric substance production by the proteobacterium could provide a niche for AOA within bioaggregates. Together, the study highlights the importance of long-term observation in identifying biotic and abiotic factors governing population dynamics in open systems such as full-scale WWTPs.
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Affiliation(s)
- Yulin Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China
| | - Wei Qin
- School of Oceanography, University of Washington, Seattle 98195, Washington, United States
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman 73019, Oklahoma, United States
| | - Xiaotao Jiang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China
| | - Feng Ju
- School of Engineering, Westlake University, 18 Shilongshan Road, Hangzhou 310024, China
| | - Yanping Mao
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, Guangdong, China
| | - Anni Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle 98195, Washington, United States
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China
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13
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The community compositions of three nitrogen removal wastewater treatment plants of different configurations in Victoria, Australia, over a 12-month operational period. Appl Microbiol Biotechnol 2020; 104:9839-9852. [DOI: 10.1007/s00253-020-10901-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 08/06/2020] [Accepted: 09/10/2020] [Indexed: 12/23/2022]
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14
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Spasov E, Tsuji JM, Hug LA, Doxey AC, Sauder LA, Parker WJ, Neufeld JD. High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant. THE ISME JOURNAL 2020; 14:1857-1872. [PMID: 32332864 PMCID: PMC7305129 DOI: 10.1038/s41396-020-0650-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 03/03/2020] [Accepted: 03/30/2020] [Indexed: 01/31/2023]
Abstract
Nitrification, the oxidation of ammonia to nitrate via nitrite, is an important process in municipal wastewater treatment plants (WWTPs). Members of the Nitrospira genus that contribute to complete ammonia oxidation (comammox) have only recently been discovered and their relevance to engineered water treatment systems is poorly understood. This study investigated distributions of Nitrospira, ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) in biofilm samples collected from tertiary rotating biological contactors (RBCs) of a municipal WWTP in Guelph, Ontario, Canada. Using quantitative PCR (qPCR), 16S rRNA gene sequencing, and metagenomics, our results demonstrate that Nitrospira species strongly dominate RBC biofilm samples and that comammox Nitrospira outnumber all other nitrifiers. Genome bins recovered from assembled metagenomes reveal multiple populations of comammox Nitrospira with distinct spatial and temporal distributions, including several taxa that are distinct from previously characterized Nitrospira members. Diverse functional profiles imply a high level of niche heterogeneity among comammox Nitrospira, in contrast to the sole detected AOA representative that was previously cultivated and characterized from the same RBC biofilm. Our metagenome bins also reveal two cyanase-encoding populations of comammox Nitrospira, suggesting an ability to degrade cyanate, which has only been shown previously for several Nitrospira representatives that are strict nitrite oxidizers. This study demonstrates the importance of RBCs as model systems for continued investigation of environmental factors that control the distributions and activities of AOB, AOA, comammox Nitrospira, and other nitrite oxidizers.
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Affiliation(s)
- Emilie Spasov
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Jackson M Tsuji
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Laura A Hug
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Andrew C Doxey
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Laura A Sauder
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Wayne J Parker
- Department of Civil and Environmental Engineering, University of Waterloo, Waterloo, ON, Canada
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, Waterloo, ON, Canada.
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15
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Roy D, McEvoy J, Khan E. Abundance and activity of ammonia oxidizing archaea and bacteria in bulk water and biofilm in water supply systems practicing chlorination and chloramination: Full and laboratory scale investigations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 715:137043. [PMID: 32041059 DOI: 10.1016/j.scitotenv.2020.137043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 01/10/2020] [Accepted: 01/30/2020] [Indexed: 05/04/2023]
Abstract
The abundance and nitrification activity of ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) in bulk water and biofilm in chloraminated and chlorinated water supply systems were investigated. The abundance of AOB varied between cold and warm periods while that was the case for AOA only in biofilm. Lower ammonia concentrations favored the abundance of AOA over AOB. AOA and AOB were found more in distal zones of the distribution system (DS). Higher numbers of AOA and AOB were observed in DS associated with chloramination compared to those associated with chlorination. Significant positive correlations between ammonia-N in bulk water and AOA indicate a possibility of involvement of AOA in nitrification in DS. A separate laboratory-based experiment simulating DS condition was conducted to understand the effects of chlorine and chloramine dosages and temperature on AOA and AOB. AOA were inhibited less than AOB in the presence of lower concentrations of chlorine and chloramine (1.5 and 2.0 mg/L chlorine; 0.05-0.1 and 0.3-0.4 mg/L chloramine) while both of them were not detected at higher dosages (2.5 mg/L chlorine and 1.5-1.6 mg/L chloramine). At a low temperature (10-12 °C), chloramine and chlorine provided similar inhibition trends in which AOB were inhibited more than AOA. At a high temperature (25 °C), chloramine was less inhibitory to AOA and AOB than chlorine.
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Affiliation(s)
- Dhritikshama Roy
- Environmental and Conservation Sciences, North Dakota State University, Fargo, ND 58108, USA
| | - John McEvoy
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58108, USA.
| | - Eakalak Khan
- Department of Civil and Environmental Engineering and Construction, University of Nevada, Las Vegas, NV 89154, USA.
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16
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Li K, Qian J, Wang P, Wang C, Lu B, Tian X, Jin W, He X, Chen H, Zhang Y, Liu Y. Differential responses of encoding-amoA nitrifiers and nir denitrifiers in activated sludge to anatase and rutile TiO 2 nanoparticles: What is active functional guild in rate limiting step of nitrogen cycle? JOURNAL OF HAZARDOUS MATERIALS 2020; 384:121388. [PMID: 31668758 DOI: 10.1016/j.jhazmat.2019.121388] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 09/26/2019] [Accepted: 10/02/2019] [Indexed: 06/10/2023]
Abstract
The long-terms effects of different crystal-composition TiO2 nanoparticles (NPs) on nitrogen-cycle-related functional guilds in activated sludge remain unclear, especially under natural light irradiation. Accordingly, activated sludge was exposed to anatase TiO2-NPs (TiO2-A) and rutile TiO2-NPs (TiO2-R) for up to 45 days. With markedly (p < 0.05) reducing nitrification-/denitrification-enzymatic-activities and abundances of ammonia-oxidizing-microorganisms (AOMs) and nitrite-reducing-bacteria (NRB), TiO2-NPs triggered bacteria and archaea UPGMA clustering and a deep modification of N-cycling functional diversity guided by crystal structure. in situ13C-DNA-SIP confirmed ammonia-oxidizing-bacteria (AOB) (Nitrosomonas and Nitrosospira) in original sludge as main active AOMs with 75.4 times more abundance than ammonia-oxidizing-archaea (AOA), while AOA within Nitrosopumilus and Nitrososphaera genera were the main active AOMs and tended to aggregate inside sludge after 10-mg/L TiO2-NPs exposure. Encoding-nirK NRB were more sensitive, while encoding-nirS Zoogloea with a total share of 4.97% to 14.93%, etc. were the main active NRB. AOB was more sensitive to TiO2-A, while TiO2-R showed the stronger toxicity to AOA and NRB resulting from differences in water environmental behaviors and crystal characteristics of two TiO2-NPs. This work expands understanding of the ecological risks of titanium-dioxide-crystal-NPs in aquatic environment and may help devise better methods to alleviate environmental stress caused by NPs at wastewater treatment plants.
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Affiliation(s)
- Kun Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing, 210098, People's Republic of China; College of Environment, Hohai University, Nanjing, 210098, People's Republic of China
| | - Jin Qian
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing, 210098, People's Republic of China; College of Environment, Hohai University, Nanjing, 210098, People's Republic of China.
