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Laux M, Ciapina LP, de Carvalho FM, Gerber AL, Guimarães APC, Apolinário M, Paes JES, Jonck CR, de Vasconcelos ATR. Living in mangroves: a syntrophic scenario unveiling a resourceful microbiome. BMC Microbiol 2024; 24:228. [PMID: 38943070 PMCID: PMC11212195 DOI: 10.1186/s12866-024-03390-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 06/19/2024] [Indexed: 07/01/2024] Open
Abstract
BACKGROUND Mangroves are complex and dynamic coastal ecosystems under frequent fluctuations in physicochemical conditions related to the tidal regime. The frequent variation in organic matter concentration, nutrients, and oxygen availability, among other factors, drives the microbial community composition, favoring syntrophic populations harboring a rich and diverse, stress-driven metabolism. Mangroves are known for their carbon sequestration capability, and their complex and integrated metabolic activity is essential to global biogeochemical cycling. Here, we present a metabolic reconstruction based on the genomic functional capability and flux profile between sympatric MAGs co-assembled from a tropical restored mangrove. RESULTS Eleven MAGs were assigned to six Bacteria phyla, all distantly related to the available reference genomes. The metabolic reconstruction showed several potential coupling points and shortcuts between complementary routes and predicted syntrophic interactions. Two metabolic scenarios were drawn: a heterotrophic scenario with plenty of carbon sources and an autotrophic scenario with limited carbon sources or under inhibitory conditions. The sulfur cycle was dominant over methane and the major pathways identified were acetate oxidation coupled to sulfate reduction, heterotrophic acetogenesis coupled to carbohydrate catabolism, ethanol production and carbon fixation. Interestingly, several gene sets and metabolic routes similar to those described for wastewater and organic effluent treatment processes were identified. CONCLUSION The mangrove microbial community metabolic reconstruction reflected the flexibility required to survive in fluctuating environments as the microhabitats created by the tidal regime in mangrove sediments. The metabolic components related to wastewater and organic effluent treatment processes identified strongly suggest that mangrove microbial communities could represent a resourceful microbial model for biotechnological applications that occur naturally in the environment.
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Affiliation(s)
- Marcele Laux
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Avenida Getúlio Vargas 333, Quitandinha Petrópolis, Rio de Janeiro, 25651-075, Brazil
| | - Luciane Prioli Ciapina
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Avenida Getúlio Vargas 333, Quitandinha Petrópolis, Rio de Janeiro, 25651-075, Brazil.
| | - Fabíola Marques de Carvalho
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Avenida Getúlio Vargas 333, Quitandinha Petrópolis, Rio de Janeiro, 25651-075, Brazil
| | - Alexandra Lehmkuhl Gerber
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Avenida Getúlio Vargas 333, Quitandinha Petrópolis, Rio de Janeiro, 25651-075, Brazil
| | - Ana Paula C Guimarães
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Avenida Getúlio Vargas 333, Quitandinha Petrópolis, Rio de Janeiro, 25651-075, Brazil
| | - Moacir Apolinário
- Petróleo Brasileiro S. A., Centro de Pesquisa Leopoldo Américo Miguez de Mello, Rio de Janeiro, RJ, Brasil
| | - Jorge Eduardo Santos Paes
- Petróleo Brasileiro S. A., Centro de Pesquisa Leopoldo Américo Miguez de Mello, Rio de Janeiro, RJ, Brasil
| | - Célio Roberto Jonck
- Petróleo Brasileiro S. A., Centro de Pesquisa Leopoldo Américo Miguez de Mello, Rio de Janeiro, RJ, Brasil
| | - Ana Tereza R de Vasconcelos
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Avenida Getúlio Vargas 333, Quitandinha Petrópolis, Rio de Janeiro, 25651-075, Brazil
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Khairunisa BH, Loganathan U, Ogejo JA, Mukhopadhyay B. Nitrogen transformation processes catalyzed by manure microbiomes in earthen pit and concrete storages on commercial dairy farms. ENVIRONMENTAL MICROBIOME 2023; 18:32. [PMID: 37041573 PMCID: PMC10091836 DOI: 10.1186/s40793-023-00483-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 03/15/2023] [Indexed: 06/19/2023]
Abstract
Storing manure is an essential aspect of nutrient management on dairy farms. It presents the opportunity to use manure efficiently as a fertilizer in crop and pasture production. Typically, the manure storages are constructed as earthen, concrete, or steel-based structures. However, storing manure can potentially emit aerial pollutants to the atmosphere, including nitrogen and greenhouse gases, through microbial and physicochemical processes. We have characterized the composition of the microbiome in two manure storage structures, a clay-lined earthen pit and an aboveground concrete storage tank, on commercial dairy farms, to discern the nitrogen transformation processes, and thereby, inform the development of mitigation practices to preserve the value of manure. First, we analyzed the 16S rRNA-V4 amplicons generated from manure samples collected from several locations and depths (0.3, 1.2, and 2.1-2.75 m below the surface) of the storages, identifying a set of Amplicon Sequence Variant (ASVs) and quantifying their abundances. Then, we inferred the respective metabolic capabilities. These results showed that the manure microbiome composition was more complex and exhibited more location-to-location variation in the earthen pit than in the concrete tank. Further, the inlet and a location with hard surface crust in the earthen pit had unique consortia. The microbiomes in both storages had the potential to generate ammonia but lacked the organisms for oxidizing it to gaseous compounds. However, the microbial conversion of nitrate to gaseous N2, NO, and N2O via denitrification and to stable ammonia via dissimilatory nitrite reduction seemed possible; minor quantities of nitrate was present in manure, potentially originating from oxidative processes occurring on the barn floor. The nitrate-transformation linked ASVs were more prevalent at the near-surface locations and all depths of the inlet. Anammox bacteria and archaeal or bacterial autotrophic nitrifiers were not detected in either storage. Hydrogenotrophic Methanocorpusculum species were the primary methanogens or methane producers, exhibiting higher abundance in the earthen pit. These findings suggested that microbial activities were not the main drivers for nitrogen loss from manure storage, and commonly reported losses are associated with the physicochemical processes. Finally, the microbiomes of stored manure had the potential to emit greenhouse gases such as NO, N2O, and methane.
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Affiliation(s)
- Bela Haifa Khairunisa
- Genetics, Bioinformatics, and Computational Biology Ph.D. Program, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Usha Loganathan
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Jactone A Ogejo
- Department of Biological System Engineering, Blacksburg, VA, 24061, USA.
| | - Biswarup Mukhopadhyay
- Genetics, Bioinformatics, and Computational Biology Ph.D. Program, Virginia Tech, Blacksburg, VA, 24061, USA.
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, 24061, USA.
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Zhao R, Babbin AR, Roerdink DL, Thorseth IH, Jørgensen SL. Nitrite accumulation and anammox bacterial niche partitioning in Arctic Mid-Ocean Ridge sediments. ISME COMMUNICATIONS 2023; 3:26. [PMID: 36991114 PMCID: PMC10060263 DOI: 10.1038/s43705-023-00230-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 02/27/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023]
Abstract
By consuming ammonium and nitrite, anammox bacteria form an important functional guild in nitrogen cycling in many environments, including marine sediments. However, their distribution and impact on the important substrate nitrite has not been well characterized. Here we combined biogeochemical, microbiological, and genomic approaches to study anammox bacteria and other nitrogen cycling groups in two sediment cores retrieved from the Arctic Mid-Ocean Ridge (AMOR). We observed nitrite accumulation in these cores, a phenomenon also recorded at 28 other marine sediment sites and in analogous aquatic environments. The nitrite maximum coincides with reduced abundance of anammox bacteria. Anammox bacterial abundances were at least one order of magnitude higher than those of nitrite reducers and the anammox abundance maxima were detected in the layers above and below the nitrite maximum. Nitrite accumulation in the two AMOR cores co-occurs with a niche partitioning between two anammox bacterial families (Candidatus Bathyanammoxibiaceae and Candidatus Scalinduaceae), likely dependent on ammonium availability. Through reconstructing and comparing the dominant anammox genomes (Ca. Bathyanammoxibius amoris and Ca. Scalindua sediminis), we revealed that Ca. B. amoris has fewer high-affinity ammonium transporters than Ca. S. sediminis and lacks the capacity to access alternative substrates and/or energy sources such as urea and cyanate. These features may restrict Ca. Bathyanammoxibiaceae to conditions of higher ammonium concentrations. These findings improve our understanding about nitrogen cycling in marine sediments by revealing coincident nitrite accumulation and niche partitioning of anammox bacteria.
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Affiliation(s)
- Rui Zhao
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Andrew R Babbin
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Desiree L Roerdink
- Centre for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, 5007, Norway
| | - Ingunn H Thorseth
- Centre for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, 5007, Norway
| | - Steffen L Jørgensen
- Centre for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, 5007, Norway.
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4
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Lai X, Li X, Song J, Yuan H, Duan L, Li N, Wang Y. Nitrogen loss from the coastal shelf of the East China Sea: Implications of the organic matter. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 854:158805. [PMID: 36113798 DOI: 10.1016/j.scitotenv.2022.158805] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/17/2022] [Accepted: 09/12/2022] [Indexed: 06/15/2023]
Abstract
Organic matter is a critical factor which regulates nitrogen loss pathways of denitrification and anammox for microbes in marine ecosystems. However, only a little attention has been paid to contrasting studies on denitrification and anammox in sandy and muddy sediments, especially in the coastal continental shelf dominated by sandy sediments. This study determined the bulk properties and associated microbial nitrogen transformation processes of surface sediments in the East China Sea coastal shelf, with the aim of gaining insight into the interaction of nitrogen loss with organic matter at the molecular level. The results illustrate that nitrogen loss dominates in organic-rich muddy sediments, and its denitrification rate (14.39 nmol N g-1 h-1) and anammox rate (2.73 nmol N g-1 h-1) are greater than those of sandy sediments (denitrification rate = 5.55 nmol N g-1 h-1, anammox rate = 1.57 nmol N g-1 h-1). Furthermore, determination of the mean summed ladderanes shows higher anammox generated in the muddy sediments with a value of 167.78 ng g-1dw. Quantitative analysis demonstrated that organic-rich muddy sediments enhanced the copy number of the denitrifying functional gene nosZ and anammox functional gene hzsB. We inferred that the greater rate of nitrogen loss in muddy sediments was due to the coupling relationship between anammox and denitrification. Overall, the community distribution and abundance of denitrifying bacteria and anammox bacteria changed intricately under the influence of organic matter. Moreover, this study further improves the understanding of nitrogen loss pathways and mechanistic factors from sediments.
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Affiliation(s)
- Xiaoshuang Lai
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Ecology and Environmental Sciences, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Xuegang Li
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Ecology and Environmental Sciences, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.
| | - Jinming Song
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Ecology and Environmental Sciences, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.
| | - Huamao Yuan
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Ecology and Environmental Sciences, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Liqin Duan
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Ecology and Environmental Sciences, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Ning Li
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Ecology and Environmental Sciences, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China; Public Technology Service Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Yingxia Wang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Ecology and Environmental Sciences, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China; Public Technology Service Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
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5
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Gao D, Liu C, Li X, Zheng Y, Dong H, Liang X, Niu Y, Yin G, Liu M, Hou L. High importance of coupled nitrification-denitrification for nitrogen removal in a large periodically low-oxygen estuary. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 846:157516. [PMID: 35872198 DOI: 10.1016/j.scitotenv.2022.157516] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/05/2022] [Accepted: 07/16/2022] [Indexed: 06/15/2023]
Abstract
The coupling between nitrification and denitrification/anammox (nitrate/nitrite used in denitrification/anammox derives from nitrification) is a significant process of reactive nitrogen (N) removal that has attracted much attention. However, the dynamics of coupled nitrification-denitrification/anammox in the periodically low-oxygen estuaries and coasts remain unclear. Here, continuous-flow experiments combined with isotope tracing techniques were conducted in periodically low-oxygen areas of the Yangtze Estuary to reveal the changes in benthic sediment denitrification and anammox as well as their coupling with nitrification. Our results showed that denitrification increased but anammox decreased during low-oxygen summer. The occurrence of low oxygen also promoted coupled nitrification-denitrification but decreased coupled nitrification-anammox. These results implied that decreased dissolved oxygen in summer did not largely restrict nitrification activity, and anaerobic denitrification/anammox regulated the magnitude of coupled nitrification-denitrification/anammox rates. Denitrification (74.95-100 %) was the dominant process in total N removal, while coupled nitrification-denitrification accounted for a higher proportion (45.68-97.05 %) of denitrification, indicating that coupling between nitrification and denitrification played a dominant role in N removal. In addition to dissolved oxygen levels, carbon and N substrate availabilities were also important variables to regulate N transformations. Overall, this study advanced our knowledge of the distribution patterns and controlling factors of N removal processes and highlighted that coupled nitrification-denitrification might have a significant but neglected role in N removal from periodically low-oxygen estuaries.
