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He Z, Feng Y, Zhang S, Wang X, Wu S, Pan X. Oxygenic denitrification for nitrogen removal with less greenhouse gas emissions: Microbiology and potential applications. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 621:453-464. [PMID: 29195194 DOI: 10.1016/j.scitotenv.2017.11.280] [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: 10/07/2017] [Revised: 11/24/2017] [Accepted: 11/24/2017] [Indexed: 06/07/2023]
Abstract
Nitrogen pollution is a worldwide problem and has been extensively treated by canonical denitrification (CDN) process. However, the CDN process generates several issues such as intensive greenhouse gas (GHG) emissions. In the past years, a novel biological nitrogen removal (BNR) process of oxygenic denitrification (O2DN) has been proposed as a promising alternative to the CDN process. The classic denitrification four steps are simplified to three steps by O2DN bacteria without producing and releasing the intermediate nitrous oxide (N2O), a potent GHG. In this article, we summarized the findings in previous literatures as well as our results, including involved microorganisms and metabolic mechanisms, functional genes and microbial detection, kinetics and influencing factors and their potential applications in wastewater treatment. Based on our knowledge and experience, the benefits and limitations of the current O2DN process were analyzed. Since O2DN is a new field in wastewater treatment, more research and application is required, especially the development of integrated processes and the quantitative assessment of the contribution of O2DN process in natural habitats and engineered systems.
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Affiliation(s)
- Zhanfei He
- College of Environment, Zhejiang University of Technology, Hangzhou, China; Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, Zhejiang University of Technology, Hangzhou, China
| | - Yudong Feng
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Shijie Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Xiaonan Wang
- Xinjiang Key Laboratory of Environmental Pollution and Bioremediation, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Shuyun Wu
- College of Environment, Zhejiang University of Technology, Hangzhou, China; Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, Zhejiang University of Technology, Hangzhou, China
| | - Xiangliang Pan
- College of Environment, Zhejiang University of Technology, Hangzhou, China; Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, Zhejiang University of Technology, Hangzhou, China.
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202
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Sønderholm M, Koren K, Wangpraseurt D, Jensen PØ, Kolpen M, Kragh KN, Bjarnsholt T, Kühl M. Tools for studying growth patterns and chemical dynamics of aggregated Pseudomonas aeruginosa exposed to different electron acceptors in an alginate bead model. NPJ Biofilms Microbiomes 2018; 4:3. [PMID: 29479470 PMCID: PMC5818519 DOI: 10.1038/s41522-018-0047-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 01/07/2018] [Accepted: 01/24/2018] [Indexed: 12/31/2022] Open
Abstract
In chronic infections, bacterial pathogens typically grow as small dense cell aggregates embedded in a matrix consisting of, e.g., wound bed sludge or lung mucus. Such biofilm growth mode exhibits extreme tolerance towards antibiotics and the immune defence system. The bacterial aggregates are exposed to physiological heterogeneity and O2 limitation due to steep chemical gradients through the matrix, which is are hypothesised to contribute to antibiotic tolerance. Using a novel combination of microsensor and bioimaging analysis, we investigated growth patterns and chemical dynamics of the pathogen Pseudomonas aeruginosa in an alginate bead model, which mimics growth in chronic infections better than traditional biofilm experiments in flow chambers. Growth patterns were strongly affected by electron acceptor availability and the presence of chemical gradients, where the combined presence of O2 and nitrate yielded highest bacterial growth by combined aerobic respiration and denitrification.
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Affiliation(s)
- Majken Sønderholm
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
| | - Klaus Koren
- Marine Biology Section, Department of Biology, University of Copenhagen, Strandpromenaden 5, DK-3000 Helsingør, Denmark
| | - Daniel Wangpraseurt
- Marine Biology Section, Department of Biology, University of Copenhagen, Strandpromenaden 5, DK-3000 Helsingør, Denmark
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Peter Østrup Jensen
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
- Department of Clinical Microbiology 9301, Copenhagen University Hospital, Rigshospitalet, Juliane Maries Vej 22, Copenhagen, Denmark
| | - Mette Kolpen
- Department of Clinical Microbiology 9301, Copenhagen University Hospital, Rigshospitalet, Juliane Maries Vej 22, Copenhagen, Denmark
| | - Kasper Nørskov Kragh
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
| | - Thomas Bjarnsholt
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
- Department of Clinical Microbiology 9301, Copenhagen University Hospital, Rigshospitalet, Juliane Maries Vej 22, Copenhagen, Denmark
| | - Michael Kühl
- Marine Biology Section, Department of Biology, University of Copenhagen, Strandpromenaden 5, DK-3000 Helsingør, Denmark
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW 2007 Australia
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203
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Abstract
Pseudomonas aeruginosa, a Gram-negative bacterium, is characterized by its versatility that enables persistent survival under adverse conditions. It can grow on diverse energy sources and readily acquire resistance to antimicrobial agents. As an opportunistic human pathogen, it also causes chronic infections inside the anaerobic mucus airways of cystic fibrosis patients. As a strict respirer, P. aeruginosa can grow by anaerobic nitrate ( [Formula: see text] ) respiration. Nitric oxide (NO) produced as an intermediate during anaerobic respiration exerts many important effects on the biological characteristics of P. aeruginosa. This review provides information regarding (i) how P. aeruginosa grows by anaerobic respiration, (ii) mechanisms by which NO is produced under such growth, and (iii) bacterial adaptation to NO. We also review the clinical relevance of NO in the fitness of P. aeruginosa and the use of NO as a potential therapeutic for treating P. aeruginosa infection.
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204
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Zhao B, Cheng DY, Tan P, An Q, Guo JS. Characterization of an aerobic denitrifier Pseudomonas stutzeri strain XL-2 to achieve efficient nitrate removal. BIORESOURCE TECHNOLOGY 2018; 250:564-573. [PMID: 29197780 DOI: 10.1016/j.biortech.2017.11.038] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 11/09/2017] [Accepted: 11/11/2017] [Indexed: 06/07/2023]
Abstract
An aerobic denitrifier was newly isolated and identified as Pseudomonas stutzeri strain XL-2. Strain XL-2 removed 97.9% of nitrate with an initial concentration about 100 mg/L. Nitrogen balance indicates that 12.4% of the initial nitrogen was converted to N2O, and 62.4% was converted to N2. Single factor experiments indicate that the optimal conditions for nitrate removal were C/N ratio of 10, temperature of 30 °C and shaking speed of 120 rpm. Sequence amplification indicates that the denitrification genes of napA, nirS, norB and nosZ were present in strain XL-2. Combined with nitrogen balance, strain XL-2 presents the metabolic pathway of NO3- → NO2- → NO → N2O → N2 under aerobic conditions. The expression of napA and nirS might be responsible for the tolerance of dissolved oxygen by strain XL-2 during denitrification process.
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Affiliation(s)
- Bin Zhao
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China; National Centre for International Research of Low-carbon and Green Buildings, Chongqing University, Chongqing 400045, PR China
| | - Dan Yang Cheng
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China
| | - Pan Tan
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China
| | - Qiang An
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China; National Centre for International Research of Low-carbon and Green Buildings, Chongqing University, Chongqing 400045, PR China.
| | - Jin Song Guo
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China; National Centre for International Research of Low-carbon and Green Buildings, Chongqing University, Chongqing 400045, PR China
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205
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Zhai S, Ji M, Zhao Y, Pavlostathis SG, Zhao Q. Effects of salinity and COD/N on denitrification and bacterial community in dicyclic-type electrode based biofilm reactor. CHEMOSPHERE 2018; 192:328-336. [PMID: 29117591 DOI: 10.1016/j.chemosphere.2017.10.108] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/17/2017] [Accepted: 10/19/2017] [Indexed: 06/07/2023]
Abstract
A dicyclic-type electrode based biofilm electrode reactor (BER) was developed for advanced nitrate removal from saline municipal wastewater. The denitrification efficiency was evaluated with a synthetic feed (NO3--N, 20 mg L-1) under different salinity and COD to nitrogen ratios (COD/N). As the salinity increased from 0% to 1.0%, the denitrification performance of both the traditional biofilm reactor (BR) and BER was inhibited; however, the BER showed better adaptation and ability to recover. The BER achieved a high nitrate removal efficiency (≥90%) at a salinity of 1.0% and a low COD/N of 2.5 (theoretical stoichiometric 2.86 ignoring microbial growth). The abundance of Methylotenera mobilis in BR and Clostridium sticklandii in BER was higher than in the initial sludge sample used as inoculum. Likewise, the abundance of napA, nirS and nosZ genes increased as the COD/N further decreased. Under high salinity stress, the BER had a higher denitrification efficiency and the consumption of the organic carbon source (i.e., methanol) was reduced compared to BR. The cooperation between heterotrophic and autotrophic denitrifiers in the BER system provides a more efficient and feasible solution for nitrate removal from saline municipal wastewater.
