151
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Wei H, Lin X. Shifts in the relative abundance and potential rates of sediment ammonia-oxidizing archaea and bacteria along environmental gradients of an urban river-estuary-adjacent sea continuum. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 771:144824. [PMID: 33545473 DOI: 10.1016/j.scitotenv.2020.144824] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in N cycling in sediments globally. However, little is known about their ammonia oxidation rates along a river-estuary-sea continuum. In this study, we investigated how the potential ammonia oxidation rates (PARs) of AOA and AOB changed spatially along a continuum comprising three habitats: the Shanghai urban river network, the Yangtze Estuary, and the adjacent East China Sea, in summer and winter. The AOA and AOB PARs (0.53 ± 0.49 and 0.72 ± 0.69 μg N g-1 d-1, mean ± SD, respectively) and their amoA gene abundance (0.47 ± 0.85 × 106 and 2.4 ± 3.54 × 106 copies g-1, respectively) decreased along the continuum, particularly from the urban river to the estuary, driven by decreasing sediment total organic C and N and other correlated inorganic nutrients (e.g., NH4+) along the gradient of anthropogenic influences. These spatial patterns were consistent between the seasons. The urban river network, where the anthropogenic influences were strongest, saw the largest seasonal differences, as both AOA and AOB had higher PARs and abundance in summer than in winter. The ratios between AOA and AOB PARs (~0.87 ± 0.51) and gene abundances (~0.25 ± 0.24), however, were predominantly <1, indicating an AOB-dominated community. Comparing the different NH4+ consumption pathways, total aerobic oxidation accounted for 12-26% of the total consumption, with the largest proportion in the estuary, where the system was well oxygenated, and the lowest in the adjacent sea, where inorganic N was highly depleted. This study revealed the spatiotemporal patterns of AOA and AOB potential rates and gene abundance along gradients of human influences and identified organic matter and nutrients as key environmental factors that shaped the variation of AOA and AOB along the continuum.
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Affiliation(s)
- Hengchen Wei
- The University of Texas at Austin Marine Science Institute, 750 Channel View Drive, Port Aransas, TX 78373, USA
| | - Xianbiao Lin
- Laboratory of Microbial Ecology and Matter Cycles, School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China; School of Geographic Sciences, Key Laboratory of Geographic Information Science of the Ministry of Education, East China Normal University, Shanghai 200241, China; Southern Laboratory of Ocean Science and Engineering (Guangdong, Zhuhai), Zhuhai 519000, China.
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152
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Liu G, Wu X, Li D, Jiang L, Huang J, Zhuang L. Long-Term Low Dissolved Oxygen Operation Decreases N 2O Emissions in the Activated Sludge Process. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:6975-6983. [PMID: 33904707 DOI: 10.1021/acs.est.0c07279] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Nitrous oxide (N2O) is an important greenhouse gas and a dominant ozone-depleting substance. Nitrification in the activated sludge process (ASP) is an important N2O emission source. This study demonstrated that a short-term low dissolved oxygen (DO) increased the N2O emissions by six times, while long-term low DO operation decreased the N2O emissions by 54% (P < 0.01). Under long-term low DO, the ammonia oxidizer abundance in the ASP increased significantly, and thus, complete nitrification was recovered and no NH3 or nitrite accumulated. Moreover, long-term low DO decreased the abundance of ammonia-oxidizing bacteria (AOB) by 28%, while increased the abundance of ammonia-oxidizing archaea (AOA) by 507%, mainly due to their higher oxygen affinity. As a result, AOA outnumbered AOB with the AOA/AOB amoA gene ratio increasing to 19.5 under long-term low DO. The efficient nitrification and decreased AOB abundance might not increase N2O production via AOB under long-term low DO conditions. The enriched AOA could decrease the N2O emissions because they were reported to lack canonical nitric oxide (NO) reductase genes that convert NO to N2O. Probably because of AOA enrichment, the positive and significant (P = 0.02) correlation of N2O emission and nitrite concentration became insignificant (P = 0.332) after 80 days of low DO operation. Therefore, ASPs can be operated with low DO and extended sludge age to synchronously reduce N2O production and carbon dioxide emissions owing to lower aeration energy without compromising the nitrification efficiency.
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Affiliation(s)
- Guoqiang Liu
- School of Environment, Guangdong Engineering Research Center of Water Treatment Processes and Materials and Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China
| | - Xianwei Wu
- School of Environment, Guangdong Engineering Research Center of Water Treatment Processes and Materials and Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China
| | - Deyong Li
- School of Environment, Guangdong Engineering Research Center of Water Treatment Processes and Materials and Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China
| | - Lugao Jiang
- School of Environment, Guangdong Engineering Research Center of Water Treatment Processes and Materials and Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China
| | - Ju Huang
- School of Environment, Guangdong Engineering Research Center of Water Treatment Processes and Materials and Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China
| | - Li Zhuang
- School of Environment, Guangdong Engineering Research Center of Water Treatment Processes and Materials and Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China
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153
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Yang Y, Zhang C, Lenton TM, Yan X, Zhu M, Zhou M, Tao J, Phelps TJ, Cao Z. The evolution pathway of ammonia-oxidizing archaea shaped by major geological events. Mol Biol Evol 2021; 38:3637-3648. [PMID: 33993308 PMCID: PMC8382903 DOI: 10.1093/molbev/msab129] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Primordial nitrification processes have been studied extensively using geochemical approaches, but the biological origination of nitrification remains unclear. Ammonia-oxidizing archaea (AOA) are widely distributed nitrifiers and implement the rate-limiting step in nitrification. They are hypothesized to have been important players in the global nitrogen cycle in Earth’s early history. We performed systematic phylogenomic and marker gene analyses to elucidate the diversification timeline of AOA evolution. Our results suggested that the AOA ancestor experienced terrestrial geothermal environments at ∼1,165 Ma (1,928–880 Ma), and gradually evolved into mesophilic soil at ∼652 Ma (767–554 Ma) before diversifying into marine settings at ∼509 Ma (629–412 Ma) and later into shallow and deep oceans, respectively. Corroborated by geochemical evidence and modeling, the timing of key diversification nodes can be linked to the global magmatism and glaciation associated with the assembly and breakup of the supercontinent Rodinia, and the later oxygenation of the deep ocean. Results of this integrated study shed light on the geological forces that may have shaped the evolutionary pathways of the AOA, which played an important role in the ancient global nitrogen cycle.
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Affiliation(s)
- Yiyan Yang
- Department of Gastroenterology, Shanghai 10th People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, 518055, P.R. China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510000, China.,Shanghai Sheshan National Geophysical Observatory, Shanghai, 201602, China
| | - Timothy M Lenton
- Global Systems Institute, University of Exeter, Exeter, EX4 4QE, United Kingdom
| | - Xinmiao Yan
- Department of Gastroenterology, Shanghai 10th People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Maoyan Zhu
- State Key Laboratory of Palaeobiology and Stratigraphy & Center for Excellence in Life and Paleoenvironment, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, 210008, P.R. China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, 100049, P.R. China
| | - Mengdi Zhou
- Department of Gastroenterology, Shanghai 10th People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jianchang Tao
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, 518055, P.R. China
| | - Tommy J Phelps
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, 518055, P.R. China
| | - Zhiwei Cao
- Department of Gastroenterology, Shanghai 10th People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
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154
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Wang Z, Ni G, Maulani N, Xia J, De Clippeleir H, Hu S, Yuan Z, Zheng M. Stoichiometric and kinetic characterization of an acid-tolerant ammonia oxidizer 'Candidatus Nitrosoglobus'. WATER RESEARCH 2021; 196:117026. [PMID: 33751975 DOI: 10.1016/j.watres.2021.117026] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/07/2021] [Accepted: 03/08/2021] [Indexed: 05/06/2023]
Abstract
Recently, acidic (i.e. pH<5) nitrification in activated-sludge is attracting attention because it enables stable nitritation (NH4+ → NO2-), and enhances sludge reduction and stabilization. However, the key acid-tolerant ammonia oxidizers involved are poorly understood. In this study, we performed stoichiometric and kinetic characterization of a new acid-tolerant ammonia-oxidizing bacterium (AOB) belonging to gamma-proteobacterium, Candidatus Nitrosoglobus. Ca. Nitrosoglobus was cultivated in activated-sludge in a laboratory membrane bioreactor over 200 days, with a relative abundance of 55.1 ± 0.5% (indicated by 16S rRNA gene amplicon sequencing) at the time of the characterization experiments. Among all known nitrifiers, Ca. Nitrosoglobus bears the highest resistance to nitrite, low pH, and free nitrous acid (FNA). These traits define Ca. Nitrosoglobus as an adversity-strategist that tends to prosper in acidic activated-sludge, where the low pH (< 5.0) and high levels of FNA (at parts per million levels) sustained and inhibited all other nitrifiers. In contrast, in the conventional pH-neutral activated-sludge process, Ca. Nitrosoglobus is less competitive with canonical AOB (e.g. Nitrosomonas) due to the relatively slow specific growth rate and low affinities to both oxygen and total ammonia. These results advance our understanding of acid-tolerant ammonia oxidizers, and support further development of the acidic activated-sludge process in which Ca. Nitrosoglobus can play a critical role.
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Affiliation(s)
- Zhiyao Wang
- Advanced Water Management Centre, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Gaofeng Ni
- Advanced Water Management Centre, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Nova Maulani
- Advanced Water Management Centre, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Jun Xia
- Advanced Water Management Centre, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Haydée De Clippeleir
- District of Columbia Water and Sewer Authority, 5000 Overlook Ave. SW, Washington, DC 20032, USA
| | - Shihu Hu
- Advanced Water Management Centre, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Zhiguo Yuan
- Advanced Water Management Centre, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Min Zheng
- Advanced Water Management Centre, The University of Queensland, St Lucia, QLD 4072, Australia.
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155
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Zhou LJ, Han P, Zhao M, Yu Y, Sun D, Hou L, Liu M, Zhao Q, Tang X, Klümper U, Gu JD, Men Y, Wu QL. Biotransformation of lincomycin and fluoroquinolone antibiotics by the ammonia oxidizers AOA, AOB and comammox: A comparison of removal, pathways, and mechanisms. WATER RESEARCH 2021; 196:117003. [PMID: 33730544 DOI: 10.1016/j.watres.2021.117003] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 06/12/2023]
Abstract
In this study, we evaluated the biotransformation mechanisms of lincomycin (LIN) and three fluoroquinolone antibiotics (FQs), ciprofloxacin (CFX), norfloxacin (NFX), and ofloxacin (OFX), which regularly enter aquatic environments through human activities, by different ammonia-oxidizing microorganisms (AOM). The organisms included a pure culture of the complete ammonia oxidizer (comammox) Nitrospira inopinata, an ammonia oxidizing archaeon (AOA) Nitrososphaera gargensis, and an ammonia-oxidizing bacterium (AOB) Nitrosomonas nitrosa Nm90. The removal of these antibiotics by the pure microbial cultures and the protein-normalized biotransformation rate constants indicated that LIN was significantly co-metabolically biotransformed by AOA and comammox, but not by AOB. CFX and NFX were significantly co-metabolized by AOA and AOB, but not by comammox. None of the tested cultures transformed OFX effectively. Generally, AOA showed the best biotransformation capability for LIN and FQs, followed by comammox and AOB. The transformation products and their related biotransformation mechanisms were also elucidated. i) The AOA performed hydroxylation, S-oxidation, and demethylation of LIN, as well as nitrosation and cleavage of the piperazine moiety of CFX and NFX; ii) the AOB utilized nitrosation to biotransform CFX and NFX; and iii) the comammox carried out hydroxylation, demethylation, and demethylthioation of LIN. Hydroxylamine, an intermediate of ammonia oxidation, chemically reacted with LIN and the selected FQs, with removals exceeding 90%. Collectively, these findings provide important fundamental insights into the roles of different ammonia oxidizers and their intermediates on LIN and FQ biotransformation in nitrifying environments including wastewater treatment systems.
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Affiliation(s)
- Li-Jun Zhou
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Ping Han
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Institute of Eco-Chongming, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China.
| | - Mengyue Zhao
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yaochun Yu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States; Department of Chemical and Environmental Engineering, University of California, Riverside, California 92521, United States
| | - Dongyao Sun
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Min Liu
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Institute of Eco-Chongming, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China
| | - Qiang Zhao
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xiufeng Tang
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Uli Klümper
- Institute for Hydrobiology, Technische Universität Dresden, Dresden 01217, Germany
| | - Ji-Dong Gu
- Environmental Engineering, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, China
| | - Yujie Men
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States; Department of Chemical and Environmental Engineering, University of California, Riverside, California 92521, United States
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; Sino-Danish Center for Science and Education, University of Chinese Academy of Sciences, Beijing, China
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156
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Boey JS, Mortimer R, Couturier A, Worrallo K, Handley KM. Estuarine microbial diversity and nitrogen cycling increase along sand-mud gradients independent of salinity and distance. Environ Microbiol 2021; 24:50-65. [PMID: 33973326 DOI: 10.1111/1462-2920.15550] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 01/22/2023]
Abstract
Estuaries are depositional environments prone to terrigenous mud sedimentation. While macrofaunal diversity and nitrogen retention are greatly affected by changes in sedimentary mud content, its impact on prokaryotic diversity and nitrogen cycling activity remains understudied. We characterized the composition of estuarine tidal flat prokaryotic communities spanning a habitat range from sandy to muddy sediments, while controlling for salinity and distance. We also determined the diversity, abundance and expression of ammonia oxidizers and N2 O-reducers within these communities by amoA and clade I nosZ gene and transcript analysis. Results show that prokaryotic communities and nitrogen cycling fractions were sensitive to changes in sedimentary mud content, and that changes in the overall community were driven by a small number of phyla. Significant changes occurred in prokaryotic communities and N2 O-reducing fractions with only a 3% increase in mud, while thresholds for ammonia oxidizers were less distinct, suggesting other factors are also important for structuring these guilds. Expression of nitrogen cycling genes was substantially higher in muddier sediments, and results indicate that the potential for coupled nitrification-denitrification became increasingly prevalent as mud content increased. Altogether, results demonstrate that mud content is a strong environmental driver of diversity and N-cycling dynamics in estuarine microbial communities.