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Affiliation(s)
- Dengzhou Gao
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Cheng Liu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China; Shandong Key Laboratory of Eco-Environmental Science for the Yellow River Delta, Binzhou University, Binzhou, Shandong 256600, China
| | - Xiaofei Li
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Yanling Zheng
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China; Key Laboratory of Geographic Information Science of the Ministry of Education, College of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Hongpo Dong
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Xia Liang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Yuhui Niu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Guoyu Yin
- Key Laboratory of Geographic Information Science of the Ministry of Education, College of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science of the Ministry of Education, College of Geographical 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, Shanghai 200241, China.
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Ding B, Li Z, Cai M, Lu M, Liu W. Feammox is more important than anammox in anaerobic ammonium loss in farmland soils around Lake Taihu, China. CHEMOSPHERE 2022; 305:135412. [PMID: 35724714 DOI: 10.1016/j.chemosphere.2022.135412] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/18/2022] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Ammonium (NH4+) oxidation is a key step in nitrogen transformation in ecosystems. Prior to the recent discovery of Feammox (anaerobic NH4+ oxidation coupled with iron reduction), anammox (anaerobic NH4+ oxidation coupled with nitrite reduction) was thought of as the only pathway by which anaerobic NH4+ loss (NH4+ directly to N2) occurs in soils. Experimental evidence has confirmed that both anammox and Feammox contribute to anaerobic NH4+ loss; however, their relative contributions to this process in farmland soils are largely unknown. Therefore, in this study, we examined the seasonal activities of anammox and Feammox in conventional tillage (CT) and no-tillage (NT) soils around Lake Taihu, China. Isotopic tracing experiments showed higher anammox and Feammox rates in summer than in other seasons, and the contribution of Feammox to anaerobic NH4+ loss from the farmland soils (54.6%-69.3%) was higher than that of anammox. Further, the Feammox rates corresponding to the two soil tillage practices were significantly different, whereas their corresponding anammox rates showed no significant differences. Furthermore, molecular analysis showed that the abundance of Geobacteraceae differed significantly with season and tillage practice, whereas the abundance of anammox bacteria showed no significant differences between CT and NT practices. Structural equation modeling also revealed that the anammox rate was directly or indirectly driven by N availability and season, whereas the Feammox rate was driven by soil moisture content, Fe(III) concentration, Fe(III) reduction rates, tillage practice, and season. Overall, this study enhances understanding regarding anaerobic NH4+ oxidation in farmland soils and highlight the importance of Feammox in NH4+ loss in such an ecosystem.
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Affiliation(s)
- Bangjing Ding
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; State Key Laboratory of Pollution Control and Resource Reuse, Nanjing University, Nanjing, 210023, China; School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Zhengkui Li
- State Key Laboratory of Pollution Control and Resource Reuse, Nanjing University, Nanjing, 210023, China; School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Miaomiao Cai
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Mingzhu Lu
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Wenzhi Liu
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
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Zhao B, Li X, Wang Y, Tan X, Qi W, Li H, Wei J, You Y, Shi W, Zhang Q. Dissimilatory nitrate reduction and functional genes in two subtropical rivers, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:68155-68173. [PMID: 34264489 DOI: 10.1007/s11356-021-15197-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 06/25/2021] [Indexed: 06/13/2023]
Abstract
Dissimilatory nitrate reduction processes, including denitrification, anaerobic ammonium oxidation (anammox), and dissimilatory nitrate reduction to ammonium (DNRA), are important pathways of nitrate transformation in the aquatic environments. In this study, we investigated potential rates of denitrification, anammox, and DNRA in the sediments of two subtropical rivers, Jinshui River and Qi River, with different intensities of human activities in their respective catchment, China. Our objectives were to assess the seasonality of dissimilatory nitrate reduction rates, quantify their respective contributions to nitrate reduction, and reveal the relationship between dissimilatory nitrate reduction rates, functional gene abundances, and physicochemicals in the river ecosystems. Our results showed higher rates of denitrification and anammox in the intensively disturbed areas in autumn and spring, and higher potential DNRA in the slightly disturbed areas in summer. Generally, denitrification, anammox, and DNRA were higher in summer, autumn, and spring, respectively. Relative contributions of nitrate reduction from denitrification, anammox, and DNRA were quite different in different seasons. Dissimilatory nitrate reduction rates and gene abundances correlated significantly with water temperature, dissolved organic carbon (DOC), sediment total organic carbon (SOC), NO3-, NH4+, DOC/NO3-, iron ions, and sulfide. Understanding dissimilatory nitrate reduction is essential for restoring nitrate reduction capacity and improving and sustaining ecohealth of the river ecosystems.
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Affiliation(s)
- Binjie Zhao
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinshuai Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Wang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiang Tan
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Wenhua Qi
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongran Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junwei Wei
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Research Center for Ecology and Environment of Qinghai-Tibetan Plateau, Tibet University, Lhasa, 850000, China
- College of Science, Tibet University, Lhasa, 850000, China
| | - Yong You
- College of Land and Resources, China West Normal University, Nanchong, 637009, China
| | - Wenjun Shi
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Quanfa Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.
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Mai Y, Liang Y, Cheng M, He Z, Yu G. Coupling oxidation of acid volatile sulfide, ferrous iron, and ammonia nitrogen from black-odorous sediment via autotrophic denitrification-anammox by nitrate addition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 790:147972. [PMID: 34082326 DOI: 10.1016/j.scitotenv.2021.147972] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/19/2021] [Accepted: 05/19/2021] [Indexed: 06/12/2023]
Abstract
The coupling removal of acid volatile sulfide (AVS), ferrous iron, and ammonia nitrogen has been applied for black-odorous sediment remediation. In this study, calcium nitrate with different N/(S + Fe) ratios (0.45, 0.90, 1.20 and 1.80) was added into black-odorous sediment in four systems named R1, R2, R3, and R4. Results showed that the removal rate of AVS was 76.40% in the R1, which was lower compared with rates in R2-R4 around 96.70%. The ferrous oxidation rate was approximately 87.00% in R2-R4, which was considerably higher than that in the R1 (24.62%). And the ammonia was reduced by 81.02%, 88.00%, 100%, and 57.18% in R1, R2, R3 and R4, respectively. During the reaction, nitrite accumulation was observed, indicating partial denitrification. Moreover, microbes related to autotrophic denitrification (e.g., genus Thiobacillus, Dok59, GOUTA19, Gallionella, with the highest abundance of 15.40%, 13.21%, 8.79%, 9.44%, respectively) were detected in all systems. Furthermore, the anammox bacteria Candidatus_Brocadia with the highest abundance of 3.44% and 4.00% in R2 and R3, respectively was also found. These findings confirmed that AVS, ferrous iron, and ammonia nitrogen could be simultaneously removed via autotrophic denitrification coupled with anammox in black-odorous sediment by nitrate addition.
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Affiliation(s)
- Yingwen Mai
- Department of Environmental Science and Engineering, College of Natural Resource and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Yuhai Liang
- Department of Environmental Science and Engineering, College of Natural Resource and Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, South China Agricultural University, Guangzhou 510642, China
| | - Mingshuang Cheng
- Department of Environmental Science and Engineering, College of Natural Resource and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Zihao He
- Department of Environmental Science and Engineering, College of Natural Resource and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Guangwei Yu
- Department of Environmental Science and Engineering, College of Natural Resource and Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, South China Agricultural University, Guangzhou 510642, China.
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9
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Organic Wastes Amended with Sorbents Reduce N2O Emissions from Sugarcane Cropping. ENVIRONMENTS 2021. [DOI: 10.3390/environments8080078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Nutrient-rich organic wastes and soil ameliorants can benefit crop performance and soil health but can also prevent crop nutrient sufficiency or increase greenhouse gas emissions. We hypothesised that nitrogen (N)-rich agricultural waste (poultry litter) amended with sorbents (bentonite clay or biochar) or compost (high C/N ratio) attenuates the concentration of inorganic nitrogen (N) in soil and reduces emissions of nitrous oxide (N2O). We tested this hypothesis with a field experiment conducted on a commercial sugarcane farm, using in vitro incubations. Treatments received 160 kg N ha−1, either from mineral fertiliser or poultry litter, with additional N (2–60 kg N ha−1) supplied by the sorbents and compost. Crop yield was similar in all N treatments, indicating N sufficiency, with the poultry litter + biochar treatment statistically matching the yield of the no-N control. Confirming our hypothesis, mineral N fertiliser resulted in the highest concentrations of soil inorganic N, followed by poultry litter and the amended poultry formulations. Reflecting the soil inorganic N concentrations, the average N2O emission factors ranked as per the following: mineral fertiliser 8.02% > poultry litter 6.77% > poultry litter + compost 6.75% > poultry litter + bentonite 5.5% > poultry litter + biochar 3.4%. All emission factors exceeded the IPCC Tier 1 default for managed soils (1%) and the Australian Government default for sugarcane soil (1.25%). Our findings reinforce concerns that current default emissions factors underestimate N2O emissions. The laboratory incubations broadly matched the field N2O emissions, indicating that in vitro testing is a cost-effective first step to guide the blending of organic wastes in a way that ensures N sufficiency for crops but minimises N losses. We conclude that suitable sorbent-waste formulations that attenuate N release will advance N efficiency and the circular nutrient economy.
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Li X, Gao D, Hou L, Qian W, Liu M, Zeng H, Chen Z, Tong C. Nitrogen loads alter the N 2 production between denitrification and anammox in Min River Estuary, a highly impacted estuary in southeast China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 277:116757. [PMID: 33647804 DOI: 10.1016/j.envpol.2021.116757] [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: 11/19/2020] [Revised: 02/08/2021] [Accepted: 02/14/2021] [Indexed: 06/12/2023]
Abstract
Estuarine sediment denitrification and anammox in response to increased nitrogen (N) loads remain poorly understood. In this study, we used N isotope tracer approach to investigate the spatial distribution of denitrification and anammox and identified the crucial controls on the partitioning of dinitrogen gas (N2) production along the Min River Estuary (MRE), a highly impacted estuary in southeast China. The results indicated that denitrification and anammox rates ranged from 10.5 to 70.7 nmol g-1 h-1 and from 0.44 to 4.31 nmol g-1 h-1, respectively. Relative contribution of anammox to N2 production (Ra) was in a range of 1.04-15.1%, tending to increase toward estuary mouth. Denitrification rates were significantly higher in upper (high N loads) than in lower estuary (low N loads), while anammox rates and Ra showed inverse distributions along the MRE. Wastewater discharge caused the N point pollution triggering denitrification but inhibiting anammox. The best predictor of the variations in denitrification rates was total nitrogen, whereas pH and NH4+ could explained the variations in anammox rates across the estuary. The crucial predictors for the partitioning of N2 production between denitrification and anammox were NH4+ and NOx-. These results suggest that the increase in human activities intensity can alter the partitioning of N2 production between denitrification and anammox, and the magnitude of this switch can be predicted by N loads in MRE and other highly impacted estuaries.
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Affiliation(s)
- Xiaofei Li
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China; Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, 350007, China.
| | - Dengzhou Gao
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China
| | - Wei Qian
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, 350007, China
| | - Min Liu
- Key Laboratory of Geographic Information Science of the Ministry of Education, School of Geographic Sciences, East China Normal University, Shanghai, 200241, China
| | - Hongda Zeng
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, 350007, China
| | - Zhibiao Chen
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, 350007, China
| | - Chuan Tong
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, 350007, China
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Abstract
Nitrogen (N) cycling in mangroves is complex, with rapid turnover of low dissolved N concentrations, but slow turnover of particulate N. Most N is stored in soils. The largest sources of N are nearly equal amounts of mangrove and benthic microalgal primary production. Dissolved N fluxes between the forests and tidal waters show net uptake, indicating N conservation. N2-fixation is underestimated as rapid rates measured on tree stems, aboveground roots and cyanobacterial mats cannot currently be accounted for at the whole-forest scale due to their extreme patchiness and the inability to extrapolate beyond a localized area. Net immobilization of NH4+ is the largest ecosystem flux, indicating N retention. Denitrification is the largest loss of N, equating to 35% of total N input. Burial equates to about 29% of total inputs and is the second largest loss of N. Total inputs slightly exceed total outputs, currently suggesting net N balance in mangroves. Mangrove PON export equates to ≈95% of PON export from the world’s tropical rivers, but only 1.5% of the entire world’s river discharge. Mangrove N2O emissions, denitrification, and burial contribute 0.4%, 0.5–2.0% and 6%, respectively, to the global coastal ocean, which are disproportionate to their small worldwide area.