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Affiliation(s)
- Siyuan Zhai
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China; School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332-0512, United States
| | - Min Ji
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China; Tianjin Engineering Center of Urban River Eco-Purification Technology, Tianjin 300350, China
| | - Yingxin Zhao
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China; Tianjin Engineering Center of Urban River Eco-Purification Technology, Tianjin 300350, China.
| | - Spyros G Pavlostathis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332-0512, United States
| | - Qing Zhao
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
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206
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Sønderholm M, Bjarnsholt T, Alhede M, Kolpen M, Jensen PØ, Kühl M, Kragh KN. The Consequences of Being in an Infectious Biofilm: Microenvironmental Conditions Governing Antibiotic Tolerance. Int J Mol Sci 2017; 18:E2688. [PMID: 29231866 PMCID: PMC5751290 DOI: 10.3390/ijms18122688] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 11/27/2017] [Accepted: 12/06/2017] [Indexed: 12/22/2022] Open
Abstract
The main driver behind biofilm research is the desire to understand the mechanisms governing the antibiotic tolerance of biofilm-growing bacteria found in chronic bacterial infections. Rather than genetic traits, several physical and chemical traits of the biofilm have been shown to be attributable to antibiotic tolerance. During infection, bacteria in biofilms exhibit slow growth and a low metabolic state due to O₂ limitation imposed by intense O₂ consumption of polymorphonuclear leukocytes or metabolically active bacteria in the biofilm periphery. Due to variable O₂ availability throughout the infection, pathogen growth can involve aerobic, microaerobic and anaerobic metabolism. This has serious implications for the antibiotic treatment of infections (e.g., in chronic wounds or in the chronic lung infection of cystic fibrosis patients), as antibiotics are usually optimized for aerobic, fast-growing bacteria. This review summarizes knowledge about the links between the microenvironment of biofilms in chronic infections and their tolerance against antibiotics.
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Affiliation(s)
- Majken Sønderholm
- Costerton Biofilm Centre, Department of Immunology and Microbiology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
| | - Thomas Bjarnsholt
- Costerton Biofilm Centre, Department of Immunology and Microbiology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
- Department of Clinical Microbiology, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark.
| | - Maria Alhede
- Costerton Biofilm Centre, Department of Immunology and Microbiology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
| | - Mette Kolpen
- Costerton Biofilm Centre, Department of Immunology and Microbiology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
- Department of Clinical Microbiology, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark.
| | - Peter Ø Jensen
- Costerton Biofilm Centre, Department of Immunology and Microbiology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
- Department of Clinical Microbiology, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark.
| | - Michael Kühl
- Marine Biology Section, Department of Biology, University of Copenhagen, DK-3000 Elsinore, Denmark.
- Climate Change Cluster, University of Technology Sydney, Ultimo NSW 2007, Australia.
| | - Kasper N Kragh
- Costerton Biofilm Centre, Department of Immunology and Microbiology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
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207
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Coates CJ, Wyman M. A denitrifying community associated with a major, marine nitrogen fixer. Environ Microbiol 2017; 19:4978-4992. [PMID: 29194965 DOI: 10.1111/1462-2920.14007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 11/15/2017] [Accepted: 11/21/2017] [Indexed: 12/11/2022]
Abstract
The diazotrophic cyanobacterium, Trichodesmium, is an integral component of the marine nitrogen cycle and contributes significant amounts of new nitrogen to oligotrophic, tropical/subtropical ocean surface waters. Trichodesmium forms macroscopic, fusiform (tufts), spherical (puffs) and raft-like colonies that provide a pseudobenthic habitat for a host of other organisms including marine invertebrates, microeukaryotes and numerous other microbes. The diversity and activity of denitrifying bacteria found in association with the colonies was interrogated using a series of molecular-based methodologies targeting the gene encoding the terminal step in the denitrification pathway, nitrous oxide reductase (nosZ). Trichodesmium spp. sampled from geographically isolated ocean provinces (the Atlantic Ocean, the Red Sea and the Indian Ocean) were shown to harbor highly similar, taxonomically related communities of denitrifiers whose members are affiliated with the Roseobacter clade within the Rhodobacteraceae (Alphaproteobacteria). These organisms were actively expressing nosZ in samples taken from the mid-Atlantic Ocean and Red Sea implying that Trichodesmium colonies are potential sites of nitrous oxide consumption and perhaps earlier steps in the denitrification pathway also. It is proposed that coupled nitrification of newly fixed N is the most likely source of nitrogen oxides supporting nitrous oxide cycling within Trichodesmium colonies.
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Affiliation(s)
- Christopher J Coates
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, Scotland, UK.,Department of Biosciences, College of Science, Swansea University, Swansea SA2 8PP, Wales, UK
| | - Michael Wyman
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, Scotland, UK
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208
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Mastrocicco M, Di Giuseppe D, Vincenzi F, Colombani N, Castaldelli G. Chlorate origin and fate in shallow groundwater below agricultural landscapes. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 231:1453-1462. [PMID: 28916282 DOI: 10.1016/j.envpol.2017.09.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/10/2017] [Accepted: 09/05/2017] [Indexed: 06/07/2023]
Abstract
In agricultural lowland landscapes, intensive agricultural is accompanied by a wide use of agrochemical application, like pesticides and fertilizers. The latter often causes serious environmental threats such as N compounds leaching and surface water eutrophication; additionally, since perchlorate can be present as impurities in many fertilizers, the potential presence of perchlorates and their by-products like chlorates and chlorites in shallow groundwater could be a reason of concern. In this light, the present manuscript reports the first temporal and spatial variation of chlorates, chlorites and major anions concentrations in the shallow unconfined aquifer belonging to Ferrara province (in the Po River plain). The study was made in 56 different locations to obtain insight on groundwater chemical composition and its sediment matrix interactions. During the monitoring period from 2010 to 2011, in June 2011 a nonpoint pollution of chlorates was found in the shallow unconfined aquifer belonging to Ferrara province. Detected chlorates concentrations ranged between 0.01 and 38 mg/l with an average value of 2.9 mg/l. Chlorates were found in 49 wells out of 56 and in all types of lithology constituting the shallow aquifer. Chlorates concentrations appeared to be linked to NO3-, volatile fatty acids (VFA) and oxygen reduction potential (ORP) variations. Chlorates behaviour was related to the biodegradation of perchlorates, since perchlorates are favourable electron acceptors for the oxidation of labile dissolved organic carbon (DOC) in groundwater. Further studies must take into consideration to monitor ClO4- in pore waters and groundwater to better elucidate the mass flux of ClO4- in shallow aquifers belonging to agricultural landscapes.
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Affiliation(s)
- Micòl Mastrocicco
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Dario Di Giuseppe
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Fabio Vincenzi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Nicolò Colombani
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.
| | - Giuseppe Castaldelli
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
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209
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Fernández-Llamosas H, Castro L, Blázquez ML, Díaz E, Carmona M. Speeding up bioproduction of selenium nanoparticles by using Vibrio natriegens as microbial factory. Sci Rep 2017; 7:16046. [PMID: 29167550 PMCID: PMC5700131 DOI: 10.1038/s41598-017-16252-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 11/10/2017] [Indexed: 11/09/2022] Open
Abstract
Selenium and selenium nanoparticles (SeNPs) are extensively used in biomedicine, electronics and some other industrial applications. The bioproduction of SeNPs is gaining interest as a green method to manufacture these biotechnologically relevant products. Several microorganisms have been used for the production of SeNPs either under aerobic or anaerobic conditions. Vibrio natriegens is a non-pathogenic fast-growing bacterium, easily cultured in different carbon sources and that has recently been engineered for easy genetic manipulation in the laboratory. Here we report that V. natriegens was able to perfectly grow aerobically in the presence of selenite concentrations up to 15 mM with a significant survival still observed at concentrations as high as 100 mM selenite. Electron microscopy and X-ray spectroscopy analyses demonstrate that V. natriegens cells growing aerobically in selenite-containing LB medium at 30 °C produced spherical electron-dense SeNPs whose size ranged from 100-400 nm. Selenite reduction just started at the beginning of the exponential growth phase and the release of SeNPs was observed after cell lysis. Remarkably, V. natriegens produced SeNPs faster than other described microorganisms that were proposed as model bioreactors for SeNPs production. Thus, the fast-growing V. natriegens bacterium becomes a suitable biocatalyst for bioremediation of selenite and for speeding-up the eco-friendly synthesis of SeNPs.
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Affiliation(s)
- Helga Fernández-Llamosas
- Environmental Biology Department, Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Laura Castro
- Department of Material Science and Metallurgical Engineering, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Av. Complutense s/n, 28040, Madrid, Spain
| | - María Luisa Blázquez
- Department of Material Science and Metallurgical Engineering, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Av. Complutense s/n, 28040, Madrid, Spain
| | - Eduardo Díaz
- Environmental Biology Department, Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Manuel Carmona
- Environmental Biology Department, Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain.