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Affiliation(s)
- Jian Sheng Boey
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand
| | - Redmond Mortimer
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand
| | - Agathe Couturier
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand.,Ecole Supérieure de Biologie Biochimie Biotechnologies, Faculté des Sciences, Université Catholique de Lyon, Lyon, France
| | - Katie Worrallo
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand
| | - Kim M Handley
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand
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157
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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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158
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Zhang Y, Dai Z, Zhou Z, Yin H, Zhang M, Zhang H, Liu Y, Li Q, Nan X, Liu X, Meng D. Development of the yeast and lactic acid bacteria co-culture agent for atmospheric ammonia removing: Genomic features and on-site applications. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 218:112287. [PMID: 33933812 DOI: 10.1016/j.ecoenv.2021.112287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/22/2021] [Accepted: 04/22/2021] [Indexed: 06/12/2023]
Abstract
Odorous gas (e.g. atmospheric ammonia) in low ventilation public places, such as public toilets and waste transfer stations, causes severe health problems. Many technologies are developed to purify the atmospheric ammonia, among which the microbial agents are supposed to be a green and economical approach. In this study, we developed a yeast, Pichia sp. J1, and a lactic acid bacterium (LAB), Lactobacillus paracasei B1, co-culture agent for atmospheric ammonia removing. The on-site application results indicated the yeast and LAB mixed fermented agent had a maximum ammonia removing efficiency of 98.78%, which is significantly higher than the pure cultures (78.93% for B1 and 75.00% for J1), indicating the co-culture agent is an excellent biological product for ammonia removal. The excellent performance of the agent is closely related to the synergy behaviors between the yeast and LAB. In the co-culture agents, some of the LAB cells adhered closely to the yeast, and the growth and lactic acid producing ability of LAB were significantly promoted by yeast. Genomic analysis indicated the complementary of nutrients, i.e. carbon and nitrogen resources, signal transduction, and adhesion proteins (regulates adhesion behavior) played roles in regulating the synergy effects. Our study offers a novel biological solution of odorous gas purification.
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Affiliation(s)
- Yanfang Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha 410083, China
| | - Zhimin Dai
- Central South Water Science and Technology Co. Ltd, Changsha 410001, China; National City Water Supply Water Quality Monitoring Network Changsha Monitoring Station, Changsha 410001, China
| | - Zhicheng Zhou
- Hunan Tobacco Science Institute, Changsha 410010, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha 410083, China
| | - Min Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha 410083, China
| | - Hetian Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha 410083, China
| | - Yongjun Liu
- Hunan Tobacco Science Institute, Changsha 410010, China
| | - Qian Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha 410083, China
| | - Xiaolong Nan
- 306 Bridge of Hunan Nuclear Geology, Changsha 410083, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha 410083, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha 410083, China.
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159
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Physical mixing in coastal waters controls and decouples nitrification via biomass dilution. Proc Natl Acad Sci U S A 2021; 118:2004877118. [PMID: 33903227 PMCID: PMC8106330 DOI: 10.1073/pnas.2004877118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Changes in both quantity and speciation of nitrogen in coastal waters impact phytoplankton communities, contributing to eutrophication and harmful algal blooms. Multidisciplinary oceanographic time series of high resolution are rare but crucial for identifying complex mechanisms that underlie such anthropogenic impacts. Analysis and modeling of such a time series from a seasonally stratified fjord showed that dilution of nitrifier biomass by variable winter mixing altered the timing and rates of nitrification, which converts ammonia to nitrite and nitrate. This reveals a link among climate-sensitive physical dynamics, nitrifier abundance, and diversity, with controls on phytoplankton ecology. The findings imply that explicit measurement and modeling of microbial communities will be required to project impacts of climate change on coastal ecosystems. Nitrification is a central process of the aquatic nitrogen cycle that controls the supply of nitrate used in other key processes, such as phytoplankton growth and denitrification. Through time series observation and modeling of a seasonally stratified, eutrophic coastal basin, we demonstrate that physical dilution of nitrifying microorganisms by water column mixing can delay and decouple nitrification. The findings are based on a 4-y, weekly time series in the subsurface water of Bedford Basin, Nova Scotia, Canada, that included measurement of functional (amoA) and phylogenetic (16S rRNA) marker genes. In years with colder winters, more intense winter mixing resulted in strong dilution of resident nitrifiers in subsurface water, delaying nitrification for weeks to months despite availability of ammonium and oxygen. Delayed regrowth of nitrifiers also led to transient accumulation of nitrite (3 to 8 μmol · kgsw−1) due to decoupling of ammonia and nitrite oxidation. Nitrite accumulation was enhanced by ammonia-oxidizing bacteria (Nitrosomonadaceae) with fast enzyme kinetics, which temporarily outcompeted the ammonia-oxidizing archaea (Nitrosopumilus) that dominated under more stable conditions. The study reveals how physical mixing can drive seasonal and interannual variations in nitrification through control of microbial biomass and diversity. Variable, mixing-induced effects on functionally specialized microbial communities are likely relevant to biogeochemical transformation rates in other seasonally stratified water columns. The detailed study reveals a complex mechanism through which weather and climate variability impacts nitrogen speciation, with implications for coastal ecosystem productivity. It also emphasizes the value of high-frequency, multiparameter time series for identifying complex controls of biogeochemical processes in aquatic systems.
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160
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Shafiee RT, Snow JT, Hester S, Zhang Q, Rickaby REM. Proteomic response of the marine ammonia-oxidising archaeon Nitrosopumilus maritimus to iron limitation reveals strategies to compensate for nutrient scarcity. Environ Microbiol 2021; 24:835-849. [PMID: 33876540 DOI: 10.1111/1462-2920.15491] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 03/25/2021] [Indexed: 11/26/2022]
Abstract
Dissolved iron (Fe) is vanishingly low in the oceans, with ecological success conferred to microorganisms that can restructure their biochemistry to maintain high growth rates during Fe scarcity. Chemolithoautotrophic ammonia-oxidising archaea (AOA) are highly abundant in the oceans, constituting ~30% of cells below the photic zone. Here we examine the proteomic response of the AOA isolate Nitrosopumilus maritimus to growth-limiting Fe concentrations. Under Fe limitation, we observed a significant reduction in the intensity of Fe-dense ferredoxins associated with respiratory complex I whilst complex III and IV proteins with more central roles in the electron transport chain remain unchanged. We concomitantly observed an increase in the intensity of Fe-free functional alternatives such as flavodoxin and plastocyanin, thioredoxin and alkyl hydroperoxide which are known to mediate electron transport and reactive oxygen species detoxification, respectively. Under Fe limitation, we found a marked increase in the intensity of the ABC phosphonate transport system (Phn), highlighting an intriguing link between Fe and P cycling in N. maritimus. We hypothesise that an elevated uptake of exogenous phosphonates under Fe limitation may either supplement N. maritimus' endogenous methylphosphonate biosynthesis pathway - which requires Fe - or enhance the production of phosphonate-containing exopolysaccharides known to efficiently bind environmental Fe.
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Affiliation(s)
- Roxana T Shafiee
- Department of Earth Sciences, South Parks Road, University of Oxford, Oxfordshire, OX1 3AN, UK
| | - Joseph T Snow
- Department of Earth Sciences, South Parks Road, University of Oxford, Oxfordshire, OX1 3AN, UK
| | - Svenja Hester
- Department of Biochemistry, South Parks Road, University of Oxford, Oxfordshire, OX1 3QU, UK
| | - Qiong Zhang
- Department of Earth Sciences, South Parks Road, University of Oxford, Oxfordshire, OX1 3AN, UK
| | - Rosalind E M Rickaby
- Department of Earth Sciences, South Parks Road, University of Oxford, Oxfordshire, OX1 3AN, UK
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161
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Differential Resilience of Soil Microbes and Ecosystem Functions Following Cessation of Long-Term Fertilization. Ecosystems 2021. [DOI: 10.1007/s10021-021-00633-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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162
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Li S, Gang D, Zhao S, Qi W, Liu H. Response of ammonia oxidation activities to water-level fluctuations in riparian zones in a column experiment. CHEMOSPHERE 2021; 269:128702. [PMID: 33162161 DOI: 10.1016/j.chemosphere.2020.128702] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/29/2020] [Accepted: 10/19/2020] [Indexed: 06/11/2023]
Abstract
Biogeochemical hotspots of nitrogen cycling such as ammonia oxidation commonly occur in riparian ecosystems. However, the responses of ammonia-oxidizing archaea (AOA) and bacteria (AOB) to water-level fluctuations (WLF) in riparian zones remain unclear. In this study, two patterns of WLF (gradual waterlogging and drying) were investigated in a 9-month column experiment, and the abundances and activities of AOA and AOB were investigated. The recovery evaluation revealed AOB abundance had not returned to the initial level at the end of the experiment, while AOA abundance had recovered nearly completely. AOA outnumbered AOB at almost all depths, and AOA showed higher resistance and adaptation to WLF than AOB. However, higher microbial abundance was not always linked to the larger contribution to nitrification. Changes in environmental parameters such as moisture and dissolved oxygen caused by WLF instead of ammonia-oxidizing microorganism (AOM) abundance might play a key role in regulating the expression of amoA gene and thus the activity of ammonia oxidizers. In addition, the community structure of AOM evolved over the incubation period. The composition of AOA species in sediment changed in the same way as that in soil, and the Nitrosopumilus cluster showed strong resistance to WLF. Conversely, waterlogging changed the community structure of AOB in soil while drying had no significant effect on the AOB community structure in sediment. This study suggests that the ammonia oxidizers will respond to WLF and eventually affect N fate in riparian ecosystems considering the coupling with other N transformation processes.
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Affiliation(s)
- Siling Li
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, 100084, Beijing, China
| | - Diga Gang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Shuangju Zhao
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Weixiao Qi
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, 100084, Beijing, China; Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
| | - Huijuan Liu
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, 100084, Beijing, China; Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
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163
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Qian J, Jin W, Hu J, Wang P, Wang C, Lu B, Li K, He X, Tang S. Stable isotope analyses of nitrogen source and preference for ammonium versus nitrate of riparian plants during the plant growing season in Taihu Lake Basin. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 763:143029. [PMID: 33129526 DOI: 10.1016/j.scitotenv.2020.143029] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 10/10/2020] [Accepted: 10/10/2020] [Indexed: 05/22/2023]
Abstract
Plants are vital components of the nitrogen (N) cycling in the riparian zones. Understanding of N uptake strategies of riparian plants, including N sources and preference in N forms (ammonium (NH4+) vs. nitrate (NO3-)), is essential to advance our knowledge on the role that plants play in regulating nutrient biogeochemical cyclings in the riparian areas. In this study, stable N isotopes (δ15N) of three riparian plants, including Acorus calamus, Canna indica and Phragmites australis, and the δ15N of NH4+ and NO3- in different sources were measured during the plant growing season (June-September) in the Taihu Lake Basin. The dissolved inorganic N (DIN) from river water, groundwater, rainwater and soil were considered as the major N sources for plants in the riparian ecosystem. Our results indicated that soil was the largest source for plant N nutrition, with significantly different (P < 0.05) contributions from soil observed among plant species (80.5 ± 4.1, 73.9 ± 2.8 and 58.7 ± 6.1% for A. calamus, C. indica, and P. australis, respectively). Meanwhile, complex water networks, shallow water tables, and high DIN content in rainwater lead to nonignorable N contributions from river water, groundwater and rainwater to plants. Groundwater contributed more percentage of N to P. australis (12.8 ± 3.2%) than A. calamus (6.1 ± 1.9%) and C. indica (8.0 ± 1.5%), which is likely attributed to the deeper roots of P. australis. All plants showed similar N preference for NO3- during the growing season. External environmental conditions and plant characteristics and adaption to more abundant soil NO3- content are possible explanations. Our research could provide important information for vegetation selections during the process of riparian ecological restoration. Reasonable choice of vegetation is essential to plant growth and water quality management, especially in agricultural watersheds where N concentrations are relatively high in agricultural runoff due to the wide uses of N fertilizers.
