1
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Ning Z, Cai P, Zhang M. Metagenomic analysis revealed highly diverse carbon fixation microorganisms in a petroleum-hydrocarbon-contaminated aquifer. ENVIRONMENTAL RESEARCH 2024; 247:118289. [PMID: 38266905 DOI: 10.1016/j.envres.2024.118289] [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: 07/07/2023] [Revised: 12/23/2023] [Accepted: 01/20/2024] [Indexed: 01/26/2024]
Abstract
As one of the ultimate products of hydrocarbon biodegradation, inorganic carbon always be used to evaluate hydrocarbon biodegradation rates in petroleum-hydrocarbon-contaminated (PHC) aquifers. The evaluation method was challenged because of the existence of carbon fixation microorganisms, which may uptake inorganic carbons and consequently cause the biodegradation rates to be underestimated. We wonder if there are carbon fixation microorganisms in PHC aquifers. Although an extremely limited number of carbon fixation microorganisms in PHC sites have been studied in previous studies, the vast majority of microorganisms that participate in carbon fixation have not been systematically identified. To systematically reveal carbon fixation microorganisms and their survival environmental conditions, high-throughput metagenomic sequencing technologies, which are characterized by culture-independent, unbiased, and comprehensive methods for the detection and taxonomic characterization of microorganisms, were introduced to analyze the groundwater samples collected from a PHC aquifer. Results showed that 1041 genera were annotated as carbon fixation microorganisms, which accounted for 49% of the total number of genera in the PHC aquifer. Carbon fixation genes involved in Calvin-Benson-Bassham (CBB), 3-hydroxy propionate (3HP), reductive tricarboxylic acid (rTCA), and Wood-Ljungdahl (WL) cycles accounted for 2%, 41%, 34%, and 23% of the total carbon fixation genes, respectively, and 3HP, rTCA, and WL can be deemed as the dominant carbon fixation pathways. Most of the identified carbon fixation microorganisms are potential hydrocarbon biodegraders, and the most abundant carbon fixation microorganisms, such as Microbacterium, Novosphingobium, and Reyranella, were just the most abundant microorganisms in the aquifer system. It's deduced that most of the microorganisms in the aquifer were facultative autotrophic, and undertaking the dual responsibilities of degrading hydrocarbons to inorganic carbon and uptaking inorganic carbon to biomass.
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Affiliation(s)
- Zhuo Ning
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, China; Key Laboratory of Groundwater Remediation of Hebei Province & China Geological Survey, China.
| | - Pingping Cai
- School of Water Resources and Environment, Hebei GEO University, China.
| | - Min Zhang
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, China; Key Laboratory of Groundwater Remediation of Hebei Province & China Geological Survey, China.
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2
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Xu Y, Wang N, Peng L, Li S, Liang C, Song K, Song S, Zhou Y. Free Nitrous Acid Inhibits Atenolol Removal during the Sidestream Partial Nitritation Process through Regulating Microbial-Induced Metabolic Types. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:11614-11624. [PMID: 35900075 DOI: 10.1021/acs.est.1c08845] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Limited studies have attempted to evaluate pharmaceutical removal during the sidestream partial nitritation (PN) process. In this work, atenolol biodegradation by PN cultures was investigated by maintaining ammonium and pH at different levels. For the first time, free nitrous acid (FNA), other than ammonium, pH, and free ammonia, was demonstrated to inhibit atenolol removal, with biodegradation efficiencies of ∼98, ∼67, and ∼28% within 6 days at average FNA levels of 0, 0.03, and 0.19 mg-N L-1, respectively. Ammonia-oxidizing bacteria (AOB)-induced metabolism was predominant despite varying FNA concentrations. In the absence of ammonium/FNA, atenolol was mostly biodegraded via AOB-induced metabolism (65%) and heterotroph-induced metabolism (33%). AOB-induced metabolism was largely inhibited (down to 29%) at 0.03 mg-N L-1 FNA, while ∼27 and ∼11% were degraded via heterotroph-induced metabolism and AOB-induced cometabolism, respectively. Higher FNA (0.19 mg-N L-1) substantially reduced atenolol biodegradation via heterotroph-induced metabolism (4%), AOB-induced metabolism (16%), and AOB-induced cometabolism (8%). Newly identified products and pathways were related to metabolic types and FNA levels: (i) deamination and decarbonylation (AOB-induced cometabolism, 0.03 mg-N L-1 FNA); (ii) deamination from atenolol acid (heterotrophic biodegradation); and (iii) nitro-substitution (reaction with nitrite). This suggests limiting FNA to realize simultaneous nitrogen and pharmaceutical removal during the sidestream process.