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210
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Santana MM, Gonzalez JM, Cruz C. Nitric Oxide Accumulation: The Evolutionary Trigger for Phytopathogenesis. Front Microbiol 2017; 8:1947. [PMID: 29067010 PMCID: PMC5641340 DOI: 10.3389/fmicb.2017.01947] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 09/22/2017] [Indexed: 01/08/2023] Open
Abstract
Many publications highlight the importance of nitric oxide (NO) in plant–bacteria interactions, either in the promotion of health and plant growth or in pathogenesis. However, the role of NO in the signaling between bacteria and plants and in the fate of their interaction, as well as the reconstruction of their interactive evolution, remains largely unknown. Despite the complexity of the evolution of life on Earth, we explore the hypothesis that denitrification and aerobic respiration were responsible for local NO accumulation, which triggered primordial antagonistic biotic interactions, namely the first phytopathogenic interactions. N-oxides, including NO, could globally accumulate via lightning synthesis in the early anoxic ocean and constitute pools for the evolution of denitrification, considered an early step of the biological nitrogen cycle. Interestingly, a common evolution may be proposed for components of denitrification and aerobic respiration pathways, namely for NO and oxygen reductases, a theory compatible with the presence of low amounts of oxygen before the great oxygenation event (GOE), which was generated by Cyanobacteria. During GOE, the increase in oxygen caused the decrease of Earth’s temperature and the consequent increase of oxygen dissolution and availability, making aerobic respiration an increasingly dominant trait of the expanding mesophilic lifestyle. Horizontal gene transfer was certainly important in the joint expansion of mesophily and aerobic respiration. First denitrification steps lead to NO formation through nitrite reductase activity, and NO may further accumulate when oxygen binds NO reductase, resulting in denitrification blockage. The consequent transient NO surplus in an oxic niche could have been a key factor for a successful outcome of an early denitrifying prokaryote able to scavenge oxygen by NO/oxygen reductase or by an independent heterotrophic aerobic respiration pathway. In fact, NO surplus could result in toxicity causing “the first disease” in oxygen-producing Cyanobacteria. We inspected in bacteria the presence of sequences similar to the NO-producing nitrite reductase nirS gene of Thermus thermophilus, an extreme thermophilic aerobe of the Thermus/Deinococcus group, which constitutes an ancient lineage related to Cyanobacteria. In silico analysis revealed the relationship between the presence of nirS genes and phytopathogenicity in Gram-negative bacteria.
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Affiliation(s)
- Margarida M Santana
- Centro de Ecologia, Evolução e Alterações Ambientais (cE3c), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Juan M Gonzalez
- Instituto de Recursos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Cristina Cruz
- Centro de Ecologia, Evolução e Alterações Ambientais (cE3c), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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211
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Carels N, Gumiel M, da Mota FF, de Carvalho Moreira CJ, Azambuja P. A Metagenomic Analysis of Bacterial Microbiota in the Digestive Tract of Triatomines. Bioinform Biol Insights 2017; 11:1177932217733422. [PMID: 28989277 PMCID: PMC5624349 DOI: 10.1177/1177932217733422] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 04/10/2017] [Indexed: 12/04/2022] Open
Abstract
The digestive tract of triatomines (DTT) is an ecological niche favored by microbiota whose enzymatic profile is adapted to the specific substrate availability in this medium. This report describes the molecular enzymatic properties that promote bacterial prominence in the DTT. The microbiota composition was assessed previously based on 16S ribosomal DNA, and whole sequenced genomes of bacteria from the same genera were used to calculate the GC level of rare and prominent bacterial species in the DTT. The enzymatic reactions encoded by coding sequences of both rare and common bacterial species were then compared and revealed key functions explaining why some genera outcompete others in the DTT. Representativeness of DTT microbiota was investigated by shotgun sequencing of DNA extracted from bacteria grown in liquid Luria-Bertani broth (LB) medium. Results showed that GC-rich bacteria outcompete GC-poor bacteria and are the dominant components of the DTT microbiota. In addition, oxidoreductases are the main enzymatic components of these bacteria. In particular, nitrate reductases (anaerobic respiration), oxygenases (catabolism of complex substrates), acetate-CoA ligase (tricarboxylic acid cycle and energy metabolism), and kinase (signaling pathway) were the major enzymatic determinants present together with a large group of minor enzymes including hydrogenases involved in energy and amino acid metabolism. In conclusion, despite their slower growth in liquid LB medium, bacteria from GC-rich genera outcompete the GC-poor bacteria because their specific enzymatic abilities impart a selective advantage in the DTT.
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Affiliation(s)
- Nicolas Carels
- Laboratório de Modelagem de Sistemas Biológicos, National Institute for Science and Technology on Innovation in Neglected Diseases (INCT-IDN), Centro de Desenvolvimento Tecnológico em Saúde (CDTS), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
| | - Marcial Gumiel
- Laboratório de Bioquímica e Fisiologia de Insetos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (IOC/FIOCRUZ), Rio de Janeiro, Brazil
| | - Fabio Faria da Mota
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (IOC/FIOCRUZ), Rio de Janeiro, Brazil
| | | | - Patricia Azambuja
- Laboratório de Bioquímica e Fisiologia de Insetos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (IOC/FIOCRUZ), Rio de Janeiro, Brazil.,Departamento de Entomologia Molecular, Instituto Nacional de Entomologia Molecular (INCT-EM), Rio de Janeiro, Brazil
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212
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Won J, Borden RC. Laboratory Column Evaluation of High Explosives Attenuation in Grenade Range Soils. JOURNAL OF ENVIRONMENTAL QUALITY 2017; 46:968-974. [PMID: 28991974 DOI: 10.2134/jeq2017.05.0180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
High explosives (HEs) deposited on military ranges can leach through the soil and contaminate groundwater. We examined the transport and fate of HEs in laboratory columns containing soils from two hand grenade bays (Bays C and T) and the impact of organic amendments on biodegradation. Soil characteristics were similar; however, Bay C had somewhat higher clay and organic C. Experimental treatments included addition of crude glycerin and lignosulfonate, and parallel control columns. Experimental results showed extensive 2,4,6-trinitrotoluene (TNT) degradation with minimal leaching, consistent with prior batch microcosm results. Amendment addition enhanced TNT degradation in both Bays C and T compared with controls. Although hexahydro-1,3,5-trinitro-1,3,5-triazine (Royal Demolition Explosive, or RDX) did not biodegrade in prior aerobic batch microcosms, 64 to 77% of RDX biodegraded in untreated soil columns with O present in the mobile soil gas. The RDX biodegradation was likely associated with short-term anoxic conditions or anoxic micro-niches. In nearly saturated Bay C columns, RDX removal increased to >92%. Amendment addition to unsaturated Bay T columns increased RDX removal to >86%. In one column, the soil remained anoxic (O < 5% by volume) for about a year after amendment addition, significantly reducing RDX leaching. Nitroso degradation products were produced equivalent to 9 to 39% of the RDX degraded, with most retained in the soil (9-37%) and 0 to 3% in the effluent. These results demonstrate that RDX biodegradation can occur in soils with measurable O, and that amendment addition can reduce RDX leaching by stimulating anaerobic biodegradation.
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213
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Marchant HK, Ahmerkamp S, Lavik G, Tegetmeyer HE, Graf J, Klatt JM, Holtappels M, Walpersdorf E, Kuypers MMM. Denitrifying community in coastal sediments performs aerobic and anaerobic respiration simultaneously. THE ISME JOURNAL 2017; 11:1799-1812. [PMID: 28463234 PMCID: PMC5520038 DOI: 10.1038/ismej.2017.51] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 02/08/2017] [Accepted: 03/03/2017] [Indexed: 01/20/2023]
Abstract
Nitrogen (N) input to the coastal oceans has increased considerably because of anthropogenic activities, however, concurrent increases have not occurred in open oceans. It has been suggested that benthic denitrification in sandy coastal sediments is a sink for this N. Sandy sediments are dynamic permeable environments, where electron acceptor and donor concentrations fluctuate over short temporal and spatial scales. The response of denitrifiers to these fluctuations are largely unknown, although previous observations suggest they may denitrify under aerobic conditions. We examined the response of benthic denitrification to fluctuating oxygen concentrations, finding that denitrification not only occurred at high O2 concentrations but was stimulated by frequent switches between oxic and anoxic conditions. Throughout a tidal cycle, in situtranscription of genes for aerobic respiration and denitrification were positively correlated within diverse bacterial classes, regardless of O2 concentrations, indicating that denitrification gene transcription is not strongly regulated by O2 in sandy sediments. This allows microbes to respond rapidly to changing environmental conditions, but also means that denitrification is utilized as an auxiliary respiration under aerobic conditions when imbalances occur in electron donor and acceptor supply. Aerobic denitrification therefore contributes significantly to N-loss in permeable sediments making the process an important sink for anthropogenic N-inputs.