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Affiliation(s)
- 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.
| | - 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
| | - Jing Hu
- Wetland Biogeochemistry Laboratory, Soil and Water Sciences Department, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Gainesville, FL, USA
| | - 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
| | - 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
| | - 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
| | - Sijing Tang
- 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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164
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Niche dimensions of a marine bacterium are identified using invasion studies in coastal seawater. Nat Microbiol 2021; 6:524-532. [PMID: 33495621 DOI: 10.1038/s41564-020-00851-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 12/11/2020] [Indexed: 01/29/2023]
Abstract
Niche theory is a foundational ecological concept that explains the distribution of species in natural environments. Identifying the dimensions of any organism's niche is challenging because numerous environmental factors can affect organism viability. We used serial invasion experiments to introduce Ruegeria pomeroyi DSS-3, a heterotrophic marine bacterium, into a coastal phytoplankton bloom on 14 dates. RNA-sequencing analysis of R. pomeroyi was conducted after 90 min to assess its niche dimensions in this dynamic ecosystem. We identified ~100 external conditions eliciting transcriptional responses, which included substrates, nutrients, metals and biotic interactions such as antagonism, resistance and cofactor synthesis. The peak bloom was characterized by favourable states for most of the substrate dimensions, but low inferred growth rates of R. pomeroyi at this stage indicated that its niche was narrowed by factors other than substrate availability, most probably negative biotic interactions with the bloom dinoflagellate. Our findings indicate chemical and biological features of the ocean environment that can constrain where heterotrophic bacteria survive.
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165
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Sakoula D, Koch H, Frank J, Jetten MSM, van Kessel MAHJ, Lücker S. Enrichment and physiological characterization of a novel comammox Nitrospira indicates ammonium inhibition of complete nitrification. THE ISME JOURNAL 2021; 15:1010-1024. [PMID: 33188298 PMCID: PMC8115096 DOI: 10.1038/s41396-020-00827-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 10/27/2020] [Accepted: 10/30/2020] [Indexed: 01/29/2023]
Abstract
The recent discovery of bacteria within the genus Nitrospira capable of complete ammonia oxidation (comammox) demonstrated that the sequential oxidation of ammonia to nitrate via nitrite can also be performed within a single bacterial cell. Although comammox Nitrospira exhibit a wide distribution in natural and engineered ecosystems, information on their physiological properties is scarce due to the limited number of cultured representatives. Additionally, most available genomic information is derived from metagenomic sequencing and high-quality genomes of Nitrospira in general are limited. In this study, we obtained a high (90%) enrichment of a novel comammox species, tentatively named "Candidatus Nitrospira kreftii", and performed a detailed genomic and physiological characterization. The complete genome of "Ca. N. kreftii" allowed reconstruction of its basic metabolic traits. Similar to Nitrospira inopinata, the enrichment culture exhibited a very high ammonia affinity (Km(app)_NH3 ≈ 0.040 ± 0.01 µM), but a higher nitrite affinity (Km(app)_NO2- = 12.5 ± 4.0 µM), indicating an adaptation to highly oligotrophic environments. Furthermore, we observed partial inhibition of ammonia oxidation at ammonium concentrations as low as 25 µM. This inhibition of "Ca. N. kreftii" indicates that differences in ammonium tolerance rather than affinity could potentially be a niche determining factor for different comammox Nitrospira.
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Affiliation(s)
- Dimitra Sakoula
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands ,grid.10420.370000 0001 2286 1424Present Address: Division of Microbial Ecology, Center for Microbiology and Environmental Systems Science, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Hanna Koch
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Jeroen Frank
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands ,grid.5590.90000000122931605Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Mike S. M. Jetten
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands ,grid.5590.90000000122931605Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Maartje A. H. J. van Kessel
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Sebastian Lücker
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
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166
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Bernhard AE, Beltz J, Giblin AE, Roberts BJ. Biogeography of ammonia oxidizers in New England and Gulf of Mexico salt marshes and the potential importance of comammox. ISME COMMUNICATIONS 2021; 1:9. [PMID: 36717686 PMCID: PMC9723745 DOI: 10.1038/s43705-021-00008-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 02/19/2021] [Accepted: 02/25/2021] [Indexed: 02/03/2023]
Abstract
Few studies have focused on broad scale biogeographic patterns of ammonia oxidizers in coastal systems, yet understanding the processes that govern them is paramount to understanding the mechanisms that drive biodiversity, and ultimately impact ecosystem processes. Here we present a meta-analysis of 16 years of data of ammonia oxidizer abundance, diversity, and activity in New England (NE) salt marshes and 5 years of data from marshes in the Gulf of Mexico (GoM). Potential nitrification rates were more than 80x higher in GoM compared to NE marshes. However, nitrifier abundances varied between regions, with ammonia-oxidizing archaea (AOA) and comammox bacteria significantly greater in GoM, while ammonia-oxidizing bacteria (AOB) were more than 20x higher in NE than GoM. Total bacterial 16S rRNA genes were also significantly greater in GoM marshes. Correlation analyses of rates and abundance suggest that AOA and comammox are more important in GoM marshes, whereas AOB are more important in NE marshes. Furthermore, ratios of nitrifiers to total bacteria in NE were as much as 80x higher than in the GoM, suggesting differences in the relative importance of nitrifiers between these systems. Communities of AOA and AOB were also significantly different between the two regions, based on amoA sequences and DNA fingerprints (terminal restriction fragment length polymorphism). Differences in rates and abundances may be due to differences in salinity, temperature, and N loading between the regions, and suggest significantly different N cycling dynamics in GoM and NE marshes that are likely driven by strong environmental differences between the regions.
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Affiliation(s)
- A E Bernhard
- Department of Biology, Connecticut College, New London, CT, USA.
| | - J Beltz
- Department of Biology, Connecticut College, New London, CT, USA
- School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - A E Giblin
- Ecosystems Center, Marine Biological Laboratory, Woods Hole, MA, USA
| | - B J Roberts
- Louisiana Universities Marine Consortium, Chauvin, LA, USA
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167
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Shafiee RT, Diver PJ, Snow JT, Zhang Q, Rickaby REM. Marine ammonia-oxidising archaea and bacteria occupy distinct iron and copper niches. ISME COMMUNICATIONS 2021; 1:1. [PMID: 37938628 PMCID: PMC9723733 DOI: 10.1038/s43705-021-00001-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/11/2020] [Accepted: 01/06/2021] [Indexed: 12/22/2022]
Abstract
Ammonia oxidation by archaea and bacteria (AOA and AOB), is the first step of nitrification in the oceans. As AOA have an ammonium affinity 200-fold higher than AOB isolates, the chemical niche allowing AOB to persist in the oligotrophic ocean remains unclear. Here we show that marine isolates, Nitrosopumilus maritimus strain SCM1 (AOA) and Nitrosococcus oceani strain C-107 (AOB) have contrasting physiologies in response to the trace metals iron (Fe) and copper (Cu), holding potential implications for their niche separation in the oceans. A greater affinity for unchelated Fe may allow AOB to inhabit shallower, euphotic waters where ammonium supply is high, but competition for Fe is rife. In contrast to AOB, AOA isolates have a greater affinity and toxicity threshold for unchelated Cu providing additional explanation to the greater success of AOA in the marine environment where Cu availability can be highly variable. Using comparative genomics, we predict that the proteomic and metal transport basis giving rise to contrasting physiologies in isolates is widespread across phylogenetically diverse marine AOA and AOB that are not yet available in pure culture. Our results develop the testable hypothesis that ammonia oxidation may be limited by Cu in large tracts of the open ocean and suggest a relatively earlier emergence of AOB than AOA when considered in the context of evolving trace metal availabilities over geologic time.
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Affiliation(s)
- Roxana T Shafiee
- Department of Earth Sciences, University of Oxford, Oxfordshire, UK.
| | - Poppy J Diver
- Department of Earth Sciences, University of Oxford, Oxfordshire, UK
| | - Joseph T Snow
- Department of Earth Sciences, University of Oxford, Oxfordshire, UK
| | - Qiong Zhang
- Department of Earth Sciences, University of Oxford, Oxfordshire, UK
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168
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Lui LM, Majumder ELW, Smith HJ, Carlson HK, von Netzer F, Fields MW, Stahl DA, Zhou J, Hazen TC, Baliga NS, Adams PD, Arkin AP. Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology. Front Microbiol 2021; 12:642422. [PMID: 33841364 PMCID: PMC8024649 DOI: 10.3389/fmicb.2021.642422] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
Over the last century, leaps in technology for imaging, sampling, detection, high-throughput sequencing, and -omics analyses have revolutionized microbial ecology to enable rapid acquisition of extensive datasets for microbial communities across the ever-increasing temporal and spatial scales. The present challenge is capitalizing on our enhanced abilities of observation and integrating diverse data types from different scales, resolutions, and disciplines to reach a causal and mechanistic understanding of how microbial communities transform and respond to perturbations in the environment. This type of causal and mechanistic understanding will make predictions of microbial community behavior more robust and actionable in addressing microbially mediated global problems. To discern drivers of microbial community assembly and function, we recognize the need for a conceptual, quantitative framework that connects measurements of genomic potential, the environment, and ecological and physical forces to rates of microbial growth at specific locations. We describe the Framework for Integrated, Conceptual, and Systematic Microbial Ecology (FICSME), an experimental design framework for conducting process-focused microbial ecology studies that incorporates biological, chemical, and physical drivers of a microbial system into a conceptual model. Through iterative cycles that advance our understanding of the coupling across scales and processes, we can reliably predict how perturbations to microbial systems impact ecosystem-scale processes or vice versa. We describe an approach and potential applications for using the FICSME to elucidate the mechanisms of globally important ecological and physical processes, toward attaining the goal of predicting the structure and function of microbial communities in chemically complex natural environments.
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Affiliation(s)
- Lauren M. Lui
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Erica L.-W. Majumder
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, United States
| | - Heidi J. Smith
- Center for Biofilm Engineering, Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Hans K. Carlson
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Frederick von Netzer
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
| | - Matthew W. Fields
- Center for Biofilm Engineering, Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - David A. Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology & Plant Biology, School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, United States
| | - Terry C. Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Knoxville, TN, United States
| | | | - Paul D. Adams
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
| | - Adam P. Arkin
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
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169
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Wang Y, Hu X, Sun Y, Wang C. Influence of the cold bottom water on taxonomic and functional composition and complexity of microbial communities in the southern Yellow Sea during the summer. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 759:143496. [PMID: 33248757 DOI: 10.1016/j.scitotenv.2020.143496] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/21/2020] [Accepted: 10/26/2020] [Indexed: 06/12/2023]
Abstract
The formation and presence of the cold bottom water (Yellow Sea Cold Water Mass, YSCWM) is a striking hydrological phenomenon in the southern Yellow Sea during the summer and has important effects on the marine ecosystem. To better understand its influence on microbial community structure and function, we compared the bacterial, archaeal and microeukaryotic communities in the cold water mass area (CWMA) and the southern area (SA) during the summer using amplicon and metagenomic sequencings. The habitat environment in the deep waters of the CWMA was characterized by higher salinity/DO/PO4-P, greater depth/distance to the coast, and lower levels of temperature/chlorophyll a/DIN/SiO3-Si/N:P ratio compared to that of the SA. Pure depth or distance to the coast explained a small portion of the microbial community variance, while environment explained a significant fraction of the variance when partialling the effects of depth and distance to the coast. Oligotrophic taxa (e.g. SAR11 clade Ia, Nitrosopumilus, Chloropicophyceae) dominated the deep water communities in the CWMA, while the common coastal taxa (e.g. Roseobacter strain HIMB11, Bacillariophyta, Noctilucophyceae) were more dominant in the deep waters of the SA, suggesting the great impact of the oligotrophic condition in the YSCWM on microbial communities. The microbial co-occurrence networks in the CWMA were less complex but contained a higher proportion of mutual exclusion relationship among prokaryotes; the prokaryotic α-diversity in the CWMA was significantly lower than in the SA while the microeukaryotic α-diversity was significantly higher in the CWMA, implying that prokaryotes and microeukaryotes respond to the cold water mass differently and the competition among prokaryotes was intensified under the impact of the YSCWM. Genes that relate to replication and repair accounted for a significantly lower proportion in the CWMA, which was likely an adaptation to the low carbon environment.