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Affiliation(s)
- Yifeng Xu
- Hubei Key Laboratory of Mineral Resources Processing and Environment, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei 430070, China
- School of Resources and Environmental Engineering, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei 430070, China
| | - Ning Wang
- School of Resources and Environmental Engineering, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei 430070, China
| | - Lai Peng
- Hubei Key Laboratory of Mineral Resources Processing and Environment, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei 430070, China
- School of Resources and Environmental Engineering, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei 430070, China
| | - Shengjun Li
- School of Resources and Environmental Engineering, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei 430070, China
| | - Chuanzhou Liang
- Hubei Key Laboratory of Mineral Resources Processing and Environment, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei 430070, China
- School of Resources and Environmental Engineering, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei 430070, China
| | - Kang Song
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Shaoxian Song
- Hubei Key Laboratory of Mineral Resources Processing and Environment, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei 430070, China
- School of Resources and Environmental Engineering, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei 430070, China
| | - Yan Zhou
- School of Civil and Environmental Engineering, Nanyang Technological University, 639798 Singapore
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Xu H, Deng Y, Li X, Liu Y, Huang S, Yang Y, Wang Z, Hu C. Effect of Increasing C/N Ratio on Performance and Microbial Community Structure in a Membrane Bioreactor with a High Ammonia Load. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:8070. [PMID: 34360363 PMCID: PMC8345800 DOI: 10.3390/ijerph18158070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/25/2021] [Accepted: 07/27/2021] [Indexed: 01/03/2023]
Abstract
Herein, the responses of the operational performance of a membrane bioreactor (MBR) with a high ammonium-nitrogen (NH4+-N) load and microbial community structure to increasing carbon to nitrogen (C/N) ratios were studied. Variation in the influent C/N ratio did not affect the removal efficiencies of chemical oxygen demand (COD) and NH4+-N but gradually abated the ammonia oxidization activity of sludge. The concentration of the sludge in the reactor at the end of the process increased four-fold compared with that of the seed sludge, ensuring the stable removal of NH4+-N. The increasing influent COD concentration resulted in an elevated production of humic acids in soluble microbial product (SMP) and accelerated the rate of membrane fouling. High-throughput sequencing analysis showed that the C/N ratio had selective effects on the microbial community structure. In the genus level, Methyloversatilis, Subsaxibacter, and Pseudomonas were enriched during the operation. However, the relative abundance of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) involved in nitrification declined gradually and were decreased by 86.54 and 90.17%, respectively, with influent COD increasing from 0 to 2000 mg/L. The present study offers a more in-depth insight into the control strategy of the C/N ratio in the operation of an MBR with a high NH4+-N load.
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Affiliation(s)
- Huaihao Xu
- Institute of Environmental Research at Greater Bay, Guangzhou Key Laboratory for Clean Energy and Materials, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China; (H.X.); (Y.D.); (X.L.); (S.H.); (Y.Y.); (C.H.)
| | - Yuepeng Deng
- Institute of Environmental Research at Greater Bay, Guangzhou Key Laboratory for Clean Energy and Materials, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China; (H.X.); (Y.D.); (X.L.); (S.H.); (Y.Y.); (C.H.)
| | - Xiuying Li
- Institute of Environmental Research at Greater Bay, Guangzhou Key Laboratory for Clean Energy and Materials, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China; (H.X.); (Y.D.); (X.L.); (S.H.); (Y.Y.); (C.H.)
| | - Yuxian Liu
- Institute of Environmental Research at Greater Bay, Guangzhou Key Laboratory for Clean Energy and Materials, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China; (H.X.); (Y.D.); (X.L.); (S.H.); (Y.Y.); (C.H.)