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing, 210098, People's Republic of China; College of Environment, Hohai University, Nanjing, 210098, People's Republic of China.
| | - Chao Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing, 210098, People's Republic of China; College of Environment, Hohai University, Nanjing, 210098, People's Republic of China
| | - Bianhe Lu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing, 210098, People's Republic of China; College of Environment, Hohai University, Nanjing, 210098, People's Republic of China
| | - Xin Tian
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing, 210098, People's Republic of China; College of Environment, Hohai University, Nanjing, 210098, People's Republic of China
| | - Wen Jin
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing, 210098, People's Republic of China; College of Environment, Hohai University, Nanjing, 210098, People's Republic of China
| | - Xixian He
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing, 210098, People's Republic of China; College of Environment, Hohai University, Nanjing, 210098, People's Republic of China
| | - Hao Chen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing, 210098, People's Republic of China; College of Environment, Hohai University, Nanjing, 210098, People's Republic of China
| | - Yuhang Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing, 210098, People's Republic of China; College of Environment, Hohai University, Nanjing, 210098, People's Republic of China
| | - Yin Liu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing, 210098, People's Republic of China; College of Environment, Hohai University, Nanjing, 210098, People's Republic of China
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17
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Freeman D, Bajón Fernández Y, Wilson A, McKew BA, Whitby C, Clark DR, Jefferson B, Coulon F, Hassard F. Nitrogen oxidation consortia dynamics influence the performance of full-scale rotating biological contactors. ENVIRONMENT INTERNATIONAL 2020; 135:105354. [PMID: 31864025 DOI: 10.1016/j.envint.2019.105354] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 11/13/2019] [Accepted: 11/20/2019] [Indexed: 06/10/2023]
Abstract
Ammonia oxidising microorganisms (AOM) play an important role in ammonia removal in wastewater treatment works (WWTW) including rotating biological contactors (RBCs). Environmental factors within RBCs are known to impact the performance of key AOM, such that only some operational RBCs have shown ability for elevated ammonia removal. In this work, long-term treatment performance of seven full-scale RBC systems along with the structure and abundance of the ammonia oxidising bacteria (AOB) and archaea (AOA) communities within microbial biofilms were examined. Long term data showed the dominance of AOB in most RBCs, although two RBCs had demonstrable shift toward an AOA dominated AOM community. Next Generation Sequencing of the 16S rRNA gene revealed diverse evolutionary ancestry of AOB from RBC biofilms while nitrite-oxidising bacteria (NOBs) were similar to reference databases. AOA were more abundant in the biofilms subject to lower organic loading and higher oxygen concentration found at the distal end of RBC systems. Modelling revealed a distinct nitrogen cycling community present within high performing RBCs, linked to efficient control of RBC process variables (retention time, organic loading and oxygen concentration). We present a novel template for enhancing the resilience of RBC systems through microbial community analysis which can guide future strategies for more effective ammonia removal. To best of the author's knowledge, this is the first comparative study reporting the use of next generation sequencing data on microbial biofilms from RBCs to inform effluent quality of small WWTW.
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Affiliation(s)
- D Freeman
- Cranfield University, College Road, Cranfield, Bedfordshire MK43 0AL, UK; Severn Trent, 2 St Johns Street, Coventry CV1 2LZ, UK
| | - Y Bajón Fernández
- Cranfield University, College Road, Cranfield, Bedfordshire MK43 0AL, UK; Severn Trent, 2 St Johns Street, Coventry CV1 2LZ, UK
| | - A Wilson
- Severn Trent, 2 St Johns Street, Coventry CV1 2LZ, UK; Atkins Global, The Axis, 10 Holliday St, Birmingham B1 1TF, UK
| | - B A McKew
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK
| | - C Whitby
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK
| | - D R Clark
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK
| | - B Jefferson
- Cranfield University, College Road, Cranfield, Bedfordshire MK43 0AL, UK
| | - F Coulon
- Cranfield University, College Road, Cranfield, Bedfordshire MK43 0AL, UK
| | - F Hassard
- Cranfield University, College Road, Cranfield, Bedfordshire MK43 0AL, UK.
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18
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Islam GM, Vi P, Gilbride KA. Functional relationship between ammonia-oxidizing bacteria and ammonia-oxidizing archaea populations in the secondary treatment system of a full-scale municipal wastewater treatment plant. J Environ Sci (China) 2019; 86:120-130. [PMID: 31787176 DOI: 10.1016/j.jes.2019.04.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 04/24/2019] [Accepted: 04/30/2019] [Indexed: 06/10/2023]
Abstract
The abundance of ammonia-oxidizing bacteria and archaea and their amoA genes from the aerobic activated sludge tanks, recycled sludge and anaerobic digesters of a full-scale wastewater treatment plant (WWTP) was determined. Polymerase chain reaction and denaturing gradient gel electrophoresis were used to generate diversity profiles, which showed that each population had a consistent profile although the abundance of individual members varied. In the aerobic tanks, the ammonia-oxidizing bacterial (AOB) population was more than 350 times more abundant than the ammonia-oxidizing archaeal (AOA) population, however in the digesters, the AOA population was more than 10 times more abundant. Measuring the activity of the amoA gene expression of the two populations using RT-PCR also showed that the AOA amoA gene was more active in the digesters than in the activated sludge tanks. Using batch reactors and ddPCR, amoA activity could be measured and it was found that when the AOB amoA activity was inhibited in the anoxic reactors, the expression of the AOA amoA gene increased fourfold. This suggests that these two populations may have a cooperative relationship for the oxidation of ammonia.
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Affiliation(s)
- Golam M Islam
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
| | - Peter Vi
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
| | - Kimberley Ann Gilbride
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada; Ryerson Urban Water, Ryerson University, 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada.
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19
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Herber J, Klotz F, Frommeyer B, Weis S, Straile D, Kolar A, Sikorski J, Egert M, Dannenmann M, Pester M. A single Thaumarchaeon drives nitrification in deep oligotrophic Lake Constance. Environ Microbiol 2019; 22:212-228. [PMID: 31657089 DOI: 10.1111/1462-2920.14840] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 08/30/2019] [Accepted: 08/30/2019] [Indexed: 12/15/2022]
Abstract
Ammonia released during organic matter mineralization is converted during nitrification to nitrate. We followed spatiotemporal dynamics of the nitrifying microbial community in deep oligotrophic Lake Constance. Depth-dependent decrease of total ammonium (0.01-0.84 μM) indicated the hypolimnion as the major place of nitrification with 15 N-isotope dilution measurements indicating a threefold daily turnover of hypolimnetic total ammonium. This was mirrored by a strong increase of ammonia-oxidizing Thaumarchaeota towards the hypolimnion (13%-21% of bacterioplankton) throughout spring to autumn as revealed by amplicon sequencing and quantitative polymerase chain reaction. Ammonia-oxidizing bacteria were typically two orders of magnitude less abundant and completely ammonia-oxidizing (comammox) bacteria were not detected. Both, 16S rRNA gene and amoA (encoding ammonia monooxygenase subunit B) analyses identified only one major species-level operational taxonomic unit (OTU) of Thaumarchaeota (99% of all ammonia oxidizers in the hypolimnion), which was affiliated to Nitrosopumilus spp. The relative abundance distribution of the single Thaumarchaeon strongly correlated to an equally abundant Chloroflexi clade CL500-11 OTU and a Nitrospira OTU that was one order of magnitude less abundant. The latter dominated among recognized nitrite oxidizers. This extremely low diversity of nitrifiers shows how vulnerable the ecosystem process of nitrification may be in Lake Constance as Central Europe's third largest lake.
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Affiliation(s)
- Janina Herber
- Department of Biology, University of Konstanz, Universitätsstrasse 10, Constance, 78457, Germany
| | - Franziska Klotz
- Department of Biology, University of Konstanz, Universitätsstrasse 10, Constance, 78457, Germany
| | - Benjamin Frommeyer
- Department of Biology, University of Konstanz, Universitätsstrasse 10, Constance, 78457, Germany
| | - Severin Weis
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Furtwangen University, Jakob-Kienzle-Str. 17, Villingen-Schwenningen, 78054, Germany
| | - Dietmar Straile
- Limnological Institute, University of Konstanz, Mainaustraße 252, Constance, 78464, Germany
| | - Allison Kolar
- Karlsruhe Institute of Technology, Institute for Meteorology and Climate Research, Atmospheric Environmental Research (IMK-IFU), Kreuzeckbahnstr. 19, 82467, Garmisch-Partenkirchen, Germany
| | - Johannes Sikorski
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, 38124, Braunschweig, Germany
| | - Markus Egert
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Furtwangen University, Jakob-Kienzle-Str. 17, Villingen-Schwenningen, 78054, Germany
| | - Michael Dannenmann
- Karlsruhe Institute of Technology, Institute for Meteorology and Climate Research, Atmospheric Environmental Research (IMK-IFU), Kreuzeckbahnstr. 19, 82467, Garmisch-Partenkirchen, Germany
| | - Michael Pester
- Department of Biology, University of Konstanz, Universitätsstrasse 10, Constance, 78457, Germany.,Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, 38124, Braunschweig, Germany.,Technical University of Braunschweig, Institute for Microbiology, Spielmannstrasse 7, Braunschweig, 38106, Germany
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20
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Gwak JH, Jung MY, Hong H, Kim JG, Quan ZX, Reinfelder JR, Spasov E, Neufeld JD, Wagner M, Rhee SK. Archaeal nitrification is constrained by copper complexation with organic matter in municipal wastewater treatment plants. ISME JOURNAL 2019; 14:335-346. [PMID: 31624348 PMCID: PMC6976641 DOI: 10.1038/s41396-019-0538-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/24/2019] [Accepted: 09/27/2019] [Indexed: 01/08/2023]
Abstract
Consistent with the observation that ammonia-oxidizing bacteria (AOB) outnumber ammonia-oxidizing archaea (AOA) in many eutrophic ecosystems globally, AOB typically dominate activated sludge aeration basins from municipal wastewater treatment plants (WWTPs). In this study, we demonstrate that the growth of AOA strains inoculated into sterile-filtered wastewater was inhibited significantly, in contrast to uninhibited growth of a reference AOB strain. In order to identify possible mechanisms underlying AOA-specific inhibition, we show that complex mixtures of organic compounds, such as yeast extract, were highly inhibitory to all AOA strains but not to the AOB strain. By testing individual organic compounds, we reveal strong inhibitory effects of organic compounds with high metal complexation potentials implying that the inhibitory mechanism for AOA can be explained by the reduced bioavailability of an essential metal. Our results further demonstrate that the inhibitory effect on AOA can be alleviated by copper supplementation, which we observed for pure AOA cultures in a defined medium and for AOA inoculated into nitrifying sludge. Our study offers a novel mechanistic explanation for the relatively low abundance of AOA in most WWTPs and provides a basis for modulating the composition of nitrifying communities in both engineered systems and naturally occurring environments.
