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Gutiérrez MC, Cáceres A, Herruzo-Ruiz AM, Siles JA, Vázquez F, Alhama J, Michán C, Martín MA. Assessment of nitrification process in a sequencing batch reactor: Modelling and genomic approach. ENVIRONMENTAL RESEARCH 2024; 246:118035. [PMID: 38199477 DOI: 10.1016/j.envres.2023.118035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024]
Abstract
Nitrification of ammoniacal nitrogen (N-NH4+) to nitrate (N-NO3-) was investigated in a lab-scale sequencing batch reactor (SBR) to evaluate its efficiency. During the nitrification process the removal of N-NH4+ reached 96%, resulting in 73% formation of N-NO3-. A lineal correlation (r2 = 0.9978) was obtained between the concentration of volatile suspended solids (VSS) and the maximal N-NO3- concentration at the end of each batch cycle under stationary state. The bacterial taxons in the initial inoculum were identified, revealing a complex diverse community mainly in the two major bacterial phyla Proteobacteria and Actinobacteria. The FAPROTAX algorithm predicted the presence in the inoculum of taxa involved in relevant processes of the nitrogen metabolism, highlighting the bacterial genera Nitrospira and Nitrosomonas that are both involved in the nitrification process. A kinetic model was formulated for predicting and validating the transformation of N-NH4+, N-NO2- and N-NO3- and the removal of organic and inorganic carbon (TOC and IC, respectively). The results showed how the increase in biomass concentration slowed down the transformation to oxidised forms of nitrogen and increased denitrification in the settling and filling stages under free aeration conditions.
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Affiliation(s)
- M C Gutiérrez
- Department of Inorganic Chemistry and Chemical Engineering, Area of Chemical Engineering, Instituto Químico para la Energía y el Medioambiente (IQUEMA), Campus de Excelencia Internacional Agroalimentario ceiA3, University of Cordoba, Campus Universitario de Rabanales, Carretera N-IV, km 396, edificio Marie Curie, 14071, Córdoba, Spain
| | - A Cáceres
- Department of Inorganic Chemistry and Chemical Engineering, Area of Chemical Engineering, Instituto Químico para la Energía y el Medioambiente (IQUEMA), Campus de Excelencia Internacional Agroalimentario ceiA3, University of Cordoba, Campus Universitario de Rabanales, Carretera N-IV, km 396, edificio Marie Curie, 14071, Córdoba, Spain
| | - A M Herruzo-Ruiz
- Department of Biochemistry and Molecular Biology, University of Cordoba, Campus de Excelencia Internacional Agroalimentario ceiA3, edificio Severo Ochoa, 14071, Córdoba, Spain
| | - J A Siles
- Department of Inorganic Chemistry and Chemical Engineering, Area of Chemical Engineering, Instituto Químico para la Energía y el Medioambiente (IQUEMA), Campus de Excelencia Internacional Agroalimentario ceiA3, University of Cordoba, Campus Universitario de Rabanales, Carretera N-IV, km 396, edificio Marie Curie, 14071, Córdoba, Spain
| | - F Vázquez
- Department of Electrical Engineering and Automation, University of Cordoba, Cordoba, 14071, Spain
| | - J Alhama
- Department of Biochemistry and Molecular Biology, University of Cordoba, Campus de Excelencia Internacional Agroalimentario ceiA3, edificio Severo Ochoa, 14071, Córdoba, Spain
| | - C Michán
- Department of Biochemistry and Molecular Biology, University of Cordoba, Campus de Excelencia Internacional Agroalimentario ceiA3, edificio Severo Ochoa, 14071, Córdoba, Spain
| | - M A Martín
- Department of Inorganic Chemistry and Chemical Engineering, Area of Chemical Engineering, Instituto Químico para la Energía y el Medioambiente (IQUEMA), Campus de Excelencia Internacional Agroalimentario ceiA3, University of Cordoba, Campus Universitario de Rabanales, Carretera N-IV, km 396, edificio Marie Curie, 14071, Córdoba, Spain.
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Kalinowska A, Pierpaoli M, Jankowska K, Fudala-Ksiazek S, Remiszewska-Skwarek A, Łuczkiewicz A. Insights into the microbial community of treated wastewater, its year-round variability and impact on the receiver, using cultivation, microscopy and amplicon-based methods. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 829:154630. [PMID: 35307432 DOI: 10.1016/j.scitotenv.2022.154630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/21/2022] [Accepted: 03/13/2022] [Indexed: 06/14/2023]
Abstract
Apart from chemical constituents, wastewater treatment plant (WWTP) effluents also release microorganisms that can be important to the receiving water bodies either from a sanitary point of view, or taking to the account the biogeochemical potential of the recipients. However, little is known about the treated wastewater microbial community, its composition, seasonal changes, functions and fate in the waters of the receiver. Thus, this study presents a synergistic approach coupling new and traditional methods: analytical chemistry, classical microbiology (cultivation- and microscopy-based methods), as well as Next Generation Sequencing and a quantitative real-time polymerase chain reaction (qPCR). The results show that in terms of bacterial community composition, treated wastewater differed from the environmental samples, irrespectively if they were related or unrelated to the WWTP effluent discharge. The canonical correspondence analysis (CCA) taking into account chemical parameters and taxonomical biodiversity indirectly confirmed the seasonal deterioration of the treated wastewater quality as a result of temperature-driven change of activated sludge community structure and biomass washout (observed also by DAPI staining). Despite seasonal fluctuations of total suspended solids and inter-related parameters (such as COD, BOD, TN, TP), the treated wastewater quality remained within current discharge limits. It was due to treatment processes intensively adjusted by WWTP operators, particularly those necessary to maintain an appropriate rate of autotrophic processes of nitrification and to support biological phosphorus removal. This can explain the observed microbiome composition similarity among WWTP effluents at high taxonomic levels. Obtained data also suggest that besides wastewater treatment efficiency, WWTP effluents are still sources of both human-related microorganisms as well as bacteria equipped in genes involved in N-cycling. Their potential of participation in nutrients cycling in the receivers is widely unknown and require critical attention and better understanding.