- Linköping University-Guangzhou University Research Center on Urban Sustainable Development, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Shuangqiu Huang
- Institute of Environmental Research at Greater Bay, Guangzhou Key Laboratory for Clean Energy and Materials, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China; (H.X.); (Y.D.); (X.L.); (S.H.); (Y.Y.); (C.H.)
| | - Yunhua Yang
- Institute of Environmental Research at Greater Bay, Guangzhou Key Laboratory for Clean Energy and Materials, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China; (H.X.); (Y.D.); (X.L.); (S.H.); (Y.Y.); (C.H.)
| | - Zhu Wang
- Institute of Environmental Research at Greater Bay, Guangzhou Key Laboratory for Clean Energy and Materials, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China; (H.X.); (Y.D.); (X.L.); (S.H.); (Y.Y.); (C.H.)
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Chun Hu
- Institute of Environmental Research at Greater Bay, Guangzhou Key Laboratory for Clean Energy and Materials, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China; (H.X.); (Y.D.); (X.L.); (S.H.); (Y.Y.); (C.H.)
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4
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Spieck E, Sass K, Keuter S, Hirschmann S, Spohn M, Indenbirken D, Kop LFM, Lücker S, Giaveno A. Defining Culture Conditions for the Hidden Nitrite-Oxidizing Bacterium Nitrolancea. Front Microbiol 2020; 11:1522. [PMID: 32849321 PMCID: PMC7365893 DOI: 10.3389/fmicb.2020.01522] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/12/2020] [Indexed: 12/26/2022] Open
Abstract
Nitrification is a key process for N-removal in engineered and natural environments, but recent findings of novel nitrifying microorganisms with surprising features revealed that our knowledge of this functional guild is still incomplete. Especially nitrite oxidation - the second step of nitrification - is catalyzed by a phylogenetically diverse bacterial group, and only recently bacteria of the phylum Chloroflexi have been identified as thermophilic nitrite-oxidizing bacteria (NOB). Among these, Nitrolancea hollandica was isolated from a laboratory-scale nitrifying bioreactor operated at 35°C with a high load of ammonium bicarbonate. However, its distribution remains cryptic as very few closely related environmental 16S rRNA gene sequences have been retrieved so far. In this study, we demonstrate how such thermophilic NOB can be enriched using modified mineral media inoculated with samples from a wastewater side-stream reactor operated at 39.5°C. Distinct cultivation conditions resulted in quick and reproducible high enrichment of two different strains of Nitrolancea, closely related to Nl. hollandica. The same cultivation approach was applied to a complex nitrite-oxidizing pre-enrichment at 42°C inoculated with biomass from a geothermal spring in the Copahue volcano area in Neuquen, Argentina. Here, an additional distinct representative of the genus Nitrolancea was obtained. This novel species had 16S rRNA and nitrite oxidoreductase alpha subunit (nxrA) gene sequence identities to Nl. hollandica of 98.5% and 97.2%, respectively. A genomic average nucleotide identity between the Argentinian strain and Nl. hollandica of 91.9% indicates that it indeed represents a distinct species. All Nitrolancea cultures formed lancet-shaped cells identical to Nl. hollandica and revealed similar physiological features, including the capability to grow at high nitrite concentrations. Growth was optimal at temperatures of 35-37°C and was strongly enhanced by ammonium supplementation. Genomic comparisons revealed that the four Nitrolancea strains share 2399 out of 3387 orthologous gene clusters and encode similar key functions. Our results define general growth conditions that enable the selective enrichment of Nitrolancea from artificial and natural environments. In most natural habitats these NOB apparently are of low abundance and their proliferation depends on the balanced presence of nitrite and ammonium, with an optimal incubation temperature of 37°C.