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Affiliation(s)
- Joo-Han Gwak
- Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, South Korea
| | - Man-Young Jung
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria
| | - Heeji Hong
- Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, South Korea
| | - Jong-Geol Kim
- Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, South Korea
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - John R Reinfelder
- Department of Environmental Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Emilie Spasov
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Michael Wagner
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria.,Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, South Korea.
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21
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Islam GM, Gilbride KA. The effect of tetracycline on the structure of the bacterial community in a wastewater treatment system and its effects on nitrogen removal. JOURNAL OF HAZARDOUS MATERIALS 2019; 371:130-137. [PMID: 30849567 DOI: 10.1016/j.jhazmat.2019.02.032] [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: 06/19/2018] [Revised: 02/08/2019] [Accepted: 02/09/2019] [Indexed: 06/09/2023]
Abstract
This study examined the impact of tetracycline at two environmentally relevant concentrations (1 μg/L and 10 μg/L) and one synthetically high concentration (500 μg/L) on the structure and function of the microbial community from the secondary treatment process of a municipal wastewater treatment plant (WWTP). Specifically, this study examined whether the introduction of tetracycline into bench scale reactors at two different replacement volume rates would cause a shift in the composition profile of the bacterial community. Furthermore concentrations of ammonia, nitrate/nitrite and total Kjeldahl nitrogen were monitored to examine the effect of the antibiotic on ammonia and nitrogen removal. At the low volume replacement rate, tetracycline was observed to have a positive impact on nitrogen removal. Total Kjeldahl nitrogen concentrations were also observed to decrease suggesting a role for tetracycline as a carbon source. However, at the higher volume replacement rate, the removal of ammonia and nitrogen were not significantly different from reactors that did not contain tetracycline. Over time, the bacterial composition profiles changed under all the conditions studied, however, the bacterial composition profiles appeared to be more influenced by the replacement volume rate than the presence of tetracycline even at concentrations many times higher than environmentally relevant amounts.
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Affiliation(s)
- G M Islam
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, Ontario, M5B 2K3, Canada
| | - K A Gilbride
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, Ontario, M5B 2K3, Canada.
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22
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Wang X, Wang S, Shi G, Wang W, Zhu G. Factors driving the distribution and role of AOA and AOB in Phragmites communis
rhizosphere in riparian zone. J Basic Microbiol 2019; 59:425-436. [DOI: 10.1002/jobm.201800581] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/01/2018] [Accepted: 12/16/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Xiaomin Wang
- Key Laboratory of Drinking Water Science and Technology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Shanyun Wang
- Key Laboratory of Drinking Water Science and Technology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
| | - Guoshuai Shi
- Key Laboratory of Drinking Water Science and Technology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
| | - Weidong Wang
- Key Laboratory of Drinking Water Science and Technology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
- University of Chinese Academy of Sciences; Beijing 100049 China
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23
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Pan KL, Gao JF, Fan XY, Li DC, Dai HH. The more important role of archaea than bacteria in nitrification of wastewater treatment plants in cold season despite their numerical relationships. WATER RESEARCH 2018; 145:552-561. [PMID: 30199800 DOI: 10.1016/j.watres.2018.08.066] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/24/2018] [Accepted: 08/30/2018] [Indexed: 05/04/2023]
Abstract
Nitrification failure of wastewater treatment plants (WWTPs) in cold season calls into investigations of the functional ammonia-oxidizing microorganisms (AOMs). In this study, we report the abundance of ammonia-oxidizing archaea (AOA), bacteria (AOB) and complete ammonia-oxidizing (comammox) Nitrospira in 23 municipal WWTPs in cold season, and explore the correlations between AOMs abundance and their relative contribution to nitrification. The copy numbers of AOA and AOB amoA gene ranged from 2.42 × 107 to 2.47 × 109 and 5.54 × 106 to 3.31 × 109 copies/g sludge, respectively. The abundance of amoA gene of Candidatus Nitrospira inopinata, an important strain of comammox Nitrospira, was stable with averaged abundance of 8.47 × 106 copies/g sludge. DNA-based stable isotope probing (DNA-SIP) assays were conducted with three typical WWTPs in which the abundance of AOA was lower than, similar to and higher than that of AOB, respectively. The results showed that considerable 13C-assimilation by AOA was detected during active nitrification in all WWTPs, whereas just a much lesser extent of 13C-incorporation by AOB and comammox Nitrospira was found in one WWTP. High-throughput sequencing with 13C-labeled DNA also showed the higher reads abundance of AOA than AOB and comammox Nitrospira. Nitrososphaera viennensis was the dominant active AOA, while Nitrosomonas oligotropha and Nitrosomonas europaea were identified as active AOB. The results obtained suggest that AOA, rather than AOB and comammox Nitrospira, dominate ammonia oxidation in WWTPs in cold season despite the numerical relationships of AOMs.
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Affiliation(s)
- Kai-Ling Pan
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing, 100124, China
| | - Jing-Feng Gao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing, 100124, China.
| | - Xiao-Yan Fan
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing, 100124, China
| | - Ding-Chang Li
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing, 100124, China
| | - Hui-Hui Dai
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing, 100124, China
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24
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Incorporation of 13C-HCO 3- by ammonia-oxidizing archaea and bacteria during ammonia oxidation of sludge from a municipal wastewater treatment plant. Appl Microbiol Biotechnol 2018; 102:10767-10777. [PMID: 30343425 DOI: 10.1007/s00253-018-9436-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 09/23/2018] [Accepted: 10/07/2018] [Indexed: 10/28/2022]
Abstract
Ammonia-oxidizing archaea (AOA) have recently been proposed as potential players for ammonia removal in wastewater treatment plants (WWTPs). However, there is little evidence directly showing the contribution of AOA to ammonia oxidation in these engineered systems. In this study, DNA-stable isotope probing (DNA-SIP) with labeled 13C-HCO3- was introduced to sludge from a municipal WWTP. Quantitative PCR demonstrated that AOA amoA genes outnumbered AOB amoA genes in this WWTP sludge. AOA amoA gene sequence analysis revealed that AOA present in this WWTP were specific to one subcluster within the group 1.1b Thaumarchaeota. When ammonia was supplied to DNA-SIP incubation, the DNA-SIP profiles demonstrated the incorporation of the 13C into AOA and AOB. However, the 13C was not found to be assimilated into both microorganisms in the incubation without ammonia. Specific primers were designed to target amoA genes of AOA belonging to the subcluster found in this WWTP. Applying the primers to DNA-SIP experiment revealed that AOA of this subcluter most likely utilized inorganic carbon during ammonia oxidation under the studied conditions.