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Affiliation(s)
- Agnieszka Kalinowska
- Department of Environmental Engineering Technology, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland.
| | - Mattia Pierpaoli
- Department of Metrology and Optoelectronics, Faculty of Electronics, Telecommunications and Informatics, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland.
| | - Katarzyna Jankowska
- Department of Environmental Engineering Technology, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland.
| | - Sylwia Fudala-Ksiazek
- Department of Sanitary Engineering, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland.
| | - Anna Remiszewska-Skwarek
- Department of Sanitary Engineering, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland.
| | - Aneta Łuczkiewicz
- Department of Environmental Engineering Technology, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland.
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3
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Zhao M, Tang X, Sun D, Hou L, Liu M, Zhao Q, Klümper U, Quan Z, Gu JD, Han P. Salinity gradients shape the nitrifier community composition in Nanliu River Estuary sediments and the ecophysiology of comammox Nitrospira inopinata. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 795:148768. [PMID: 34247082 DOI: 10.1016/j.scitotenv.2021.148768] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/24/2021] [Accepted: 06/27/2021] [Indexed: 06/13/2023]
Abstract
The recent discovery of complete ammonia oxidizers (comammox), which convert ammonia to nitrate in a single organism, revolutionized the conventional understanding that two types of nitrifying microorganisms have to be involved in the nitrification process for more than 100 years. However, how different types of nitrifiers in response to salinity change remains largely unclear. This study not only investigated nitrifier community (including ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), comammox and nitrite-oxidizing Nitrospira) in the Nanliu estuary to find the ecological relationship between salinity and functional communities and also studied the physiology of a typical comammox Nitrospira inopinata in response to a salinity gradient. Based on sequences retrieved with four sets of functional gene primes, comammox Nitrospira was in general, mainly composed of clade A, with a clear separation of clade A1 subgroup in all samples and clade A2 subgroup in low salinity ones. As expected, group I.1b and group I.1a AOA dominated the AOA community in low- and high-salinity samples, respectively. Nitrosomonas-AOB were detected in all samples while Nitrosospira-AOB were mainly found in relatively high-salinity samples. Regarding general Nitrospira, lineages II and IV were the major groups in most of the samples, while lineage I Nitrospira was only detected in low-salinity samples. Furthermore, the comammox pure culture of N. inopinata showed an optimal salinity at 0.5‰ and ceased to grow at 12.8‰ for ammonia oxidation, but remained active for nitrite oxidation. These results show new evidence regarding niche specificity of different nitrifying microorganisms modulated mainly by salinity, and also a clear response by comammox N. inopinata to a wide range of simulated salinity levels.
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Affiliation(s)
- Mengyue Zhao
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xiufeng Tang
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Dongyao Sun
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Institute of Eco-Chongming, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China
| | - Qiang Zhao
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Uli Klümper
- Institute for Hydrobiology, Technische Universität Dresden, 01062 Dresden, Germany
| | - Zhexue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ji-Dong Gu
- Environmental Engineering, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, China
| | - Ping Han
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Institute of Eco-Chongming, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China.
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Challenges in Treatment of Digestate Liquid Fraction from Biogas Plant. Performance of Nitrogen Removal and Microbial Activity in Activated Sludge Process. ENERGIES 2021. [DOI: 10.3390/en14217321] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Even thoughdigestate, which is continually generated in anaerobic digestion process, can only be used as fertilizer during the growing season, digestate treatment is still a critical, environmental problem. That is why the present work aims to develop a method to manage digestate in agricultural biogas plant in periods when its use as fertilizer is not possible. A lab-scale system for the biological treatment of the digestate liquid fraction using the activated sludge method with a separate denitrification chamber was constructed and tested. The nitrogen load that was added tothe digestate liquid fraction accounted for 78.53% of the total nitrogen load fed into the reactor. External carbon sources, such as acetic acid, as well as flume water and molasses, i.e., wastewater and by-products from a sugar factory, were used to support the denitrification process. The best results were obtained using an acetic acid and COD (Chemical Oxygen Demand)/NO3–N (Nitrate Nitrogen) ratio of 7.5. The removal efficiency of TN (Total Nitrogen), NH4–N (Ammonia Nitrogen) and COD was 83.73%, 99.94%, 86.26%, respectively. It was interesting to see results obtained that were similar to those obtained when using flume water and COD/NO3–N at a ratio of 8.7. This indicates that flume water can be used as an alternative carbon source to intensify biological nitrogen removal from digestate.