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Affiliation(s)
- Eva Spieck
- Department of Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany
| | - Katharina Sass
- Department of Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany
| | - Sabine Keuter
- Department of Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany
| | - Sophia Hirschmann
- Department of Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany
| | - Michael Spohn
- Technology Platform Next Generation Sequencing, Heinrich Pette Institut, Hamburg, Germany
| | - Daniela Indenbirken
- Technology Platform Next Generation Sequencing, Heinrich Pette Institut, Hamburg, Germany
| | - Linnea F. M. Kop
- Department of Microbiology, IWWR, Radboud University, Nijmegen, Netherlands
| | - Sebastian Lücker
- Department of Microbiology, IWWR, Radboud University, Nijmegen, Netherlands
| | - Alejandra Giaveno
- PROBIEN (CONICET-UNCo), Departamento de Química, Facultad de Ingeniería, Universidad Nacional del Comahue, Neuquén, Argentina
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5
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Isshiki R, Fujitani H, Tsuneda S. Transcriptome Analysis of the Ammonia-Oxidizing Bacterium Nitrosomonas mobilis Ms1 Reveals Division of Labor between Aggregates and Free-living Cells. Microbes Environ 2020; 35. [PMID: 32115437 PMCID: PMC7308568 DOI: 10.1264/jsme2.me19148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Bacteria change their metabolic states to increase survival by forming aggregates. Ammonia-oxidizing bacteria also form aggregates in response to environmental stresses. Nitrosomonas mobilis, an ammonia-oxidizing bacterium with high stress tolerance, often forms aggregates mainly in wastewater treatment systems. Despite the high frequency of aggregate formation by N. mobilis, its relationship with survival currently remains unclear. In the present study, aggregates were formed in the late stage of culture with the accumulation of nitrite as a growth inhibitor. To clarify the significance of aggregate formation in N. mobilis Ms1, a transcriptome analysis was performed. Comparisons of the early and late stages of culture revealed that the expression of stress response genes (chaperones and proteases) increased in the early stage. Aggregate formation may lead to stress avoidance because stress response genes were not up-regulated in the late stage of culture during which aggregates formed. Furthermore, comparisons of free-living cells with aggregates in the early stage of culture showed differences in gene expression related to biosynthesis (ATP synthase and ribosomal proteins) and motility and adhesion (flagella, pilus, and chemotaxis). Biosynthesis genes for growth were up-regulated in free-living cells, while motility and adhesion genes for adaptation were up-regulated in aggregates. These results indicate that N. mobilis Ms1 cells adapt to an unfavorable environment and grow through the division of labor between aggregates and free-living cells.
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Affiliation(s)
- Rino Isshiki
- Department of Life Science and Medical Bioscience, Waseda University
| | - Hirotsugu Fujitani
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology.,Research Organization for Nano & Life Innovation, Waseda University
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, Waseda University.,Research Organization for Nano & Life Innovation, Waseda University
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6
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Picioreanu C, Pérez J, van Loosdrecht MCM. Impact of cell cluster size on apparent half-saturation coefficients for oxygen in nitrifying sludge and biofilms. WATER RESEARCH 2016; 106:371-382. [PMID: 27750126 DOI: 10.1016/j.watres.2016.10.017] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 10/06/2016] [Accepted: 10/07/2016] [Indexed: 05/08/2023]
Abstract
A three-dimensional (3-D) diffusion-reaction model was used to assess the effects of nitrifiers growing in cell clusters on the apparent oxygen half-saturation coefficients in activated sludge flocs. The model allows conciliation of seemingly contradictory reports by several research groups. Although intrinsic half-saturation coefficients (i.e., not affected by diffusion) show a better affinity for oxygen for ammonia oxidizing (AOB) than for nitrite oxidizing bacteria (NOB) (KO,AOB < KO,NOB), measurements in flocs often produced reversed apparent values (KO,AOB,app > KO,NOB,app), which can now be explained by the 3-D model with AOB and NOB microcolonies. This effect cannot be described with a conventional 1-D homogeneous model because the reversion of the AOB/NOB apparent KO is caused by the high biomass density and resulting concentration gradients inside the microcolonies. Two main factors explain the reversion of the half-saturation coefficients: the difference in oxygen yields (for NOB lower than for AOB) and the difference in colony size (NOB colonies are smaller than those of AOB). The strongest increase in the apparent half-saturation coefficients is linked to the colony size, rather than to the floc size. For high-density microbial aggregates (i.e., granular sludge), the need for a stratified population (AOB outer shell, NOB inner layers) was revealed in order to outcompete NOB. This study stresses the need for a more detailed description of the biomass distribution in activated sludge, granular sludge and biofilm reactors when elucidating the mechanisms for NOB repression.