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Affiliation(s)
- Yibo Wang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoke Hu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yanyu Sun
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Caixia Wang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; University of Chinese Academy of Sciences, Beijing 100049, China
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170
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Baker KD, Kellogg CTE, McClelland JW, Dunton KH, Crump BC. The Genomic Capabilities of Microbial Communities Track Seasonal Variation in Environmental Conditions of Arctic Lagoons. Front Microbiol 2021; 12:601901. [PMID: 33643234 PMCID: PMC7906997 DOI: 10.3389/fmicb.2021.601901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/04/2021] [Indexed: 11/30/2022] Open
Abstract
In contrast to temperate systems, Arctic lagoons that span the Alaska Beaufort Sea coast face extreme seasonality. Nine months of ice cover up to ∼1.7 m thick is followed by a spring thaw that introduces an enormous pulse of freshwater, nutrients, and organic matter into these lagoons over a relatively brief 2–3 week period. Prokaryotic communities link these subsidies to lagoon food webs through nutrient uptake, heterotrophic production, and other biogeochemical processes, but little is known about how the genomic capabilities of these communities respond to seasonal variability. Replicate water samples from two lagoons and one coastal site near Kaktovik, AK were collected in April (full ice cover), June (ice break up), and August (open water) to represent winter, spring, and summer, respectively. Samples were size fractionated to distinguish free-living and particle-attached microbial communities. Multivariate analysis of metagenomes indicated that seasonal variability in gene abundances was greater than variability between size fractions and sites, and that June differed significantly from the other months. Spring (June) gene abundances reflected the high input of watershed-sourced nutrients and organic matter via spring thaw, featuring indicator genes for denitrification possibly linked to greater organic carbon availability, and genes for processing phytoplankton-derived organic matter associated with spring blooms. Summer featured fewer indicator genes, but had increased abundances of anoxygenic photosynthesis genes, possibly associated with elevated light availability. Winter (April) gene abundances suggested low energy inputs and autotrophic bacterial metabolism, featuring indicator genes for chemoautotrophic carbon fixation, methane metabolism, and nitrification. Winter indicator genes for nitrification belonged to Thaumarchaeota and Nitrosomonadales, suggesting these organisms play an important role in oxidizing ammonium during the under-ice period. This study shows that high latitude estuarine microbial assemblages shift metabolic capabilities as they change phylogenetic composition between these extreme seasons, providing evidence that these communities may be resilient to large hydrological events in a rapidly changing Arctic.
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Affiliation(s)
- Kristina D Baker
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | | | - James W McClelland
- The University of Texas at Austin Marine Science Institute, Port Aransas, TX, United States
| | - Kenneth H Dunton
- The University of Texas at Austin Marine Science Institute, Port Aransas, TX, United States
| | - Byron C Crump
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States
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171
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Relationships between nitrogen cycling microbial community abundance and composition reveal the indirect effect of soil pH on oak decline. THE ISME JOURNAL 2021; 15:623-635. [PMID: 33067585 PMCID: PMC8027100 DOI: 10.1038/s41396-020-00801-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 09/11/2020] [Accepted: 09/30/2020] [Indexed: 01/30/2023]
Abstract
Tree decline is a global concern and the primary cause is often unknown. Complex interactions between fluctuations in nitrogen (N) and acidifying compounds have been proposed as factors causing nutrient imbalances and decreasing stress tolerance of oak trees. Microorganisms are crucial in regulating soil N available to plants, yet little is known about the relationships between soil N-cycling and tree health. Here, we combined high-throughput sequencing and qPCR analysis of key nitrification and denitrification genes with soil chemical analyses to characterise ammonia-oxidising bacteria (AOB), archaea (AOA) and denitrifying communities in soils associated with symptomatic (declining) and asymptomatic (apparently healthy) oak trees (Quercus robur and Q. petraea) in the United Kingdom. Asymptomatic trees were associated with a higher abundance of AOB that is driven positively by soil pH. No relationship was found between AOA abundance and tree health. However, AOA abundance was driven by lower concentrations of NH4+, further supporting the idea of AOA favouring lower soil NH4+ concentrations. Denitrifier abundance was influenced primarily by soil C:N ratio, and correlations with AOB regardless of tree health. These findings indicate that amelioration of soil acidification by balancing C:N may affect AOB abundance driving N transformations, reducing stress on declining oak trees.
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172
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Bai J, Yu P, Wen X, Wang W, Jia J, Wang X. Effects of cadmium addition on net nitrogen mineralization processes in the urban constructed wetland soils of a Chinese delta. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2021; 43:1155-1164. [PMID: 32419088 DOI: 10.1007/s10653-020-00597-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 05/04/2020] [Indexed: 06/11/2023]
Abstract
Heavy metal pollution is a serious problem in wetland ecosystems, and the toxicity of heavy metals affects microorganisms, thus influencing the biogeochemical process of nitrogen (N). To investigate the effects of heavy metal cadmium (Cd) pollution on N mineralization in urban constructed wetland soils of the Pearl River Delta, a 40-day aerobic incubation experiment was conducted under three Cd addition treatments [no Cd addition (control), low Cd addition (LCA) and high Cd addition (HCA)]. The results showed that compared with the control, the LCA treatment enhanced the soil N mineralization rate (RM), while the HCA treatment inhibited RM, with the average RM values in the control treatment of 0.40 mg kg-1 day-1, LCA treatments (0.66 mg kg-1 day-1), and HCA treatments (0.21 mg kg-1 day-1). The average ammonification rate values in the LCA treatments (- 3.15 to 2.25 mg kg-1 day-1) were higher than those in the HCA treatments (- 2.39 to 0.74 mg kg-1 day-1) and the control treatment (- 0.68 to 0.90 mg kg-1 day-1) (P < 0.05). However, the nitrification values in the HCA treatments (- 0.37 to 3.36 mg kg-1 day-1) were higher than those in the LCA treatments (0.42-1.93 mg kg-1 day-1) and the control treatment (0.20-1.45 mg kg-1 day-1) (P < 0.05). The net N mineralization accumulation generally increased over the entire incubation time in different Cd addition treatments. The percentage of NH4+-N to total inorganic N showed a decrease, while an increase was observed for NO3--N over the incubation time. The urease activities were significantly inhibited in the LCA and HCA treatments and showed a "decreasing before increasing" trend. The abundance of ammonia oxidizing archaea (AOA) was higher in the two Cd addition treatments than the control treatment, and higher in the LCA treatments than in the HCA treatment. AOA was the dominant microorganism in the ammonia oxidation process of N mineralization in constructed wetland soils. The findings of this work indicate that Cd addition has a profound effect on the balance of N mineralization and may further impact the plant productivity and water quality of constructed wetlands.
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Affiliation(s)
- Junhong Bai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China.
| | - Peidong Yu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Xiaojun Wen
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Wei Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Jia Jia
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Xin Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, People's Republic of China
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173
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Zhou X, Wang A, Hobbie EA, Zhu F, Qu Y, Dai L, Li D, Liu X, Zhu W, Koba K, Li Y, Fang Y. Mature conifers assimilate nitrate as efficiently as ammonium from soils in four forest plantations. THE NEW PHYTOLOGIST 2021; 229:3184-3194. [PMID: 33226653 DOI: 10.1111/nph.17110] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 11/16/2020] [Indexed: 06/11/2023]
Abstract
Conifers are considered to prefer to take up ammonium (NH4+ ) over nitrate (NO3- ). However, this conclusion is mainly based on hydroponic experiments that separate roots from soils. It remains unclear to what extent mature conifers can use nitrate compared to ammonium under field conditions where both roots and soil microbes compete for nitrogen (N). We conducted an in situ whole mature tree nitrogen-15 (15 N) labeling experiment (15 NH4+ vs 15 NO3- ) over 15 d to quantify ammonium and nitrate uptake and assimilation rates in four 40-yr-old monoculture coniferous plantations (Pinus koraiensis, Pinus sylvestris, Picea koraiensis and Larix olgensis, respectively). For the whole tree, 15 NO3- contributed 39% to 90% to total 15 N tracer uptake among four plantations during the study period. At day 3, the 15 NO3- accounted for 77%, 64%, 62% and 59% by Larix olgensis, Pinus koraiensis, Pinus sylvestris and Picea koraiensis, respectively. Our study indicates that mature coniferous trees assimilated nitrate as efficiently as ammonium from soils even at low soil nitrate concentration, in contrast to the results from hydroponic experiments showing that ammonium uptake dominated over nitrate. This implies that mature conifers can adapt to increasing availability of nitrate in soil, for example, under the context of globalization of N deposition and global warming.
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Affiliation(s)
- Xulun Zhou
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, China
- School of Resources and Civil Engineering, Northeastern University, Shenyang, 110819, China
- Key Laboratory of Stable Isotope Techniques and Applications, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Ang Wang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, China
- Key Laboratory of Stable Isotope Techniques and Applications, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
- Qingyuan Forest CERN, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Erik A Hobbie
- Earth Systems Research Center, Morse Hall, University of New Hampshire, Durham, NH, 03824, USA
| | - Feifei Zhu
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, China
- Key Laboratory of Stable Isotope Techniques and Applications, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
- Qingyuan Forest CERN, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Yuying Qu
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, China
- Key Laboratory of Stable Isotope Techniques and Applications, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
- Qingyuan Forest CERN, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Luming Dai
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, China
- Qingyuan Forest CERN, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Dejun Li
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Xueyan Liu
- Insititute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China
| | - Weixing Zhu
- Department of Biological Sciences, Binghamton University, The State University of New York, Binghamton, NY, 13902, USA
| | - Keisuke Koba
- Center for Ecological Research, Kyoto University, Otsu, 520-2113, Japan
| | - Yinghua Li
- School of Resources and Civil Engineering, Northeastern University, Shenyang, 110819, China
| | - Yunting Fang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, China
- Key Laboratory of Stable Isotope Techniques and Applications, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
- Qingyuan Forest CERN, Chinese Academy of Sciences, Shenyang, 110016, China
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174
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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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175
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Semedo M, Lopes E, Baptista MS, Oller-Ruiz A, Gilabert J, Tomasino MP, Magalhães C. Depth Profile of Nitrifying Archaeal and Bacterial Communities in the Remote Oligotrophic Waters of the North Pacific. Front Microbiol 2021; 12:624071. [PMID: 33732221 PMCID: PMC7959781 DOI: 10.3389/fmicb.2021.624071] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/01/2021] [Indexed: 12/21/2022] Open
Abstract
Nitrification is a vital ecosystem function in the open ocean that regenerates inorganic nitrogen and promotes primary production. Recent studies have shown that the ecology and physiology of nitrifying organisms is more complex than previously postulated. The distribution of these organisms in the remote oligotrophic ocean and their interactions with the physicochemical environment are relatively understudied. In this work, we aimed to evaluate the depth profile of nitrifying archaea and bacteria in the Eastern North Pacific Subtropical Front, an area with limited biological surveys but with intense trophic transferences and physicochemical gradients. Furthermore, we investigated the dominant physicochemical and biological relationships within and between ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB) as well as with the overall prokaryotic community. We used a 16S rRNA gene sequencing approach to identify and characterize the nitrifying groups within the first 500 m of the water column and to analyze their abiotic and biotic interactions. The water column was characterized mainly by two contrasting environments, warm O2-rich surface waters with low dissolved inorganic nitrogen (DIN) and a cold O2-deficient mesopelagic layer with high concentrations of nitrate (NO3–). Thaumarcheotal AOA and bacterial NOB were highly abundant below the deep chlorophyll maximum (DCM) and in the mesopelagic. In the mesopelagic, AOA and NOB represented up to 25 and 3% of the total prokaryotic community, respectively. Interestingly, the AOA community in the mesopelagic was dominated by unclassified genera that may constitute a novel group of AOA highly adapted to the conditions observed at those depths. Several of these unclassified amplicon sequence variants (ASVs) were positively correlated with NO3– concentrations and negatively correlated with temperature and O2, whereas known thaumarcheotal genera exhibited the opposite behavior. Additionally, we found a large network of positive interactions within and between putative nitrifying ASVs and other prokaryotic groups, including 13230 significant correlations and 23 sub-communities of AOA, AOB, NOB, irrespective of their taxonomic classification. This study provides new insights into our understanding of the roles that AOA may play in recycling inorganic nitrogen in the oligotrophic ocean, with potential consequences to primary production in these remote ecosystems.