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Xia F, Jiang QY, Zhu T, Zou B, Liu H, Quan ZX. Ammonium promoting methane oxidation by stimulating the Type Ia methane-oxidizing bacteria in tidal flat sediments of the Yangtze River estuary. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 793:148470. [PMID: 34166901 DOI: 10.1016/j.scitotenv.2021.148470] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 06/13/2023]
Abstract
Estuary and coastal environments have essential ecosystem functions in greenhouse gas sinks and removal of nitrogen pollution. Methane-oxidizing bacteria (MOB) and ammonia-oxidizing bacteria (AOB) communities play critical functions in the estuary's tidal flat sediments. Therefore, the effects of ammonium on MOB communities and methane on AOB communities need to be further explained. In this study, microcosm incubations with different contents of ammonium or methane were conducted for a relatively short (24 h) or long (28 days) period with tidal flat sediments from the Yangtze River estuary. Subsequently, the tagged highly degenerate primer PCR and DNA-based stable isotope probing method were employed to demonstrate the effects on MOB and AOB populations. The results indicated that the methane consumption was enhanced with ammonium supplements within 24 h of incubation. Supplement of 2 μmol/g d.w.s (μmol per gram dry weight soil) NH4+ increased the amount of MOB and its proportion to the total bacteria (p < 0.05) for 28 days incubation. The ammonium supplement increased the proportion of Methylomonas and Methylobacter based on the 16S rRNA gene. According to the functional gene analysis, the MOB primarily engaged in methane oxidation include Methylomonas, Methylobacter, Methylomicrobium, and Methylosarcina, which were associated with Type Ia MOB. It suggested that ammonium supplement may promote methane oxidation by stimulating the Type Ia MOB in tidal flat sediments of the Yangtze River estuary. The current research helps understand the effect of ammonium on methane consumption in the estuary and coastal environments.
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Affiliation(s)
- Fei Xia
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China; Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Qiu-Yue Jiang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Ting Zhu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Bin Zou
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Huan Liu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China.
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Guo J, Zhou Y, Guo H, Min W. Saline and alkaline stresses alter soil properties and composition and structure of gene-based nitrifier and denitrifier communities in a calcareous desert soil. BMC Microbiol 2021; 21:246. [PMID: 34521348 PMCID: PMC8442331 DOI: 10.1186/s12866-021-02313-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 09/06/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Saline and alkaline stresses damages the health of soil systems. Meanwhile, little is known about how saline or alkaline stress affects soil nitrifier and denitrifier communities. Therefore, we compared the responses of gene-based nitrifier and denitrifier communities to chloride (CS), sulfate (SS), and alkaline (AS) stresses with those in a no-stress control (CK) in pots with a calcareous desert soil. RESULTS Compared with CK, saline and alkaline stress decreased potential nitrification rate (PNR) and NO3-N; increased pH, salinity, water content, and NH4-N; and decreased copy numbers of amoA-AOA and amoA-AOB genes but increased those of denitrifier nirS and nosZ genes. Copies of nirK increased in SS and AS but decreased in CS. There were more copies of amoA-AOB than of amoA-AOA and of nirS than of nirK or nosZ. Compared with CK, SS and AS decreased operational taxonomic units (OTUs) of amoA-AOB but increased those of nirS and nosZ, whereas CS decreased nirK OTUs but increased those of nosZ. The numbers of OTUs and amoA-AOB genes were greater than those of amoA-AOA. There were positive linear relations between PNR and amoA-AOA and amoA-AOB copies. Compared with CK, the Chao 1 index of amoA-AOA and amoA-AOB decreased in AS, that of nirK increased in CS and SS, but that of nirS and nosZ increased in all treatments. The Shannon index of amoA-AOB decreased but that of nirS increased in CS and SS, whereas the index of nirK decreased in all treatments. Saline and alkaline stress greatly affected the structure of nitrifier and denitrifier communities and decreased potential biomarkers of nirS-type; however, AS increased those of nirK- and nosZ-type, and SS decreased those of nosZ-type. Soil water content, pH, and salinity were important in shaping amoA-AOA and denitrifier communities, whereas soil water and pH were important to amoA-AOB communities. CONCLUSION These results indicate that the nitrifier and denitrifier communities respond to saline and alkaline stresses conditions. Communities of amoA-AOA and amoA-AOB contribute to nitrification in alluvial gray desert soil, and those of nirS are more important in denitrification than those of nirK or nosZ.
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Affiliation(s)
- Jiaxin Guo
- Department of Resources and Environmental Science, Agriculture College, Shihezi University, Box #425, Shihezi, Xinjiang, 832003, People's Republic of China
| | - Yongxue Zhou
- Department of Resources and Environmental Science, Agriculture College, Shihezi University, Box #425, Shihezi, Xinjiang, 832003, People's Republic of China
| | - Huijuan Guo
- Department of Resources and Environmental Science, Agriculture College, Shihezi University, Box #425, Shihezi, Xinjiang, 832003, People's Republic of China
| | - Wei Min
- Department of Resources and Environmental Science, Agriculture College, Shihezi University, Box #425, Shihezi, Xinjiang, 832003, People's Republic of China.
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Wei H, Lin X. Shifts in the relative abundance and potential rates of sediment ammonia-oxidizing archaea and bacteria along environmental gradients of an urban river-estuary-adjacent sea continuum. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 771:144824. [PMID: 33545473 DOI: 10.1016/j.scitotenv.2020.144824] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in N cycling in sediments globally. However, little is known about their ammonia oxidation rates along a river-estuary-sea continuum. In this study, we investigated how the potential ammonia oxidation rates (PARs) of AOA and AOB changed spatially along a continuum comprising three habitats: the Shanghai urban river network, the Yangtze Estuary, and the adjacent East China Sea, in summer and winter. The AOA and AOB PARs (0.53 ± 0.49 and 0.72 ± 0.69 μg N g-1 d-1, mean ± SD, respectively) and their amoA gene abundance (0.47 ± 0.85 × 106 and 2.4 ± 3.54 × 106 copies g-1, respectively) decreased along the continuum, particularly from the urban river to the estuary, driven by decreasing sediment total organic C and N and other correlated inorganic nutrients (e.g., NH4+) along the gradient of anthropogenic influences. These spatial patterns were consistent between the seasons. The urban river network, where the anthropogenic influences were strongest, saw the largest seasonal differences, as both AOA and AOB had higher PARs and abundance in summer than in winter. The ratios between AOA and AOB PARs (~0.87 ± 0.51) and gene abundances (~0.25 ± 0.24), however, were predominantly <1, indicating an AOB-dominated community. Comparing the different NH4+ consumption pathways, total aerobic oxidation accounted for 12-26% of the total consumption, with the largest proportion in the estuary, where the system was well oxygenated, and the lowest in the adjacent sea, where inorganic N was highly depleted. This study revealed the spatiotemporal patterns of AOA and AOB potential rates and gene abundance along gradients of human influences and identified organic matter and nutrients as key environmental factors that shaped the variation of AOA and AOB along the continuum.