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Affiliation(s)
- Cristian Picioreanu
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Julio Pérez
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
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7
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Cabrol L, Poly F, Malhautier L, Pommier T, Lerondelle C, Verstraete W, Lepeuple AS, Fanlo JL, Le Roux X. Management of Microbial Communities through Transient Disturbances Enhances the Functional Resilience of Nitrifying Gas-Biofilters to Future Disturbances. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:338-48. [PMID: 26651080 DOI: 10.1021/acs.est.5b02740] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Microbial communities have a key role for the performance of engineered ecosystems such as waste gas biofilters. Maintaining constant performance despite fluctuating environmental conditions is of prime interest, but it is highly challenging because the mechanisms that drive the response of microbial communities to disturbances still have to be disentangled. Here we demonstrate that the bioprocess performance and stability can be improved and reinforced in the face of disturbances, through a rationally predefined strategy of microbial resource management (MRM). This strategy was experimentally validated in replicated pilot-scale nitrifying gas-biofilters, for the two steps of nitrification. The associated biological mechanisms were unraveled through analysis of functions, abundances and community compositions for the major actors of nitrification in these biofilters, that is, ammonia-oxidizing bacteria (AOB) and Nitrobacter-like nitrite-oxidizers (NOB). Our MRM strategy, based on the application of successive, transient perturbations of increasing intensity, enabled to steer the nitrifier community in a favorable way through the selection of more resistant AOB and NOB sharing functional gene sequences close to those of, respectively, Nitrosomonas eutropha and Nitrobacter hamburgensis that are well adapted to high N load. The induced community shifts resulted in significant enhancement of nitrification resilience capacity following the intense perturbation.
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Affiliation(s)
- Léa Cabrol
- Laboratoire Génie de l'Environnement Industriel, Ecole des Mines d'Alès , Rue Jules Renard, 30100 Alès, France
- Veolia Environnement Recherche et Innovation, Chemin de la Digue, BP76, 78600, Maisons Laffitte, France
- Pontificia Universidad Católica de Valparaíso, Escuela de Ingeniería Bioquímica, Avenida Brasil 2185, Valparaíso, Chile
| | - Franck Poly
- Laboratoire d'Ecologie Microbienne, Université de Lyon, Université Lyon 1, CNRS, INRA, UMR CNRS 5557, USC INRA 1364, Bâtiment Gregor Mendel, 16, rue Raphael Dubois, 69622, Villeurbanne Cedex, France
| | - Luc Malhautier
- Laboratoire Génie de l'Environnement Industriel, Ecole des Mines d'Alès , Rue Jules Renard, 30100 Alès, France
| | - Thomas Pommier
- Laboratoire d'Ecologie Microbienne, Université de Lyon, Université Lyon 1, CNRS, INRA, UMR CNRS 5557, USC INRA 1364, Bâtiment Gregor Mendel, 16, rue Raphael Dubois, 69622, Villeurbanne Cedex, France
| | - Catherine Lerondelle
- Laboratoire d'Ecologie Microbienne, Université de Lyon, Université Lyon 1, CNRS, INRA, UMR CNRS 5557, USC INRA 1364, Bâtiment Gregor Mendel, 16, rue Raphael Dubois, 69622, Villeurbanne Cedex, France
| | - Willy Verstraete
- LabMET, Faculty Bio-Science Engineering, Ghent University , Coupure L 653, 9000 Gent, Belgium
| | - Anne-Sophie Lepeuple
- Veolia Environnement Recherche et Innovation, Chemin de la Digue, BP76, 78600, Maisons Laffitte, France
| | - Jean-Louis Fanlo
- Laboratoire Génie de l'Environnement Industriel, Ecole des Mines d'Alès , Rue Jules Renard, 30100 Alès, France
| | - Xavier Le Roux
- Laboratoire d'Ecologie Microbienne, Université de Lyon, Université Lyon 1, CNRS, INRA, UMR CNRS 5557, USC INRA 1364, Bâtiment Gregor Mendel, 16, rue Raphael Dubois, 69622, Villeurbanne Cedex, France
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8