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Affiliation(s)
- Miguel Semedo
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
| | - Eva Lopes
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
| | - Mafalda S Baptista
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal.,Faculty of Sciences, University of Porto, Porto, Portugal.,International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| | - Ainhoa Oller-Ruiz
- Department of Chemical & Environmental Engineering, Universidad Politécnica de Cartagena (UPCT), Cartagena, Spain
| | - Javier Gilabert
- Department of Chemical & Environmental Engineering, Universidad Politécnica de Cartagena (UPCT), Cartagena, Spain
| | - Maria Paola Tomasino
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
| | - Catarina Magalhães
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal.,Faculty of Sciences, University of Porto, Porto, Portugal.,School of Science, Faculty of Science and Engineering, University of Waikato, Hamilton, New Zealand
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176
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Su Q, Schittich AR, Jensen MM, Ng H, Smets BF. Role of Ammonia Oxidation in Organic Micropollutant Transformation during Wastewater Treatment: Insights from Molecular, Cellular, and Community Level Observations. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:2173-2188. [PMID: 33543927 DOI: 10.1021/acs.est.0c06466] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Organic micropollutants (OMPs) are a threat to aquatic environments, and wastewater treatment plants may act as a source or a barrier of OMPs entering the environment. Understanding the fate of OMPs in wastewater treatment processes is needed to establish efficient OMP removal strategies. Enhanced OMP biotransformation has been documented during biological nitrogen removal and has been attributed to the cometabolic activity of ammonia-oxidizing bacteria (AOB) and, specifically, to the ammonia monooxygenase (AMO) enzyme. Yet, the exact mechanisms of OMP biotransformation are often unknown. This critical review aims to fundamentally and quantitatively evaluate the role of ammonia oxidation in OMP biotransformation during wastewater treatment processes. OMPs can be transformed by AOB via direct and indirect enzymatic reactions: AMO directly transforms OMPs primarily via hydroxylation, while biologically produced reactive nitrogen species (hydroxylamine (NH2OH), nitrite (NO2-), and nitric oxide (NO)) can chemically transform OMPs through nitration, hydroxylation, and deamination and can contribute significantly to the observed OMP transformations. OMPs containing alkyl, aliphatic hydroxyl, ether, and sulfide functional groups as well as substituted aromatic rings and aromatic primary amines can be biotransformed by AMO, while OMPs containing alkyl groups, phenols, secondary amines, and aromatic primary amines can undergo abiotic transformations mediated by reactive nitrogen species. Higher OMP biotransformation efficiencies and rates are obtained in AOB-dominant microbial communities, especially in autotrophic reactors performing nitrification or nitritation, than in non-AOB-dominant microbial communities. The biotransformations of OMPs in wastewater treatment systems can often be linked to ammonium (NH4+) removal following two central lines of evidence: (i) Similar transformation products (i.e., hydroxylated, nitrated, and desaminated TPs) are detected in wastewater treatment systems as in AOB pure cultures. (ii) Consistency in OMP biotransformation (rbio, μmol/g VSS/d) to NH4+ removal (rNH4+, mol/g VSS/d) rate ratios (rbio/rNH4+) is observed for individual OMPs across different systems with similar rNH4+ and AOB abundances. In this review, we conclude that AOB are the main drivers of OMP biotransformation during wastewater treatment processes. The importance of biologically driven abiotic OMP transformation is quantitatively assessed, and functional groups susceptible to transformations by AMO and reactive nitrogen species are systematically classified. This critical review will improve the prediction of OMP transformation and facilitate the design of efficient OMP removal strategies during wastewater treatment.
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Affiliation(s)
- Qingxian Su
- National University of Singapore Environmental Research Institute, 5A Engineering Drive 1, 117411 Singapore, Singapore
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs., Lyngby, Denmark
| | - Anna-Ricarda Schittich
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs., Lyngby, Denmark
| | - Marlene Mark Jensen
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs., Lyngby, Denmark
| | - Howyong Ng
- National University of Singapore Environmental Research Institute, 5A Engineering Drive 1, 117411 Singapore, Singapore
- Centre for Water Research, Department of Civil & Environmental Engineering, National University of Singapore, 1 Engineering Drive 2, 117576 Singapore, Singapore
| | - Barth F Smets
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs., Lyngby, Denmark
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177
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Production and Excretion of Polyamines To Tolerate High Ammonia, a Case Study on Soil Ammonia-Oxidizing Archaeon " Candidatus Nitrosocosmicus agrestis". mSystems 2021; 6:6/1/e01003-20. [PMID: 33594004 PMCID: PMC8573960 DOI: 10.1128/msystems.01003-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Ammonia tolerance is a universal characteristic among the ammonia-oxidizing bacteria (AOB); in contrast, the known species of ammonia-oxidizing archaea (AOA) have been regarded as ammonia sensitive, until the identification of the genus “Candidatus Nitrosocosmicus.” However, the mechanism of its ammonia tolerance has not been reported. In this study, the AOA species “Candidatus Nitrosocosmicus agrestis,” obtained from agricultural soil, was determined to be able to tolerate high concentrations of NH3 (>1,500 μM). In the genome of this strain, which was recovered from metagenomic data, a full set of genes for the pathways of polysaccharide metabolism, urea hydrolysis, arginine synthesis, and polyamine synthesis was identified. Among them, the genes encoding cytoplasmic carbonic anhydrase (CA) and a potential polyamine transporter (drug/metabolite exporter [DME]) were found to be unique to the genus “Ca. Nitrosocosmicus.” When “Ca. Nitrosocosmicus agrestis” was grown with high levels of ammonia, the genes that participate in CO2/HCO3− conversion, glutamate/glutamine syntheses, arginine synthesis, polyamine synthesis, and polyamine excretion were significantly upregulated, and the polyamines, including putrescine and spermidine, had significant levels of production. Based on genome analysis, gene expression quantification, and polyamine determination, we propose that the production and excretion of polyamines is probably one of the reasons for the ammonia tolerance of “Ca. Nitrosocosmicus agrestis,” and even of the genus “Ca. Nitrosocosmicus.” IMPORTANCE Ammonia tolerance of AOA is usually much lower than that of the AOB, which makes the AOB rather than AOA a predominant ammonia oxidizer in agricultural soils, contributing to global N2O emission. Recently, some AOA species from the genus “Ca. Nitrosocosmicus” were also found to have high ammonia tolerance. However, the reported mechanism for the ammonia tolerance is very rare and indeterminate for AOB and for AOA species. In this study, an ammonia-tolerant AOA strain of the species “Ca. Nitrosocosmicus agrestis” was identified and its potential mechanisms for ammonia tolerance were explored. This study will be of benefit for determining more of the ecological role of AOA in agricultural soils or other environments.
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178
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Shao YH, Wu JH. Comammox Nitrospira Species Dominate in an Efficient Partial Nitrification-Anammox Bioreactor for Treating Ammonium at Low Loadings. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:2087-2098. [PMID: 33440936 DOI: 10.1021/acs.est.0c05777] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Bacteria capable of complete ammonia oxidation (comammox) are widespread and contribute to nitrification in wastewater treatment facilities. However, their roles in partial nitrification-anaerobic ammonium oxidation (anammox) systems remain unclear. In this study, a bench-scale bioreactor with continuous stirring was operated for more than 1000 days with limited oxygen supply to achieve efficient nitrogen removal (70.1 ± 2.7%) at a low ammonium loading of 35.2 mg-N/L/day. High-throughput amplicon sequencing analysis of the comammox ammonia monooxygenase subunit A (amoA) gene revealed seven sequence types from two clusters in clade A of comammox Nitrospira. Quantitative polymerase chain reaction analyses suggested that the comammox species dominated the ammonia-oxidizing community, with an abundance as high as 89.2 ± 7.9% in total prokaryotic amoA copies. Multiple linear regression further revealed the substantial contribution of the comammox Nitrospira to ammonia oxidation in the bioreactor. The investigation with bioreactor and batch experiments consistently showed that activities of comammox Nitrospira were inhibited by free ammonia far more severely than other ammonia-oxidizing microbes. Overall, this study provided new insight into the ecology of comammox Nitrospira under hypoxic conditions and suggested comammox-associated partial nitrification-anammox as a potential method for treating low-strength ammonium-containing wastewater.
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Affiliation(s)
- Yung-Hsien Shao
- Department of Environmental Engineering, National Cheng Kung University, Tainan City 701, Taiwan
| | - Jer-Horng Wu
- Department of Environmental Engineering, National Cheng Kung University, Tainan City 701, Taiwan
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179
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Ward LM, Johnston DT, Shih PM. Phanerozoic radiation of ammonia oxidizing bacteria. Sci Rep 2021; 11:2070. [PMID: 33483596 PMCID: PMC7822890 DOI: 10.1038/s41598-021-81718-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/11/2021] [Indexed: 01/30/2023] Open
Abstract
The modern nitrogen cycle consists of a web of microbially mediated redox transformations. Among the most crucial reactions in this cycle is the oxidation of ammonia to nitrite, an obligately aerobic process performed by a limited number of lineages of bacteria (AOB) and archaea (AOA). As this process has an absolute requirement for O2, the timing of its evolution-especially as it relates to the Great Oxygenation Event ~ 2.3 billion years ago-remains contested and is pivotal to our understanding of nutrient cycles. To estimate the antiquity of bacterial ammonia oxidation, we performed phylogenetic and molecular clock analyses of AOB. Surprisingly, bacterial ammonia oxidation appears quite young, with crown group clades having originated during Neoproterozoic time (or later) with major radiations occurring during Paleozoic time. These results place the evolution of AOB broadly coincident with the pervasive oxygenation of the deep ocean. The late evolution AOB challenges earlier interpretations of the ancient nitrogen isotope record, predicts a more substantial role for AOA during Precambrian time, and may have implications for understanding of the size and structure of the biogeochemical nitrogen cycle through geologic time.
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Affiliation(s)
- L M Ward
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, USA.
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.
| | - D T Johnston
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, USA
| | - P M Shih
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
- Department of Energy, Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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180
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Convergent Evolution of a Promiscuous 3-Hydroxypropionyl-CoA Dehydratase/Crotonyl-CoA Hydratase in Crenarchaeota and Thaumarchaeota. mSphere 2021; 6:6/1/e01079-20. [PMID: 33472982 PMCID: PMC7845616 DOI: 10.1128/msphere.01079-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Inorganic carbon fixation is the most important biosynthetic process on Earth and the oldest type of metabolism. The autotrophic HP/HB cycle functions in Crenarchaea of the order Sulfolobales and in ammonia-oxidizing Archaea of the phylum Thaumarchaeota that are highly abundant in marine, terrestrial, and geothermal environments. The autotrophic 3-hydroxypropionate/4-hydroxybutyrate (HP/HB) cycle functions in thermoacidophilic, (micro)aerobic, hydrogen-oxidizing Crenarchaeota of the order Sulfolobales as well as in mesophilic, aerobic, ammonia-oxidizing Thaumarchaeota. Notably, the HP/HB cycle evolved independently in these two archaeal lineages, and crenarchaeal and thaumarchaeal versions differ regarding their enzyme properties and phylogeny. These differences result in altered energetic efficiencies between the variants. Compared to the crenarchaeal HP/HB cycle, the thaumarchaeal variant saves two ATP equivalents per turn, rendering it the most energy-efficient aerobic pathway for carbon fixation. Characteristically, the HP/HB cycle includes two enoyl coenzyme A (CoA) hydratase reactions: the 3-hydroxypropionyl-CoA dehydratase reaction and the crotonyl-CoA hydratase reaction. In this study, we show that both reactions are catalyzed in the aforementioned archaeal groups by a promiscuous 3-hydroxypropionyl-CoA dehydratase/crotonyl-CoA hydratase (Msed_2001 in crenarchaeon Metallosphaera sedula and Nmar_1308 in thaumarchaeon Nitrosopumilus maritimus). Although these two enzymes are homologous, they are closely related to bacterial enoyl-CoA hydratases and were retrieved independently from the same enzyme pool by the ancestors of Crenarchaeota and Thaumarchaeota, despite the existence of multiple alternatives. This striking similarity in the emergence of enzymes involved in inorganic carbon fixation from two independently evolved pathways highlights that convergent evolution of autotrophy could be much more widespread than anticipated. IMPORTANCE Inorganic carbon fixation is the most important biosynthetic process on Earth and the oldest type of metabolism. The autotrophic HP/HB cycle functions in Crenarchaeota of the order Sulfolobales and in ammonia-oxidizing Archaea of the phylum Thaumarchaeota that are highly abundant in marine, terrestrial, and geothermal environments. Bioinformatic prediction of the autotrophic potential of microorganisms or microbial communities requires identification of enzymes involved in autotrophy. However, many microorganisms possess several isoenzymes that may potentially catalyze the reactions of the cycle. Here, we studied the enzymes catalyzing 3-hydroxypropionyl-CoA dehydration and crotonyl-CoA hydration in Nitrosopumilus maritimus (Thaumarchaeota) as well as in Metallosphaera sedula (Crenarchaeota). We showed that both reactions were catalyzed by homologous promiscuous enzymes, which evolved independently from each other from their bacterial homologs. Furthermore, the HP/HB cycle is of applied value, and knowledge of its enzymes is necessary to transfer them to a heterologous host for synthesis of various value-added products.
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181
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Kaushal R, Lai CC, Shiah FK, Liang MC. Utilization of Δ 17O for nitrate dynamics in a subtropical freshwater reservoir. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 753:141836. [PMID: 32911164 DOI: 10.1016/j.scitotenv.2020.141836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 08/18/2020] [Accepted: 08/19/2020] [Indexed: 06/11/2023]
Abstract
Feitsui Reservoir, a freshwater body in Taiwan with minimal anthropogenic stress, meets the water demand for the population of more than five million living in Taipei city. In view of the biogeochemical processes controlling the long-term trophic status of this socio-economically and ecologically important aquatic system, probing the nitrogen cycle and its dynamics is essential. Here, we monitored the concentration and stable isotopic compositions (δ15N, δ18O, and Δ17O) of nitrate in the Feitsui Reservoir and in the atmospheric wet deposition at intervals of 1-2 weeks for a year, along with measurements of environmental data such as chlorophyll a, dissolved oxygen, and community respiration. Emphasis was laid on Δ17O (= δ17O - 0.52 × δ18O) because of the mass-conservative behavior of Δ17O during partial assimilation and denitrification. The present approach offered an effective method to quantify the gross nitrification and removal/uptake rates of nitrate in the reservoir. The atmospheric nitrate exhibited elevated Δ17O values ranging from 12.6‰ to 30.1‰ (23.3 ± 5.0‰), compared to the lower Δ17O values of ~0 to 4.6‰ (1.1 ± 0.7‰) recorded in the reservoir nitrate. Utilizing Δ17O for dissolved nitrates, we observed a seasonal trend of higher nitrification and removal rates during the summer than in the winter. Our estimates showed annually-averaged nitrification rate of 55 ± 11 mmol m-2 d-1 and removal/uptake rate of 57 ± 11 mmol m-2 d-1 (or a nitrate turnover time of ~2.5 months), representing the active nature of nitrogen cycling in this preserved subtropical reservoir.