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Affiliation(s)
- Hengchen Wei
- The University of Texas at Austin Marine Science Institute, 750 Channel View Drive, Port Aransas, TX 78373, USA
| | - Xianbiao Lin
- Laboratory of Microbial Ecology and Matter Cycles, School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China; School of Geographic Sciences, Key Laboratory of Geographic Information Science of the Ministry of Education, East China Normal University, Shanghai 200241, China; Southern Laboratory of Ocean Science and Engineering (Guangdong, Zhuhai), Zhuhai 519000, China.
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Effect of biomass immobilization and reduced graphene oxide on the microbial community changes and nitrogen removal at low temperatures. Sci Rep 2021; 11:840. [PMID: 33436937 PMCID: PMC7804202 DOI: 10.1038/s41598-020-80747-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 12/28/2020] [Indexed: 11/08/2022] Open
Abstract
The slow growth rate and high optimal temperatures for the anaerobic ammonium oxidation (anammox) bacteria are significant limitations of the anammox processes application in the treatment of mainstream of wastewater entering wastewater treatment plant (WWTP). In this study, we investigate the nitrogen removal and microbial community changes in sodium alginate (SA) and sodium alginate–reduced graphene oxide (SA-RGO) carriers, depending on the process temperature, with a particular emphasis on the temperature close to the mainstream of wastewater entering the WWTP. The RGO addition to the SA matrix causes suppression of the beads swelling, which intern modifies the mechanical properties of the gel beads. The effect of the temperature drop on the nitrogen removal rate was reduced for biomass entrapped in SA and SA-RGO gel beads in comparison to non-immobilized biomass, this suggests a ‘‘protective” effect caused by immobilization. However, analyses performed using next-generation sequencing (NGS) and qPCR revealed that the microbial community composition and relative gene abundance changed significantly, after the implementation of the new process conditions. The microbial community inside the gel beads was completely remodelled, in comparison with inoculum, and denitrification contributed to the nitrogen transformation inside the beads.
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9
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Wang X, Liu J, Liang J, Sun H, Zhang XH. Spatiotemporal dynamics of the total and active Vibrio spp. populations throughout the Changjiang estuary in China. Environ Microbiol 2020; 22:4438-4455. [PMID: 33462948 PMCID: PMC7689709 DOI: 10.1111/1462-2920.15152] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 07/03/2020] [Indexed: 11/27/2022]
Abstract
Vibrio is ubiquitously distributed in marine environments and is the most extensively characterized group within Gammaproteobacteria. Studies have investigated Vibrio spp. worldwide, but mostly focused on pathogenic vibrios and based on cultivation methods. Here, using a combination of molecular and culturing methods, we investigated the dynamics of the total and active Vibrio spp. throughout the Changjiang estuary in China. The total Vibrio abundance was higher in summer (~6.59 × 103 copies ml−1) than in winter (~1.85 × 103 copies ml−1) and increased from freshwater to saltwater (e.g. 8.04 × 101 to 9.39 × 103 copies ml−1 in summer). The ratio of active to total Vibrio (Va/Vt) revealed a high activity of vibrios, with remarkable differences between freshwater and saltwater (p < 0.05). Based on the community compositions of the culturable, total and active Vibrio, Vibrio atlanticus and Vibrio owensii were the dominant and active species in winter and summer, respectively. The distribution of Vibrio was governed by the effects of diverse environmental factors, such as temperature, salinity, pH, dissolved oxygen and SiO32−. Our study clearly demonstrates the spatiotemporal dynamics of total and active Vibrio spp. and lays a foundation for fully understanding the ecological roles of marine Vibrio.
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Affiliation(s)
- Xiaolei Wang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Jiwen Liu
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.,Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266100, China
| | - Jinchang Liang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Hao Sun
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.,Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266100, China
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10
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Response of ammonia-oxidizing Bacteria and Archaea to long-term saline water irrigation in alluvial grey desert soils. Sci Rep 2020; 10:489. [PMID: 31949227 PMCID: PMC6965641 DOI: 10.1038/s41598-019-57402-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/30/2019] [Indexed: 11/16/2022] Open
Abstract
Soil nitrification via ammonia oxidation is a key ecosystem process in terrestrial environments, but little is known of how increasing irrigation of farmland soils with saline waters effects these processes. We investigated the effects of long-term irrigation with saline water on the abundances and community structures of ammonia-oxidizing bacteria (AOB) and archaea (AOA). Irrigation with brackish or saline water increased soil salinity (EC1:5) and NH4-N compared to irrigation with freshwater, while NO3-N, potential nitrification rates (PNR) and amoA gene copy numbers of AOA and AOB decreased markedly under irrigation regimes with saline waters. Moreover, irrigation with brackish water lowered AOA/AOB ratios. PNR was positively correlated with AOA and AOB amoA gene copy numbers across treatments. Saline and brackish water irrigation significantly increased the diversity of AOA, as noted by Shannon index values, while saline water irrigation markedly reduced AOB diversity. In addition, irrigation with brackish or fresh waters resulted in higher proportions of unclassified taxa in the AOB communities. However, irrigation with saline water led to higher proportions of unclassified taxa in the AOA communities along with the Candidatus Nitrosocaldus genus, as compared to soils irrigated with freshwater. AOA community structures were closely associated with soil salinity, NO3−N, and pH, while AOB communities were only significantly associated with NO3−N and pH. These results suggest that salinity was the dominant factor affecting the growth of ammonia-oxidizing microorganisms and community structure. These results can provide a scientific basis for further exploring the response mechanism of ammonia-oxidizing microorganisms and their roles in nitrogen transformation in alluvial grey desert soils of arid areas.