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Affiliation(s)
| | | | - Gaute Lavik
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Halina E Tegetmeyer
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
| | - Jon Graf
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Judith M Klatt
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Geomicrobiology Laboratory, Department of Earth & Environmental Sciences, University of Michigan, Ann Arbor MI, USA
| | - Moritz Holtappels
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
- Marum—Centre for Marine Environmental Science, Bremen, Germany
| | - Eva Walpersdorf
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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214
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Ding A, Zheng P, Zhang M, Zhang Q. Impacts of electron donor and acceptor on the performance of electrotrophic denitrification. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:19693-19702. [PMID: 28685327 DOI: 10.1007/s11356-017-9455-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 06/01/2017] [Indexed: 06/07/2023]
Abstract
Electrotrophic denitrification is a novel nitrogen removal technique. In this study, the performance and the mechanism of electrotrophic denitrification were investigated at different nitrate concentrations and current intensities. The results showed that the performance of electrotrophic denitrification was good with a sludge loading of 0.39 kg N/kg VSS day. The half-saturation constant for nitrate-N was 1894.03 mg/L. The optimal nitrate-N concentration and current intensity were 1500 mg/L and 20 μA, respectively. Electrotrophic denitrification was defined as the process of direct use of electron for nitrate reduction, and electrotrophic denitrifier was proposed to be the microbe of using electricity as energy source directly. The present work will benefit the development and application of electrotrophic denitrification. Graphical abstract ᅟ.
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Affiliation(s)
- Aqiang Ding
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, People's Republic of China.
| | - Meng Zhang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Qianqian Zhang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, People's Republic of China
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215
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Gui M, Chen Q, Ni J. Effect of sulfamethoxazole on aerobic denitrification by strain Pseudomonas stutzeri PCN-1. BIORESOURCE TECHNOLOGY 2017; 235:325-331. [PMID: 28376383 DOI: 10.1016/j.biortech.2017.03.131] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/19/2017] [Accepted: 03/22/2017] [Indexed: 06/07/2023]
Abstract
Sulfamethoxazole (SMX), as a common sulfonamide antibiotic, was reported to affect conventional anaerobic denitrification. This study presented effects of SMX on aerobic denitrification by an aerobic denitrifier strain Pseudomonas stutzeri PCN-1. Results demonstrated serious inhibition of N2O reduction as SMX reached 4μg/L, leading to higher N2O emission ratio (251-fold). Increase of SMX (∼8μg/L) would induce highest nitrite accumulation (95.3mg/L) without reduction, and severe inhibition of nitrate reduction resulted in lower nitrate removal rate (0.15mg/L/h) as SMX reached 20μg/L. Furthermore, corresponding inhibition of SMX on denitrifying genes expression (nosZ>nirS>cnorB>napA) was found with a time-lapse expression between nosZ and cnorB. Meanwhile, the decline in electron transport activity and active microbial biomass of strain PCN-1 was revealed. The insight into mechanism of SMX influence on aerobic denitrifier is of particular significance to upgrade nitrogen removal process in antibiotics-containing wastewater treatment plant.
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Affiliation(s)
- Mengyao Gui
- Department of Environmental Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Qian Chen
- Department of Environmental Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Jinren Ni
- Department of Environmental Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China.
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216
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Zhong L, Lai CY, Shi LD, Wang KD, Dai YJ, Liu YW, Ma F, Rittmann BE, Zheng P, Zhao HP. Nitrate effects on chromate reduction in a methane-based biofilm. WATER RESEARCH 2017; 115:130-137. [PMID: 28273443 DOI: 10.1016/j.watres.2017.03.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 02/27/2017] [Accepted: 03/01/2017] [Indexed: 06/06/2023]
Abstract
The effects of nitrate (NO3-) on chromate (Cr(VI)) reduction in a membrane biofilm reactor (MBfR) were studied when CH4 was the sole electron donor supplied with a non-limiting delivery capacity. A high surface loading of NO3- gave significant and irreversible inhibition of Cr(VI) reduction. At a surface loading of 500 mg Cr/m2-d, the Cr(VI)-removal percentage was 100% when NO3- was absent (Stage 1), but was dramatically lowered to < 25% with introduction of 280 mg N m-2-d NO3- (Stage 2). After ∼50 days operation in Stage 2, the Cr(VI) reduction recovered to only ∼70% in Stage 3, when NO3- was removed from the influent; thus, NO3- had a significant long-term inhibition effect on Cr(VI) reduction. Weighted PCoA and UniFrac analyses proved that the introduction of NO3- had a strong impact on the microbial community in the biofilms, and the changes possibly were linked to the irreversible inhibition of Cr(VI) reduction. For example, Meiothermus, the main genus involved in Cr(VI) reduction at first, declined with introduction of NO3-. The denitrifier Chitinophagaceae was enriched after the addition of NO3-, while Pelomonas became important when nitrate was removed, suggesting its potential role as a Cr(VI) reducer. Moreover, introducing NO3- led to a decrease in the number of genes predicted (by PICRUSt) to be related to chromate reduction, but genes predicted to be related to denitrification, methane oxidation, and fermentation increased.
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Affiliation(s)
- Liang Zhong
- Department of Environmental Engineering, College of Environmental and Resource Science, Zhejiang University, Hangzhou, China
| | - Chun-Yu Lai
- Department of Environmental Engineering, College of Environmental and Resource Science, Zhejiang University, Hangzhou, China; Zhejiang Province Key Lab Water Pollut Control & Envi, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ling-Dong Shi
- Department of Environmental Engineering, College of Environmental and Resource Science, Zhejiang University, Hangzhou, China
| | - Kai-Di Wang
- Department of Environmental Engineering, College of Environmental and Resource Science, Zhejiang University, Hangzhou, China
| | - Yu-Jie Dai
- Department of Environmental Engineering, College of Environmental and Resource Science, Zhejiang University, Hangzhou, China
| | - Yao-Wei Liu
- Department of Environmental Engineering, College of Environmental and Resource Science, Zhejiang University, Hangzhou, China
| | - Fang Ma
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, P.O. Box 875701, Tempe, AZ 85287-5701, USA
| | - Ping Zheng
- Department of Environmental Engineering, College of Environmental and Resource Science, Zhejiang University, Hangzhou, China; Zhejiang Province Key Lab Water Pollut Control & Envi, Zhejiang University, Hangzhou, Zhejiang, China
| | - He-Ping Zhao
- Department of Environmental Engineering, College of Environmental and Resource Science, Zhejiang University, Hangzhou, China; Zhejiang Province Key Lab Water Pollut Control & Envi, Zhejiang University, Hangzhou, Zhejiang, China; State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
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217
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Zhai S, Zhao Y, Ji M, Qi W. Simultaneous removal of nitrate and chromate in groundwater by a spiral fiber based biofilm reactor. BIORESOURCE TECHNOLOGY 2017; 232:278-284. [PMID: 28237899 DOI: 10.1016/j.biortech.2017.01.076] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/19/2017] [Accepted: 01/22/2017] [Indexed: 06/06/2023]
Abstract
A spiral fiber based biofilm reactor was developed to remove nitrate and chromate simultaneously. The denitrification and Cr(VI) removal efficiency was evaluated with synthetic groundwater (NO3--N=50mg/L) under different Cr(VI) concentrations (0-1.0mg/L), carbon nitrogen ratios (C/N) (0.8-1.2), hydraulic retention times (HRT) (2-16h) and initial pHs (4-10). Nitrate and Cr(VI) were completely removed without nitrite accumulation when the Cr(VI) concentration was lower than 0.4mg/L. As Cr(VI) up to 1.0mg/L, the system was obviously inhibited, but it recovered rapidly within 6days due to the strong adaption and domestication of microorganisms in the biofilm reactor. The results demonstrated that high removal efficiency of nitrate (≥99%) and Cr(VI) (≥95%) were achieved at lower C/N=0.9, HRT=8h, initial pH=7, and Cr(VI)=1.0mg/L. The technology proposed in present study can be alternative for simultaneous removal of co-contaminants in groundwater.