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25
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Ammonia-Oxidizing Archaea (AOA) Play with Ammonia-Oxidizing Bacteria (AOB) in Nitrogen Removal from Wastewater. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2018; 2018:8429145. [PMID: 30302054 PMCID: PMC6158934 DOI: 10.1155/2018/8429145] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/17/2018] [Indexed: 12/17/2022]
Abstract
An increase in the number of publications in recent years indicates that besides ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) may play an important role in nitrogen removal from wastewater, gaining wide attention in the wastewater engineering field. This paper reviews the current knowledge on AOA and AOB involved in wastewater treatment systems and summarises the environmental factors affecting AOA and AOB. Current findings reveal that AOA have stronger environmental adaptability compared with AOB under extreme environmental conditions (such as low temperature and low oxygen level). However, there is still little information on the cooperation and competition relationship between AOA and AOB, and other microbes related to nitrogen removal, which needs further exploration. Furthermore, future studies are proposed to develop novel nitrogen removal processes dominated by AOA by parameter optimization.
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26
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Sabba F, Terada A, Wells G, Smets BF, Nerenberg R. Nitrous oxide emissions from biofilm processes for wastewater treatment. Appl Microbiol Biotechnol 2018; 102:9815-9829. [DOI: 10.1007/s00253-018-9332-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 08/13/2018] [Accepted: 08/15/2018] [Indexed: 01/21/2023]
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27
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Lee KH, Wang YF, Wang Y, Gu JD, Jiao JJ. Abundance and Diversity of Aerobic/Anaerobic Ammonia/Ammonium-Oxidizing Microorganisms in an Ammonium-Rich Aquitard in the Pearl River Delta of South China. MICROBIAL ECOLOGY 2018; 76:81-91. [PMID: 27448106 DOI: 10.1007/s00248-016-0815-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 07/04/2016] [Indexed: 06/06/2023]
Abstract
Natural occurring groundwater with abnormally high ammonium concentrations was discovered in the aquifer-aquitard system in the Pearl River Delta, South China. The community composition and abundance of aerobic/anaerobic ammonia/ammonium-oxidizing microorganisms (AOM) in the aquitard were investigated in this study. The alpha subunit of ammonia monooxygenase gene (amoA) was used as the biomarker for the detection of aerobic ammonia-oxidizing archaea (AOA) and bacteria (AOB), and also partial 16S rRNA gene for Plantomycetes and anaerobic ammonium-oxidizing (anammox) bacteria. Phylogenetic analysis showed that AOA in this aquitard were affiliated with those from water columns and wastewater treatment plants; and AOB were dominated by sequences among the Nitrosomonas marina/Nitrosomonas oligotropha lineage, which were affiliated with environmental sequences from coastal eutrophic bay and subtropical estuary. The richness and diversity of both AOA and AOB communities had very little variations with the depth. Candidatus Scalindua-related sequences dominated the anammox bacterial community. AOB amoA gene abundances were always higher than those of AOA at different depths in this aquitard. The Pearson moment correlation analysis showed that AOA amoA gene abundance positively correlated with pH and ammonium concentration, whereas AOB amoA gene abundance negatively correlated with C/N ratio. This is the first report that highlights the presence with low diversity of AOM communities in natural aquitard of rich ammonium.
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Affiliation(s)
- Kwok-Ho Lee
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People's Republic of China
| | - Yong-Feng Wang
- Guangdong Provincial Key Laboratory of Bio-control for the Forest Disease and Pest, Guangdong Academy of Forestry, No. 233 Guangshan 1st Road, Guangzhou, People's Republic of China
| | - Ya Wang
- School of Earth Science and Geological Engineering, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Ji-Dong Gu
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People's Republic of China.
| | - Jiu Jimmy Jiao
- Department of Earth Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People's Republic of China
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28
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Pan KL, Gao JF, Li HY, Fan XY, Li DC, Jiang H. Ammonia-oxidizing bacteria dominate ammonia oxidation in a full-scale wastewater treatment plant revealed by DNA-based stable isotope probing. BIORESOURCE TECHNOLOGY 2018; 256:152-159. [PMID: 29438915 DOI: 10.1016/j.biortech.2018.02.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 01/31/2018] [Accepted: 02/02/2018] [Indexed: 05/04/2023]
Abstract
A full-scale wastewater treatment plant (WWTP) with three separate treatment processes was selected to investigate the effects of seasonality and treatment process on the community structures of ammonia-oxidizing archaea (AOA) and bacteria (AOB). And then DNA-based stable isotope probing (DNA-SIP) was applied to explore the active ammonia oxidizers. The results of high-throughput sequencing indicated that treatment processes varied AOB communities rather than AOA communities. AOA slightly outnumbered AOB in most of the samples, whose abundance was significantly correlated with temperature. DNA-SIP results showed that the majority of AOB amoA gene was labeled by 13C-substrate, while just a small amount of AOA amoA gene was labeled. As revealed by high-throughput sequencing of heavy DNA, Nitrosomonadaceae-like AOB, Nitrosomonas sp. NP1, Nitrosomonas oligotropha and Nitrosomonas marina were the active AOB, and Nitrososphaera viennensis dominated the active AOA. The results indicated that AOB, not AOA, dominated active ammonia oxidation in the test WWTP.
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Affiliation(s)
- Kai-Ling Pan
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing 100124, China
| | - Jing-Feng Gao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing 100124, China.
| | - Hong-Yu Li
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing 100124, China
| | - Xiao-Yan Fan
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing 100124, China
| | - Ding-Chang Li
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing 100124, China
| | - Hao Jiang
- Research Department of Microbiology, Allwegene Technology Co., Ltd, Beijing 102209, China
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29
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Effect of Tidal Cycling Rate on the Distribution and Abundance of Nitrogen-Oxidizing Bacteria in a Bench-Scale Fill-and-Drain Bioreactor. WATER 2018. [DOI: 10.3390/w10040492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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30
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Peng Y, Li J, Lu J, Xiao L, Yang L. Characteristics of microbial community involved in early biofilms formation under the influence of wastewater treatment plant effluent. J Environ Sci (China) 2018; 66:113-124. [PMID: 29628077 DOI: 10.1016/j.jes.2017.05.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 02/09/2017] [Accepted: 05/09/2017] [Indexed: 06/08/2023]
Abstract
Effluents from wastewater treatment plants (WWTPs) containing microorganisms and residual nutrients can influence the biofilm formation. Although the process and mechanism of bacterial biofilm formation have been well characterized, little is known about the characteristics and interaction of bacteria, archaea and eukaryotes in the early colonization, especially under the influence of WWTP effluent. The aim of this study was to characterize the important bacterial, archaeal and eukaryotic species in the early stage of biofilm formation downstream of the WWTP outlet. Water and biofilm samples were collected 24 and 48hr after the deposition of bio-cords in the stream. Illumina Miseq sequencing of the 16S and 18S rDNA showed that, among the three domains, the bacterial biofilm community had the largest alpha and beta diversity. The early bacterial colonizers appeared to be "biofilm-specific", with only a few dominant operational taxonomic units (OTUs) shared between the biofilm and the ambient water environment. Alpha-proteobacteria and Ciliophora tended to dominate the bacterial and eukaryotic communities, respectively, of the early biofilm already at 24hr, whereas archaea played only a minor role during the early stage of colonization. The network analysis showed that the three domains of microbial community connected highly during the early colonization and it might be a characteristic of the microbial communities in the biofilm formation process where co-occurrence relationships could drive coexistence and diversity maintenance within the microbial communities.
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Affiliation(s)
- Yuke Peng
- School of the Environment, State Key Laboratory for Pollution Control and Resource Reuse (SKL-PCRR), Nanjing University, Nanjing 210023, China.
| | - Jie Li
- School of the Environment, State Key Laboratory for Pollution Control and Resource Reuse (SKL-PCRR), Nanjing University, Nanjing 210023, China
| | - Junling Lu
- School of the Environment, State Key Laboratory for Pollution Control and Resource Reuse (SKL-PCRR), Nanjing University, Nanjing 210023, China
| | - Lin Xiao
- School of the Environment, State Key Laboratory for Pollution Control and Resource Reuse (SKL-PCRR), Nanjing University, Nanjing 210023, China.