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Yang Y, Li M, Li H, Li XY, Lin JG, Denecke M, Gu JD. Specific and effective detection of anammox bacteria using PCR primers targeting the 16S rRNA gene and functional genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 734:139387. [PMID: 32460079 DOI: 10.1016/j.scitotenv.2020.139387] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 05/09/2020] [Accepted: 05/10/2020] [Indexed: 05/05/2023]
Abstract
Anaerobic ammonium-oxidizing (anammox) bacteria play an important role in the nitrogen cycle by coupling ammonium and nitrite to produce dinitrogen gas (N2). Polymerase chain reaction (PCR) is a fast, simple, and sensitive method that is widely used to assess the diversity, abundance, and activity of the slow-growing bacteria. In this review, we summarize and evaluate the wide variety of PCR primers targeting the 16S rRNA gene and functional genes (hzo, nir, and hzs) of anammox bacteria for their effectiveness and efficiencies in detecting this group of bacteria in different sample types. Furthermore, the efficiencies of different universal high-throughput sequencing 16S rRNA gene primers in anammox bacteria investigations were also evaluated to provide a reference for primer selection. Based on our in silico evaluation results, none of the 16S rRNA gene primers could recover all of the known anammox bacteria, but multiple hzo and hzs gene primers could accomplish this task. However, uncertain copies (1-3 copies) of hzo genes were identified in the genomes, and the hydrazine oxidation reaction catalyzed by hydrazine oxidoreductases (HZOs) can also be catalyzed by other hydroxylamine oxidoreductases (HAOs) in anammox bacteria, which can potentially result in large deviations in hzo-based qPCR and RT-qPCR analyses and results. Therefore, the use of optimal primers targeting unique hzs genes are recommended, although the efficiencies of these newly designed primers need further verification in practical applications. This article provides comprehensive information for the effective and specific detection of anammox bacteria using specific primers targeting the 16S rRNA gene and functional genes and serves as a basis for future high-quality primer design.
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Affiliation(s)
- Yuchun Yang
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, Hong Kong, People's Republic of China; Environmental Engineering, Guangdong Technion Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, People's Republic of China
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, People's Republic of China.
| | - Hui Li
- School of Resource and Environmental Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, People's Republic of China
| | - Xiao-Yan Li
- Department of Civil and Environmental Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, People's Republic of China
| | - Jih-Gaw Lin
- Institute of Environmental Engineering, National Chiao Tung University, 1001 University Road, Hsinchu City 30010, Taiwan
| | - Martin Denecke
- Department of Urban Water- and Waste Management, University of Duisburg-Essen, Universitätsstraße 15, 45141 Essen, Germany
| | - Ji-Dong Gu
- School of Food and Biotechnology, Guangdong Industry Polytechnic, Guangzhou, Guangdong 510300, People's Republic of China; Environmental Engineering, Guangdong Technion Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, People's Republic of China.
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13
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Pan H, Qin Y, Wang Y, Liu S, Yu B, Song Y, Wang X, Zhu G. Dissimilatory nitrate/nitrite reduction to ammonium (DNRA) pathway dominates nitrate reduction processes in rhizosphere and non-rhizosphere of four fertilized farmland soil. ENVIRONMENTAL RESEARCH 2020; 186:109612. [PMID: 32668552 DOI: 10.1016/j.envres.2020.109612] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 04/26/2020] [Accepted: 04/26/2020] [Indexed: 06/11/2023]
Abstract
Nitrate (NO3-) reduction partitioning between denitrification, anaerobic ammonium oxidation (anammox), denitrifying anaerobic methane oxidation (DAMO), and dissimilatory nitrate reduction to ammonium (DNRA), can influence the nitrogen (N) use efficiency and crop production in arid farmland. The microbial structure, function and potential rates of denitrification, anammox, DAMO and DNRA, and their respective contributions to total NO3- reduction were investigated in rhizosphere and non-rhizosphere soil of four typical crops in north China by functional gene amplification, high-throughput sequencing, network analysis and isotopic tracing technique. The measured denitrification and DNRA rate varied from 0.0294 to 20.769 nmol N g-1 h-1and 2.4125-58.682 nmol N g-1 h-1, respectively, based on which DNRA pathway contributed to 84.44 ± 14.40% of dissimilatory NO3- reduction, hence dominated NO3- reduction processes compared to denitrification. Anammox and DAMO were not detected. High-throughput sequencing analysis on DNRA nrfA gene, and denitrification nirS and nirK genes demonstrated that these two processes did not correlate to corresponding gene abundance or dominant genus. RDA and Pearson's correlation analysis illustrated that DNRA rate was significantly correlated with the abundance of Chthiniobacter, as well as total organic matter (TOM); denitrification rate was significantly correlated with the abundance of Lautropia, so did TOM. Network analysis showed that the genus performed DNRA was the key connector in the microbial community of dissimilatory nitrate reducers. This study simultaneously investigated the dissimilatory nitrate reduction processes in rhizosphere and non-rhizosphere soils in arid farmland, highlighting that DNRA dominated NO3- reduction processes against denitrification. As denitrification results in N loss, whereas DNRA contributes to N retention, the relative contributions of DNRA versus denitrification activities should be considered appropriately when assessing N transformation processes and N fertilizer management in arid farmland fields.
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Affiliation(s)
- Huawei Pan
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yu Qin
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuantao Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Shiguang Liu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Bin Yu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yiping Song
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Xiaomin Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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Zheng Y, Hou L, Liu M, Yin G. Dynamics and environmental importance of anaerobic ammonium oxidation (anammox) bacteria in urban river networks. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 254:112998. [PMID: 31422342 DOI: 10.1016/j.envpol.2019.112998] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 07/03/2019] [Accepted: 07/27/2019] [Indexed: 06/10/2023]
Abstract
Anaerobic ammonium oxidation (anammox) is recognized as an important bioprocess for nitrogen removal, yet little is known about the associated microbial communities in urban river networks which are intensively disturbed by human activity. In the present study, we investigated the community composition and abundance of anammox bacteria in the urban river network of Shanghai, and explored their potential correlations with nitrogen removal activities and the environmental parameters. High biodiversity of anammox bacteria was detected in the sediment of urban river networks, including Candidatus Brocadia, Scalindua, Jettenia, and Kuenenia. Anammox bacterial abundance ranged from 3.7 × 106 to 3.9 × 107 copies g-1 dry sediment based on 16S rRNA gene, which was strongly correlated to the metabolic activity of anammox bacteria (P < 0.01). A strong linkage between anammox bacteria and denitrifiers was detected (P < 0.05), implying a potential metabolic interdependence between these two nitrogen-removing microbes was existed in urban river networks. Sediment ammonium (NH4+) made a significant contribution to the anammox bacterial community-environment relationship, while anammox bacterial abundance related significantly with sediment total organic carbon (TOC) and silt contents (P < 0.05). However, no statistically significant correlation was observed between cell-specific anammox rate and the measured environmental factors (P > 0.05). In general, the community composition and abundance of anammox bacteria in different hierarchies of the river network was homogeneous, without significant spatial variations (P > 0.05). These results provided an opportunity to further understand the microbial mechanism of nitrogen removal bioprocesses in urban river networks.
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Affiliation(s)
- Yanling Zheng
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China.
| | - Min Liu
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China
| | - Guoyu Yin
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China
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Wang J, Kan J, Qian G, Chen J, Xia Z, Zhang X, Liu H, Sun J. Denitrification and anammox: Understanding nitrogen loss from Yangtze Estuary to the east China sea (ECS). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 252:1659-1670. [PMID: 31284208 DOI: 10.1016/j.envpol.2019.06.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 05/18/2019] [Accepted: 06/06/2019] [Indexed: 06/09/2023]
Abstract
The Yangtze River, which is the largest in Euro-Asian, receives tremendous anthropogenic nitrogen input and is typically characterized by severe eutrophication and hypoxia. Two major processes, denitrification and anaerobic ammonium oxidation (anammox), play vital roles for removing nitrogen global in nitrogen cycling. In the current study, sediment samples were collected from both latitudinal and longitudinal transects along the coastal Yangtze River and the East China Sea (ECS). We investigated community composition and distributions of nosZ gene-encoded denitrifiers by high throughput sequencing, and also quantified the relative abundances of both denitrifying and anammox bacteria by q-PCR analysis. Denitrifying communities showed distinct spatial distribution patterns that were impacted by physical (water current and river runoffs) and chemical (nutrient availability and organic content) processes. Both denitrifying and anammox bacteria contributed to the nitrogen removal in Yangtze Estuary and the adjacent ECS, and these two processes shifted from coastal to open ocean with reverse trends: the abundance of nosZ gene decreased from coastal to open ocean while anammox exhibited an increasing trend based on quantifications of hzsB and 16S rRNA genes. Further correspondence correlation analysis revealed that salinity and nutrients were the main factors in structuring composition and distribution of denitrifying and anammox bacteria. This study improved our understanding of dynamic processes in nitrogen removal from estuarine to open ocean. We hypothesize that denitrification is the major nitrogen removal pathway in estuaries, but in open oceans, low nutrient and organic matter concentrations restrict denitrification, thus increasing the importance of anammox as a nitrogen removal process.
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Affiliation(s)
- Jing Wang
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, 300457, PR China; Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, SOA, Hangzhou, 310012, PR China
| | - Jinjun Kan
- Stroud Water Research Center, 970 Spencer Road, Avondale, PA, 19311, USA
| | - Gang Qian
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Jianfang Chen
- Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, SOA, Hangzhou, 310012, PR China
| | - Zhiqiang Xia
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Xiaodong Zhang
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Haijiao Liu
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Jun Sun
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, 300457, PR China; Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and Technology, Tianjin, 300457, PR China.
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Kraiem K, Wahab MA, Kallali H, Fra-Vazquez A, Pedrouso A, Mosquera-Corral A, Jedidi N. Effects of short- and long-term exposures of humic acid on the Anammox activity and microbial community. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:19012-19024. [PMID: 30039484 DOI: 10.1007/s11356-018-2786-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 07/17/2018] [Indexed: 06/08/2023]
Abstract
Humic acid has a controversial effect on the biological treatment processes. Here, we have investigated humic acid effects on the Anammox activity by studying the nitrogen removal efficiencies in batch and continuous conditions and analyzing the microbial community using Fluorescence in situ hybridization (FISH) technique. The results showed that the Anammox activity was affected by the presence of humic acid at a concentration higher than 70 mg/L. In fact, in the presence of humic acid concentration of 200 mg/L, the Anammox activity decreased to 57% in batch and under continuous condition, the ammonium removal efficiencies of the reactor decreased from 78 to 41%. This reduction of Anammox activity after humic acid addition was highlighted by FISH analysis which revealed a considerable reduction of the abundance of Anammox bacteria and the bacteria living in symbiosis with them. Furthermore, a total inhibition of Candidatus Brocadia fulgida was observed. However, humic acid has promoted heterotrophic denitrifying bacteria which became dominant in the reactor. In fact, the evolution of the organic matter in the reactor showed that the added humic acid was used as carbon source by heterotrophic bacteria which explained the shift of metabolism to the favor of heterotrophic denitrifying bacteria. Accordingly, humic acid should be controlled in the influent to avoid Anammox activity inhibition.