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Ginawi A, Wang L, Wang H, Yu B, Yunjun Y. Effects of environmental variables on abundance of ammonia-oxidizing communities in sediments of Luotian River, China. PeerJ 2020; 8:e8256. [PMID: 31934502 PMCID: PMC6951284 DOI: 10.7717/peerj.8256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 11/20/2019] [Indexed: 12/14/2022] Open
Abstract
Ammonia-oxidizing communities play important functional roles in the nitrification. However, environmental stresses can significantly affect this process by controlling the abundant communities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities. In this study, we examined the abundance variations of ammonia-oxidizing communities using quantitative polymerase chain reaction (qPCR) and terminal-restriction fragment length polymorphism (T-RFLP) in a typical subtropical river, Luotian County, South Dabie Mountains, China. Clone libraries were conducted to evaluate the community structure and abundance of AOA and AOB in sediments. Results showed that Nitrososphaera sp and Nitrosopumilus sp were the most dominant AOA. The abundance of the AOA and AOB amoA gene ranged from 5.28 × 108 gene copies (g-soil−1) to 2.23 × 108 gene copies (g-soil−1) and 5.45 × 108 gene copies (g-soil−1) to 3.30 × 107 gene copies (g-soil−1), respectively. Five environmental variables, namely, ORP, DO, NO\documentclass[12pt]{minimal}
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}{}${}_{4}^{+}$\end{document}4+ were played a major function in microbial communities of AOA and AOB in sediments. The T-RFLP profiles of AOA showed that 488 and 116 bp T-RFs were dominated. Overall, the results of this study showed that anthropogenic activities andenvironmental stress in rivers can alter the structure and function of microbes in their variable environment.
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Affiliation(s)
- Amjed Ginawi
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Faculty of Marine Science and Fisheries, Red Sea University, Port Sudan, Red Sea State, Sudan
| | - Lixiao Wang
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Huading Wang
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Bingbing Yu
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yan Yunjun
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
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12
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Banach-Wiśniewska A, Tomaszewski M, Cema G, Ziembińska-Buczyńska A. Medium shift influence on nitrogen removal bacteria: Ecophysiology and anammox process performance. CHEMOSPHERE 2020; 238:124597. [PMID: 31450106 DOI: 10.1016/j.chemosphere.2019.124597] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/22/2019] [Accepted: 08/14/2019] [Indexed: 06/10/2023]
Abstract
In this study, we focused on the proportion of particular bacterial groups and changes in microbial community structure in relation to the anammox process parameters and the feeding medium strategy in the Sequencing Batch Reactor (SBR). In order to present an insight into the microbial dynamics while feeding medium shift from synthetic wastewater to landfill leachate, fluorescent in situ hybridization (FISH), Real Time PCR, PCR - DGGE (Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis) and Reverse Transcription PCR-DGGE analysis were used. Feeding medium change has the strongest impact on relative abundance of denitrifiers and representatives of Planctomycetes. The relative abundancy of specific genes for all investigated nitrogen removal bacterial groups dropped after landfill leachate implementation. However, anammox consortium were able to adapt to the new reactor operating conditions and time for adaptation was estimated at the level of 90 days.
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Affiliation(s)
- Anna Banach-Wiśniewska
- Silesian University of Technology, Faculty of Power and Environmental Engineering, Environmental Biotechnology Department, Akademicka 2, 44-100, Gliwice, Poland.
| | - Mariusz Tomaszewski
- Silesian University of Technology, Faculty of Power and Environmental Engineering, Environmental Biotechnology Department, Akademicka 2, 44-100, Gliwice, Poland
| | - Grzegorz Cema
- Silesian University of Technology, Faculty of Power and Environmental Engineering, Environmental Biotechnology Department, Akademicka 2, 44-100, Gliwice, Poland
| | - Aleksandra Ziembińska-Buczyńska
- Silesian University of Technology, Faculty of Power and Environmental Engineering, Environmental Biotechnology Department, Akademicka 2, 44-100, Gliwice, Poland
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13
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Fahim R, Lu X, Jilani G, Hussain J, Hussain I. Comparison of floating-bed wetland and gravel filter amended with limestone and sawdust for sewage treatment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:20400-20410. [PMID: 31102209 DOI: 10.1007/s11356-019-05325-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/30/2019] [Indexed: 06/09/2023]
Abstract
Advancements in the design and technology of constructed wetlands for efficient removal of wastewater contaminants are ever in progress to develop situation-based economical systems. Here, we entrenched two horizontal sub-surface flow constructed wetlands (HSFCW) with either chemical, viz. limestone (HSFCW-LS) or organic, viz. sawdust (HSFCW-SD) substrates, and compared them with biological method, viz. growing of water spinach in floating-bed-constructed wetland (FBCW-WS) to enhance the performance of CWs. Same sewage wastewater was used as influent in each fortified CW replicated thrice. Sewage was replaced weekly, for a total of 12 weeks of experimentation. Sampling of raw sewage from influent was undertaken at the inlet in the beginning, and that of treated effluent from the outlet after a week of treatments. Quality of raw sewage used weekly during experimentation remained almost uniform and near to the wastewater standards. Cumulative data of treated wastewater depicted that the FBCW-WS achieved the highest performance in the removal of total nitrogen (TN), [Formula: see text]-N, and total phosphorus (TP) with average removal efficiencies of 75.9, 90.5, and 94.3%, respectively. Whereas, HSFCW-SD performed better for [Formula: see text]-N, FC, and TSS with corresponding removal efficiency of 77.5, 64.3, and 74.2% while HSFCW-LS showed average performance. This study concludes that performance of biological method of macrophyte cultivation (FBCW-WS) is significantly superior to chemical and organic substrates, so it could be more effective, economical, and sustainable approach for sewage treatment.