| | - Liuyan Yang
- School of the Environment, State Key Laboratory for Pollution Control and Resource Reuse (SKL-PCRR), Nanjing University, Nanjing 210023, China
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31
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Tatari K, Musovic S, Gülay A, Dechesne A, Albrechtsen HJ, Smets BF. Density and distribution of nitrifying guilds in rapid sand filters for drinking water production: Dominance of Nitrospira spp. WATER RESEARCH 2017; 127:239-248. [PMID: 29055829 DOI: 10.1016/j.watres.2017.10.023] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 10/07/2017] [Accepted: 10/09/2017] [Indexed: 05/04/2023]
Abstract
We investigated the density and distribution of total bacteria, canonical Ammonia Oxidizing Bacteria (AOB) (Nitrosomonas plus Nitrosospira), Ammonia Oxidizing Archaea (AOA), as well as Nitrobacter and Nitrospira in rapid sand filters used for groundwater treatment. To investigate the spatial distribution of these guilds, filter material was sampled at four drinking water treatment plants (DWTPs) in parallel filters of the pre- and after-filtration stages at different locations and depths. The target guilds were quantified by qPCR targeting 16S rRNA and amoA genes. Total bacterial densities (ignoring 16S rRNA gene copy number variation) were high and ranged from 109 to 1010 per gram (1015 to 1016 per m3) of filter material. All examined guilds, except AOA, were stratified at only one of the four DWTPs. Densities varied spatially within filter (intra-filter variation) at two of the DWTPs and in parallel filters (inter-filter variation) at one of the DWTPs. Variation analysis revealed random sampling as the most efficient strategy to yield accurate mean density estimates, with collection of at least 7 samples suggested to obtain an acceptable (below half order of magnitude) density precision. Nitrospira was consistently the most dominant guild (5-10% of total community), and was generally up to 4 orders of magnitude more abundant than Nitrobacter and up to 2 orders of magnitude more abundant than canonical AOBs. These results, supplemented with further analysis of the previously reported diversity of Nitrospira in the studied DWTPs based on 16S rRNA and nxrB gene phylogeny (Gülay et al., 2016; Palomo et al., 2016), indicate that the high Nitrospira abundance is due to their comammox (complete ammonia oxidation) physiology. AOA densities were lower than AOB densities, except in the highly stratified filters, where they were of similar abundance. In conclusion, rapid sand filters are microbially dense, with varying degrees of spatial heterogeneity, which requires replicate sampling for a sufficiently precise determination of total microbial community and specific population densities. A consistently high Nitrospira to bacterial and archaeal AOB density ratio suggests that non-canonical pathways for nitrification may dominate the examined RSFs.
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Affiliation(s)
- Karolina Tatari
- Department of Environmental Engineering, Technical University of Denmark, Miljøvej 113, 2800 Kgs. Lyngby, Denmark
| | - Sanin Musovic
- Department of Environmental Engineering, Technical University of Denmark, Miljøvej 113, 2800 Kgs. Lyngby, Denmark
| | - Arda Gülay
- Department of Environmental Engineering, Technical University of Denmark, Miljøvej 113, 2800 Kgs. Lyngby, Denmark
| | - Arnaud Dechesne
- Department of Environmental Engineering, Technical University of Denmark, Miljøvej 113, 2800 Kgs. Lyngby, Denmark
| | - Hans-Jørgen Albrechtsen
- Department of Environmental Engineering, Technical University of Denmark, Miljøvej 113, 2800 Kgs. Lyngby, Denmark
| | - Barth F Smets
- Department of Environmental Engineering, Technical University of Denmark, Miljøvej 113, 2800 Kgs. Lyngby, Denmark.
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32
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Roy D, McEvoy J, Blonigen M, Amundson M, Khan E. Seasonal variation and ex-situ nitrification activity of ammonia oxidizing archaea in biofilm based wastewater treatment processes. BIORESOURCE TECHNOLOGY 2017; 244:850-859. [PMID: 28841790 DOI: 10.1016/j.biortech.2017.08.060] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 08/09/2017] [Accepted: 08/10/2017] [Indexed: 05/04/2023]
Abstract
The abundance of ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) was investigated in full-scale two-stage trickling filters (TF) and moving bed bioreactor (MBBR) treating municipal wastewater. Biofilm samples were collected for 17months from nitrifying TF (NTF), biochemical oxygen demand TF (BTF), and MBBR media. The abundance of AOA and AOB was determined using a quantitative PCR approach targeting the ammonia monooxygenase subunit A gene of archaea and bacteria. AOA were dominant in the NTF and MBBR, while AOB dominated in the BTF. AOA and AOB were more abundant during warmer months, and AOA were detected in the BTF only during warmer months. In laboratory nitrification activity experiments, ammonia oxidation to nitrite decreased when AOA populations from the NTF and MBBR were inhibited, demonstrating that AOA contributed to nitrification. This study has shown that AOA outnumber AOB and contribute to ammonia oxidation in full-scale nitrifying biofilm processes.
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Affiliation(s)
- Dhritikshama Roy
- Environmental and Conservation Sciences Program (#2820), North Dakota State University, Fargo, ND 58108-6050, USA; Department of Civil and Environmental Engineering (#2470), North Dakota State University, Fargo, ND 58108-6050, USA
| | - John McEvoy
- Department of Veterinary and Microbiological Science (#7690), North Dakota State University, Fargo, ND 58108-6050, USA
| | - Mark Blonigen
- City of Fargo, 3400 North Broadway, Fargo, ND 58102, USA
| | - Maria Amundson
- City of Moorhead, 2121 28th Street N, Moorhead, MN 56560, USA
| | - Eakalak Khan
- Department of Civil and Environmental Engineering (#2470), North Dakota State University, Fargo, ND 58108-6050, USA.
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33
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Duff AM, Zhang LM, Smith CJ. Small-scale variation of ammonia oxidisers within intertidal sediments dominated by ammonia-oxidising bacteria Nitrosomonas sp. amoA genes and transcripts. Sci Rep 2017; 7:13200. [PMID: 29038459 PMCID: PMC5643298 DOI: 10.1038/s41598-017-13583-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 09/25/2017] [Indexed: 11/08/2022] Open
Abstract
While numerous studies have investigated the abundance of ammonia oxidising bacteria and archaea (AOB/AOA) via the ammonia monooxygenase gene amoA, less is known about their small-scale variation and if amoA gene abundance equates to activity. Here we present a spatial and temporal study of ammonia oxidation in two small intertidal bays, Rusheen and Clew bay, Ireland. Potential Nitrification Rate (PNR) was ten-fold higher in Rusheen bay (Clew: 0.27 ± SD 0.55; Rusheen: 2.46 ± SD 3.4 NO2- µg-1 g-1 day-1, P < 0.001) than in Clew bay but amoA gene abundances were similar between bays, and comparable to those in other coastal ecosystems. Within bays AOB genes increased towards the muddy sediments and were positively correlated with PNR and pH. Less spatial variation was observed in AOA abundances which nevertheless positively correlated with pH and temperature and negatively with salinity and ammonia. Transcriptionally active AOB and AOA were quantified from all sites in Rusheen bay, February 2014, following the general trends observed at DNA level. AOB phylotypes predominantly from the known Nitrosomonas group were distributed across the bay, while Nitrosomonas group B phylotypes were absent from low salinity sites. AOA genes and transcripts were primarily affiliated with Thaumarchaeota group I.1a.
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Affiliation(s)
- Aoife M Duff
- Microbiology, School of Natural Sciences, NUI Galway, Galway, Ireland
- Infrastructure and Environment, School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Science, Chinese Academy of Sciences, 18 Shuangqing Rd., Haidan Beijing, 100085, P.R. China
| | - Cindy J Smith
- Microbiology, School of Natural Sciences, NUI Galway, Galway, Ireland.
- Infrastructure and Environment, School of Engineering, University of Glasgow, Glasgow, United Kingdom.