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Affiliation(s)
- Khadija Kraiem
- Laboratory of Wastewater Treatment and Valorization, Water Research and Technologies Center, CERTE, Technopark Tourist Route of Soliman Nabeul, PO Box No. 273, 8020, Soliman, Tunisia
- Faculty of Sciences of Tunis, University of Tunis El Manar, Rommana, B.P. no. 94, 1068, Tunis, Tunisia
| | - Mohamed Ali Wahab
- Laboratory of Wastewater Treatment and Valorization, Water Research and Technologies Center, CERTE, Technopark Tourist Route of Soliman Nabeul, PO Box No. 273, 8020, Soliman, Tunisia.
| | - Hamadi Kallali
- Laboratory of Wastewater Treatment and Valorization, Water Research and Technologies Center, CERTE, Technopark Tourist Route of Soliman Nabeul, PO Box No. 273, 8020, Soliman, Tunisia
| | - Andrea Fra-Vazquez
- Department of Chemical Engineering, Institute of Technological Research, School of Engineering, Universidade de Santiago de Compostela, Rua Lope Gómez de Marzoa s/n, 15782, Santiago de Compostela, Spain
| | - Alba Pedrouso
- Department of Chemical Engineering, Institute of Technological Research, School of Engineering, Universidade de Santiago de Compostela, Rua Lope Gómez de Marzoa s/n, 15782, Santiago de Compostela, Spain
| | - Anuska Mosquera-Corral
- Department of Chemical Engineering, Institute of Technological Research, School of Engineering, Universidade de Santiago de Compostela, Rua Lope Gómez de Marzoa s/n, 15782, Santiago de Compostela, Spain
| | - Naceur Jedidi
- Laboratory of Wastewater Treatment and Valorization, Water Research and Technologies Center, CERTE, Technopark Tourist Route of Soliman Nabeul, PO Box No. 273, 8020, Soliman, Tunisia
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Kraiem K, Kallali H, Wahab MA, Fra-Vazquez A, Mosquera-Corral A, Jedidi N. Comparative study on pilots between ANAMMOX favored conditions in a partially saturated vertical flow constructed wetland and a hybrid system for rural wastewater treatment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 670:644-653. [PMID: 30909042 DOI: 10.1016/j.scitotenv.2019.03.220] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 03/02/2019] [Accepted: 03/14/2019] [Indexed: 06/09/2023]
Abstract
The objective of this research was to evaluate the nitrogen removal in a single stage rural wastewater treatment system. It was a modified subsurface vertical flow (SSVF) constructed wetland. The so-called Anaerobic Ammonium Oxidation(ANAMMOX) process is favored by imposing a saturated zone at the bottom of the basin. The nitrogen removal performances of this modified SSVF were compared to those of a conventional hybrid system where the well-known nitrification-denitrification process is performed. This study was carried out using three lab-scale pilots of constructed wetlands during four months: (1) a hybrid constructed wetlands with a reed-Phragmites australis SSVF bed in serial with a cattail-Typha angustofolia SSHF bed (SSVFp + SSHF). (2) A reed-Phragmites australis SSVF bed partially saturated at 40% of its depth (SSVFPS); (3) A cattail-Typha angustofolia SSVF bed partially saturated at 40% of its depth (SSVFTS). The results showed that the three configurations used in this study were efficient for most of the pollutants reduction. In fact, single-stage reactors have achieved similar chemical oxygen demand (COD) removal in comparison to the two-stage reactor independently of the macrophytes species. However, for Total Kjeldahl Nitrogen (TKN), a slightly higher nitrogen removal efficiency was recorded for (SSVF p + SSHF) with an average removal rate of 53% versus 48% and 51% for SSVF PS and SSVFTS respectively. These findings were highlighted with fluorescent in situ hybridization (FISH) analysis, which demonstrated the presence of major differences in the community composition and abundance of the bacteria involved with denitrification and nitrification in the three systems. In fact, SSVFP of the hybrid system was characterized by highest relative abundance of nitrifying bacteria (13% Nitrosomonas, 11% Nitrosospira, 14% Nitrospira and 10% Nitrobacter). While, the SSHF of hybrid system had larger number of denitrifying species than SSVF, with relative abundances of pseudomonas (3%), Paracoccus (9%), Zoogloea (6%), Thauera (4%), Thiobacillus (2%) and Aeromonas (1%). Interestingly, in the SSVFST (planted with Thypha angustofolia) where the relative abundance of nitrifying bacteria was very low (4% Nitrosomonas, 4% Nitrosospira, 4% Nitrospira and 1% Nitrobacter), we have detected the presence of ANAMMOX bacteria (3%). Accordingly SSVFST in the presence of Thypha angustofolia have favored the development of ANAMMOX activity in comparison to the other configurations.
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Affiliation(s)
- Khadija Kraiem
- Effluent Treatment and Valorization Laboratory (ETVL), Water Research and Technology Center (WATREC), Carthage University, Technopark Tourist Route of Soliman Nabeul, PO-box N°273-8020, Soliman, Tunisia; Faculty of Sciences of Tunis, University of Tunis El Manar, B.P. no. 94 - ROMMANA, Tunis 1068, Tunisia.
| | - Hamadi Kallali
- Effluent Treatment and Valorization Laboratory (ETVL), Water Research and Technology Center (WATREC), Carthage University, Technopark Tourist Route of Soliman Nabeul, PO-box N°273-8020, Soliman, Tunisia
| | - Mohamed Ali Wahab
- Effluent Treatment and Valorization Laboratory (ETVL), Water Research and Technology Center (WATREC), Carthage University, Technopark Tourist Route of Soliman Nabeul, PO-box N°273-8020, Soliman, Tunisia
| | - Andrea Fra-Vazquez
- Department of Chemical Engineering, Institute of Technological Research, School of Engineering, Universidade de Santiago de Compostela, Rua Lope Gómez de Marzoa s/n, E-15782 Santiago de Compostela, Spain
| | - Anukha Mosquera-Corral
- Department of Chemical Engineering, Institute of Technological Research, School of Engineering, Universidade de Santiago de Compostela, Rua Lope Gómez de Marzoa s/n, E-15782 Santiago de Compostela, Spain
| | - Naceur Jedidi
- Effluent Treatment and Valorization Laboratory (ETVL), Water Research and Technology Center (WATREC), Carthage University, Technopark Tourist Route of Soliman Nabeul, PO-box N°273-8020, Soliman, Tunisia
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Li Y, Zheng L, Zhang Y, Liu H, Jing H. Comparative metagenomics study reveals pollution induced changes of microbial genes in mangrove sediments. Sci Rep 2019; 9:5739. [PMID: 30952929 PMCID: PMC6450915 DOI: 10.1038/s41598-019-42260-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 03/26/2019] [Indexed: 01/21/2023] Open
Abstract
Mangrove forests are widespread along the subtropical and tropical coasts. They provide a habitat for a wide variety of plants, animals and microorganisms, and act as a buffer zone between the ocean and land. Along with other coastal environments, mangrove ecosystems are under increasing pressure from human activities, such as excessive input of nutrients and toxic pollutants. Despite efforts to understand the diversity of microbes in mangrove sediments, their metabolic capability in pristine and contaminated mangrove sediments remains largely unknown. By using metagenomic approach, we investigated the metabolic capacity of microorganisms in contaminated (CMS) and pristine (PMS) mangrove sediments at subtropical and tropical coastal sites. When comparing the CMS with PMS, we found that the former had a reduced diazotroph abundance and nitrogen fixing capability, but an enhanced metabolism that is related to the generation of microbial greenhouse gases via increased methanogenesis and sulfate reduction. In addition, a high concentration of heavy metals (mainly Zn, Cd, and Pb) and abundance of metal/antibiotic resistance encoding genes were found in CMS. Together, these data provide evidence that contamination in mangrove sediment can markedly change microbial community and metabolism; however, no significant differences in gene distribution were found between the subtropical and tropical mangrove sediments. In summary, contamination in mangrove sediments might weaken the microbial metabolisms that enable the mangrove ecosystems to act as a buffer zone for terrestrial nutrients deposition, and induce bioremediation processes accompanied with an increase in greenhouse gas emission.
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Affiliation(s)
- Yingdong Li
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, China
| | - Liping Zheng
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Yue Zhang
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Hongbin Liu
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, China.
| | - Hongmei Jing
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.
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Shen L, Ouyang L, Zhu Y, Trimmer M. Spatial separation of anaerobic ammonium oxidation and nitrite‐dependent anaerobic methane oxidation in permeable riverbeds. Environ Microbiol 2019; 21:1185-1195. [DOI: 10.1111/1462-2920.14554] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/21/2019] [Accepted: 02/01/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Lidong Shen
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Jiangsu Key Laboratory of Agricultural MeteorologyDepartment of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology Nanjing 210044 China
- School of Biological & Chemical Sciences, Queen Mary University of London E1 4NS, London UK
| | - Liao Ouyang
- School of Biological & Chemical Sciences, Queen Mary University of London E1 4NS, London UK
| | - Yizhu Zhu
- School of Biological & Chemical Sciences, Queen Mary University of London E1 4NS, London UK
| | - Mark Trimmer
- School of Biological & Chemical Sciences, Queen Mary University of London E1 4NS, London UK
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Zhou X, Wang M, Wen C, Liu D. Nitrogen release and its influence on anammox bacteria during the decay of Potamogeton crispus with different values of initial debris biomass. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 650:604-615. [PMID: 30208346 DOI: 10.1016/j.scitotenv.2018.08.358] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 07/03/2018] [Accepted: 08/25/2018] [Indexed: 06/08/2023]
Abstract
Aquatic macrophytes play a significant role in the nutrient cycle of freshwater ecosystems. However, nutrients from plant debris release into both sediments and overlying water if not timely harvested. To date, minimal information is available regarding nutrient release and its subsequent influences on bacterial communities with decaying debris. In this study, Potamogeton crispus was used as a model plant. Debris biomass levels of 0 g (control, J-CK), 10 g dry weight (DW) (100 g DW/m2, J-10 g), 40 g DW (400 g DW/m2, J-40 g) and 80 g DW (800 g DW/m2, J-80 g) were used to simulate the different biomass densities of P. crispus in field. The physicochemical parameters of overlying water and sediment samples were analysed. The community composition of anammox bacteria in the sediment was also analysed using 16S rRNA genes as markers. The results showed that dissolved oxygen and pH dramatically decreased, whereas total nitrogen (TN) and NH4+-N concentrations increased in the overlying water in the initial stage of P. crispus decomposition. However, NO3--N concentration changes in the overlying water were more complicated. The concentrations of organic matter, TN and NH4+-N in the sediment all increased, but the rate of increase varied among the groups with different initial biomass levels, indicating that these physicochemical properties in sediment are significantly affected by debris biomass level and decay time. In addition, the order of anammox bacteria abundance was J-40 g > J-CK > J-80 g > J-10 g. Moreover, the community structure of anammox bacteria were simpler compared to that of J-CK as debris biomass level increased. The results demonstrate that P. crispus debris decomposition could affect the ecological distribution of anammox bacteria. Such influence clearly varies with varying amounts of P. crispus biomass debris. This information could be useful for the management of aquatic macrophytes in freshwater ecosystems.
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Affiliation(s)
- Xiaohong Zhou
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China.
| | - Mingyuan Wang
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Chunzi Wen
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Dan Liu
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
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21
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Fu L, Chen Y, Li S, He H, Mi T, Zhen Y, Yu Z. Shifts in the anammox bacterial community structure and abundance in sediments from the Changjiang Estuary and its adjacent area. Syst Appl Microbiol 2019; 42:383-396. [PMID: 30679000 DOI: 10.1016/j.syapm.2018.12.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 12/13/2018] [Accepted: 12/19/2018] [Indexed: 10/27/2022]
Abstract
Anaerobic ammonium oxidation (anammox) is an important process in marine nitrogen cycle. In this study, diverse anammox bacteria were identified in the sediments of the Changjiang (Yangtze) Estuary and its adjacent area. Specifically, the community characters of anammox bacteria in the studied area were studied by quantitative polymerase chain reaction (qPCR), as well as 16S rRNA gene- and functional gene (hzo)-based Roche 454 sequencing. The abundance of denitrifying bacteria detected by the nirS gene was greater than that of anammox bacteria. 16S rRNA and hzo gene fragments affiliating with known anammox bacterial lineages were recovered, and the two major phylotypes belonged to the Candidatus Scalindua (Ca. Scalindua) genus, with >90% sequence similarity. A phylogenetic analysis detected the Scalindua and Brocadia genera together with some anammox-like bacterial clusters, which suggested a higher diversity in the studied ecosystem than in open ocean environment, where only Scalindua genus was detected. A redundancy analysis (RDA) showed that total organic carbon (TOC) and total nitrogen (TN) content in sediments significantly influenced anammox bacterial abundance of. Spearman correlation analyses confirmed that the spatial variation in anammox bacterial abundance was highly correlated with TOC (P<0.01) and TN (P<0.01) contents in sediments.