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Affiliation(s)
- Raana Fahim
- Department of Environmental Science & Engineering, School of Energy and Environment, Southeast University, Nanjing, 210096, China.
| | - Xiwu Lu
- Department of Environmental Science & Engineering, School of Energy and Environment, Southeast University, Nanjing, 210096, China.
| | - Ghulam Jilani
- Institute of Soil Science, PMAS Arid Agriculture University Rawalpindi, Rawalpindi, 46300, Pakistan
| | - Javid Hussain
- Department of Environmental Science & Engineering, Faculty of Life Sciences and Informatics, Balochistan University of Information Technology, Engineering & Management Sciences, Quetta, Pakistan
| | - Ittehad Hussain
- Department of Environmental Science & Engineering, School of Energy and Environment, Southeast University, Nanjing, 210096, China
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14
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Hira D, Aiko N, Yabuki Y, Fujii T. Impact of aerobic acclimation on the nitrification performance and microbial community of landfill leachate sludge. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2018; 209:188-194. [PMID: 29291488 DOI: 10.1016/j.jenvman.2017.12.056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 12/16/2017] [Accepted: 12/20/2017] [Indexed: 06/07/2023]
Abstract
Nitrogenous pollution of water is regarded as a global environmental problem, and nitrogen removal has become an important issue in wastewater treatment processes. Landfill leachate is a typical large source of nitrogenous wastewater. Although the characteristics of leachate vary according to the age of the landfill, leachates of mature landfill have high concentrations of nitrogenous compounds. Most nitrogen in these leachates is in the form of ammonium nitrogen. In this study, we investigated the bacterial community of sludge from a landfill leachate lagoon by pyrosequencing of the bacterial 16S rRNA gene. The sludge was acclimated in a laboratory-scale reactor with aeration using a mechanical stirrer to promote nitrification. On 149 days, nitrification was achieved and then the bacterial community was also analyzed. The bacterial community was also analyzed after nitrification was achieved. Pyrosequencing analyses revealed that the abundances of ammonia-oxidizing and nitrite-oxidizing bacteria were increased by acclimation and their total proportions increased to >15% of total biomass. Changes in the sulfate-reducing and sulfur-oxidizing bacteria were also observed during the acclimation process. The aerobic acclimation process enriched a nitrifying microbial community from the landfill leachate sludge. These results suggested that the aerobic acclimation is a processing method for the nitrification ammonium oxidizing throw the enrichment of nitrifiers. Improvement of this acclimation method would allow nitrogen removal from leachate by nitrification and sulfur denitrification.
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Affiliation(s)
- Daisuke Hira
- Department of Applied Life Science, Faculty of Biotechnology and Life Science, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan.
| | - Nobuyuki Aiko
- Key Laboratory of Research Institute of Environment, Agriculture and Fisheries, Osaka Prefectural Government, 1-3-62 Nakamichi, Higashinari-ku, Osaka 537-0025, Japan
| | - Yoshinori Yabuki
- Key Laboratory of Research Institute of Environment, Agriculture and Fisheries, Osaka Prefectural Government, 1-3-62 Nakamichi, Higashinari-ku, Osaka 537-0025, Japan
| | - Takao Fujii
- Department of Applied Life Science, Faculty of Biotechnology and Life Science, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
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15
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Geochemical and Microbial Community Attributes in Relation to Hyporheic Zone Geological Facies. Sci Rep 2017; 7:12006. [PMID: 28931901 PMCID: PMC5607297 DOI: 10.1038/s41598-017-12275-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 08/30/2017] [Indexed: 11/18/2022] Open
Abstract
The hyporheic zone (HZ) is the active ecotone between the surface stream and groundwater, where exchanges of nutrients and organic carbon have been shown to stimulate microbial activity and transformations of carbon and nitrogen. To examine the relationship between sediment texture, biogeochemistry, and biological activity in the Columbia River HZ, the grain size distributions for sediment samples were characterized to define geological facies, and the relationships among physical properties of the facies, physicochemical attributes of the local environment, and the structure and activity of associated microbial communities were examined. Mud and sand content and the presence of microbial heterotrophic and nitrifying communities partially explained the variability in many biogeochemical attributes such as C:N ratio and %TOC. Microbial community analysis revealed a high relative abundance of putative ammonia-oxidizing Thaumarchaeota and nitrite-oxidizing Nitrospirae. Network analysis showed negative relationships between sets of co-varying organisms and sand and mud contents, and positive relationships with total organic carbon. Our results indicate grain size distribution is a good predictor of biogeochemical properties, and that subsets of the overall microbial community respond to different sediment texture. Relationships between facies and hydrobiogeochemical properties enable facies-based conditional simulation/mapping of these properties to inform multiscale modeling of hyporheic exchange and biogeochemical processes.