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34
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Khangembam CD, Sharma JG, Chakrabarti R. Diversity and Abundance of Ammonia-Oxidizing Bacteria and Archaea in a Freshwater Recirculating Aquaculture System. HAYATI JOURNAL OF BIOSCIENCES 2017. [DOI: 10.1016/j.hjb.2017.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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35
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Abundance and diversity of ammonia-oxidizing archaea in a biological aerated filter process. ANN MICROBIOL 2017. [DOI: 10.1007/s13213-017-1272-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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36
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Sauder LA, Albertsen M, Engel K, Schwarz J, Nielsen PH, Wagner M, Neufeld JD. Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system. ISME JOURNAL 2017; 11:1142-1157. [PMID: 28195581 PMCID: PMC5398378 DOI: 10.1038/ismej.2016.192] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 11/10/2016] [Accepted: 11/16/2016] [Indexed: 02/07/2023]
Abstract
Thaumarchaeota have been detected in several industrial and municipal wastewater treatment plants (WWTPs), despite the fact that ammonia-oxidizing archaea (AOA) are thought to be adapted to low ammonia environments. However, the activity, physiology and metabolism of WWTP-associated AOA remain poorly understood. We report the cultivation and complete genome sequence of Candidatus Nitrosocosmicus exaquare, a novel AOA representative from a municipal WWTP in Guelph, Ontario (Canada). In enrichment culture, Ca. N. exaquare oxidizes ammonia to nitrite stoichiometrically, is mesophilic, and tolerates at least 15 mm of ammonium chloride or sodium nitrite. Microautoradiography (MAR) for enrichment cultures demonstrates that Ca. N. exaquare assimilates bicarbonate in association with ammonia oxidation. However, despite using inorganic carbon, the ammonia-oxidizing activity of Ca. N. exaquare is greatly stimulated in enrichment culture by the addition of organic compounds, especially malate and succinate. Ca. N. exaquare cells are coccoid with a diameter of ~1–2 μm. Phylogenetically, Ca. N. exaquare belongs to the Nitrososphaera sister cluster within the Group I.1b Thaumarchaeota, a lineage which includes most other reported AOA sequences from municipal and industrial WWTPs. The 2.99 Mbp genome of Ca. N. exaquare encodes pathways for ammonia oxidation, bicarbonate fixation, and urea transport and breakdown. In addition, this genome encodes several key genes for dealing with oxidative stress, including peroxidase and catalase. Incubations of WWTP biofilm demonstrate partial inhibition of ammonia-oxidizing activity by 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO), suggesting that Ca. N. exaquare-like AOA may contribute to nitrification in situ. However, CARD-FISH-MAR showed no incorporation of bicarbonate by detected Thaumarchaeaota, suggesting that detected AOA may incorporate non-bicarbonate carbon sources or rely on an alternative and yet unknown metabolism.
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Affiliation(s)
- Laura A Sauder
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Mads Albertsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Katja Engel
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Jasmin Schwarz
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network 'Chemistry meets Microbiology', University of Vienna, Vienna, Austria
| | - Per H Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Michael Wagner
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network 'Chemistry meets Microbiology', University of Vienna, Vienna, Austria
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
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Men Y, Achermann S, Helbling DE, Johnson DR, Fenner K. Relative contribution of ammonia oxidizing bacteria and other members of nitrifying activated sludge communities to micropollutant biotransformation. WATER RESEARCH 2017; 109:217-226. [PMID: 27898334 DOI: 10.1016/j.watres.2016.11.048] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/17/2016] [Accepted: 11/20/2016] [Indexed: 05/27/2023]
Abstract
Improved micropollutant (MP) biotransformation during biological wastewater treatment has been associated with high ammonia oxidation activities, suggesting co-metabolic biotransformation by ammonia oxidizing bacteria as an underlying mechanism. The goal of this study was to clarify the contribution of ammonia oxidizing bacteria to increased MP degradation in nitrifying activated sludge (NAS) communities using a series of inhibition experiments. To this end, we treated a NAS community with two different ammonia oxidation inhibitors, namely octyne (OCT), a mechanistic inhibitor that covalently binds to ammonia monooxygenases, and allylthiourea (ATU), a copper chelator that depletes copper ions from the active center of ammonia monooxygenases. We investigated the biotransformation of 79 structurally different MPs by the inhibitor-treated and untreated sludge communities. Fifty-five compounds exhibited over 20% removal in the untreated control after a 46 h-incubation. Of these, 31 compounds were significantly inhibited by either ATU and/or OCT. For 17 of the 31 MPs, the inhibition by ATU at 46 h was substantially higher than by OCT despite the full inhibition of ammonia oxidation by both inhibitors. This was particularly the case for almost all thioether and phenylurea compounds tested, suggesting that in nitrifying activated sludge communities, ATU does not exclusively act as an inhibitor of bacterial ammonia oxidation. Rather, ATU also inhibited enzymes contributing to MP biotransformation but not to bulk ammonia oxidation. Thus, inhibition studies with ATU tend to overestimate the contribution of ammonia-oxidizing bacteria to MP biotransformation in nitrifying activated sludge communities. Biolog tests revealed only minor effects of ATU on the heterotrophic respiration of common organic substrates by the sludge community, suggesting that ATU did not affect enzymes that were essential in energy conservation and central metabolism of heterotrophs. By comparing ATU- and OCT-treated samples, as well as before and after ammonia oxidation was recovered in OCT-treated samples, we were able to demonstrate that ammonia-oxidizing bacteria were highly involved in the biotransformation of four compounds: asulam, clomazone, monuron and trimethoprim.
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Affiliation(s)
- Yujie Men
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland; Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Stefan Achermann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland; Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, 8092 Zürich, Switzerland
| | - Damian E Helbling
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA
| | - David R Johnson
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Kathrin Fenner
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland; Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, 8092 Zürich, Switzerland
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Lu X, Seuradge BJ, Neufeld JD. Biogeography of soil Thaumarchaeota in relation to soil depth and land usage. FEMS Microbiol Ecol 2016; 93:fiw246. [DOI: 10.1093/femsec/fiw246] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/27/2016] [Accepted: 12/07/2016] [Indexed: 01/02/2023] Open
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Jung MY, Kim JG, Sinninghe Damsté JS, Rijpstra WIC, Madsen EL, Kim SJ, Hong H, Si OJ, Kerou M, Schleper C, Rhee SK. A hydrophobic ammonia-oxidizing archaeon of the Nitrosocosmicus clade isolated from coal tar-contaminated sediment. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:983-992. [PMID: 27700018 DOI: 10.1111/1758-2229.12477] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 09/20/2016] [Accepted: 09/20/2016] [Indexed: 06/06/2023]
Abstract
A wide diversity of ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaeota exists and plays a key role in the N cycle in a variety of habitats. In this study, we isolated and characterized an ammonia-oxidizing archaeon, strain MY3, from a coal tar-contaminated sediment. Phylogenetically, strain MY3 falls in clade 'Nitrosocosmicus' of the thaumarchaeotal group I.1b. The cells of strain MY3 are large 'walnut-like' cocci, divide by binary fission along a central cingulum, and form aggregates. Strain MY3 is mesophilic and neutrophilic. An assay of 13 C-bicarbonate incorporation into archaeal membrane lipids indicated that strain MY3 is capable of autotrophy. In contrast to some other AOA, TCA cycle intermediates, i.e. pruvate, oxaloacetate and α-ketoglutarate, did not affect the growth rates and yields of strain MY3. The attachment of cells of strain MY3 to XAD-7 hydrophobic beads and to the adsorbent vermiculite demonstrated the potential of strain MY3 to form biofilms. The cell surface was confirmed to be hydrophobic by the extraction of strain MY3 from an aqueous medium with p-xylene. Our finding of a strong potential for surface attachment by strain MY3 may reflect an adaptation to the selective pressures in hydrophobic terrestrial environments.
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Affiliation(s)
- Man-Young Jung
- Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, South Korea
| | - Jong-Geol Kim
- Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, South Korea
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, P.O. Box 59, AB Den Burg, 1790, The Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, P.O. Box 80.021, Utrecht, 3508, TA, The Netherlands
| | - W Irene C Rijpstra
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, P.O. Box 59, AB Den Burg, 1790, The Netherlands
| | - Eugene L Madsen
- Department of Microbiology, Cornell University, Ithaca, NY, 14853-8101, USA
| | - So-Jeong Kim
- Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, South Korea
| | - Heeji Hong
- Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, South Korea
| | - Ok-Ja Si
- Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, South Korea
| | - Melina Kerou
- Department of Genetics in Ecology, University of Vienna, Vienna, A-1090, Austria
| | - Christa Schleper
- Department of Genetics in Ecology, University of Vienna, Vienna, A-1090, Austria
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, South Korea
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Insights into microbial diversity in wastewater treatment systems: How far have we come? Biotechnol Adv 2016; 34:790-802. [DOI: 10.1016/j.biotechadv.2016.04.003] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 02/15/2016] [Accepted: 04/07/2016] [Indexed: 11/16/2022]
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Men Y, Han P, Helbling DE, Jehmlich N, Herbold C, Gulde R, Onnis-Hayden A, Gu AZ, Johnson DR, Wagner M, Fenner K. Biotransformation of Two Pharmaceuticals by the Ammonia-Oxidizing Archaeon Nitrososphaera gargensis. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:4682-92. [PMID: 27046099 PMCID: PMC4981450 DOI: 10.1021/acs.est.5b06016] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 03/25/2016] [Accepted: 04/05/2016] [Indexed: 05/20/2023]
Abstract
The biotransformation of some micropollutants has previously been observed to be positively associated with ammonia oxidation activities and the transcript abundance of the archaeal ammonia monooxygenase gene (amoA) in nitrifying activated sludge. Given the increasing interest in and potential importance of ammonia-oxidizing archaea (AOA), we investigated the capabilities of an AOA pure culture, Nitrososphaera gargensis, to biotransform ten micropollutants belonging to three structurally similar groups (i.e., phenylureas, tertiary amides, and tertiary amines). N. gargensis was able to biotransform two of the tertiary amines, mianserin (MIA) and ranitidine (RAN), exhibiting similar compound specificity as two ammonia-oxidizing bacteria (AOB) strains that were tested for comparison. The same MIA and RAN biotransformation reactions were carried out by both the AOA and AOB strains. The major transformation product (TP) of MIA, α-oxo MIA was likely formed via a two-step oxidation reaction. The first hydroxylation step is typically catalyzed by monooxygenases. Three RAN TP candidates were identified from nontarget analysis. Their tentative structures and possible biotransformation pathways were proposed. The biotransformation of MIA and RAN only occurred when ammonia oxidation was active, suggesting cometabolic transformations. Consistently, a comparative proteomic analysis revealed no significant differential expression of any protein-encoding gene in N. gargensis grown on ammonium with MIA or RAN compared with standard cultivation on ammonium only. Taken together, this study provides first important insights regarding the roles played by AOA in micropollutant biotransformation.