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Affiliation(s)
- Lulu Fu
- College of Marine Life Science, Ocean University of China, Qingdao 266003, PR China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China; Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao 266100, PR China
| | - Yangyang Chen
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China; Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao 266100, PR China; College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, PR China
| | - Siqi Li
- College of Marine Life Science, Ocean University of China, Qingdao 266003, PR China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China; Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao 266100, PR China
| | - Hui He
- College of Marine Life Science, Ocean University of China, Qingdao 266003, PR China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China; Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao 266100, PR China; Key Laboratory of Marine Chemical Theory and Technology, Ministry of Education, Qingdao 266100, PR China
| | - Tiezhu Mi
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China; Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao 266100, PR China; College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, PR China
| | - Yu Zhen
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China; Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao 266100, PR China; College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, PR China.
| | - Zhigang Yu
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China; Key Laboratory of Marine Chemical Theory and Technology, Ministry of Education, Qingdao 266100, PR China
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LUVIZOTTO DANICEM, ARAUJO JULIANAE, SILVA MICHELEDECÁSSIAP, DIAS ARMANDOCF, KRAFT BEATE, TEGETMEYE HALINA, STROUS MARC, ANDREOTE FERNANDOD. The rates and players of denitrification, dissimilatory nitrate reduction to ammonia (DNRA) and anaerobic ammonia oxidation (anammox) in mangrove soils. ACTA ACUST UNITED AC 2019; 91:e20180373. [DOI: 10.1590/0001-3765201820180373] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 06/29/2018] [Indexed: 11/22/2022]
Affiliation(s)
| | | | | | | | - BEATE KRAFT
- Max Planck Institute for Marine Microbiology, Germany; University of Southern Denmark, Denmark
| | - HALINA TEGETMEYE
- Max Planck Institute for Marine Microbiology, Germany; University of Bielefeld, Germany
| | - MARC STROUS
- Max Planck Institute for Marine Microbiology, Germany; University of Bielefeld, Germany; University of Calgary, Canada
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23
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Shen LD, Liu X, Wu HS. Importance of anaerobic ammonium oxidation as a nitrogen removal pathway in freshwater marsh sediments. J Appl Microbiol 2018; 125:1423-1434. [DOI: 10.1111/jam.14042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 06/04/2018] [Accepted: 07/04/2018] [Indexed: 12/26/2022]
Affiliation(s)
- L.-D. Shen
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters; Jiangsu Key Laboratory of Agricultural Meteorology; School of Applied Meteorology; Nanjing University of Information Science and Technology; Nanjing China
- Department of Ecology; School of Applied Meteorology; Nanjing University of Information Science and Technology; Nanjing China
| | - X. Liu
- Department of Ecology; School of Applied Meteorology; Nanjing University of Information Science and Technology; Nanjing China
| | - H.-S. Wu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters; Jiangsu Key Laboratory of Agricultural Meteorology; School of Applied Meteorology; Nanjing University of Information Science and Technology; Nanjing China
- Department of Ecology; School of Applied Meteorology; Nanjing University of Information Science and Technology; Nanjing China
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24
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Akbarzadeh Z, Laverman AM, Rezanezhad F, Raimonet M, Viollier E, Shafei B, Van Cappellen P. Benthic nitrite exchanges in the Seine River (France): An early diagenetic modeling analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 628-629:580-593. [PMID: 29454199 DOI: 10.1016/j.scitotenv.2018.01.319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 01/10/2018] [Accepted: 01/30/2018] [Indexed: 06/08/2023]
Abstract
Nitrite is a toxic intermediate compound in the nitrogen (N) cycle. Elevated concentrations of nitrite have been observed in the Seine River, raising questions about its sources and fate. Here, we assess the role of bottom sediments as potential sources or sinks of nitrite along the river continuum. Sediment cores were collected from two depocenters, one located upstream, the other downstream, from the largest wastewater treatment plant (WWTP) servicing the conurbation of Paris. Pore water profiles of oxygen, nitrate, nitrite and ammonium were measured. Ammonium, nitrate and nitrite fluxes across the sediment-water interface (SWI) were determined in separate core incubation experiments. The data were interpreted with a one-dimensional, multi-component reactive transport model, which accounts for the production and consumption of nitrite through nitrification, denitrification, anammox and dissimilatory nitrate reduction to ammonium (DNRA). In all core incubation experiments, nitrate uptake by the sediments was observed, indicative of high rates of denitrification. In contrast, for both sampling locations, the sediments in cores collected in August 2012 acted as sinks for nitrite, but those collected in October 2013 released nitrite to the overlying water. The model results suggest that the first step of nitrification generated most pore water nitrite at the two locations. While nitrification was also the main pathway consuming nitrite in the sediments upstream of the WWTP, anammox dominated nitrite removal at the downstream site. Sensitivity analyses indicated that the magnitude and direction of the benthic nitrite fluxes most strongly depend on bottom water oxygenation and the deposition flux of labile organic matter.
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Affiliation(s)
- Zahra Akbarzadeh
- Ecohydrology Research Group, Water Institute and Department of Earth and Environmental Sciences, University of Waterloo, Canada.
| | | | - Fereidoun Rezanezhad
- Ecohydrology Research Group, Water Institute and Department of Earth and Environmental Sciences, University of Waterloo, Canada
| | - Mélanie Raimonet
- UMR 7619 METIS, Université Pierre et Marie Curie, Paris 6, Sorbonne Universités, Paris, France
| | - Eric Viollier
- Laboratoire de Géochimie des Eaux, UMR 7154, Université Paris Diderot, Paris 7 and Institut de Physique du Globe (IPGP), Paris, France
| | - Babak Shafei
- AquaNRG Consulting Inc., Houston, TX, United States
| | - Philippe Van Cappellen
- Ecohydrology Research Group, Water Institute and Department of Earth and Environmental Sciences, University of Waterloo, Canada
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25
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Wang S, Wang W, Liu L, Zhuang L, Zhao S, Su Y, Li Y, Wang M, Wang C, Xu L, Zhu G. Microbial Nitrogen Cycle Hotspots in the Plant-Bed/Ditch System of a Constructed Wetland with N 2O Mitigation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:6226-6236. [PMID: 29750509 DOI: 10.1021/acs.est.7b04925] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Artificial microbial nitrogen (N) cycle hotspots in the plant-bed/ditch system were developed and investigated based on intact core and slurry assays measurement using isotopic tracing technology, quantitative PCR and high-throughput sequencing. By increasing hydraulic retention time and periodically fluctuating water level in heterogeneous riparian zones, hotspots of anammox, nitrification, denitrification, ammonium (NH4+) oxidation, nitrite (NO2-) oxidation, nitrate (NO3-) reduction and DNRA were all stimulated at the interface sediments, with the abundance and activity being about 1-3 orders of magnitude higher than those in nonhotspots. Isotopic pairing experiments revealed that in microbial hotspots, nitrite sources were higher than the sinks, and both NH4+ oxidation (55.8%) and NO3- reduction (44.2%) provided nitrite for anammox, which accounted for 43.0% of N-loss and 44.4% of NH4+ removal in riparian zones but did not involve nitrous oxide (N2O) emission risks. High-throughput analysis identified that bacterial quorum sensing mediated this anammox hotspot with B.fulgida dominating the anammox community, but it was B. anammoxidans and Jettenia sp. that contributed more to anammox activity. In the nonhotspot zones, the NO2- source (NO3- reduction dominated) was lower than the sink, limiting the effects on anammox. The in situ N2O flux measurement showed that the microbial hotspot had a 27.1% reduced N2O emission flux compared with the nonhotspot zones.
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Affiliation(s)
- Shanyun Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing , China
| | - Weidong Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing , China
| | - Lu Liu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing , China
| | - Linjie Zhuang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing , China
| | - Siyan Zhao
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Yu Su
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Yixiao Li
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing , China
| | - Mengzi Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing , China
| | - Cheng Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Liya Xu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing , China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
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Bulmer RH, Schwendenmann L, Lohrer AM, Lundquist CJ. Sediment carbon and nutrient fluxes from cleared and intact temperate mangrove ecosystems and adjacent sandflats. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 599-600:1874-1884. [PMID: 28545214 DOI: 10.1016/j.scitotenv.2017.05.139] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/12/2017] [Accepted: 05/15/2017] [Indexed: 06/07/2023]
Abstract
The loss of mangrove ecosystems is associated with numerous impacts on coastal and estuarine function, including sediment carbon and nutrient cycling. In this study we compared in situ fluxes of carbon dioxide (CO2) from the sediment to the atmosphere, and fluxes of dissolved inorganic nutrients and oxygen across the sediment-water interface, in intact and cleared mangrove and sandflat ecosystems in a temperate estuary. Measurements were made 20 and 25months after mangrove clearance, in summer and winter, respectively. Sediment CO2 efflux was over two-fold higher from cleared than intact mangrove ecosystems at 20 and 25months after mangrove clearance. The higher CO2 efflux from the cleared site was explained by an increase in respiration of dead root material along with sediment disturbance following mangrove clearance. In contrast, sediment CO2 efflux from the sandflat site was negligible (≤9.13±1.18mmolm-2d-1), associated with lower sediment organic matter content. The fluxes of inorganic nutrients (NH4+, NOx and PO43-) from intact and cleared mangrove sediments were low (≤20.37±18.66μmolm-2h-1). The highest NH4+ fluxes were measured at the sandflat site (69.21±13.49μmolm-2h-1). Lower inorganic nutrient fluxes within the cleared and intact mangrove sites compared to the sandflat site were associated with lower abundance of larger burrowing macrofauna. Further, a higher fraction of organic matter, silt and clay content in mangrove sediments may have limited nutrient exchange.
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Affiliation(s)
- Richard H Bulmer
- National Institute of Water and Atmospheric Research Ltd (NIWA), Hamilton, New Zealand; Institute of Marine Science, University of Auckland, Auckland, New Zealand.
| | | | - Andrew M Lohrer
- National Institute of Water and Atmospheric Research Ltd (NIWA), Hamilton, New Zealand
| | - Carolyn J Lundquist
- National Institute of Water and Atmospheric Research Ltd (NIWA), Hamilton, New Zealand; Institute of Marine Science, University of Auckland, Auckland, New Zealand
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27
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Assessment of molecular detection of anaerobic ammonium-oxidizing (anammox) bacteria in different environmental samples using PCR primers based on 16S rRNA and functional genes. Appl Microbiol Biotechnol 2017; 101:7689-7702. [PMID: 28932888 DOI: 10.1007/s00253-017-8502-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/10/2017] [Accepted: 08/26/2017] [Indexed: 10/18/2022]
Abstract
Eleven published PCR primer sets for detecting genes encoding 16S ribosomal RNA (rRNA), hydrazine oxidoreductase (HZO), cytochrome cd 1-containing nitrite reductase (NirS), and hydrazine synthase subunit A (HzsA) of anaerobic ammonium-oxidizing (anammox) bacteria were assessed for the diversity and abundance of anammox bacteria in samples of three environments: wastewater treatment plant (WWTP), wetland of Mai Po Nature Reserve (MP), and the South China Sea (SCS). Consistent phylogenetic results of three biomarkers (16S rRNA, hzo, and hzsA) of anammox bacteria were obtained from all samples. WWTP had the lowest diversity with Candidatus Kuenenia dominating while the SCS was dominated by Candidatus Scalindua. MP showed the highest diversity of anammox bacteria including C. Scalindua, C. Kuenenia, and Candidatus Brocadia. Comparing different primer sets, no significant differences in specificity for 16S rRNA gene could be distinguished. Primer set CL1 showed relatively high efficiency in detecting the anammox bacterium hzo gene from all samples, while CL2 showed greater selectivity for WWTP samples. The recently reported primer sets of the hzsA gene resulted in high efficiencies in detecting anammox bacteria while nirS primer sets were more selective for specific samples. Results collectively indicate that the distribution of anammox bacteria is niche-specific within different ecosystems and primer specificity may cause biases on the diversity detected.
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28
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Sulfide-Induced Dissimilatory Nitrate Reduction to Ammonium Supports Anaerobic Ammonium Oxidation (Anammox) in an Open-Water Unit Process Wetland. Appl Environ Microbiol 2017; 83:AEM.00782-17. [PMID: 28526796 DOI: 10.1128/aem.00782-17] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 05/14/2017] [Indexed: 02/01/2023] Open
Abstract
Open-water unit process wetlands host a benthic diatomaceous and bacterial assemblage capable of nitrate removal from treated municipal wastewater with unexpected contributions from anammox processes. In exploring mechanistic drivers of anammox, 16S rRNA gene sequencing profiles of the biomat revealed significant microbial community shifts along the flow path and with depth. Notably, there was an increasing abundance of sulfate reducers (Desulfococcus and other Deltaproteobacteria) and anammox microorganisms (Brocadiaceae) with depth. Pore water profiles demonstrated that nitrate and sulfate concentrations exhibited a commensurate decrease with biomat depth accompanied by the accumulation of ammonium. Quantitative PCR targeting the anammox hydrazine synthase gene, hzsA, revealed a 3-fold increase in abundance with biomat depth as well as a 2-fold increase in the sulfate reductase gene, dsrA These microbial and geochemical trends were most pronounced in proximity to the influent region of the wetland where the biomat was thickest and influent nitrate concentrations were highest. While direct genetic queries for dissimilatory nitrate reduction to ammonium (DNRA) microorganisms proved unsuccessful, an increasing depth-dependent dominance of Gammaproteobacteria and diatoms that have previously been functionally linked to DNRA was observed. To further explore this potential, a series of microcosms containing field-derived biomat material confirmed the ability of the community to produce sulfide and reduce nitrate; however, significant ammonium production was observed only in the presence of hydrogen sulfide. Collectively, these results suggest that biogenic sulfide induces DNRA, which in turn can explain the requisite coproduction of ammonium and nitrite from nitrified effluent necessary to sustain the anammox community.IMPORTANCE This study aims to increase understanding of why and how anammox is occurring in an engineered wetland with limited exogenous contributions of ammonium and nitrite. In doing so, the study has implications for how geochemical parameters could potentially be leveraged to impact nutrient cycling and attenuation during the operation of treatment wetlands. The work also contributes to ongoing discussions about biogeochemical signatures surrounding anammox processes and enhances our understanding of the contributions of anammox processes in freshwater environments.