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Sorokin DY, Vejmelkova D, Lücker S, Streshinskaya GM, Rijpstra WIC, Sinninghe Damsté JS, Kleerbezem R, van Loosdrecht M, Muyzer G, Daims H. Nitrolancea hollandica gen. nov., sp. nov., a chemolithoautotrophic nitrite-oxidizing bacterium isolated from a bioreactor belonging to the phylum Chloroflexi. Int J Syst Evol Microbiol 2014; 64:1859-1865. [DOI: 10.1099/ijs.0.062232-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel nitrite-oxidizing bacterium (NOB), strain LbT, was isolated from a nitrifying bioreactor with a high loading of ammonium bicarbonate in a mineral medium with nitrite as the energy source. The cells were oval (lancet-shaped) rods with pointed edges, non-motile, Gram-positive (by staining and from the cell wall structure) and non-spore-forming. Strain LbT was an obligately aerobic, chemolitoautotrophic NOB, utilizing nitrite or formate as the energy source and CO2 as the carbon source. Ammonium served as the only source of assimilated nitrogen. Growth with nitrite was optimal at pH 6.8–7.5 and at 40 °C (maximum 46 °C). The membrane lipids consisted of C20 alkyl 1,2-diols with the dominant fatty acids being 10MeC18 and C18 : 1ω9. The peptidoglycan lacked meso-DAP but contained ornithine and lysine. The dominant lipoquinone was MK-8. Phylogenetic analyses of the 16s rRNA gene sequence placed strain LbT into the class
Thermomicrobia
of the phylum
Chloroflexi
with
Sphaerobacter thermophilus
as the closest relative. On the basis of physiological and phylogenetic data, it is proposed that strain LbT represents a novel species of a new genus, with the suggested name Nitrolancea hollandica gen. nov., sp. nov. The type strain of the type species is LbT ( = DSM 23161T = UNIQEM U798T).
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Affiliation(s)
- Dimitry Y. Sorokin
- Department of Biotechnology, TU Delft, The Netherlands
- Winogradsky Institute of Microbiology RAS, Moscow, Russia
| | | | - Sebastian Lücker
- Department of Microbial Ecology, Ecology Centre, University of Vienna, Vienna, Austria
| | - Galina M. Streshinskaya
- Microbiology Department, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - W. Irene C. Rijpstra
- 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
| | | | | | - Gerard Muyzer
- Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Holger Daims
- Department of Microbial Ecology, Ecology Centre, University of Vienna, Vienna, Austria
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9
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Hoang V, Delatolla R, Abujamel T, Mottawea W, Gadbois A, Laflamme E, Stintzi A. Nitrifying moving bed biofilm reactor (MBBR) biofilm and biomass response to long term exposure to 1 °C. WATER RESEARCH 2014; 49:215-24. [PMID: 24333509 DOI: 10.1016/j.watres.2013.11.018] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 11/04/2013] [Accepted: 11/12/2013] [Indexed: 05/12/2023]
Abstract
This study aims to investigate moving bed biofilm reactor (MBBR) nitrification rates, nitrifying biofilm morphology, biomass viability as well as bacterial community shifts during long-term exposure to 1 °C. Long-term exposure to 1 °C is the key operational condition for potential ammonia removal upgrade units to numerous northern region treatment systems. The average laboratory MBBR ammonia removal rate after long-term exposure to 1 °C was measured to be 18 ± 5.1% as compared to the average removal rate at 20 °C. Biofilm morphology and specifically the thickness along with biomass viability at various depths in the biofilm were investigated using variable pressure electron scanning microscope (VPSEM) imaging and confocal laser scanning microscope (CLSM) imaging in combination with viability live/dead staining. The biofilm thickness along with the number of viable cells showed significant increases after long-term exposure to 1 °C. Hence, this study observed nitrifying bacteria with higher activities at warm temperatures and a slightly greater quantity of nitrifying bacteria with lower activities at cold temperatures in nitrifying MBBR biofilms. Using DNA sequencing analysis, Nitrosomonas and Nitrosospira (ammonia oxidizers) as well as Nitrospira (nitrite oxidizer) were identified and no population shift was observed between 20 °C and after long-term exposure to 1 °C.