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Affiliation(s)
- Siyuan Zhai
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Yinxin Zhao
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China; Tianjin Engineering Research Center of Urban River Eco-Purification Technology, Tianjin 300350, China.
| | - Min Ji
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China; Tianjin Engineering Research Center of Urban River Eco-Purification Technology, Tianjin 300350, China
| | - Wenfang Qi
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
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218
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Jensen PØ, Kolpen M, Kragh KN, Kühl M. Microenvironmental characteristics and physiology of biofilms in chronic infections of CF patients are strongly affected by the host immune response. APMIS 2017; 125:276-288. [PMID: 28407427 DOI: 10.1111/apm.12668] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 01/04/2017] [Indexed: 01/14/2023]
Abstract
In vitro studies of Pseudomonas aeruginosa and other pathogenic bacteria in biofilm aggregates have yielded detailed insight into their potential growth modes and metabolic flexibility under exposure to gradients of substrate and electron acceptor. However, the growth pattern of P. aeruginosa in chronic lung infections of cystic fibrosis (CF) patients is very different from what is observed in vitro, for example, in biofilms grown in flow chambers. Dense in vitro biofilms of P. aeruginosa exhibit rapid O2 depletion within <50-100 μm due to their own aerobic metabolism. In contrast, in vivo investigations show that P. aeruginosa persists in the chronically infected CF lung as relatively small cell aggregates that are surrounded by numerous PMNs, where the activity of PMNs is the major cause of O2 depletion rendering the P. aeruginosa aggregates anoxic. High levels of nitrate and nitrite enable P. aeruginosa to persist fueled by denitrification in the PMN-surrounded biofilm aggregates. This configuration creates a potentially long-term stable ecological niche for P. aeruginosa in the CF lung, which is largely governed by slow growth and anaerobic metabolism and enables persistence and resilience of this pathogen even under the recurring aggressive antimicrobial treatments of CF patients. As similar slow growth of other CF pathogens has recently been observed in endobronchial secretions, there is now a clear need for better in vitro models that simulate such in vivo growth patterns and anoxic microenvironments in order to help unravel the efficiency of existing or new antimicrobials targeting anaerobic metabolism in P. aeruginosa and other CF pathogens. We also advocate that host immune responses such as PMN-driven O2 depletion play a central role in the formation of anoxic microniches governing bacterial persistence in other chronic infections such as chronic wounds.
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Affiliation(s)
- Peter Ø Jensen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark.,Department of International Health, Immunology and Microbiology, UC-CARE, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mette Kolpen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark.,Department of International Health, Immunology and Microbiology, UC-CARE, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kasper N Kragh
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark.,Department of International Health, Immunology and Microbiology, UC-CARE, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark.,Climate Change Cluster, University of Technology, Sydney, NSW, Australia
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219
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Effect of NaCl on aerobic denitrification by strain Achromobacter sp. GAD-3. Appl Microbiol Biotechnol 2017; 101:5139-5147. [DOI: 10.1007/s00253-017-8191-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/08/2017] [Accepted: 02/10/2017] [Indexed: 10/20/2022]
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220
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Hutt LP, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy T, Daum C, Shapiro N, Ivanova N, Kyrpides N, Woyke T, Boden R. Permanent draft genome of Thiobacillus thioparus DSM 505 T, an obligately chemolithoautotrophic member of the Betaproteobacteria. Stand Genomic Sci 2017; 12:10. [PMID: 28127420 PMCID: PMC5248467 DOI: 10.1186/s40793-017-0229-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/08/2017] [Indexed: 01/20/2023] Open
Abstract
Thiobacillus thioparus DSM 505T is one of first two isolated strains of inorganic sulfur-oxidising Bacteria. The original strain of T. thioparus was lost almost 100 years ago and the working type strain is Culture CT (=DSM 505T = ATCC 8158T) isolated by Starkey in 1934 from agricultural soil at Rutgers University, New Jersey, USA. It is an obligate chemolithoautotroph that conserves energy from the oxidation of reduced inorganic sulfur compounds using the Kelly-Trudinger pathway and uses it to fix carbon dioxide It is not capable of heterotrophic or mixotrophic growth. The strain has a genome size of 3,201,518 bp. Here we report the genome sequence, annotation and characteristics. The genome contains 3,135 protein coding and 62 RNA coding genes. Genes encoding the transaldolase variant of the Calvin-Benson-Bassham cycle were also identified and an operon encoding carboxysomes, along with Smith’s biosynthetic horseshoe in lieu of Krebs’ cycle sensu stricto. Terminal oxidases were identified, viz. cytochrome c oxidase (cbb3, EC 1.9.3.1) and ubiquinol oxidase (bd, EC 1.10.3.10). There is a partial sox operon of the Kelly-Friedrich pathway of inorganic sulfur-oxidation that contains soxXYZAB genes but lacking soxCDEF, there is also a lack of the DUF302 gene previously noted in the sox operon of other members of the ‘Proteobacteria’ that can use trithionate as an energy source. In spite of apparently not growing anaerobically with denitrification, the nar, nir, nor and nos operons encoding enzymes of denitrification are found in the T. thioparus genome, in the same arrangements as in the true denitrifier T. denitrificans.
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Affiliation(s)
- Lee P Hutt
- School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth, PL4 8AA UK.,Sustainable Earth Institute, University of Plymouth, Drake Circus, Plymouth, PL4 8AA UK
| | | | - Alicia Clum
- DOE Joint Genome Institute, 94598 Walnut Creek, CA USA
| | - Manoj Pillay
- DOE Joint Genome Institute, 94598 Walnut Creek, CA USA
| | | | - Neha Varghese
- DOE Joint Genome Institute, 94598 Walnut Creek, CA USA
| | | | | | | | - Chris Daum
- DOE Joint Genome Institute, 94598 Walnut Creek, CA USA
| | | | | | | | - Tanja Woyke
- DOE Joint Genome Institute, 94598 Walnut Creek, CA USA
| | - Rich Boden
- School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth, PL4 8AA UK.,Sustainable Earth Institute, University of Plymouth, Drake Circus, Plymouth, PL4 8AA UK
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221
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Padhi SK, Maiti NK. Molecular insight into the dynamic central metabolic pathways of Achromobacter xylosoxidans CF-S36 during heterotrophic nitrogen removal processes. J Biosci Bioeng 2017; 123:46-55. [DOI: 10.1016/j.jbiosc.2016.07.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 06/23/2016] [Accepted: 07/14/2016] [Indexed: 10/21/2022]
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222
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Zheng M, Li C, Liu S, Gui M, Ni J. Potential application of aerobic denitrifying bacterium Pseudomonas aeruginosa PCN-2 in nitrogen oxides (NOx) removal from flue gas. JOURNAL OF HAZARDOUS MATERIALS 2016; 318:571-578. [PMID: 27469045 DOI: 10.1016/j.jhazmat.2016.07.047] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 06/16/2016] [Accepted: 07/18/2016] [Indexed: 06/06/2023]
Abstract
Conventional biological removal of nitrogen oxides (NOx) from flue gas has been severely restricted by the presence of oxygen. This paper presents an efficient alternative for NOx removal at varying oxygen levels using the newly isolated bacterial strain Pseudomonas aeruginosa PCN-2 which was capable of aerobic and anoxic denitrification. Interestingly, nitric oxide (NO), as the obligatory intermediate, was negligibly accumulated during nitrate and nitrite reduction. Moreover, normal nitrate reduction with decreasing NO accumulation was realized under O2 concentration ranging from 0 to 100%. Reverse transcription and real-time quantitative polymerase chain reaction (RT-qPCR) analysis revealed that high efficient NO removal was attributed to the coordinate regulation of gene expressions including napA (for periplasmic nitrate reductase), nirS (for cytochrome cd1 nitrite reductase) and cnorB (for NO reductase). Further batch experiments demonstrated the immobilized strain PCN-2 possessed high capability of removing NO and nitrogen dioxide (NO2) at O2 concentration of 0-10%. A biotrickling filter established with present strain achieved high NOx removal efficiencies of 91.94-96.74% at inlet NO concentration of 100-500ppm and O2 concentration of 0-10%, which implied promising potential applications in purifying NOx contaminated flue gas.
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Affiliation(s)
- Maosheng Zheng
- MOE Key Laboratory of Regional Energy Systems Optimization, Resources and Environmental Research Academy, North China Electric Power University, Beijing 102206, China
| | - Can Li
- Department of Environmental Engineering, Peking University, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Shufeng Liu
- Department of Environmental Engineering, Peking University, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Mengyao Gui
- Department of Environmental Engineering, Peking University, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Jinren Ni
- Department of Environmental Engineering, Peking University, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China.