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29
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Shen LD, Cheng HX, Liu X, Li JH, Liu Y. Potential role of anammox in nitrogen removal in a freshwater reservoir, Jiulonghu Reservoir (China). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:3890-3899. [PMID: 27905043 DOI: 10.1007/s11356-016-8126-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Accepted: 11/16/2016] [Indexed: 06/06/2023]
Abstract
Currently, the nitrogen removal potential of anaerobic ammonium oxidation (anammox) and its regulating factors in reservoir systems remain uncertain. Here, we provided the molecular and isotopic evidence for anammox in the freshwater sediment of Jiulonghu Reservoir that is located in Quzhou, Zhejiang Province, China. Diverse 16S rRNA gene sequences related to Candidatus Kuenenia and Candidatus Brocadia were detected by using high-throughput (Illumina MiSeq) sequencing of total bacterial 16S rRNA genes, and the Candidatus Brocadia was the most frequently detected anammox bacterial genus. The anammox bacterial abundance was determined based on quantitative PCR on hzsA (the alpha subunit of the hydrazine synthase) genes and varied from 3.1 × 105 to 1.1 × 106 copies g-1 dry sediment. Homogenized sediments were further incubated with 15NO3- amendments to measure the potential anammox rates and determine the contribution of this process to dinitrogen gas (N2) production. The potential rates of anammox ranged between 8.1 and 30.8 nmol N2 g-1 dry sediment day-1, and anammox accounted for 7.7-20.5% of total N2 production in sediment. Higher levels of anammox bacterial diversity, abundance, and activity were observed in the downstream with greater human disturbance than those in the upstream with less human disturbance. Correlation analyses suggested that the inorganic nitrogen level in sediment could be a key factor for the anammox bacterial abundance and activity. The results showed that the nitrogen removal via anammox may not be negligible in the examined reservoir and indicated that human activities could influence the anammox process in reservoir systems.
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Affiliation(s)
- Li-Dong Shen
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Jiangsu Key Laboratory of Agricultural Meteorology, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Hai-Xiang Cheng
- College of Chemistry and Materials Engineering, Quzhou University, Quzhou, 324000, China.
| | - Xu Liu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Jiangsu Key Laboratory of Agricultural Meteorology, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Jian-Hui Li
- Quzhou Academy of Agricultural Sciences, Quzhou, 324000, China
| | - Yan Liu
- Wuxijiang National Wetland Park Service, Quzhou, 324000, China
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Brin LD, Giblin AE, Rich JJ. Similar temperature responses suggest future climate warming will not alter partitioning between denitrification and anammox in temperate marine sediments. GLOBAL CHANGE BIOLOGY 2017; 23:331-340. [PMID: 27225536 DOI: 10.1111/gcb.13370] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 05/06/2016] [Accepted: 05/09/2016] [Indexed: 06/05/2023]
Abstract
Removal of biologically available nitrogen (N) by the microbially mediated processes denitrification and anaerobic ammonium oxidation (anammox) affects ecosystem N availability. Although few studies have examined temperature responses of denitrification and anammox, previous work suggests that denitrification could become more important than anammox in response to climate warming. To test this hypothesis, we determined whether temperature responses of denitrification and anammox differed in shelf and estuarine sediments from coastal Rhode Island over a seasonal cycle. The influence of temperature and organic C availability was further assessed in a 12-week laboratory microcosm experiment. Temperature responses, as characterized by thermal optima (Topt ) and apparent activation energy (Ea ), were determined by measuring potential rates of denitrification and anammox at 31 discrete temperatures ranging from 3 to 59 °C. With a few exceptions, Topt and Ea of denitrification and anammox did not differ in Rhode Island sediments over the seasonal cycle. In microcosm sediments, Ea was somewhat lower for anammox compared to denitrification across all treatments. However, Topt did not differ between processes, and neither Ea nor Topt changed with warming or carbon addition. Thus, the two processes behaved similarly in terms of temperature responses, and these responses were not influenced by warming. This led us to reject the hypothesis that anammox is more cold-adapted than denitrification in our study system. Overall, our study suggests that temperature responses of both processes can be accurately modeled for temperate regions in the future using a single set of parameters, which are likely not to change over the next century as a result of predicted climate warming. We further conclude that climate warming will not directly alter the partitioning of N flow through anammox and denitrification.
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Affiliation(s)
- Lindsay D Brin
- Canadian Rivers Institute, University of New Brunswick, 100 Tucker Park Road, Saint John, NB, E2L 4L5, Canada
| | - Anne E Giblin
- Ecosystems Center, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 02543, USA
| | - Jeremy J Rich
- School of Marine Sciences, Darling Marine Center, University of Maine, Walpole, ME, 04573, USA
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Tikilili PV, Chirwa E. Searching for indigenous anaerobic ammonium oxidizing (anammox) bacteria in South African habitats: Pretoria region. BIOTECHNOL BIOTEC EQ 2016. [DOI: 10.1080/13102818.2016.1225515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Phumza Vuyokazi Tikilili
- Water Utilization Division, Department of Chemical Engineering, University of Pretoria , South Campus, Pretoria, South Africa
| | - Evans Chirwa
- Water Utilization Division, Department of Chemical Engineering, University of Pretoria , South Campus, Pretoria, South Africa
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Lipsewers YA, Hopmans EC, Meysman FJR, Sinninghe Damsté JS, Villanueva L. Abundance and Diversity of Denitrifying and Anammox Bacteria in Seasonally Hypoxic and Sulfidic Sediments of the Saline Lake Grevelingen. Front Microbiol 2016; 7:1661. [PMID: 27812355 PMCID: PMC5071380 DOI: 10.3389/fmicb.2016.01661] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/05/2016] [Indexed: 11/13/2022] Open
Abstract
Denitrifying and anammox bacteria are involved in the nitrogen cycling in marine sediments but the environmental factors that regulate the relative importance of these processes are not well constrained. Here, we evaluated the abundance, diversity, and potential activity of denitrifying, anammox, and sulfide-dependent denitrifying bacteria in the sediments of the seasonally hypoxic saline Lake Grevelingen, known to harbor an active microbial community involved in sulfur oxidation pathways. Depth distributions of 16S rRNA gene, nirS gene of denitrifying and anammox bacteria, aprA gene of sulfur-oxidizing and sulfate-reducing bacteria, and ladderane lipids of anammox bacteria were studied in sediments impacted by seasonally hypoxic bottom waters. Samples were collected down to 5 cm depth (1 cm resolution) at three different locations before (March) and during summer hypoxia (August). The abundance of denitrifying bacteria did not vary despite of differences in oxygen and sulfide availability in the sediments, whereas anammox bacteria were more abundant in the summer hypoxia but in those sediments with lower sulfide concentrations. The potential activity of denitrifying and anammox bacteria as well as of sulfur-oxidizing, including sulfide-dependent denitrifiers and sulfate-reducing bacteria, was potentially inhibited by the competition for nitrate and nitrite with cable and/or Beggiatoa-like bacteria in March and by the accumulation of sulfide in the summer hypoxia. The simultaneous presence and activity of organoheterotrophic denitrifying bacteria, sulfide-dependent denitrifiers, and anammox bacteria suggests a tight network of bacteria coupling carbon-, nitrogen-, and sulfur cycling in Lake Grevelingen sediments.
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Affiliation(s)
- Yvonne A Lipsewers
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University Den Burg, Netherlands
| | - Ellen C Hopmans
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University Den Burg, Netherlands
| | - Filip J R Meysman
- Department of Estuarine and Delta Systems, Royal Netherlands Institute for Sea Research, Utrecht University Den Burg, Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht UniversityDen Burg, Netherlands; Faculty of Geosciences, Department of Earth Sciences, Utrecht UniversityUtrecht, Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University Den Burg, Netherlands
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Zheng Y, Hou L, Liu M, Yin G, Gao J, Jiang X, Lin X, Li X, Yu C, Wang R. Community composition and activity of anaerobic ammonium oxidation bacteria in the rhizosphere of salt-marsh grass Spartina alterniflora. Appl Microbiol Biotechnol 2016; 100:8203-12. [DOI: 10.1007/s00253-016-7625-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Revised: 05/03/2016] [Accepted: 05/07/2016] [Indexed: 11/28/2022]
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Rios-Del Toro EE, Cervantes FJ. Coupling between anammox and autotrophic denitrification for simultaneous removal of ammonium and sulfide by enriched marine sediments. Biodegradation 2016; 27:107-18. [DOI: 10.1007/s10532-016-9759-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 03/15/2016] [Indexed: 10/22/2022]
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Huygens D, Trimmer M, Rütting T, Müller C, Heppell CM, Lansdown K, Boeckx P. Biogeochemical Nitrogen Cycling in Wetland Ecosystems: Nitrogen-15 Isotope Techniques. METHODS IN BIOGEOCHEMISTRY OF WETLANDS 2015. [DOI: 10.2136/sssabookser10.c30] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Dries Huygens
- Isotope Bioscience Laboratory-ISOFYS; Ghent Univ.; B-9000 Gent Belgium
| | - Mark Trimmer
- School of Biological and Chemical Sciences; Queen Mary Univ. of London; London E1 4NS UK
| | - Tobias Rütting
- Dep. of Earth Sciences; Univ. of Gothenburg; 405 30 Gothenburg Sweden
| | - Christoph Müller
- Dep. of Plant Ecology; Justus-Liebig Univ., Giessen; 35392 Giessen Germany
| | | | - Katrina Lansdown
- School of Geography; Queen Mary Univ. of London; London E1 4NS UK
| | - Pascal Boeckx
- Isotope Bioscience Laboratory-ISOFYS; Ghent Univ.; B-9000 Gent Belgium
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Hou L, Zheng Y, Liu M, Li X, Lin X, Yin G, Gao J, Deng F, Chen F, Jiang X. Anaerobic ammonium oxidation and its contribution to nitrogen removal in China's coastal wetlands. Sci Rep 2015; 5:15621. [PMID: 26494435 PMCID: PMC4616045 DOI: 10.1038/srep15621] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 09/28/2015] [Indexed: 11/09/2022] Open
Abstract
Over the past several decades, human activities have caused substantial enrichment of reactive nitrogen in China’s coastal wetlands. Although anaerobic ammonium oxidation (anammox), the process of oxidizing ammonium into dinitrogen gas through the reduction of nitrite, is identified as an important process for removing reactive nitrogen, little is known about the dynamics of anammox and its contribution to nitrogen removal in nitrogen-enriched environments. Here, we examine potential rates of anammox and associate them with bacterial diversity and abundance across the coastal wetlands of China using molecular and isotope tracing techniques. High anammox bacterial diversity was detected in China’s coastal wetlands and included Candidatus Scalindua, Kuenenia, Brocadia, and Jettenia. Potential anammox rates were more closely associated with the abundance of anammox bacteria than to their diversity. Among all measured environmental variables, temperature was a key environmental factor, causing a latitudinal distribution of the anammox bacterial community composition, biodiversity and activity along the coastal wetlands of China. Based on nitrogen isotope tracing experiments, anammox was estimated to account for approximately 3.8–10.7% of the total reactive nitrogen removal in the study area. Combined with denitrification, anammox can remove 20.7% of the total external terrigenous inorganic nitrogen annually transported into China’s coastal wetland ecosystems.