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Affiliation(s)
- Yujie Men
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Department
of Civil and Environmental Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Yujie Men. Address: 3209 Newmark
Civil Engineering Laboratory, MC-250 205 North Mathews Ave., Urbana,
IL 61801-2352, USA. . Phone: (217) 244-8259
| | - Ping Han
- Department
of Microbiology and Ecosystem Science, Division of Microbial Ecology,
Research Network “Chemistry meets Microbiology”, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Damian E. Helbling
- School
of Civil and Environmental Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Nico Jehmlich
- Department
of Proteomics, Helmholtz-Centre for Environmental
Research − UFZ, 04318 Leipzig, Germany
| | - Craig Herbold
- Department
of Microbiology and Ecosystem Science, Division of Microbial Ecology,
Research Network “Chemistry meets Microbiology”, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Rebekka Gulde
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Annalisa Onnis-Hayden
- Department
of Civil and Environmental Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - April Z. Gu
- Department
of Civil and Environmental Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - David R. Johnson
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Michael Wagner
- Department
of Microbiology and Ecosystem Science, Division of Microbial Ecology,
Research Network “Chemistry meets Microbiology”, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Kathrin Fenner
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Department
of Environmental Systems Science, ETH Zürich, 8092 Zürich, Switzerland
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Sauder LA, Ross AA, Neufeld JD. Nitric oxide scavengers differentially inhibit ammonia oxidation in ammonia-oxidizing archaea and bacteria. FEMS Microbiol Lett 2016; 363:fnw052. [PMID: 26946536 DOI: 10.1093/femsle/fnw052] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2016] [Indexed: 11/14/2022] Open
Abstract
Differential inhibitors are important for measuring the relative contributions of microbial groups, such as ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), to biogeochemical processes in environmental samples. In particular, 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO) represents a nitric oxide scavenger used for the specific inhibition of AOA, implicating nitric oxide as an intermediate of thaumarchaeotal ammonia oxidation. This study investigated four alternative nitric oxide scavengers for their ability to differentially inhibit AOA and AOB in comparison to PTIO. Caffeic acid, curcumin, methylene blue hydrate and trolox were tested onNitrosopumilus maritimus, two unpublished AOA representatives (AOA-6f and AOA-G6) as well as the AOB representative Nitrosomonas europaea All four scavengers inhibited ammonia oxidation by AOA at lower concentrations than for AOB. In particular, differential inhibition of AOA and AOB by caffeic acid (100 μM) and methylene blue hydrate (3 μM) was comparable to carboxy-PTIO (100 μM) in pure and enrichment culture incubations. However, when added to aquarium sponge biofilm microcosms, both scavengers were unable to inhibit ammonia oxidation consistently, likely due to degradation of the inhibitors themselves. This study provides evidence that a variety of nitric oxide scavengers result in differential inhibition of ammonia oxidation in AOA and AOB, and provides support to the proposed role of nitric oxide as a key intermediate in the thaumarchaeotal ammonia oxidation pathway.
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Affiliation(s)
- Laura A Sauder
- Department of Biology, University of Waterloo, 200 University Ave. W. Waterloo, ON N2L 3G1, Canada
| | - Ashley A Ross
- Department of Biology, University of Waterloo, 200 University Ave. W. Waterloo, ON N2L 3G1, Canada
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, 200 University Ave. W. Waterloo, ON N2L 3G1, Canada
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Gao JF, Fan XY, Luo X, Pan KL. Insight into the short-term effect of titanium dioxide nanoparticles on active ammonia oxidizing microorganisms in a full-scale wastewater treatment plant: a DNA-stable isotope probing study. RSC Adv 2016. [DOI: 10.1039/c6ra13066f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are two distinct ammonia-oxidizing microorganisms (AOMs) responsible for nitrification in wastewater treatment plants (WWTPs).
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Affiliation(s)
- Jing-Feng Gao
- College of Environmental and Energy Engineering
- Beijing University of Technology
- Beijing 100124
- China
| | - Xiao-Yan Fan
- College of Environmental and Energy Engineering
- Beijing University of Technology
- Beijing 100124
- China
| | - Xin Luo
- College of Environmental and Energy Engineering
- Beijing University of Technology
- Beijing 100124
- China
| | - Kai-Ling Pan
- College of Environmental and Energy Engineering
- Beijing University of Technology
- Beijing 100124
- China
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Ross AA, Neufeld JD. Microbial biogeography of a university campus. MICROBIOME 2015; 3:66. [PMID: 26620848 PMCID: PMC4666157 DOI: 10.1186/s40168-015-0135-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 11/17/2015] [Indexed: 05/10/2023]
Abstract
BACKGROUND Microorganisms are distributed on surfaces within homes, workplaces, and schools, with the potential to impact human health and disease. University campuses represent a unique opportunity to explore the distribution of microorganisms within built environments because of high human population densities, throughput, and variable building usage. For example, the main campus of the University of Waterloo spans four square kilometres, hosts over 40,000 individuals daily, and is comprised of a variety of buildings, including lecture halls, gyms, restaurants, residences, and a daycare. RESULTS Representative left and right entrance door handles from each of the 65 buildings at the University of Waterloo were swabbed at three time points during an academic term in order to determine if microbial community assemblages coincided with building usage and whether these communities are stable temporally. Across all door handles, the dominant phyla were Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes, which comprised 89.0 % of all reads. A total of 713 genera were observed, 16 of which constituted a minimum of 1 % of the 2,458,094 classified and rarefied reads. Archaea were found in low abundance (~0.03 %) but were present on 42.8 % of the door handles on 96 % of buildings across all time points, indicating that they are ubiquitous at very low levels on door handle surfaces. Although inter-handle variability was high, several individual building entrances harbored distinct microbial communities that were consistent over time. The presence of visible environmental debris on a subset of handles was associated with distinct microbial communities (beta diversity), increased richness (alpha diversity), and higher biomass (adenosine 5'-triphosphate; ATP). CONCLUSIONS This study demonstrates highly variable microbial communities associated with frequently contacted door handles on a university campus. Nonetheless, the data also revealed several building-specific and temporally stable bacterial and archaeal community patterns, with a potential impact of accumulated debris, a possible result of low human throughput, on detected microbial communities.
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Affiliation(s)
- Ashley A Ross
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada.
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada.
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Gan XH, Zhang FQ, Gu JD, Guo YD, Li ZQ, Zhang WQ, Xu XY, Zhou Y, Wen XY, Xie GG, Wang YF. Differential distribution patterns of ammonia-oxidizing archaea and bacteria in acidic soils of Nanling National Nature Reserve forests in subtropical China. Antonie van Leeuwenhoek 2015; 109:237-51. [DOI: 10.1007/s10482-015-0627-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 11/19/2015] [Indexed: 10/22/2022]
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Sterngren AE, Hallin S, Bengtson P. Archaeal Ammonia Oxidizers Dominate in Numbers, but Bacteria Drive Gross Nitrification in N-amended Grassland Soil. Front Microbiol 2015; 6:1350. [PMID: 26648926 PMCID: PMC4663241 DOI: 10.3389/fmicb.2015.01350] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/16/2015] [Indexed: 12/02/2022] Open
Abstract
Both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) play an important role in nitrification in terrestrial environments. Most often AOA outnumber AOB, but the relative contribution of AOA and AOB to nitrification rates remains unclear. The aim of this experiment was to test the hypotheses that high nitrogen availability would favor AOB and result in high gross nitrification rates, while high carbon availability would result in low nitrogen concentrations that favor the activity of AOA. The hypotheses were tested in a microcosm experiment where sugars, ammonium, or amino acids were added regularly to a grassland soil for a period of 33 days. The abundance of amoA genes from AOB increased markedly in treatments that received nitrogen, suggesting that AOB were the main ammonia oxidizers here. However, AOB could not account for the entire ammonia oxidation activity observed in treatments where the soil was deficient in available nitrogen. The findings suggest that AOA are important drivers of nitrification under nitrogen-poor conditions, but that input of easily available nitrogen results in increased abundance, activity, and relative importance of AOB for gross nitrification in grassland soil.