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Affiliation(s)
- Ritika Kaushal
- Institute of Earth Sciences, Academia Sinica, Taipei, Taiwan
| | - Chao-Chen Lai
- Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan
| | - Fuh-Kwo Shiah
- Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan
| | - Mao-Chang Liang
- Institute of Earth Sciences, Academia Sinica, Taipei, Taiwan.
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182
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Roveto PM, Gupta A, Schuler AJ. Effects of surface skewness on local shear stresses, biofilm activity, and microbial communities for wastewater treatment. BIORESOURCE TECHNOLOGY 2021; 320:124251. [PMID: 33157445 DOI: 10.1016/j.biortech.2020.124251] [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: 08/13/2020] [Revised: 10/05/2020] [Accepted: 10/08/2020] [Indexed: 06/11/2023]
Abstract
This study's objective was to assess attachment surface skewness (asymmetric surface height variation) effects on biofilm development. 3D printed molds were used to create surfaces with 300 μm features to provide opposite skewness but identical roughness values. Surfaces with negative skewness had consistently greater nitrite oxidation and biomass growth than other surfaces during biofilm development when studied in annular bioreactor systems. CFD modelling predicted local shear stress differences that could explain experimental results. 16 s rRNA gene amplicon sequencing revealed population differences, including relatively high Acinetobacter and Terrimonas fractions on the negative skew surfaces, and PCoA analyses indicated the flat surface populations diverged from the skew surfaces by the study's end. The results suggest skewness is particularly important in systems where biofilms have not overgrown surface features, as in system startup, thin biofilms, and shorter time frame studies, which includes much previous microbial attachment research.
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Affiliation(s)
- Philip M Roveto
- University of New Mexico, 1 University Blvd, Albuquerque, NM 87131, United States.
| | - Adwaith Gupta
- Paanduv Applications, 124 Parwana Nagar, Bareilly, UP 243122, India.
| | - Andrew J Schuler
- University of New Mexico, 1 University Blvd, Albuquerque, NM 87131, United States.
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183
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Zhou Y, Suenaga T, Qi C, Riya S, Hosomi M, Terada A. Temperature and oxygen level determine N 2 O respiration activities of heterotrophic N 2 O-reducing bacteria: Biokinetic study. Biotechnol Bioeng 2020; 118:1330-1341. [PMID: 33305820 DOI: 10.1002/bit.27654] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/23/2020] [Accepted: 12/09/2020] [Indexed: 12/24/2022]
Abstract
Nitrous oxide (N2 O), a potent greenhouse gas, is reduced to N2 gas by N2 O-reducing bacteria (N2 ORB), a process which represents an N2 O sink in natural and engineered ecosystems. The N2 O sink activity by N2 ORB depends on temperature and O2 exposure, yet the specifics are not yet understood. This study explores the effects of temperature and oxygen exposure on biokinetics of pure culture N2 ORB. Four N2 ORB, representing either clade I type nosZ (Pseudomonas stutzeri JCM5965 and Paracoccus denitrificans NBRC102528) or clade II type nosZ (Azospira sp. strains I09 and I13), were individually tested. The higher activation energy for N2 O by Azospira sp. strain I13 (114.0 ± 22.6 kJ mol-1 ) compared with the other tested N2 ORB (38.3-60.1 kJ mol-1 ) indicates that N2 ORB can adapt to different temperatures. The O2 inhibition constants (KI ) of Azospira sp. strain I09 and Ps. stutzeri JCM5965 increased from 0.06 ± 0.05 and 0.05 ± 0.02 μmol L-1 to 0.92 ± 0.24 and 0.84 ± 0.31 μmol L-1 , respectively, as the temperature increased from 15°C to 35°C, while that of Azospira sp. strain I13 was temperature-independent (p = 0.106). Within the range of temperatures examined, Azospira sp. strain I13 had a faster recovery after O2 exposure compared with Azospira sp. strain I09 and Ps. stutzeri JCM5965 (p < 0.05). These results suggest that temperature and O2 exposure result in the growth of ecophysiologically distinct N2 ORB as N2 O sinks. This knowledge can help develop a suitable N2 O mitigation strategy according to the physiologies of the predominant N2 ORB.
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Affiliation(s)
- Yiwen Zhou
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Toshikazu Suenaga
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Chuang Qi
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan.,School of Environment, Nanjing Normal University, Nanjing, China
| | - Shohei Riya
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Masaaki Hosomi
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Akihiko Terada
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan.,Global Innovation Research Institute, Tokyo University of Agriculture and Technology, Tokyo, Japan
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184
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Vitamin B 12-dependent biosynthesis ties amplified 2-methylhopanoid production during oceanic anoxic events to nitrification. Proc Natl Acad Sci U S A 2020; 117:32996-33004. [PMID: 33318211 DOI: 10.1073/pnas.2012357117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Bacterial hopanoid lipids are ubiquitous in the geologic record and serve as biomarkers for reconstructing Earth's climatic and biogeochemical evolution. Specifically, the abundance of 2-methylhopanoids deposited during Mesozoic ocean anoxic events (OAEs) and other intervals has been interpreted to reflect proliferation of nitrogen-fixing marine cyanobacteria. However, there currently is no conclusive evidence for 2-methylhopanoid production by extant marine cyanobacteria. As an alternative explanation, here we report 2-methylhopanoid production by bacteria of the genus Nitrobacter, cosmopolitan nitrite oxidizers that inhabit nutrient-rich freshwater, brackish, and marine environments. The model organism Nitrobacter vulgaris produced only trace amounts of 2-methylhopanoids when grown in minimal medium or with added methionine, the presumed biosynthetic methyl donor. Supplementation of cultures with cobalamin (vitamin B12) increased nitrite oxidation rates and stimulated a 33-fold increase of 2-methylhopanoid abundance, indicating that the biosynthetic reaction mechanism is cobalamin dependent. Because Nitrobacter spp. cannot synthesize cobalamin, we postulate that they acquire it from organisms inhabiting a shared ecological niche-for example, ammonia-oxidizing archaea. We propose that during nutrient-rich conditions, cobalamin-based mutualism intensifies upper water column nitrification, thus promoting 2-methylhopanoid deposition. In contrast, anoxia underlying oligotrophic surface ocean conditions in restricted basins would prompt shoaling of anaerobic ammonium oxidation, leading to low observed 2-methylhopanoid abundances. The first scenario is consistent with hypotheses of enhanced nutrient loading during OAEs, while the second is consistent with the sedimentary record of Pliocene-Pleistocene Mediterranean sapropel events. We thus hypothesize that nitrogen cycling in the Pliocene-Pleistocene Mediterranean resembled modern, highly stratified basins, whereas no modern analog exists for OAEs.
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185
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Wang C, Wu R, Song Y, Guo J, Liu R, Cui Y. Differences in nitrification and ammonium-oxidising prokaryotes in the process of wetland restoration. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2020; 56:136-144. [PMID: 33259261 DOI: 10.1080/10934529.2020.1852845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 11/06/2020] [Accepted: 11/12/2020] [Indexed: 06/12/2023]
Abstract
Ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB) are ammonium oxidising prokaryotes that can drive soil nitrification in wetlands. During the restoration of wetlands, different types of land use soils (agricultural soil [AS], restored wetland soil [RS], and natural wetland soil [NWS]) are present. However, studies on the effects of changes in the types of land use in wetlands during restoration on nitrification and the community composition of AOA and AOB are still not well understood. In this study, the differences in the potential nitrification rate (PNR) and community composition of AOA and AOB in AS, RS, and NWS were compared and discussed. The results indicated that the PNRs in the AS, RS, and NWS were on the same order of magnitude. Nitrification was mainly driven by AOB. High-throughput sequencing results showed that the genus Nitrososphaera of AOA and unclassified_o_Nitrosomonadales of AOB were only detected in the AS. Redundancy analysis (RDA) results indicated that the community composition of AOA was mostly influenced by pH, while TC was the most influential variable on the community composition of AOB. Our study provides a basis for distinguishing the roles of ammonium-oxidising prokaryotes in nitrification and further understanding the changes in nitrifying activity in wetlands during restoration.
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Affiliation(s)
- Chunyong Wang
- School of Chemical and Environmental Engineering, Liaoning University of Technology, Jinzhou, PR China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, PR China
| | - Rui Wu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, PR China
| | - Yi Song
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, PR China
| | - Jianbo Guo
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, PR China
| | - Ruyin Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, PR China
| | - Yanshan Cui
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, PR China
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186
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Séneca J, Pjevac P, Canarini A, Herbold CW, Zioutis C, Dietrich M, Simon E, Prommer J, Bahn M, Pötsch EM, Wagner M, Wanek W, Richter A. Composition and activity of nitrifier communities in soil are unresponsive to elevated temperature and CO 2, but strongly affected by drought. THE ISME JOURNAL 2020; 14:3038-3053. [PMID: 32770119 PMCID: PMC7784676 DOI: 10.1038/s41396-020-00735-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 07/21/2020] [Accepted: 07/30/2020] [Indexed: 11/23/2022]
Abstract
Nitrification is a fundamental process in terrestrial nitrogen cycling. However, detailed information on how climate change affects the structure of nitrifier communities is lacking, specifically from experiments in which multiple climate change factors are manipulated simultaneously. Consequently, our ability to predict how soil nitrogen (N) cycling will change in a future climate is limited. We conducted a field experiment in a managed grassland and simultaneously tested the effects of elevated atmospheric CO2, temperature, and drought on the abundance of active ammonia-oxidizing bacteria (AOB) and archaea (AOA), comammox (CMX) Nitrospira, and nitrite-oxidizing bacteria (NOB), and on gross mineralization and nitrification rates. We found that N transformation processes, as well as gene and transcript abundances, and nitrifier community composition were remarkably resistant to individual and interactive effects of elevated CO2 and temperature. During drought however, process rates were increased or at least maintained. At the same time, the abundance of active AOB increased probably due to higher NH4+ availability. Both, AOA and comammox Nitrospira decreased in response to drought and the active community composition of AOA and NOB was also significantly affected. In summary, our findings suggest that warming and elevated CO2 have only minor effects on nitrifier communities and soil biogeochemical variables in managed grasslands, whereas drought favors AOB and increases nitrification rates. This highlights the overriding importance of drought as a global change driver impacting on soil microbial community structure and its consequences for N cycling.
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Affiliation(s)
- Joana Séneca
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Petra Pjevac
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
| | - Alberto Canarini
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
| | - Craig W Herbold
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Christos Zioutis
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Marlies Dietrich
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Eva Simon
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Judith Prommer
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Michael Bahn
- Department of Ecology, University of Innsbruck, 6020, Innsbruck, Austria
| | - Erich M Pötsch
- Agricultural Research and Education Centre Raumberg-Gumpenstein, Altirdning 11, 8952, Irdning, Austria
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Wolfgang Wanek
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
- International Institute for Applied Systems Analysis, Laxenburg, Austria.
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187
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Monthly distribution of ammonia-oxidizing microbes in a tropical bay. J Microbiol 2020; 59:10-19. [PMID: 33201437 DOI: 10.1007/s12275-021-0287-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 09/28/2020] [Accepted: 09/28/2020] [Indexed: 10/23/2022]
Abstract
Ammonia oxidation, performed by ammonia-oxidizing archaea (AOA) and bacteria (AOB), plays a critical role in the cycle of nitrogen in the ocean. For now, environmental variables controlling distribution of ammonia-oxidizing microbes are still largely unknown in oceanic environments. In this study, we used real-time quantitative PCR and high-throughput sequencing methods to investigate the abundance and diversity of AOA and AOB from sediment and water in Zhanjiang Bay. Phylogenic analysis revealed that the majority of AOA amoA sequences in water and sediment were affiliated with the genus Nitrosopumilus, whereas the Nitrosotalea cluster was only detected with low abundance in water. Nitrosomonas and Nitrosospira dominated AOB amoA sequences in water and sediment, respectively. The amoA copy numbers of both AOA and AOB varied significantly with month for both sediment and water. When water and sediment temperature dropped to 17-20°C in December and February, respectively, the copy number of AOB amoA genes increased markedly and was much higher than for AOA amoA genes. Also, AOA abundance in water peaked in December when water temperature was lowest (17-20°C). Stepwise multiple regression analyses revealed that temperature was the most key factor driving monthly changes of AOA or AOB abundance. It is inferred that low water temperature may inhibit growth of phytoplankton and other microbes and so reduce competition for a common substrate, ammonium.