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Affiliation(s)
- Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, China
| | - Yanling Zheng
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, China.,College of Geographical Sciences, East China Normal University, Shanghai 200241, China
| | - Min Liu
- College of Geographical Sciences, East China Normal University, Shanghai 200241, China
| | - Xiaofei Li
- College of Geographical Sciences, East China Normal University, Shanghai 200241, China
| | - Xianbiao Lin
- College of Geographical Sciences, East China Normal University, Shanghai 200241, China
| | - Guoyu Yin
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, China.,College of Geographical Sciences, East China Normal University, Shanghai 200241, China
| | - Juan Gao
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, China
| | - Fengyu Deng
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, China
| | - Fei Chen
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, China
| | - Xiaofen Jiang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, China
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Occurrence and importance of anaerobic ammonium-oxidising bacteria in vegetable soils. Appl Microbiol Biotechnol 2015; 99:5709-18. [PMID: 25690313 DOI: 10.1007/s00253-015-6454-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 01/28/2015] [Accepted: 02/01/2015] [Indexed: 12/27/2022]
Abstract
The quantitative importance of anaerobic ammonium oxidation (anammox) has been described in paddy fields, while the presence and importance of anammox in subsurface soil from vegetable fields have not been determined yet. Here, we investigated the occurrence and activity of anammox bacteria in five different types of vegetable fields located in Jiangsu Province, China. Stable isotope experiments confirmed the anammox activity in the examined soils, with the potential rates of 2.1 and 23.2 nmol N2 g(-1) dry soil day(-1), and the anammox accounted for 5.9-20.5% of total soil dinitrogen gas production. It is estimated that a total loss of 7.1-78.2 g N m(-2) year(-1) could be linked to the anammox process in the examined vegetable fields. Phylogenetic analyses showed that multiple co-occurring anammox genera were present in the examined soils, including Candidatus Brocadia, Candidatus Kuenenia, Candidatus Anammoxoglobus and Candidatus Jettenia, and Candidatus Brocadia appeared to be the most common anammox genus. Quantitative PCR further confirmed the presence of anammox bacteria in the examined soils, with the abundance varying from 2.8 × 10(5) to 3.0 × 10(6) copies g(-1) dry soil. Correlation analyses suggested that the soil ammonium concentration had significant influence on the activity and abundance of anammox bacteria in the examined soils. The results of our study showed the presence of diverse anammox bacteria and indicated that the anammox process could serve as an important nitrogen loss pathway in vegetable fields.
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Potential contribution of anammox to nitrogen loss from paddy soils in Southern China. Appl Environ Microbiol 2014; 81:938-47. [PMID: 25416768 DOI: 10.1128/aem.02664-14] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The anaerobic oxidation of ammonium (anammox) process has been observed in diverse terrestrial ecosystems, while the contribution of anammox to N2 production in paddy soils is not well documented. In this study, the anammox activity and the abundance and diversity of anammox bacteria were investigated to assess the anammox potential of 12 typical paddy soils collected in southern China. Anammox bacteria related to "Candidatus Brocadia" and "Candidatus Kuenenia" and two novel unidentified clusters were detected, with "Candidatus Brocadia" comprising 50% of the anammox population. The prevalence of the anammox was confirmed by the quantitative PCR results based on hydrazine synthase (hzsB) genes, which showed that the abundance ranged from 1.16 × 10(4) to 9.65 × 10(4) copies per gram of dry weight. The anammox rates measured by the isotope-pairing technique ranged from 0.27 to 5.25 nmol N per gram of soil per hour in these paddy soils, which contributed 0.6 to 15% to soil N2 production. It is estimated that a total loss of 2.50 × 10(6) Mg N per year is linked to anammox in the paddy fields in southern China, which implied that ca. 10% of the applied ammonia fertilizers is lost via the anammox process. Anammox activity was significantly correlated with the abundance of hzsB genes, soil nitrate concentration, and C/N ratio. Additionally, ammonia concentration and pH were found to be significantly correlated with the anammox bacterial structure.
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Evidence for the cooccurrence of nitrite-dependent anaerobic ammonium and methane oxidation processes in a flooded paddy field. Appl Environ Microbiol 2014; 80:7611-9. [PMID: 25261523 DOI: 10.1128/aem.02379-14] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Anaerobic ammonium oxidation (anammox) and nitrite-dependent anaerobic methane oxidation (n-damo) are two of the most recent discoveries in the microbial nitrogen cycle. In the present study, we provide direct evidence for the cooccurrence of the anammox and n-damo processes in a flooded paddy field in southeastern China. Stable isotope experiments showed that the potential anammox rates ranged from 5.6 to 22.7 nmol N2 g(-1) (dry weight) day(-1) and the potential n-damo rates varied from 0.2 to 2.1 nmol CO2 g(-1) (dry weight) day(-1) in different layers of soil cores. Quantitative PCR showed that the abundance of anammox bacteria ranged from 1.0 × 10(5) to 2.0 × 10(6) copies g(-1) (dry weight) in different layers of soil cores and the abundance of n-damo bacteria varied from 3.8 × 10(5) to 6.1 × 10(6) copies g(-1) (dry weight). Phylogenetic analyses of the recovered 16S rRNA gene sequences showed that anammox bacteria affiliated with "Candidatus Brocadia" and "Candidatus Kuenenia" and n-damo bacteria related to "Candidatus Methylomirabilis oxyfera" were present in the soil cores. It is estimated that a total loss of 50.7 g N m(-2) per year could be linked to the anammox process, which is at intermediate levels for the nitrogen flux ranges of aerobic ammonium oxidation and denitrification reported in wetland soils. In addition, it is estimated that a total of 0.14 g CH4 m(-2) per year could be oxidized via the n-damo process, while this rate is at the lower end of the aerobic methane oxidation rates reported in wetland soils.
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Lipsewers YA, Bale NJ, Hopmans EC, Schouten S, Sinninghe Damsté JS, Villanueva L. Seasonality and depth distribution of the abundance and activity of ammonia oxidizing microorganisms in marine coastal sediments (North Sea). Front Microbiol 2014; 5:472. [PMID: 25250020 PMCID: PMC4155873 DOI: 10.3389/fmicb.2014.00472] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 08/20/2014] [Indexed: 11/13/2022] Open
Abstract
Microbial processes such as nitrification and anaerobic ammonium oxidation (anammox) are important for nitrogen cycling in marine sediments. Seasonal variations of archaeal and bacterial ammonia oxidizers (AOA and AOB) and anammox bacteria, as well as the environmental factors affecting these groups, are not well studied. We have examined the seasonal and depth distribution of the abundance and potential activity of these microbial groups in coastal marine sediments of the southern North Sea. This was achieved by quantifying specific intact polar lipids as well as the abundance and gene expression of their 16S rRNA gene, the ammonia monooxygenase subunit A (amoA) gene of AOA and AOB, and the hydrazine synthase (hzsA) gene of anammox bacteria. AOA, AOB, and anammox bacteria were detected and transcriptionally active down to 12 cm sediment depth. In all seasons, the abundance of AOA was higher compared to the AOB abundance suggesting that AOA play a more dominant role in aerobic ammonia oxidation in these sediments. Anammox bacteria were abundant and active even in oxygenated and bioturbated parts of the sediment. The abundance of AOA and AOB was relatively stable with depth and over the seasonal cycle, while anammox bacteria abundance and transcriptional activity were highest in August. North Sea sediments thus seem to provide a common, stable, ecological niche for AOA, AOB, and anammox bacteria.
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Affiliation(s)
- Yvonne A Lipsewers
- Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research Den Burg, Netherlands
| | - Nicole J Bale
- Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research Den Burg, Netherlands
| | - Ellen C Hopmans
- Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research Den Burg, Netherlands
| | - Stefan Schouten
- Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research Den Burg, Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research Den Burg, Netherlands
| | - Laura Villanueva
- Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research Den Burg, Netherlands
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Zhou S, Borjigin S, Riya S, Terada A, Hosomi M. The relationship between anammox and denitrification in the sediment of an inland river. THE SCIENCE OF THE TOTAL ENVIRONMENT 2014; 490:1029-1036. [PMID: 24914531 DOI: 10.1016/j.scitotenv.2014.05.096] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 05/12/2014] [Accepted: 05/21/2014] [Indexed: 06/03/2023]
Abstract
This study measured the microbial processes of anaerobic ammonium oxidation (anammox) and denitrification in sediment sampled from two sites in the estuary of an inland river (Koisegawa River, Ibaragi prefecture, Japan) using a nitrogen isotope pairing technique (IPT). The responses of anammox and denitrification activities to temperature and nitrate concentration were also evaluated. Further, to elucidate the correlation between anammox and denitrification processes, an inhibition experiment was conducted, using chlorate to inhibit the first step of denitrification. Denitrification activity was much higher than anammox activity, and it reached a maximum at the surface layer in February 2012. Denitrification activity decreased as sediment depth increased, and a similar phenomenon was observed for anammox activity in the sediment of site A, where aquatic plants were absent from the surroundings. The activities of both denitrification and anammox were temperature-dependent, but they responded differently to changes in incubation temperature. Compared to a linear increase in denitrification as temperature rose to 35 °C, the optimal temperature for anammox was 25 °C, after which the activity decreased sharply. At the same time, both anammox and denitrification activities increased with NO3(-) concentration. The Michaelis-Menten kinetic constants (Vmax and Km) of denitrification were significantly higher than those of the anammox process. Furthermore, anammox activity decreased accordingly when the first step of denitrification was inhibited, which probably reduced the amount of the intermediate NO2(-). Our study provides the first direct exploration of the denitrification-dependent correlation of anammox activity in the sediment of inland river.
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Affiliation(s)
- Sheng Zhou
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, No. 1000 Jinqi Road, Shanghai 201403, China; Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
| | - Sodbilig Borjigin
- Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Shohei Riya
- Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Akihiko Terada
- Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Masaaki Hosomi
- Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
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Sun W, Xia C, Xu M, Guo J, Wang A, Sun G. Diversity and distribution of planktonic anaerobic ammonium-oxidizing bacteria in the Dongjiang River, China. Microbiol Res 2014; 169:897-906. [PMID: 24932882 DOI: 10.1016/j.micres.2014.05.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 02/16/2014] [Accepted: 05/14/2014] [Indexed: 01/21/2023]
Abstract
Anaerobic ammonium-oxidizing (anammox) process has recently been recognized as an important pathway for removing fixed nitrogen (N) from aquatic ecosystems. Anammox organisms are widely distributed in freshwater environments. However, little is known about their presence in the water column of riverine ecosystems. Here, the existence of a diverse anammox community was revealed in the water column of the Dongjiang River by analyzing 16S rRNA and hydrazine oxidation (hzo) genes of anammox bacteria. Phylogenetic analyses of hzo genes showed that Candidatus Jettenia related clades of anammox bacteria were dominant in the river, suggesting the ecological microniche distinction from freshwater/estuary and marine anammox bacteria with Ca. Brocadia and Kuenenia genera mainly detected in freshwater/estuary ecosystems, and Ca. Scalindua genus mainly detected in marine ecosystems. The abundance and diversity of anammox bacteria along the river were both significantly correlated with concentrations of NH4(+)-N based on Pearson and partial correlation analyses. Redundancy analyses showed the contents of NH4(+)-N, NO3(-)-N and the ratio of NH4(+)-N to NO2(-)-N significantly influenced the spatial distributions of anammox bacteria in the water column of the Dongjiang River. These results expanded our understanding of the distribution and potential roles of anammox bacteria in the water column of the river ecosystem.
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Affiliation(s)
- Wei Sun
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510070, China; School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510070, China; State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, China
| | - Chunyu Xia
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510070, China; State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, China
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510070, China; State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, China.
| | - Jun Guo
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510070, China; State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, China
| | - Aijie Wang
- Harbin Institute of Technology, Harbin 150090, China
| | - Guoping Sun
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou 510070, China; State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, China.
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Bale NJ, Villanueva L, Fan H, Stal LJ, Hopmans EC, Schouten S, Sinninghe Damsté JS. Occurrence and activity of anammox bacteria in surface sediments of the southern North Sea. FEMS Microbiol Ecol 2014; 89:99-110. [DOI: 10.1111/1574-6941.12338] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 03/25/2014] [Accepted: 03/27/2014] [Indexed: 11/26/2022] Open
Affiliation(s)
- Nicole J. Bale
- Department of Marine Organic Biogeochemistry; NIOZ Royal Netherlands Institute for Sea Research; Den Burg the Netherlands
| | - Laura Villanueva
- Department of Marine Organic Biogeochemistry; NIOZ Royal Netherlands Institute for Sea Research; Den Burg the Netherlands
| | - Haoxin Fan
- Department of Marine Microbiology; NIOZ Royal Netherlands Institute for Sea Research; Yerseke the Netherlands
| | - Lucas J. Stal
- Department of Marine Microbiology; NIOZ Royal Netherlands Institute for Sea Research; Yerseke the Netherlands
| | - Ellen C. Hopmans
- Department of Marine Organic Biogeochemistry; NIOZ Royal Netherlands Institute for Sea Research; Den Burg the Netherlands
| | - Stefan Schouten
- Department of Marine Organic Biogeochemistry; NIOZ Royal Netherlands Institute for Sea Research; Den Burg the Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Organic Biogeochemistry; NIOZ Royal Netherlands Institute for Sea Research; Den Burg the Netherlands
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Song B, Buckner CT, Hembury DJ, Mills RA, Palmer MR. Impact of volcanic ash on anammox communities in deep sea sediments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:159-166. [PMID: 24596289 DOI: 10.1111/1758-2229.12137] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Accepted: 12/11/2013] [Indexed: 06/03/2023]
Abstract
Subaerial explosive volcanism contributes substantial amounts of material to the oceans, but little is known about the impact of volcanic ash on sedimentary microbial activity. We have studied anammox communities in deep sea sediments near the volcanically active island of Montserrat, Lesser Antilles. The rates of anammox and denitrification in the sediments were measured using (15)N isotope pairing incubation experiments, while 16S rRNA genes were used to examine anammox community structures. The higher anammox rates were measured in sediment containing the lower accumulation of volcanic ash in the surface sediments, while the lowest activities were found in sediments with the highest ash deposit. 16S rRNA gene analysis revealed the presence of 'Candidatus Scalindua spp.' in the sediments. The lowest diversity of anammox bacteria was observed in the sediments with the highest ash deposit. Overall, this study demonstrates that the deposition of volcanic material in deep sea sediments has negative impacts on activity and diversity of the anammox community. Since anammox may account for up to 79% of N2 production in marine ecosystems, periods of extensive explosive volcanism in Earth history may have had a hitherto unrecognized negative impact on the sedimentary nitrogen removal processes.