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16
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Zhao D, He X, Huang R, Yan W, Yu Z. Emergent macrophytes modify the abundance and community composition of ammonia oxidizers in their rhizosphere sediments. J Basic Microbiol 2017; 57:625-632. [DOI: 10.1002/jobm.201700035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Revised: 03/31/2017] [Accepted: 04/30/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Dayong Zhao
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering; Hohai University; Nanjing China
- College of Hydrology and Water Resources; Hohai University; Nanjing China
| | - Xiaowei He
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering; Hohai University; Nanjing China
- College of Hydrology and Water Resources; Hohai University; Nanjing China
| | - Rui Huang
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering; Hohai University; Nanjing China
- College of Hydrology and Water Resources; Hohai University; Nanjing China
| | - Wenming Yan
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering; Hohai University; Nanjing China
| | - Zhongbo Yu
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering; Hohai University; Nanjing China
- College of Hydrology and Water Resources; Hohai University; Nanjing China
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17
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Zhao D, Luo J, Wang J, Huang R, Guo K, Li Y, Wu QL. The influence of land use on the abundance and diversity of ammonia oxidizers. Curr Microbiol 2014; 70:282-9. [PMID: 25331793 DOI: 10.1007/s00284-014-0714-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Accepted: 09/06/2014] [Indexed: 11/30/2022]
Abstract
Nitrification plays a significant role in soil nitrogen cycling, a process in which the first step can be catalyzed by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). In this study, six soil samples with distinct land-use regimes (forestland soil, paddy soil, wheat-planted soil, fruit-planted soil, grassland soil, and rape-planted soil) were collected from Chuzhou city in the Anhui province to elucidate the effects of land use on the abundance and diversity of AOA and AOB. The abundance of the archaeal amoA gene ranged from 2.12 × 10(4) copies per gram of dry soil to 2.57 × 10(5) copies per gram of dry soil, while the abundance of the bacterial amoA gene ranged from 5.58 × 10(4) copies per gram of dry soil to 1.59 × 10(8) copies per gram of dry soil. The grassland and the rape-planted soil samples maintained the highest abundance of the bacterial and archaeal amoA genes, respectively. The abundance of the archaeal amoA gene was positively correlated with the pH (P < 0.05). The ammonia concentrations exhibited a significantly positive relation with the abundance of the bacterial amoA gene (P < 0.01) and the number of OTUs of AOB (P < 0.05). The community composition of AOB was more sensitive to the land-use regimes than that of AOA. The data obtained in this study may be useful to better understand the nitrification process in soils with different land-use regimes.
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Affiliation(s)
- Dayong Zhao
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China,
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18
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Hou M, Xiong J, Wang K, Ye X, Ye R, Wang Q, Hu C, Zhang D. Communities of sediment ammonia-oxidizing bacteria along a coastal pollution gradient in the East China Sea. MARINE POLLUTION BULLETIN 2014; 86:147-153. [PMID: 25110045 DOI: 10.1016/j.marpolbul.2014.07.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 07/08/2014] [Accepted: 07/20/2014] [Indexed: 06/03/2023]
Abstract
Anthropogenic nitrogen (N) discharges has caused eutrophication in coastal zones. Ammonia-oxidizing bacteria (AOB) convert ammonia to nitrite and play important roles in N transformation. Here, we used pyrosequencing based on the amoA gene to investigate the response of the sediment AOB community to an N pollution gradient in the East China Sea. The results showed that AOB assemblages were primarily affiliated with Nitrosospira-like lineages, and only 0.4% of those belonged to Nitrosomonas-like lineage. The Nitrosospira-like lineage was separated into four clusters that were most similar to the sediment AOB communities detected in adjacent marine regions. Additionally, one clade was out grouped from the AOB lineages, which shared the high similarities with pmoA gene. The AOB community structures substantially changed along the pollution gradient, which were primarily shaped by NH4(+)-N, NO3(-)-N, SO4(2)(-)-S, TP and Eh. These results demonstrated that coastal pollution could dramatically influence AOB communities, which, in turn, may change ecosystem function.
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Affiliation(s)
- Manhua Hou
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Jinbo Xiong
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; 2011 Center of Modern Marine Aquaculture of East China Sea, Ningbo 315211, China
| | - Kai Wang
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; 2011 Center of Modern Marine Aquaculture of East China Sea, Ningbo 315211, China
| | - Xiansen Ye
- Marine Environmental Monitoring Center of Ningbo, SOA, Ningbo 315012, China
| | - Ran Ye
- Marine Environmental Monitoring Center of Ningbo, SOA, Ningbo 315012, China
| | - Qiong Wang
- Marine Environmental Monitoring Center of Ningbo, SOA, Ningbo 315012, China
| | - Changju Hu
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Demin Zhang
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; 2011 Center of Modern Marine Aquaculture of East China Sea, Ningbo 315211, China.
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19
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Narihiro T, Tamaki H, Akiba A, Takasaki K, Nakano K, Kamagata Y, Hanada S, Maji T. Microbial community structure of relict niter-beds previously used for saltpeter production. PLoS One 2014; 9:e104752. [PMID: 25111392 PMCID: PMC4128746 DOI: 10.1371/journal.pone.0104752] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 07/14/2014] [Indexed: 11/24/2022] Open
Abstract
From the 16th to the 18th centuries in Japan, saltpeter was produced using a biological niter-bed process and was formed under the floor of gassho-style houses in the historic villages of Shirakawa-go and Gokayama, which are classified as United Nations Educational, Scientific and Cultural Organization (UNESCO) World Heritage Sites. The relict niter-beds are now conserved in the underfloor space of gassho-style houses, where they are isolated from destabilizing environmental factors and retain the ability to produce nitrate. However, little is known about the nitrifying microbes in such relict niter-bed ecosystems. In this study, the microbial community structures within nine relict niter-bed soils were investigated using 454 pyrotag analysis targeting the 16S rRNA gene and the bacterial and archaeal ammonia monooxygenase gene (amoA). The 16S rRNA gene pyrotag analysis showed that members of the phyla Proteobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Gemmatimonadetes, and Planctomycetes were major microbial constituents, and principal coordinate analysis showed that the NO3−, Cl−, K+, and Na+ contents were potential determinants of the structures of entire microbial communities in relict niter-bed soils. The bacterial and archaeal amoA libraries indicated that members of the Nitrosospira-type ammonia-oxidizing bacteria (AOB) and “Ca. Nitrososphaera”-type ammonia-oxidizing archaea (AOA), respectively, predominated in relict niter-bed soils. In addition, soil pH and organic carbon content were important factors for the ecological niche of AOB and AOA in relict niter-bed soil ecosystems.