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Affiliation(s)
- Anna E Sterngren
- Microbial Ecology, Department of Biology, Lund University Lund, Sweden
| | - Sara Hallin
- Department of Microbiology, Uppsala BioCenter, Swedish University of Agricultural Sciences Uppsala, Sweden
| | - Per Bengtson
- Microbial Ecology, Department of Biology, Lund University Lund, Sweden
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Li X, Zhang M, Liu F, Li Y, He Y, Zhang S, Wu J. The Significance of Myriophyllum elatinoides for Swine Wastewater Treatment: Abundance and Community Structure of Ammonia-Oxidizing Microorganisms in Sediments. PLoS One 2015; 10:e0139778. [PMID: 26444015 PMCID: PMC4596523 DOI: 10.1371/journal.pone.0139778] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 09/17/2015] [Indexed: 11/19/2022] Open
Abstract
Myriophyllum elatinoides was reported to effectively treat wastewater by removing nitrogen (N) and phosphorus (P). However, little is known about the abundance and community structure of ammonia-oxidizing microorganisms associated with M. elatinoides purification systems. The objective of this research was to characterize the abundance and community structure of ammonia-oxidizing microorganisms in swine wastewater and determine the main nitrogen removal pathways. In this study, five different waters were treated by M. elatinoides in microcosms for one month. The five waters included tap water (Control), swine wastewater (SW), 50% diluted swine wastewater (50% SW), and two synthetic wastewaters: 200 mg NH4+-N L−1 (200 NH4+-N) and 400 mg NH4+-N L−1 (400 NH4+-N). The most dramatic changes were in NH4+-N and total N (TN) concentrations, with average removal rates of 84% and 90%, respectively, in the treatments containing swine wastewater. On days 7, 14, and 28, the dissolved oxygen (DO) increased by 81.8%, 210.4% and 136.5%, respectively, compared with on day 0, in the swine wastewater. The results also showed that the bacterial amoA (AOB) copy numbers in the sediments of the treatments were significantly higher than those of archaeal amoA (AOA) copy numbers (p = 0.015). In addition, the high DO concentrations in swine wastewater responded well to the high abundance of AOB. The AOA and AOB community distributions were positively related with NO3-N and were negatively related with DO in swine wastewater treatments. In summary, our experimental results suggested that the M. elatinoides purification system could improve the activity of ammonia-oxidizing microorganisms and consequently might contribute to the significant N removal from the swine wastewater.
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Affiliation(s)
- Xi Li
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, P. R. China
- Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, P. R. China
| | - Miaomiao Zhang
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, P. R. China
- Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, P. R. China
| | - Feng Liu
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, P. R. China
- Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, P. R. China
- * E-mail: (FL); (YL); (JW)
| | - Yong Li
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, P. R. China
- Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, P. R. China
- * E-mail: (FL); (YL); (JW)
| | - Yang He
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, P. R. China
- Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, P. R. China
- Graduate University of Chinese Academy of Sciences, Beijing, 100039, P. R. China
| | - Shunan Zhang
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, P. R. China
- Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, P. R. China
- Graduate University of Chinese Academy of Sciences, Beijing, 100039, P. R. China
| | - Jinshui Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, P. R. China
- Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, P. R. China
- * E-mail: (FL); (YL); (JW)
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Zhang Y, Tian Z, Liu M, Shi ZJ, Hale L, Zhou J, Yang M. High Concentrations of the Antibiotic Spiramycin in Wastewater Lead to High Abundance of Ammonia-Oxidizing Archaea in Nitrifying Populations. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:9124-9132. [PMID: 26125322 DOI: 10.1021/acs.est.5b01293] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
To evaluate the potential effects of antibiotics on ammonia-oxidizing microbes, multiple tools including quantitative PCR (qPCR), 454-pyrosequencing, and a high-throughput functional gene array (GeoChip) were used to reveal the distribution of ammonia-oxidizing archaea (AOA) and archaeal amoA (Arch-amoA) genes in three wastewater treatment systems receiving spiramycin or oxytetracycline production wastewaters. The qPCR results revealed that the copy number ratios of Arch-amoA to ammonia-oxidizing bacteria (AOB) amoA genes were the highest in the spiramycin full-scale (5.30) and pilot-scale systems (1.49 × 10(-1)), followed by the oxytetracycline system (4.90 × 10(-4)), with no Arch-amoA genes detected in the control systems treating sewage or inosine production wastewater. The pyrosequencing result showed that the relative abundance of AOA affiliated with Thaumarchaeota accounted for 78.5-99.6% of total archaea in the two spiramycin systems, which was in accordance with the qPCR results. Mantel test based on GeoChip data showed that Arch-amoA gene signal intensity correlated with the presence of spiramycin (P < 0.05). Antibiotics explained 25.8% of variations in amoA functional gene structures by variance partitioning analysis. This study revealed the selection of AOA in the presence of high concentrations of spiramycin in activated sludge systems.
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Affiliation(s)
- Yu Zhang
- †State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P.O. Box 2871, Beijing 100085, China
| | - Zhe Tian
- †State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P.O. Box 2871, Beijing 100085, China
| | - Miaomiao Liu
- †State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P.O. Box 2871, Beijing 100085, China
| | - Zhou Jason Shi
- ‡Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Lauren Hale
- ‡Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Jizhong Zhou
- ‡Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
- §Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- ∥State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Min Yang
- †State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P.O. Box 2871, Beijing 100085, China
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Denaturing Gradient Gel Electrophoresis (DGGE) for Microbial Community Analysis. SPRINGER PROTOCOLS HANDBOOKS 2015. [DOI: 10.1007/8623_2015_99] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Temporal and spatial stability of ammonia-oxidizing archaea and bacteria in aquarium biofilters. PLoS One 2014; 9:e113515. [PMID: 25479061 PMCID: PMC4257543 DOI: 10.1371/journal.pone.0113515] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 10/29/2014] [Indexed: 11/19/2022] Open
Abstract
Nitrifying biofilters are used in aquaria and aquaculture systems to prevent accumulation of ammonia by promoting rapid conversion to nitrate via nitrite. Ammonia-oxidizing archaea (AOA), as opposed to ammonia-oxidizing bacteria (AOB), were recently identified as the dominant ammonia oxidizers in most freshwater aquaria. This study investigated biofilms from fixed-bed aquarium biofilters to assess the temporal and spatial dynamics of AOA and AOB abundance and diversity. Over a period of four months, ammonia-oxidizing microorganisms from six freshwater and one marine aquarium were investigated at 4–5 time points. Nitrogen balances for three freshwater aquaria showed that active nitrification by aquarium biofilters accounted for ≥81–86% of total nitrogen conversion in the aquaria. Quantitative PCR (qPCR) for bacterial and thaumarchaeal ammonia monooxygenase (amoA) genes demonstrated that AOA were numerically dominant over AOB in all six freshwater aquaria tested, and contributed all detectable amoA genes in three aquarium biofilters. In the marine aquarium, however, AOB outnumbered AOA by three to five orders of magnitude based on amoA gene abundances. A comparison of AOA abundance in three carrier materials (fine sponge, rough sponge and sintered glass or ceramic rings) of two three-media freshwater biofilters revealed preferential growth of AOA on fine sponge. Denaturing gel gradient electrophoresis (DGGE) of thaumarchaeal 16S rRNA genes indicated that community composition within a given biofilter was stable across media types. In addition, DGGE of all aquarium biofilters revealed low AOA diversity, with few bands, which were stable over time. Nonmetric multidimensional scaling (NMDS) based on denaturing gradient gel electrophoresis (DGGE) fingerprints of thaumarchaeal 16S rRNA genes placed freshwater and marine aquaria communities in separate clusters. These results indicate that AOA are the dominant ammonia-oxidizing microorganisms in freshwater aquarium biofilters, and that AOA community composition within a given aquarium is stable over time and across biofilter support material types.
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