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Affiliation(s)
- Bongkeun Song
- Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC, USA; Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, USA
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Shao S, Luan X, Dang H, Zhou H, Zhao Y, Liu H, Zhang Y, Dai L, Ye Y, Klotz MG. Deep-sea methane seep sediments in the Okhotsk Sea sustain diverse and abundant anammox bacteria. FEMS Microbiol Ecol 2013; 87:503-16. [DOI: 10.1111/1574-6941.12241] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 10/14/2013] [Accepted: 10/20/2013] [Indexed: 11/28/2022] Open
Affiliation(s)
- Sudong Shao
- State Key Laboratory of Marine Environmental Science; Xiamen University; Xiamen China
- Institute of Marine Microbes and Ecospheres; Xiamen University; Xiamen China
- Department of Ocean Science and Engineering; Zhejiang University; Hangzhou China
- State Key Laboratory of Heavy Oil Processing; Key Laboratory of Bioengineering and Biotechnology in Universities of Shandong; Centre for Bioengineering and Biotechnology; China University of Petroleum (East China); Qingdao China
| | - Xiwu Luan
- Key Laboratory of Marine Hydrocarbon Resources and Environmental Geology; Ministry of Land and Resources of China; Qingdao China
- Qingdao Institute of Marine Geology; Qingdao China
| | - Hongyue Dang
- State Key Laboratory of Marine Environmental Science; Xiamen University; Xiamen China
- Institute of Marine Microbes and Ecospheres; Xiamen University; Xiamen China
- State Key Laboratory of Heavy Oil Processing; Key Laboratory of Bioengineering and Biotechnology in Universities of Shandong; Centre for Bioengineering and Biotechnology; China University of Petroleum (East China); Qingdao China
| | - Haixia Zhou
- State Key Laboratory of Heavy Oil Processing; Key Laboratory of Bioengineering and Biotechnology in Universities of Shandong; Centre for Bioengineering and Biotechnology; China University of Petroleum (East China); Qingdao China
| | - Yakun Zhao
- College of Chemical Engineering; China University of Petroleum (East China); Qingdao China
| | - Haitao Liu
- College of Chemical Engineering; China University of Petroleum (East China); Qingdao China
| | - Yunbo Zhang
- College of Chemical Engineering; China University of Petroleum (East China); Qingdao China
| | - Lingqing Dai
- State Key Laboratory of Marine Environmental Science; Xiamen University; Xiamen China
- Institute of Marine Microbes and Ecospheres; Xiamen University; Xiamen China
- Department of Ocean Science and Engineering; Zhejiang University; Hangzhou China
- State Key Laboratory of Heavy Oil Processing; Key Laboratory of Bioengineering and Biotechnology in Universities of Shandong; Centre for Bioengineering and Biotechnology; China University of Petroleum (East China); Qingdao China
| | - Ying Ye
- Department of Ocean Science and Engineering; Zhejiang University; Hangzhou China
| | - Martin G. Klotz
- State Key Laboratory of Marine Environmental Science; Xiamen University; Xiamen China
- Institute of Marine Microbes and Ecospheres; Xiamen University; Xiamen China
- State Key Laboratory of Heavy Oil Processing; Key Laboratory of Bioengineering and Biotechnology in Universities of Shandong; Centre for Bioengineering and Biotechnology; China University of Petroleum (East China); Qingdao China
- Department of Biology; University of North Carolina; Charlotte NC USA
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Weng B, Xie X, Yang J, Liu J, Lu H, Yan C. Research on the nitrogen cycle in rhizosphere of Kandelia obovata under ammonium and nitrate addition. MARINE POLLUTION BULLETIN 2013; 76:227-240. [PMID: 24047638 DOI: 10.1016/j.marpolbul.2013.08.034] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 08/25/2013] [Accepted: 08/26/2013] [Indexed: 06/02/2023]
Abstract
The present study investigated nitrogen process in rhizosphere of Kandelia obovata under nitrogen input. Results showed that nitrogen additions significantly increased 4 kinds of enzyme activities (Urease, Nitrate reductase, Nitrite reductase and hydroxylamine reductase). The pH value increased to 7.1 under ammonium addition, but decreased to 6.9 under nitrate addition. Potential Nitrification Intensity (PNI) increased 200-1500% compared with control under ammonium addition, and Potential Denitrification Intensity (PDI) increased more than 200% under nitrate addition. Ten types of organic acids were detected from root exudates, which mainly included oxalic acid, tartaric acid, formic acid, acetic acid, and citric acid. The abundance of 5 kinds of microbial functional groups (nifH, AOA, AOB, nirS, nirK) responded differently. Total nitrogen in organs of K. obovata increased more than 200%. This indicated that nitrogen additions accelerated the transformation of nitrogen directly and stimulated the exudation of root exudates and 5 kinds of genes indirectly.
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Affiliation(s)
- Bosen Weng
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361005, PR China
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Sun W, Xu MY, Wu WM, Guo J, Xia CY, Sun GP, Wang AJ. Molecular diversity and distribution of anammox community in sediments of the Dongjiang River, a drinking water source of Hong Kong. J Appl Microbiol 2013; 116:464-76. [DOI: 10.1111/jam.12367] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Revised: 09/21/2013] [Accepted: 10/08/2013] [Indexed: 11/27/2022]
Affiliation(s)
- W. Sun
- School of Bioscience and Bioengineering; South China University of Technology; Guangzhou China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application; Guangdong Institute of Microbiology; Guangzhou China
- State Key Laboratory of Applied Microbiology (Ministry-Guangdong Province Jointly Breeding Base), South China; Guangzhou China
| | - M.-Y. Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application; Guangdong Institute of Microbiology; Guangzhou China
- State Key Laboratory of Applied Microbiology (Ministry-Guangdong Province Jointly Breeding Base), South China; Guangzhou China
| | - W.-M. Wu
- Department of Civil & Environmental Engineering; Center for Sustainable Development & Global Competitiveness; Stanford University; Stanford CA USA
| | - J. Guo
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application; Guangdong Institute of Microbiology; Guangzhou China
- State Key Laboratory of Applied Microbiology (Ministry-Guangdong Province Jointly Breeding Base), South China; Guangzhou China
| | - C.-Y. Xia
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application; Guangdong Institute of Microbiology; Guangzhou China
- State Key Laboratory of Applied Microbiology (Ministry-Guangdong Province Jointly Breeding Base), South China; Guangzhou China
| | - G.-P. Sun
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application; Guangdong Institute of Microbiology; Guangzhou China
- State Key Laboratory of Applied Microbiology (Ministry-Guangdong Province Jointly Breeding Base), South China; Guangzhou China
| | - A.-J. Wang
- Harbin Institute of Technology; Harbin China
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Zhao Y, Xia Y, Kana TM, Wu Y, Li X, Yan X. Seasonal variation and controlling factors of anaerobic ammonium oxidation in freshwater river sediments in the Taihu Lake region of China. CHEMOSPHERE 2013; 93:2124-2131. [PMID: 23978673 DOI: 10.1016/j.chemosphere.2013.07.063] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 07/18/2013] [Accepted: 07/22/2013] [Indexed: 06/02/2023]
Abstract
Anaerobic ammonium oxidation (anammox) has been recently recognized as an important pathway for the removal of fixed nitrogen (N) from aquatic systems. However, the functions of anammox in freshwater river systems remain uncertain. In this study, we evaluated the occurrence of anammox activity in two rivers in the Taihu Lake region in China during a seasonal survey. Homogenized sediments were incubated with (15)N-labeled NO3(-) and NH4(+) amendments to determine the potential importance of the anammox process relative to canonical denitrification. Production of (29)N2 and (30)N2 in slurries was determined using membrane inlet mass spectrometry. Potential anammox rates in the two river sediments ranged from 0.11±0.07 to 6.79±1.28 μmol N m(-2) h(-1) and the remove of N by anammox accounted for 0.8±0.00% to 10.7±0.03% of total N2 production. Potential anammox rates varied spatially and temporally in the two rivers, with the highest and lowest mean anammox rates appearing during summer and early autumn and during winter, respectively. The variation of the percentage of anammox to total N2 production displayed the same trend with potential anammox rates. Water temperature and NO3(-) content in sediments were the main factors affecting anammox activity. Anammox bacteria were detected in sediment samples using barcode pyrosequencing. The 16S rRNA anammox gene sequences in the river sediments were affiliated with Candidatus Kuenenia, Candidatus Jettenia, and Candidatus Scalindua, among which C. Kuenenia dominated the anammox bacterial communities. Our results confirmed the presence of anammox bacteria but their role is relatively small in removing fixed N from freshwater river systems.
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Affiliation(s)
- Yongqiang Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
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Wastewater effluent impacts ammonia-oxidizing prokaryotes of the Grand River, Canada. Appl Environ Microbiol 2013; 79:7454-65. [PMID: 24056472 DOI: 10.1128/aem.02202-13] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Grand River (Ontario, Canada) is impacted by wastewater treatment plants (WWTPs) that release ammonia (NH3 and NH4+) into the river. In-river microbial communities help transform this ammonia into more oxidized compounds (e.g., NO3- or N2), although the spatial distribution and relative abundance of freshwater autotrophic ammonia-oxidizing prokaryotes (AOP) are not well characterized. This study investigated freshwater N cycling within the Grand River, focusing on sediment and water columns, both inside and outside a WWTP effluent plume. The diversity, relative abundance, and nitrification activity of AOP were investigated by denaturing gradient gel electrophoresis (DGGE), quantitative real-time PCR (qPCR), and reverse transcriptase qPCR (RT-qPCR), targeting both 16S rRNA and functional genes, together with activity assays. The analysis of bacterial 16S rRNA gene fingerprints showed that the WWTP effluent strongly affected autochthonous bacterial patterns in the water column but not those associated with sediment nucleic acids. Molecular and activity data demonstrated that ammonia-oxidizing archaea (AOA) were numerically and metabolically dominant in samples taken from outside the WWTP plume, whereas ammonia-oxidizing bacteria (AOB) dominated numerically within the WWTP effluent plume. Potential nitrification rate measurements supported the dominance of AOB activity in downstream sediment. Anaerobic ammonia-oxidizing (anammox) bacteria were detected primarily in sediment nucleic acids. In-river AOA patterns were completely distinct from effluent AOA patterns. This study demonstrates the importance of combined molecular and activity-based studies for disentangling molecular signatures of wastewater effluent from autochthonous prokaryotic communities.
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Siegert M, Taubert M, Seifert J, von Bergen-Tomm M, Basen M, Bastida F, Gehre M, Richnow HH, Krüger M. The nitrogen cycle in anaerobic methanotrophic mats of the Black Sea is linked to sulfate reduction and biomass decomposition. FEMS Microbiol Ecol 2013; 86:231-45. [DOI: 10.1111/1574-6941.12156] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 05/16/2013] [Accepted: 05/29/2013] [Indexed: 11/27/2022] Open
Affiliation(s)
- Michael Siegert
- Bundesanstalt für Geowissenschaften und Rohstoffe Hannover; Hannover; Germany
| | - Martin Taubert
- School of Environmental Sciences; University of East Anglia; Norwich; UK
| | - Jana Seifert
- Institute of Animal Nutrition; University of Hohenheim; Stuttgart; Germany
| | | | - Mirko Basen
- Max-Planck-Institut für Marine Mikrobiologie; Bremen; Germany
| | - Felipe Bastida
- Department of Isotope Biogeochemistry; Helmholtz Centre for Environmental Research - UFZ; Leipzig; Germany
| | - Matthias Gehre
- Department of Isotope Biogeochemistry; Helmholtz Centre for Environmental Research - UFZ; Leipzig; Germany
| | - Hans-Hermann Richnow
- Department of Isotope Biogeochemistry; Helmholtz Centre for Environmental Research - UFZ; Leipzig; Germany
| | - Martin Krüger
- Bundesanstalt für Geowissenschaften und Rohstoffe Hannover; Hannover; Germany
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