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223
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Dynamics of Bacterial Community Abundance and Structure in Horizontal Subsurface Flow Wetland Mesocosms Treating Municipal Wastewater. WATER 2016. [DOI: 10.3390/w8100457] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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224
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Sarkar J, Kazy SK, Gupta A, Dutta A, Mohapatra B, Roy A, Bera P, Mitra A, Sar P. Biostimulation of Indigenous Microbial Community for Bioremediation of Petroleum Refinery Sludge. Front Microbiol 2016; 7:1407. [PMID: 27708623 PMCID: PMC5030240 DOI: 10.3389/fmicb.2016.01407] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 08/25/2016] [Indexed: 11/18/2022] Open
Abstract
Nutrient deficiency severely impairs the catabolic activity of indigenous microorganisms in hydrocarbon rich environments (HREs) and limits the rate of intrinsic bioremediation. The present study aimed to characterize the microbial community in refinery waste and evaluate the scope for biostimulation based in situ bioremediation. Samples recovered from the wastewater lagoon of Guwahati refinery revealed a hydrocarbon enriched [high total petroleum hydrocarbon (TPH)], oxygen-, moisture-limited, reducing environment. Intrinsic biodegradation ability of the indigenous microorganisms was enhanced significantly (>80% reduction in TPH by 90 days) with nitrate amendment. Preferred utilization of both higher- (>C30) and middle- chain (C20-30) length hydrocarbons were evident from GC-MS analysis. Denaturing gradient gel electrophoresis and community level physiological profiling analyses indicated distinct shift in community’s composition and metabolic abilities following nitrogen (N) amendment. High throughput deep sequencing of 16S rRNA gene showed that the native community was mainly composed of hydrocarbon degrading, syntrophic, methanogenic, nitrate/iron/sulfur reducing facultative anaerobic bacteria and archaebacteria, affiliated to γ- and δ-Proteobacteria and Euryarchaeota respectively. Genes for aerobic and anaerobic alkane metabolism (alkB and bssA), methanogenesis (mcrA), denitrification (nirS and narG) and N2 fixation (nifH) were detected. Concomitant to hydrocarbon degradation, lowering of dissolve O2 and increase in oxidation-reduction potential (ORP) marked with an enrichment of N2 fixing, nitrate reducing aerobic/facultative anaerobic members [e.g., Azovibrio, Pseudoxanthomonas and Comamonadaceae members] was evident in N amended microcosm. This study highlighted that indigenous community of refinery sludge was intrinsically diverse, yet appreciable rate of in situ bioremediation could be achieved by supplying adequate N sources.
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Affiliation(s)
- Jayeeta Sarkar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, India
| | - Sufia K Kazy
- Department of Biotechnology, National Institute of Technology Durgapur, India
| | - Abhishek Gupta
- Department of Biotechnology, Indian Institute of Technology Kharagpur, India
| | - Avishek Dutta
- School of Bioscience, Indian Institute of Technology Kharagpur, India
| | - Balaram Mohapatra
- Department of Biotechnology, Indian Institute of Technology Kharagpur, India
| | - Ajoy Roy
- Department of Biotechnology, National Institute of Technology Durgapur, India
| | - Paramita Bera
- Department of Agricultural and Food Engineering, Indian Institute of Technology Kharagpur, India
| | - Adinpunya Mitra
- Department of Agricultural and Food Engineering, Indian Institute of Technology Kharagpur, India
| | - Pinaki Sar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, India
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225
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Wan R, Chen Y, Zheng X, Su Y, Li M. Effect of CO2 on Microbial Denitrification via Inhibiting Electron Transport and Consumption. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:9915-22. [PMID: 27562440 DOI: 10.1021/acs.est.5b05850] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Increasing anthropogenic CO2 emissions have been reported to influence global biogeochemical processes; however, in the literature the effects of CO2 on denitrification have mainly been attributed to the changes it causes in environmental factors, while the direct effects of CO2 on denitrification remain unknown. In this study, increasing CO2 from 0 to 30 000 ppm under constant environmental conditions decreased total nitrogen removal efficiency from 97% to 54%, but increased N2O generation by 240 fold. A subsequent mechanistic study revealed that CO2 damaged the bacterial membrane and directly inhibited the transport and consumption of intracellular electrons by causing intracellular reactive nitrogen species (RNS) accumulation, suppressing the expression of key electron transfer proteins (flavoprotein, succinate dehydrogenase, and cytochrome c) and the synthesis and activity of key denitrifying enzymes. Further study indicated that the inhibitory effects of CO2 on the transport and consumption of electrons were caused by the decrease of intracellular iron due to key iron transporters (AfuA, FhuC, and FhuD) being down-regulated. Overall, this study suggests that the direct effect of CO2 on denitrifying microbes via inhibition of intracellular electron transport and consumption is an important reason for its negative influence on denitrification.
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Affiliation(s)
- Rui Wan
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University , 1239 Siping Road, Shanghai 200092
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University , 1239 Siping Road, Shanghai 200092
| | - Xiong Zheng
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University , 1239 Siping Road, Shanghai 200092
| | - Yinglong Su
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University , 1239 Siping Road, Shanghai 200092
| | - Mu Li
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University , 1239 Siping Road, Shanghai 200092
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Fernández-Llamosas H, Castro L, Blázquez ML, Díaz E, Carmona M. Biosynthesis of selenium nanoparticles by Azoarcus sp. CIB. Microb Cell Fact 2016; 15:109. [PMID: 27301452 PMCID: PMC4908764 DOI: 10.1186/s12934-016-0510-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 06/07/2016] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Different bacteria have been reported so far that link selenite resistance to the production of metallic selenium nanoparticles (SeNPs). Although SeNPs have many biotechnological applications in diverse areas, the molecular mechanisms involved in their microbial genesis are not fully understood. The Azoarcus genus is a physiologically versatile group of beta-proteobacteria of great environmental relevance. Azoarcus sp. CIB is a facultative anaerobe that combines the ability to degrade under aerobic and/or anaerobic conditions a wide range of aromatic compounds, including some toxic hydrocarbons such as toluene and m-xylene, with an endophytic life style in the root of rice. We unravel here an additional physiological feature of the strain CIB that is related to its resistance to selenium oxyanions and the formation of SeNPs. RESULTS This work is the first report of a member of the Azoarcus genus that is able to anaerobically grow in the presence of selenite. Electron microscopy preparations and X-ray spectroscopy analyses demonstrate the reduction of selenite to spherical electron-dense SeNPs whose average size was 123 ± 35 nm of diameter. Our data suggest that the main molecular mechanism of selenite resistance resides on an energy-dependent selenite exporter. Azoarcus cells trigger the synthesis of SeNPs when they reach the stationary-phase of growth, and either the exhaustion of electron donor or acceptor, both of which lead to starvation conditions, produce the reduction of selenite to red elemental selenium. Azoarcus becomes a promising biocatalyst, either as whole cells or cellular extracts, for the anaerobic and/or aerobic green synthesis of SeNPs. CONCLUSIONS Azoarcus turns out to be a new eco-friendly system to reduce selenite and produce spherical SeNPs. Moreover, this is the first report of a rice endophyte able to produce SeNPs. Since Azoarcus is also able to degrade both aerobically and anaerobically toxic aromatic compounds of great environmental concern, it becomes a suitable candidate for a more sustainable agricultural practice and for bioremediation strategies.
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Affiliation(s)
- Helga Fernández-Llamosas
- />Environmental Biology Department, Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Laura Castro
- />Material Science and Metallurgical Engineering Department, Facultad de Químicas, Universidad Complutense de Madrid, Madrid, Spain
| | - María Luisa Blázquez
- />Material Science and Metallurgical Engineering Department, Facultad de Químicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Eduardo Díaz
- />Environmental Biology Department, Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Manuel Carmona
- />Environmental Biology Department, Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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Srivastava M, Kaushik MS, Singh A, Singh D, Mishra AK. Molecular phylogeny of heterotrophic nitrifiers and aerobic denitrifiers and their potential role in ammonium removal. J Basic Microbiol 2016; 56:907-21. [PMID: 27037833 DOI: 10.1002/jobm.201500689] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 03/09/2016] [Indexed: 11/06/2022]
Abstract
To investigate the physiology and taxonomic composition of the key players of nitrification and denitrification processes in paddy fields, culture dependent and independent studies have been carried out. A total of 28 bacterial strains have been screened in which six were capable of reducing nitrate and nitrite as well as having significant ammonium removal potential. 16S rRNA-PCR-DGGE-based molecular typing of enriched batch culture was done with time duration to explore and identify dominant and stable soil denitrifiers. Notably, three isolates namely PDN3, PDN19, PDN14 were found to be efficiently involved in the removal of 70.32, 71.46, and 81.50% of NH4 (+) and showed closest similarity (>98%) with Bacillus cereus, Bacillus subtilis, and Pseudomonas aeruginosa strains, respectively. The bacterial strain PDN14 showed maximum growth with highest ammonium removal rate (2.78 gN/(m(3) ·h) has also been characterized based on nosZ gene which showed similarity to uncultured γ- Proteobacteria, P. aeruginosa sp. B3. Median joining (MJ) network and rRNA secondary structure have been analyzed for their detailed taxonomic diversity and derived haplotype-based co-occurrence. Results demonstrated that such strains can serve as good candidate for in situ nitrogen transformation in paddy soils and improvingly characterized by physiological and detailed phylogenetic approaches.