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188
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Rui M, Chen H, Ye Y, Deng H, Wang H. Effect of Flow Configuration on Nitrifiers in Biological Activated Carbon Filters for Potable Water Production. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:14646-14655. [PMID: 33118354 DOI: 10.1021/acs.est.0c02479] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Up-flow biological activated carbon (BAC) filters have been empirically employed in drinking water treatment plants (DWTPs) to address the challenges of its down-flow counterparts (e.g., high head loss and insufficient use of BAC beds), yet their performances and mechanisms toward ammonia removal are not fully evaluated. This study characterized the occurrence, distribution, and diversities of nitrifiers in up-flow and down-flow BAC filters by investigating 18 full-scale drinking water treatment trains in different geographic locations. Quantitative polymerase chain reaction analysis of gene markers of target microorganisms demonstrated higher numbers of total bacteria, ammonia-oxidizing bacteria (AOB), and Nitrospira in the up-flow filters relative to the down-flow filters (P < 0.05), implying enhanced biological activities and nitrification potential within up-flow filters. The dominance of ammonia-oxidizing archaea (AOA) over AOB (i.e., 1.3-4.0 log10 gene copies higher) in 17 BAC filters illustrated the critical role of AOA in drinking water nitrification. Stratification of biomass was mainly found in the down-flow filters rather than the up-flow filters, suggesting better mixing of filter media across up-flow filter beds. Analysis of similarity results revealed that the AOA and Nitrospira community compositions were mainly affected by water sources and locations (P < 0.05) but not flow configurations. These results provide insight into nitrification mechanisms in BAC filters with different flow configurations in real-world DWTPs.
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Affiliation(s)
- Min Rui
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
- Shanghai Municipal Engineering Design Institute (Group) Co., Ltd., Shanghai 200092, China
| | - Haoshen Chen
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
- Shanghai Municipal Engineering Design Institute (Group) Co., Ltd., Shanghai 200092, China
| | - Yinyin Ye
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
- Department of Civil, Structural and Environmental Engineering, University at Buffalo, Buffalo, New York 14260, United States
| | - Huiping Deng
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, P.R. China
| | - Hong Wang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, P.R. China
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189
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Liang D, Ouyang Y, Tiemann L, Robertson GP. Niche Differentiation of Bacterial Versus Archaeal Soil Nitrifiers Induced by Ammonium Inhibition Along a Management Gradient. Front Microbiol 2020; 11:568588. [PMID: 33281763 PMCID: PMC7689314 DOI: 10.3389/fmicb.2020.568588] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 10/12/2020] [Indexed: 01/08/2023] Open
Abstract
Soil nitrification, mediated mainly by ammonia oxidizing archaea (AOA) and bacteria (AOB), converts ammonium (NH4+) to nitrite (NO2−) and thence nitrate (NO3−). To better understand ecological differences between AOA and AOB, we investigated the nitrification kinetics of AOA and AOB under eight replicated cropped and unmanaged ecosystems (including two fertilized natural systems) along a long-term management intensity gradient in the upper U.S. Midwest. For five of eight ecosystems, AOB but not AOA exhibited Haldane kinetics (inhibited by high NH4+ additions), especially in perennial and successional systems. In contrast, AOA predominantly exhibited Michaelis-Menten kinetics, suggesting greater resistance to high nitrogen inputs than AOB. These responses suggest the potential for NH4+-induced niche differentiation between AOA and AOB. Additionally, long-term fertilization significantly enhanced maximum nitrification rates (Vmax) in the early successional systems for both AOA and AOB, but not in the deciduous forest systems. This was likely due to pH suppression of nitrification in the acidic forest soils, corroborated by a positive correlation of Vmax with soil pH but not with amoA gene abundance. Results also demonstrated that soil nitrification potentials were relatively stable, as there were no seasonal differences. Overall, results suggest that (1) NH4+ inhibition of AOB but not AOA could be another factor contributing to niche differentiation between AOA and AOB in soil, and (2) nitrification by both AOA and AOB can be significantly promoted by long-term nitrogen inputs.
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Affiliation(s)
- Di Liang
- Department of Plant, Soil and Microbial Sciences and Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, United States.,W. K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, United States
| | - Yang Ouyang
- Department of Plant, Soil and Microbial Sciences and Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, United States
| | - Lisa Tiemann
- Department of Plant, Soil and Microbial Sciences and Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, United States
| | - G Philip Robertson
- Department of Plant, Soil and Microbial Sciences and Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, United States.,W. K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, United States
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190
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Xia WW, Zhao J, Zheng Y, Zhang HM, Zhang JB, Chen RR, Lin XG, Jia ZJ. Active Soil Nitrifying Communities Revealed by In Situ Transcriptomics and Microcosm-Based Stable-Isotope Probing. Appl Environ Microbiol 2020; 86:e01807-20. [PMID: 32978127 PMCID: PMC7657639 DOI: 10.1128/aem.01807-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/17/2020] [Indexed: 01/19/2023] Open
Abstract
Long-term nitrogen field fertilization often results in significant changes in nitrifying communities that catalyze a key step in the global N cycle. However, whether microcosm studies are able to inform the dynamic changes in communities of ammonia-oxidizing bacteria (AOB) and archaea (AOA) under field conditions remains poorly understood. This study aimed to evaluate the transcriptional activities of nitrifying communities under in situ conditions, and we found that they were largely similar to those of 13C-labeled nitrifying communities in the urea-amended microcosms of soils that had received different N fertilization regimens for 22 years. High-throughput sequencing of 16S rRNA genes and transcripts suggested that Nitrosospira cluster 3-like AOB and Nitrososphaera viennensis-like AOA were significantly stimulated in N-fertilized fresh soils. Real-time quantitative PCR demonstrated that the significant increase of AOA and AOB in fresh soils upon nitrogen fertilization could be preserved in the air-dried soils. DNA-based stable-isotope probing (SIP) further revealed the greatest labeling of Nitrosospira cluster 3-like AOB and Nitrosospira viennensis-like AOA, despite the strong advantage of AOB over AOA in the N-fertilized soils. Nitrobacter-like nitrite-oxidizing bacteria (NOB) played more important roles than Nitrospira-like NOB in urea-amended SIP microcosms, while the situation was the opposite under field conditions. Our results suggest that long-term fertilization selected for physiologically versatile AOB and AOA that could have been adapted to a wide range of substrate ammonium concentrations. It also provides compelling evidence that the dominant communities of transcriptionally active nitrifiers under field conditions were largely similar to those revealed in 13C-labeled microcosms.IMPORTANCE The role of manipulated microcosms in microbial ecology has been much debated, because they cannot entirely represent the in situ situation. We collected soil samples from 20 field plots, including 5 different treatments with and without nitrogen fertilizers for 22 years, in order to assess active nitrifying communities by in situ transcriptomics and microcosm-based stable-isotope probing. The results showed that chronic N enrichment led to competitive advantages of Nitrosospira cluster 3-like AOB over N. viennensis-like AOA in soils under field conditions. Microcosm labeling revealed similar results for active AOA and AOB, although an apparent discrepancy was observed for nitrite-oxidizing bacteria. This study suggests that the soil microbiome represents a relatively stable community resulting from complex evolutionary processes over a large time scale, and microcosms can serve as powerful tools to test the theory of environmental filtering on the key functional microbial guilds.
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Affiliation(s)
- Wei-Wei Xia
- Jiangsu Key Laboratory of Agricultural Meteorology, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jun Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yan Zheng
- School of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou, China
| | - Hui-Min Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jia-Bao Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Rui-Rui Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Xian-Gui Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Zhong-Jun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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191
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Cardarelli EL, Bargar JR, Francis CA. Diverse Thaumarchaeota Dominate Subsurface Ammonia-oxidizing Communities in Semi-arid Floodplains in the Western United States. MICROBIAL ECOLOGY 2020; 80:778-792. [PMID: 32535638 DOI: 10.1007/s00248-020-01534-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 05/29/2020] [Indexed: 06/11/2023]
Abstract
Subsurface microbial communities mediate biogeochemical transformations that drive both local and ecosystem-level cycling of essential elements, including nitrogen. However, their study has been largely limited to the deep ocean, terrestrial mines, caves, and topsoils (< 30 cm). Here, we present regional insights into the microbial ecology of aerobic ammonia oxidation within the terrestrial subsurface of five semi-arid riparian sites spanning a 900-km N-S transect. We sampled sediments, profiled communities to depths of ≤ 10 m, and compared them to reveal trends regionally within and surrounding the Upper Colorado River Basin (CRB). The diversity and abundance of ammonia-oxidizing microbial communities were evaluated in the context of subsurface geochemistry by applying a combination of amoA (encoding ammonia monooxygenase subunit A) gene sequencing, quantitative PCR, and geochemical techniques. Analysis of 898 amoA sequences from ammonia-oxidizing archaea (AOA) and bacteria (AOB) revealed extensive ecosystem-scale diversity, including archaeal amoA sequences from four of the five major AOA lineages currently found worldwide as well as distinct AOA ecotypes associated with naturally reduced zones (NRZs) and hydrogeochemical zones (unsaturated, capillary fringe, and saturated). Overall, AOA outnumber AOB by 2- to 5000-fold over this regional scale, suggesting that AOA may play a prominent biogeochemical role in nitrification within terrestrial subsurface sediments.
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Affiliation(s)
- Emily L Cardarelli
- Department of Earth System Science, Stanford University, Stanford, CA, 94305-4216, USA
| | - John R Bargar
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Christopher A Francis
- Department of Earth System Science, Stanford University, Stanford, CA, 94305-4216, USA.
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192
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Islam W, Noman A, Naveed H, Huang Z, Chen HYH. Role of environmental factors in shaping the soil microbiome. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:41225-41247. [PMID: 32829437 DOI: 10.1007/s11356-020-10471-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 08/10/2020] [Indexed: 05/09/2023]
Abstract
The soil microbiome comprises one of the most important and complex components of all terrestrial ecosystems as it harbors millions of microbes including bacteria, fungi, archaea, viruses, and protozoa. Together, these microbes and environmental factors contribute to shaping the soil microbiome, both spatially and temporally. Recent advances in genomic and metagenomic analyses have enabled a more comprehensive elucidation of the soil microbiome. However, most studies have described major modulators such as fungi and bacteria while overlooking other soil microbes. This review encompasses all known microbes that may exist in a particular soil microbiome by describing their occurrence, abundance, diversity, distribution, communication, and functions. Finally, we examined the role of several abiotic factors involved in the shaping of the soil microbiome.
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Affiliation(s)
- Waqar Islam
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, 350007, China
- Institute of Geography, Fujian Normal University, Fuzhou, 350007, China
- Faculty of Natural Resources Management, Lakehead University, 955 Oliver Rd, Thunder Bay, ON, P7B 5E1, Canada
| | - Ali Noman
- Department of Botany, Government College University, Faisalabad, 38000, Pakistan
| | - Hassan Naveed
- College of Life Science, Leshan Normal University, Leshan, 614004, Sichuan, China
| | - Zhiqun Huang
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, 350007, China.
- Institute of Geography, Fujian Normal University, Fuzhou, 350007, China.
| | - Han Y H Chen
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, 350007, China.
- Institute of Geography, Fujian Normal University, Fuzhou, 350007, China.
- Faculty of Natural Resources Management, Lakehead University, 955 Oliver Rd, Thunder Bay, ON, P7B 5E1, Canada.
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193
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Poghosyan L, Koch H, Frank J, van Kessel MAHJ, Cremers G, van Alen T, Jetten MSM, Op den Camp HJM, Lücker S. Metagenomic profiling of ammonia- and methane-oxidizing microorganisms in two sequential rapid sand filters. WATER RESEARCH 2020; 185:116288. [PMID: 32810745 DOI: 10.1016/j.watres.2020.116288] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/17/2020] [Accepted: 08/09/2020] [Indexed: 05/22/2023]
Abstract
Elevated concentrations of ammonium and methane in groundwater are often associated with microbiological, chemical and sanitary problems during drinking water production and distribution. To avoid their accumulation, raw water in the Netherlands and many other countries is purified by sand filtration. These drinking water filtration systems select for microbial communities that mediate the biodegradation of organic and inorganic compounds. In this study, the top layers and wall biofilm of a Dutch drinking water treatment plant (DWTP) were sampled from the filtration units of the plant over three years. We used high-throughput sequencing in combination with differential coverage and sequence composition-based binning to recover 56 near-complete metagenome-assembled genomes (MAGs) with an estimated completion of ≥70% and with ≤10% redundancy. These MAGs were used to characterize the microbial communities involved in the conversion of ammonia and methane. The methanotrophic microbial communities colonizing the wall biofilm (WB) and the granular material of the primary rapid sand filter (P-RSF) were dominated by members of the Methylococcaceae and Methylophilaceae. The abundance of these bacteria drastically decreased in the secondary rapid sand filter (S-RSF) samples. In all samples, complete ammonia-oxidizing (comammox) Nitrospira were the most abundant nitrifying guild. Clade A comammox Nitrospira dominated the P-RSF, while clade B was most abundant in WB and S-RSF, where ammonium concentrations were much lower. In conclusion, the knowledge obtained in this study contributes to understanding the role of microorganisms in the removal of carbon and nitrogen compounds during drinking water production. We furthermore found that drinking water treatment plants represent valuable model systems to study microbial community function and interaction.