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Affiliation(s)
- V Hoang
- Department of Civil Engineering, University of Ottawa, 161 Louis Pasteur, Ottawa, Ontario K1N 6N5, Canada
| | - R Delatolla
- Department of Civil Engineering, University of Ottawa, 161 Louis Pasteur, Ottawa, Ontario K1N 6N5, Canada.
| | - T Abujamel
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ontario K1H 8M5, Canada
| | - W Mottawea
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ontario K1H 8M5, Canada
| | - A Gadbois
- John Meunier Inc., Montreal, Quebec H4S 2B3, Canada
| | - E Laflamme
- John Meunier Inc., Montreal, Quebec H4S 2B3, Canada
| | - A Stintzi
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ontario K1H 8M5, Canada
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Wang Z, Zhang XX, Huang K, Miao Y, Shi P, Liu B, Long C, Li A. Metagenomic profiling of antibiotic resistance genes and mobile genetic elements in a tannery wastewater treatment plant. PLoS One 2013; 8:e76079. [PMID: 24098424 PMCID: PMC3787945 DOI: 10.1371/journal.pone.0076079] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 08/20/2013] [Indexed: 11/18/2022] Open
Abstract
Antibiotics are often used to prevent sickness and improve production in animal agriculture, and the residues in animal bodies may enter tannery wastewater during leather production. This study aimed to use Illumina high-throughput sequencing to investigate the occurrence, diversity and abundance of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in aerobic and anaerobic sludge of a full-scale tannery wastewater treatment plant (WWTP). Metagenomic analysis showed that Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria dominated in the WWTP, but the relative abundance of archaea in anaerobic sludge was higher than in aerobic sludge. Sequencing reads from aerobic and anaerobic sludge revealed differences in the abundance of functional genes between both microbial communities. Genes coding for antibiotic resistance were identified in both communities. BLAST analysis against Antibiotic Resistance Genes Database (ARDB) further revealed that aerobic and anaerobic sludge contained various ARGs with high abundance, among which sulfonamide resistance gene sul1 had the highest abundance, occupying over 20% of the total ARGs reads. Tetracycline resistance genes (tet) were highly rich in the anaerobic sludge, among which tet33 had the highest abundance, but was absent in aerobic sludge. Over 70 types of insertion sequences were detected in each sludge sample, and class 1 integrase genes were prevalent in the WWTP. The results highlighted prevalence of ARGs and MGEs in tannery WWTPs, which may deserve more public health concerns.
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Affiliation(s)
- Zhu Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, China
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11
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Jin RC, Zhang QQ, Liu JH, Yang BE, Wu K, Zheng P. Performance and stability of the partial nitrification process for nitrogen removal from monosodium glutamate wastewater. Sep Purif Technol 2013. [DOI: 10.1016/j.seppur.2012.10.042] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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12
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Liu S, Horn H, Müller E. A systematic insight into a single-stage deammonification process operated in granular sludge reactor with high-loaded reject-water: characterization and quantification of microbiological community. J Appl Microbiol 2012; 114:339-51. [DOI: 10.1111/jam.12042] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2012] [Revised: 09/04/2012] [Accepted: 09/11/2012] [Indexed: 11/28/2022]
Affiliation(s)
- S.T. Liu
- Institute of Water Quality Control; Technische Universität München; Garching Germany
- Department of Environmental Engineering; Peking University; The Key Laboratory of Water and Sediment Sciences; Ministry of Education; Beijing China
| | - H. Horn
- Karlsruhe Institute of Technology (KIT); Engler-Bunte-Institute; Water Chemistry and Water Technology; Karlsruhe Germany
| | - E. Müller
- Institute of Water Quality Control; Technische Universität München; Garching Germany
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Gabarró J, Ganigué R, Gich F, Ruscalleda M, Balaguer MD, Colprim J. Effect of temperature on AOB activity of a partial nitritation SBR treating landfill leachate with extremely high nitrogen concentration. BIORESOURCE TECHNOLOGY 2012; 126:283-289. [PMID: 23079415 DOI: 10.1016/j.biortech.2012.09.011] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 09/04/2012] [Accepted: 09/05/2012] [Indexed: 06/01/2023]
Abstract
This study investigates the effects of temperature on ammonia oxidizing bacteria activity in a partial nitritation (PN) sequencing batch reactor. Stable PN was achieved in a 250 L SBR with a minimum operating volume of 111L treating mature landfill leachate containing an ammonium concentration of around 6000 mg N-NH(4)(+)L(-1) at both 25 and 35 °C. A suitable influent to feed an anammox reactor was achieved in both cases. A kinetic model was applied to study the influence of free ammonia (FA), the free nitrous acid (FNA) inhibition, and the inorganic carbon (IC) limitation. NH(4)(+) and NO(2)(-) concentrations were similar at 25 and 35 °C experiments (about 2500 mg N-NH(4)(+)L(-1) and 3500 mg N-NO(2)(-)L(-1)), FA and FNA concentrations differed due to the strong temperature dependence. FNA was the main source of inhibition at 25 °C, while at 35 °C combined FA and FNA inhibition occurred. DGGE results demonstrated that PN-SBR sludge was enriched on the same AOB phylotypes in both experiments.