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Affiliation(s)
- Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
- * E-mail:
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Aya Akiba
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | | | | | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan
| | - Satoshi Hanada
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Taizo Maji
- Shubun University, Ichinomiya, Aichi, Japan
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20
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Hu Z, Meng H, Shi JH, Bu NS, Fang CM, Quan ZX. Community size and composition of ammonia oxidizers and denitrifiers in an alluvial intertidal wetland ecosystem. Front Microbiol 2014; 5:371. [PMID: 25101072 PMCID: PMC4107847 DOI: 10.3389/fmicb.2014.00371] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 07/02/2014] [Indexed: 11/30/2022] Open
Abstract
Global nitrogen cycling is mainly mediated by the activity of microorganisms. Nitrogen cycle processes are mediated by functional groups of microorganisms that are affected by constantly changing environmental conditions and substrate availability. In this study, we investigated the temporal and spatial patterns of nitrifier and denitrifier communities in an intertidal wetland. Soil samples were collected over four distinct seasons from three locations with different vegetative cover. Multiple environmental factors and process rates were measured and analyzed together with the community size and composition profiles. We observed that the community size and composition of the nitrifiers and denitrifiers are affected significantly by seasonal factors, while vegetative cover affected the community composition. The seasonal impacts on the community size of ammonia oxidizing archaea (AOA) are much higher than that of ammonia oxidizing bacteria (AOB). The seasonal change was a more important indicator for AOA community composition patterns, while vegetation was more important for the AOB community patterns. The microbial process rates were correlated with both the community size and composition.
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Affiliation(s)
- Ziye Hu
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan UniversityShanghai, China
| | - Han Meng
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan UniversityShanghai, China
| | - Jin-Huan Shi
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan UniversityShanghai, China
| | - Nai-Shun Bu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan UniversityShanghai, China
| | - Chang-Ming Fang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan UniversityShanghai, China
| | - Zhe-Xue Quan
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan UniversityShanghai, China
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21
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Liu B, Li Y, Zhang J, Zhou X, Wu C. Abundance and diversity of ammonia-oxidizing microorganisms in the sediments of Jinshan Lake. Curr Microbiol 2014; 69:751-7. [PMID: 25008777 DOI: 10.1007/s00284-014-0646-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 05/12/2014] [Indexed: 11/25/2022]
Abstract
Community structures of ammonia-oxidizing microorganisms were investigated using PCR primers designed to specifically target the ammonia monooxygenase α-subunit (amoA) gene in the sediment of Jinshan Lake. Relationships between the abundance and diversity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), and physicochemical parameters were also explored. The AOA abundance decreased sharply from west to east; however, the AOB abundance changed slightly with AOB outnumbering AOA in two of the four sediment samples (JS), JS3 and JS4. The AOA abundance was significantly correlated with the NH4-N, NO3-N, and TP. No significant correlations were observed between the AOB abundance and environmental variables. AOB had a higher diversity and richness of amoA genes than AOA. Among the 76 archaeal amoA sequences retrieved, 57.89, 38.16, and 3.95 % fell within the Nitrosopumilus, Nitrososphaera, and Nitrososphaera sister clusters, respectively. The 130 bacterial amoA gene sequences obtained in this study were grouped with known AOB sequences in the Nitrosomonas and Nitrosospira genera, which occupied 72.31 % and 27.69 % of the AOB group, respectively. Compared to the other three sample sites, the AOA and AOB community compositions at JS4 showed a large difference. This work could enhance our understanding of the roles of ammonia-oxidizing microorganisms in freshwater lake environment.
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Affiliation(s)
- Biao Liu
- Department of Environment Engineering, School of Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, China,
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22
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Wang X, Wang C, Bao L, Xie S. Abundance and community structure of ammonia-oxidizing microorganisms in reservoir sediment and adjacent soils. Appl Microbiol Biotechnol 2013; 98:1883-92. [PMID: 23949998 DOI: 10.1007/s00253-013-5174-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Revised: 07/25/2013] [Accepted: 08/01/2013] [Indexed: 12/01/2022]
Abstract
Ammonia oxidation is an important process for global nitrogen cycling. Both ammonia-oxidizing bacteria (AOB) and archaea (AOA) can be the important players in nitrification process. However, their relative contribution to nitrification remains controversial. This study investigated the abundance and community structure of AOA and AOB in sediment of Miyun Reservoir and adjacent soils. Quantitative PCR assays indicated that the highest AOA abundance occurred in unplanted riparian soil, followed by reservoir sediment, reed-planted riparian soil and agricultural soil. The AOB community size in agricultural soil was much larger than that in the other habitats. Large variations in the structures of AOA and AOB were also observed among the different habitats. The abundance of Nitrosospira-like AOB species were detected in the agricultural soil and reservoir sediment. Pearson's correlation analysis showed the AOB diversity had positive significant correlations with pH and total nitrogen, while the AOA diversity might be negatively affected by nitrate nitrogen and ammonia nitrogen. This work could add new insights towards nitrification in aquatic and terrestrial ecosystems.
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Affiliation(s)
- Xiaoyan Wang
- College of Resources, Environment & Tourism, Capital Normal University, Beijing, 100048, China
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