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Affiliation(s)
- Lianna Poghosyan
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen 6525AJ, the Netherlands
| | - Hanna Koch
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen 6525AJ, the Netherlands
| | - Jeroen Frank
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen 6525AJ, the Netherlands
| | - Maartje A H J van Kessel
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen 6525AJ, the Netherlands
| | - Geert Cremers
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen 6525AJ, the Netherlands
| | - Theo van Alen
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen 6525AJ, the Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen 6525AJ, the Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen 6525AJ, the Netherlands
| | - Sebastian Lücker
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen 6525AJ, the Netherlands.
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194
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Deep amoA amplicon sequencing reveals community partitioning within ammonia-oxidizing bacteria in the environmentally dynamic estuary of the River Elbe. Sci Rep 2020; 10:17165. [PMID: 33051504 PMCID: PMC7555866 DOI: 10.1038/s41598-020-74163-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/24/2020] [Indexed: 11/25/2022] Open
Abstract
The community composition of betaproteobacterial ammonia-oxidizing bacteria (ß-AOB) in the River Elbe Estuary was investigated by high throughput sequencing of ammonia monooxygenase subunit A gene (amoA) amplicons. In the course of the seasons surface sediment samples from seven sites along the longitudinal profile of the upper Estuary of the Elbe were investigated. We observed striking shifts of the ß-AOB community composition according to space and time. Members of the Nitrosomonas oligotropha-lineage and the genus Nitrosospira were found to be the dominant ß-AOB within the river transect, investigated. However, continuous shifts of balance between members of both lineages along the longitudinal profile were determined. A noticeable feature was a substantial increase of proportion of Nitrosospira-like sequences in autumn and of sequences affiliated with the Nitrosomonas marina-lineage at downstream sites in spring and summer. Slightly raised relative abundances of sequences affiliated with the Nitrosomonas europaea/Nitrosomonas mobilis-lineage and the Nitrosomonas communis-lineage were found at sampling sites located in the port of Hamburg. Comparisons between environmental parameters and AOB-lineage (ecotype) composition revealed promising clues that processes happening in the fluvial to marine transition zone of the Elbe estuary are reflected by shifts in the relative proportion of ammonia monooxygenase sequence abundance, and hence, we propose ß-AOB as appropriate indicators for environmental dynamics and the ecological condition of the Elbe Estuary.
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195
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Stahl DA. The path leading to the discovery of the ammoniaoxidizing archaea. Environ Microbiol 2020; 22:4507-4519. [PMID: 32955155 DOI: 10.1111/1462-2920.15239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 11/28/2022]
Affiliation(s)
- David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, 98195, USA
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196
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Sun D, Tang X, Zhao M, Zhang Z, Hou L, Liu M, Wang B, Klümper U, Han P. Distribution and Diversity of Comammox Nitrospira in Coastal Wetlands of China. Front Microbiol 2020; 11:589268. [PMID: 33123118 PMCID: PMC7573150 DOI: 10.3389/fmicb.2020.589268] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/15/2020] [Indexed: 12/17/2022] Open
Abstract
Complete ammonia oxidizers (comammox), able to individually oxidize ammonia to nitrate, are considered to play a significant role in the global nitrogen cycle. However, the distribution of comammox Nitrospira in estuarine tidal flat wetland and the environmental drivers affecting their abundance and diversity remain unknown. Here, we present a large-scale investigation on the geographical distribution of comammox Nitrospira along the estuarine tidal flat wetlands of China, where comammox Nitrospira were successfully detected in 9 of the 16 sampling sites. The abundance of comammox Nitrospira ranged from 4.15 × 105 to 6.67 × 106 copies/g, 2.21- to 5.44-folds lower than canonical ammonia oxidizers: ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Phylogenetic analysis based on the alpha subunit of the ammonia monooxygenase encoding gene (amoA) revealed that comammox Nitrospira Clade A, mainly originating from upstream river inputs, accounts for more than 80% of the detected comammox Nitrospira, whereas comammox Nitrospira clade B were rarely detected. Comammox Nitrospira abundance and dominant comammox Nitrospira OTUs varied within the estuarine samples, showing a geographical pattern. Salinity and pH were the most important environmental drivers affecting the distribution of comammox Nitrospira in estuarine tidal flat wetlands. The abundance of comammox Nitrospira was further negatively correlated with high ammonia and nitrite concentrations. Altogether, this study revealed the existence, abundance and distribution of comammox Nitrospira and the driving environmental factors in estuarine ecosystems, thus providing insights into the ecological niches of this recently discovered nitrifying consortium and their contributions to nitrification in global estuarine environments.
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Affiliation(s)
- Dongyao Sun
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, Shanghai, China
| | - Xiufeng Tang
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, Shanghai, China
| | - Mengyue Zhao
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, Shanghai, China
| | - Zongxiao Zhang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Min Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, Shanghai, China.,Institute of Eco-Chongming, East China Normal University, Shanghai, China
| | - Baozhan Wang
- Key Laboratory of Microbiology for Agricultural Environment (Ministry of Agriculture), College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Uli Klümper
- Institute for Hydrobiology, Technische Universität Dresden, Dresden, Germany
| | - Ping Han
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, Shanghai, China.,State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China.,Institute of Eco-Chongming, East China Normal University, Shanghai, China
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197
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Tang S, Liao Y, Xu Y, Dang Z, Zhu X, Ji G. Microbial coupling mechanisms of nitrogen removal in constructed wetlands: A review. BIORESOURCE TECHNOLOGY 2020; 314:123759. [PMID: 32654809 DOI: 10.1016/j.biortech.2020.123759] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 06/11/2023]
Abstract
Nitrogen removal through microorganisms is the most important pathway in constructed wetlands (CWs). In this review, we summarize the microbial coupling mechanisms of nitrogen removal, which are the common methods of nitrogen transformation. The electron pathways are shortened and consumption of oxygen and energy is reduced during the coupling of nitrogen transformation functional microorganisms. The highly efficient nitrogen removal mechanisms are cultivated from the design conditions in CWs, such as intermittent aeration and tidal flow. The coupling of microorganisms and substrates enhances nitrogen removal mainly by supplying electrons, and plants affect nitrogen transformation functional microorganisms by the release of oxygen and exudates from root systems as well as providing carriers for microbial attachment. In addition, inorganic elements such as Fe, S and H act as electron donors to drive the autotrophic denitrification process in CWs.
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Affiliation(s)
- Shuangyu Tang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing 100871, China
| | - Yinhao Liao
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing 100871, China
| | - Yichan Xu
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing 100871, China
| | - Zhengzhu Dang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing 100871, China
| | - Xianfang Zhu
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing 100871, China
| | - Guodong Ji
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing 100871, China.
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198
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Fuchsman CA, Stüeken EE. Using modern low-oxygen marine ecosystems to understand the nitrogen cycle of the Paleo- and Mesoproterozoic oceans. Environ Microbiol 2020; 23:2801-2822. [PMID: 32869502 DOI: 10.1111/1462-2920.15220] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 08/25/2020] [Accepted: 08/27/2020] [Indexed: 11/29/2022]
Abstract
During the productive Paleoproterozoic (2.4-1.8 Ga) and less productive Mesoproterozoic (1.8-1.0 Ga), the ocean was suboxic to anoxic and multicellular organisms had not yet evolved. Here, we link geologic information about the Proterozoic ocean to microbial processes in modern low-oxygen systems. High iron concentrations and rates of Fe cycling in the Proterozoic are the largest differences from modern oxygen-deficient zones. In anoxic waters, which composed most of the Paleoproterozoic and ~40% of the Mesoproterozoic ocean, nitrogen cycling dominated. Rates of N2 production by denitrification and anammox were likely linked to sinking organic matter fluxes and in situ primary productivity under anoxic conditions. Additionally autotrophic denitrifiers could have used reduced iron or methane. 50% of the Mesoproterozoic ocean may have been suboxic, promoting nitrification and metal oxidation in the suboxic water and N2 O and N2 production by partial and complete denitrification in anoxic zones in organic aggregates. Sulfidic conditions may have composed ~10% of the Mesoproterozoic ocean focused along continental margins. Due to low nitrate concentrations in offshore regions, anammox bacteria likely dominated N2 production immediately above sulfidic zones, but in coastal regions, higher nitrate concentrations probably promoted complete S-oxidizing autotrophic denitrification at the sulfide interface.
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Affiliation(s)
- Clara A Fuchsman
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, 21613, USA
| | - Eva E Stüeken
- School of Earth & Environmental Sciences, University of St Andrews, St Andrews, KY16 9AL, Scotland, UK
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199
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Voegel TM, Larrabee MM, Nelson LM. Development of droplet digital PCR assays to quantify genes involved in nitrification and denitrification, comparison with quantitative real-time PCR and validation of assays in vineyard soil. Can J Microbiol 2020; 67:174-187. [PMID: 32910858 DOI: 10.1139/cjm-2020-0033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Quantifying genes in soil is important to relate the abundance of soil bacteria to biogeochemical cycles. Quantitative real-time PCR is widely used for quantification, but its use with environmental samples is limited by poor reaction efficiencies or by PCR inhibition through co-purified soil substances. Droplet digital PCR (ddPCR) is a technology for absolute, sensitive quantification of genes. This study optimized eight ddPCR assays to quantify total bacteria and archaea as well as the nitrification (bacterial and archaeal amoA) and denitrification (nirS, nirK, nosZI, nosZII) genes involved in the generation or reduction of the greenhouse gas nitrous oxide. Detection and quantification thresholds were compared with those of quantitative real-time PCR and were equal to, or improved, in ddPCR. To validate the assays using environmental samples, soil DNA was isolated from two vineyards in the Okanagan valley in British Columbia, Canada, over the 2017 growing season. Soil properties related to the observed gene abundances were determined. Total bacteria, nirK, and nosZII increased with time and the soil C/N ratio and NH4+-N concentration affected total archaea and archaeal amoA negatively. The results, compared with those of other studies, showed that ddPCR is a valid alternative to qPCR to quantify genes involved in nitrification or denitrification.
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Affiliation(s)
- Tanja M Voegel
- Irving K. Barber Faculty of Science, Department of Biology, University of British Columbia Okanagan, 1177 Research Road, Kelowna, BC V1V 1V7, Canada.,Irving K. Barber Faculty of Science, Department of Biology, University of British Columbia Okanagan, 1177 Research Road, Kelowna, BC V1V 1V7, Canada
| | - Melissa M Larrabee
- Irving K. Barber Faculty of Science, Department of Biology, University of British Columbia Okanagan, 1177 Research Road, Kelowna, BC V1V 1V7, Canada.,Irving K. Barber Faculty of Science, Department of Biology, University of British Columbia Okanagan, 1177 Research Road, Kelowna, BC V1V 1V7, Canada
| | - Louise M Nelson
- Irving K. Barber Faculty of Science, Department of Biology, University of British Columbia Okanagan, 1177 Research Road, Kelowna, BC V1V 1V7, Canada.,Irving K. Barber Faculty of Science, Department of Biology, University of British Columbia Okanagan, 1177 Research Road, Kelowna, BC V1V 1V7, Canada
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200
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Genomic Characteristics of a Novel Species of Ammonia-Oxidizing Archaea from the Jiulong River Estuary. Appl Environ Microbiol 2020; 86:AEM.00736-20. [PMID: 32631866 DOI: 10.1128/aem.00736-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/30/2020] [Indexed: 11/20/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA) are ubiquitous in diverse ecosystems and play a pivotal role in global nitrogen and carbon cycling. Although AOA diversity and distribution are widely studied, mainly based on the amoA (alpha subunit of ammonia monooxygenase) genotypes, only limited investigations have addressed the relationship between AOA genetic adaptation, metabolic features, and ecological niches, especially in estuaries. Here, we describe the AOA communities along the Jiulong River estuary in southern China. Nine high-quality AOA metagenome-assembled genomes (MAGs) were obtained by metagenomics. Five of the MAGs are proposed to constitute a new species, "Candidatus Nitrosopumilus aestuariumsis" sp. nov., based on the phylogenies of the 16S and 23S rRNA genes and concatenated ribosomal proteins, as well as the average amino acid identity. Comparative genomic analysis revealed unique features of the new species, including a high number of genes related to diverse carbohydrate-active enzymes, phosphatases, heavy-metal transport systems, flagellation, and chemotaxis. These genes may be crucial for AOA adaptation to the eutrophic and heavy-metal-contaminated Jiulong River estuary. The uncovered detailed genomic characteristics of the new estuarine AOA species highlight AOA contributions to ammonia oxidation in the Jiulong River estuary.IMPORTANCE In this study, AOA communities along a river in southern China were characterized, and metagenome-assembled genomes (MAGs) of a novel AOA clade were also obtained. Based on the characterization of AOA genomes, the study suggests adaptation of the novel AOAs to estuarine environments, providing new information on the ecology of estuarine AOA and the nitrogen cycle in contaminated estuarine environments.
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