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Affiliation(s)
- Meenakshi Srivastava
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, India
| | - Manish Singh Kaushik
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, India
| | - Anumeha Singh
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, India
| | - Deepti Singh
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, India
| | - Arun Kumar Mishra
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, India
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228
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Yuan L, Zhi W, Liu Y, Smiley E, Gallagher D, Chen X, Dietrich A, Zhang H. Aerobic and anaerobic microbial degradation of crude (4-methylcyclohexyl)methanol in river sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 547:78-86. [PMID: 26780132 DOI: 10.1016/j.scitotenv.2015.12.144] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 12/15/2015] [Accepted: 12/29/2015] [Indexed: 06/05/2023]
Abstract
Cyclohexane and some of its derivatives have been a major concern because of their significant adverse human health effects and widespread occurrence in the environment. The 2014 West Virginia chemical spill has raised public attention to (4-methylcyclohexyl)methanol (4-MCHM), one cyclohexane derivative, which is widely used in coal processing but largely ignored. In particular, the environmental fate of its primary components, cis- and trans-4-MCHM, remains largely unexplored. This study aimed to investigate the degradation kinetics and mineralization of cis- and trans-4-MCHM by sediment microorganisms under aerobic and anaerobic conditions. We found the removal of cis- and trans-4-MCHM was mainly attributed to biodegradation with little contribution from sorption. A nearly complete aerobic degradation of 4-MCHM occurred within 14 days, whereas the anaerobic degradation was reluctant with residual percentages of 62.6% of cis-4-MCHM and 85.0% of trans-4-MCHM after 16-day incubation. The cis-4-MCHM was degraded faster than the trans under both aerobic and anaerobic conditions, indicating an isomer-specific degradation could occur during the 4-MCHM degradation. Nitrate addition enhanced 4-MCHM mineralization by about 50% under both aerobic and anaerobic conditions. Both cis- and trans-4-MCHM fit well with the first-order kinetic model with respective degradation rates of 0.46-0.52 and 0.19-0.31 day(-)(1) under aerobic condition. Respective degradation rates of 0.041-0.095 and 0.013-0.052 day(-)(1) occurred under anaerobic condition. One bacterial strain capable of effectively degrading 4-MCHM isomers was isolated from river sediments and identified as Bacillus pumilus at the species level based on 16S rRNA gene sequence and 97% identity. Our findings will provide critical information for improving the prediction of the environmental fate of 4-MCHM and other cyclohexane derivatives with similar structure as well as enhancing the development of feasible treatment technologies to mitigate these compounds.
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Affiliation(s)
- Li Yuan
- College of Environmental Sciences and Engineering, Peking University, Haidian District, Beijing 100871, China; Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, United States; Department of Earth and Environmental Engineering, Columbia University, New York, NY 10027, United States
| | - Wei Zhi
- College of Environmental Sciences and Engineering, Peking University, Haidian District, Beijing 100871, China; John and Willie Leone Department of Energy and Mineral Engineering, The Pennsylvania State University, University Park, PA 16802, United States
| | - Yangsheng Liu
- College of Environmental Sciences and Engineering, Peking University, Haidian District, Beijing 100871, China.
| | - Elizabeth Smiley
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, United States
| | - Daniel Gallagher
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, United States
| | - Xi Chen
- Department of Earth and Environmental Engineering, Columbia University, New York, NY 10027, United States
| | - Andrea Dietrich
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, United States
| | - Husen Zhang
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, United States.
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229
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Li M, Su Y, Chen Y, Wan R, Zheng X, Liu K. The effects of fulvic acid on microbial denitrification: promotion of NADH generation, electron transfer, and consumption. Appl Microbiol Biotechnol 2016; 100:5607-18. [PMID: 26894403 DOI: 10.1007/s00253-016-7383-1] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 02/01/2016] [Accepted: 02/03/2016] [Indexed: 12/16/2022]
Abstract
The heterotrophic denitrification requires the participation of electrons which are derived from direct electron donor (usually nicotinamide adenine dinucleotide (NADH)), and the electrons are transferred via electron transport system in denitrifiers and then consumed by denitrifying enzymes. Despite the reported electron transfer ability of humic substances (HS), the influences of fulvic acid (FA), an ubiquitous major component of HS, on promoting NADH generation, electron transfer, and consumption in denitrification process have never been reported. The presence of FA, compared with the control, was found not only significantly improved the total nitrogen (TN) removal efficiency (99.9 % versus 74.8 %) but remarkably reduced the nitrite accumulation (0.2 against 43.8 mg/L) and N2O emission (0.003 against 0.240 mg nitrogen/mg TN removed). The mechanisms study showed that FA increased the metabolism of carbon source via glycolysis and tricarboxylic acid (TCA) cycle pathways to produce more available NADH. FA also facilitated the electron transfer activities from NADH to denitrifying enzymes via complex I and complex III in electron transport system, which improved the reduction of nitrate and accelerated the transformations of nitrite and N2O, and lower nitrite and N2O accumulations were therefore observed. In addition, the consumption of electrons in denitrification was enhanced due to FA stimulating the synthesis and the catalytic activity of key denitrifying enzymes, especially nitrite reductase and N2O reductase. It will provide an important new insight into the potential effect of FA on microbial denitrification metabolism process and even nitrogen cycle in nature niches.
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Affiliation(s)
- Mu Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Yinglong Su
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China.
| | - Rui Wan
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Xiong Zheng
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Kun Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China
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Hanke A, Berg J, Hargesheimer T, Tegetmeyer HE, Sharp CE, Strous M. Selective Pressure of Temperature on Competition and Cross-Feeding within Denitrifying and Fermentative Microbial Communities. Front Microbiol 2016; 6:1461. [PMID: 26779132 PMCID: PMC4703780 DOI: 10.3389/fmicb.2015.01461] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 12/07/2015] [Indexed: 11/13/2022] Open
Abstract
In coastal marine sediments, denitrification and fermentation are important processes in the anaerobic decomposition of organic matter. Microbial communities performing these two processes were enriched from tidal marine sediments in replicated, long term chemostat incubations at 10 and 25°C. Whereas denitrification rates at 25°C were more or less stable over time, at 10°C denitrification activity was unstable and could only be sustained either by repeatedly increasing the amount of carbon substrates provided or by repeatedly decreasing the dilution rate. Metagenomic and transcriptomic sequencing was performed at different time points and provisional whole genome sequences (WGS) and gene activities of abundant populations were compared across incubations. These analyses suggested that a temperature of 10°C selected for populations related to Vibrionales/Photobacterium that contributed to both fermentation (via pyruvate/formate lyase) and nitrous oxide reduction. At 25°C, denitrifying populations affiliated with Rhodobacteraceae were more abundant. The latter performed complete denitrification, and may have used carbon substrates produced by fermentative populations (cross-feeding). Overall, our results suggest that a mixture of competition-for substrates between fermentative and denitrifying populations, and for electrons between both pathways active within a single population -, and cross feeding-between fermentative and denitrifying populations-controlled the overall rate of denitrification. Temperature was shown to have a strong selective effect, not only on the populations performing either process, but also on the nature of their ecological interactions. Future research will show whether these results can be extrapolated to the natural environment.
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Affiliation(s)
- Anna Hanke
- Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Jasmine Berg
- Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Theresa Hargesheimer
- Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Halina E Tegetmeyer
- Center for Biotechnology, Institute for Genome Research and Systems Biology, University of Bielefeld Bielefeld, Germany
| | - Christine E Sharp
- Energy Bioengineering Group, Department of Geoscience, University of Calgary Calgary, AB, Canada
| | - Marc Strous
- Microbial Fitness Group, Max Planck Institute for Marine MicrobiologyBremen, Germany; Center for Biotechnology, Institute for Genome Research and Systems Biology, University of BielefeldBielefeld, Germany; Energy Bioengineering Group, Department of Geoscience, University of CalgaryCalgary, AB, Canada
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231
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Skennerton CT, Ward LM, Michel A, Metcalfe K, Valiente C, Mullin S, Chan KY, Gradinaru V, Orphan VJ. Genomic Reconstruction of an Uncultured Hydrothermal Vent Gammaproteobacterial Methanotroph (Family Methylothermaceae) Indicates Multiple Adaptations to Oxygen Limitation. Front Microbiol 2015; 6:1425. [PMID: 26779119 PMCID: PMC4688376 DOI: 10.3389/fmicb.2015.01425] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 11/30/2015] [Indexed: 11/13/2022] Open
Abstract
Hydrothermal vents are an important contributor to marine biogeochemistry, producing large volumes of reduced fluids, gasses, and metals and housing unique, productive microbial and animal communities fueled by chemosynthesis. Methane is a common constituent of hydrothermal vent fluid and is frequently consumed at vent sites by methanotrophic bacteria that serve to control escape of this greenhouse gas into the atmosphere. Despite their ecological and geochemical importance, little is known about the ecophysiology of uncultured hydrothermal vent-associated methanotrophic bacteria. Using metagenomic binning techniques, we recovered and analyzed a near-complete genome from a novel gammaproteobacterial methanotroph (B42) associated with a white smoker chimney in the Southern Lau basin. B42 was the dominant methanotroph in the community, at ∼80x coverage, with only four others detected in the metagenome, all on low coverage contigs (7x–12x). Phylogenetic placement of B42 showed it is a member of the Methylothermaceae, a family currently represented by only one sequenced genome. Metabolic inferences based on the presence of known pathways in the genome showed that B42 possesses a branched respiratory chain with A- and B-family heme copper oxidases, cytochrome bd oxidase and a partial denitrification pathway. These genes could allow B42 to respire over a wide range of oxygen concentrations within the highly dynamic vent environment. Phylogenies of the denitrification genes revealed they are the result of separate horizontal gene transfer from other Proteobacteria and suggest that denitrification is a selective advantage in conditions where extremely low oxygen concentrations require all oxygen to be used for methane activation.