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Affiliation(s)
- J Gabarró
- LEQUIA, Institute of the Environment, University of Girona, Campus Montilivi, E-17071 Girona, Catalonia, Spain.
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Laplante K, Derome N. Parallel changes in the taxonomical structure of bacterial communities exposed to a similar environmental disturbance. Ecol Evol 2012; 1:489-501. [PMID: 22393517 PMCID: PMC3287327 DOI: 10.1002/ece3.37] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Accepted: 08/24/2011] [Indexed: 11/25/2022] Open
Abstract
Bacterial communities play a central role in ecosystems, by regulating biogeochemical fluxes. Therefore, understanding how multiple functional interactions between species face environmental perturbations is a major concern in conservation biology. Because bacteria can use several strategies, including horizontal gene transfers (HGT), to cope with rapidly changing environmental conditions, potential decoupling between function and taxonomy makes the use of a given species as a general bioindicator problematic. The present work is a first step to characterize the impact of a recent polymetallic gradient over the taxonomical networks of five lacustrine bacterial communities. Given that evolutionary convergence represents one of the best illustration of natural selection, we focused on a system composed of two pairs of impacted and clean lakes in order to test whether similar perturbation exerts a comparable impact on the taxonomical networks of independent bacterial communities. First, we showed that similar environmental stress drove parallel structural changes at the taxonomic level on two independent bacterial communities. Second, we showed that a long-term exposure to contaminant gradients drove significant taxonomic structure changes within three interconnected bacterial communities. Thus, this model lake system is relevant to characterize the strategies, namely acclimation and/or adaptation, of bacterial communities facing environmental perturbations, such as metal contamination.
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Affiliation(s)
- Karine Laplante
- Institut de Biologie Intégrative et des Systèmes (IBIS) 1030 rue de la Médecine Université Laval, Québec, Canada
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Sorokin DY, Lücker S, Vejmelkova D, Kostrikina NA, Kleerebezem R, Rijpstra WIC, Damsté JSS, Le Paslier D, Muyzer G, Wagner M, van Loosdrecht MCM, Daims H. Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi. ISME JOURNAL 2012; 6:2245-56. [PMID: 22763649 PMCID: PMC3504966 DOI: 10.1038/ismej.2012.70] [Citation(s) in RCA: 202] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Nitrite-oxidizing bacteria (NOB) catalyze the second step of nitrification, a major process of the biogeochemical nitrogen cycle, but the recognized diversity of this guild is surprisingly low and only two bacterial phyla contain known NOB. Here, we report on the discovery of a chemolithoautotrophic nitrite oxidizer that belongs to the widespread phylum Chloroflexi not previously known to contain any nitrifying organism. This organism, named Nitrolancetus hollandicus, was isolated from a nitrifying reactor. Its tolerance to a broad temperature range (25–63 °C) and low affinity for nitrite (Ks=1 mℳ), a complex layered cell envelope that stains Gram positive, and uncommon membrane lipids composed of 1,2-diols distinguish N. hollandicus from all other known nitrite oxidizers. N. hollandicus grows on nitrite and CO2, and is able to use formate as a source of energy and carbon. Genome sequencing and analysis of N. hollandicus revealed the presence of all genes required for CO2 fixation by the Calvin cycle and a nitrite oxidoreductase (NXR) similar to the NXR forms of the proteobacterial nitrite oxidizers, Nitrobacter and Nitrococcus. Comparative genomic analysis of the nxr loci unexpectedly indicated functionally important lateral gene transfer events between Nitrolancetus and other NOB carrying a cytoplasmic NXR, suggesting that horizontal transfer of the NXR module was a major driver for the spread of the capability to gain energy from nitrite oxidation during bacterial evolution. The surprising discovery of N. hollandicus significantly extends the known diversity of nitrifying organisms and likely will have implications for future research on nitrification in natural and engineered ecosystems.
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Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
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