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Affiliation(s)
- Connor T Skennerton
- Division of Geological and Planetary Sciences, California Institute of Technology Pasadena, CA, USA
| | - Lewis M Ward
- Division of Geological and Planetary Sciences, California Institute of Technology Pasadena, CA, USA
| | - Alice Michel
- Division of Geological and Planetary Sciences, California Institute of Technology Pasadena, CA, USA
| | - Kyle Metcalfe
- Division of Geological and Planetary Sciences, California Institute of Technology Pasadena, CA, USA
| | - Chanel Valiente
- Division of Geological and Planetary Sciences, California Institute of Technology Pasadena, CA, USA
| | - Sean Mullin
- Division of Geological and Planetary Sciences, California Institute of Technology Pasadena, CA, USA
| | - Ken Y Chan
- Division of Biology and Bioengineering, California Institute of Technology Pasadena, CA, USA
| | - Viviana Gradinaru
- Division of Biology and Bioengineering, California Institute of Technology Pasadena, CA, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology Pasadena, CA, USA
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232
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Yu L, Yuan Y, Chen S, Zhuang L, Zhou S. Direct uptake of electrode electrons for autotrophic denitrification by Thiobacillus denitrificans. Electrochem commun 2015. [DOI: 10.1016/j.elecom.2015.08.025] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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233
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Kolpen M, Appeldorff CF, Brandt S, Mousavi N, Kragh KN, Aydogan S, Uppal HA, Bjarnsholt T, Ciofu O, Høiby N, Jensen PØ. Increased bactericidal activity of colistin on Pseudomonas aeruginosa biofilms in anaerobic conditions. Pathog Dis 2015; 74:ftv086. [PMID: 26458402 PMCID: PMC4655427 DOI: 10.1093/femspd/ftv086] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2015] [Indexed: 12/19/2022] Open
Abstract
Tolerance towards antibiotics of Pseudomonas aeruginosa biofilms is recognized as a major cause of therapeutic failure of chronic lung infection in cystic fibrosis (CF) patients. This lung infection is characterized by antibiotic-tolerant biofilms in mucus with zones of O2 depletion mainly due to polymorphonuclear leukocytic activity. In contrast to the main types of bactericidal antibiotics, it has not been possible to establish an association between the bactericidal effects of colistin and the production of detectable levels of OH ˙ on several strains of planktonic P. aeruginosa. Therefore, we propose that production of OH ˙ may not contribute significantly to the bactericidal activity of colistin on P. aeruginosa biofilm. Thus, we investigated the effect of colistin treatment on biofilm of wild-type PAO1, a catalase-deficient mutant (ΔkatA) and a colistin-resistant CF isolate cultured in microtiter plates in normoxic- or anoxic atmosphere with 1 mM nitrate. The killing of bacteria during colistin treatment was measured by CFU counts, and the OH⋅ formation was measured by 3(')-(p-hydroxylphenyl fluorescein) fluorescein (HPF) fluorescence. Validation of the assay was done by hydrogen peroxide treatment. OH⋅ formation was undetectable in aerobic PAO1 biofilms during 3 h of colistin treatment. Interestingly, we demonstrate increased susceptibility of P. aeruginosa biofilms towards colistin during anaerobic conditions. In fact, the maximum enhancement of killing by anaerobic conditions exceeded 2 logs using 4 mg L(-1) of colistin compared to killing at aerobic conditions.
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Affiliation(s)
- Mette Kolpen
- Department of Clinical Microbiology, Rigshospitalet, 2100 Copenhagen, Denmark Department of Immunology and Microbiology, UC-CARE, Faculty of Health Sciences University of Copenhagen, 2200 Copenhagen, Denmark
| | | | - Sarah Brandt
- Department of Clinical Microbiology, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Nabi Mousavi
- Department of Clinical Microbiology, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Kasper N Kragh
- Department of Immunology and Microbiology, UC-CARE, Faculty of Health Sciences University of Copenhagen, 2200 Copenhagen, Denmark
| | - Sevtap Aydogan
- Department of Clinical Microbiology, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Haleema A Uppal
- Department of Clinical Microbiology, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Thomas Bjarnsholt
- Department of Clinical Microbiology, Rigshospitalet, 2100 Copenhagen, Denmark Department of Immunology and Microbiology, UC-CARE, Faculty of Health Sciences University of Copenhagen, 2200 Copenhagen, Denmark
| | - Oana Ciofu
- Department of Immunology and Microbiology, UC-CARE, Faculty of Health Sciences University of Copenhagen, 2200 Copenhagen, Denmark
| | - Niels Høiby
- Department of Clinical Microbiology, Rigshospitalet, 2100 Copenhagen, Denmark Department of Immunology and Microbiology, UC-CARE, Faculty of Health Sciences University of Copenhagen, 2200 Copenhagen, Denmark
| | - Peter Ø Jensen
- Department of Clinical Microbiology, Rigshospitalet, 2100 Copenhagen, Denmark
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235
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He D, Zheng M, Ma T, Li C, Ni J. Interaction of Cr(VI) reduction and denitrification by strain Pseudomonas aeruginosa PCN-2 under aerobic conditions. BIORESOURCE TECHNOLOGY 2015; 185:346-352. [PMID: 25795449 DOI: 10.1016/j.biortech.2015.02.109] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 02/23/2015] [Accepted: 02/27/2015] [Indexed: 06/04/2023]
Abstract
Inhibition of efficient denitrification in presence of toxic heavy metals is one of the current problems encountered in municipal wastewater treatment plants. This paper presents how to remove hexavalent chromium (Cr(VI)) and nitrate simultaneously by the novel strain Pseudomonas aeruginosa PCN-2 under aerobic conditions. The capability of strain PCN-2 for Cr(VI) and nitrate reduction was confirmed by PCR analysis of gene ChrR, napA, nirS, cnorB, nosZ, while Cr(VI) reduction was proved via an initial single-electron transfer through Cr(V) detection using electron paramagnetic resonance. Experimental results demonstrated that Cr(VI) and nitrate reduction by strain PCN-2 was much faster at pH 8-9 and higher initial cell concentration. However, increasing Cr(VI) concentration would inhibit aerobic denitrification process and result in an significant delay of nitrate reduction or N2O accumulation, which was attributed to competition between three electron acceptors, i.e., Cr(VI), O2 and nitrate in the electron transport chain.
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Affiliation(s)
- Da He
- Shenzhen Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China; Department of Environmental Engineering, Peking University, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Maosheng Zheng
- Department of Environmental Engineering, Peking University, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Tao Ma
- Department of Environmental Engineering, Peking University, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Can Li
- Department of Environmental Engineering, Peking University, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Jinren Ni
- Department of Environmental Engineering, Peking University, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China.
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Chen D, Yang K, Wang H, Lv B, Ma F. Characteristics of nitrate removal in a bio-ceramsite reactor by aerobic denitrification. ENVIRONMENTAL TECHNOLOGY 2015; 36:1457-1463. [PMID: 25441228 DOI: 10.1080/09593330.2014.993729] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A newly aerobic denitrifying bacterial strain, Pseudomonas sp. X31, which was isolated from activated sludge, was added to a newly developed aerobic denitrification bio-ceramsite reactor as an inoculum to treat nitrate-polluted water and the denitrification activities of this system under different air-water ratio, hydraulic loading, and C/N (carbon/nitrogen ratio) conditions were investigated. It demonstrated excellent capability for denitrification in the bio-ceramsite reactor at air-water ratios that varied from 6.5:1 to 8:1. The optimal hydraulic loading for the bio-ceramsite reactor was 0.75 m/h with the optimum denitrification efficiency of 95.18%. The optimal C/N was 4.5:1 with a maximum nitrate removal efficiency of 98.48%. COD could be completely removed under the most appropriate condition (air-water ratio 6.5:1-8:1, hydraulic loading 0.75 m/h, and C/N 4.5:1). The quantity of the biomass in the reactor decreased along with flow, which was in accordance with the variety of the available substrate concentrations in the water. However, the biofilm activity was not proportional to the biomass in the bio-ceramsite reactor, but increased with the quantity of the biomass up to a peak value and then decreased.
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Affiliation(s)
- Dan Chen
- a School of Civil Engineering , Wuhan University , Wuhan 430072 , People's Republic of China
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237
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Kits KD, Klotz MG, Stein LY. Methane oxidation coupled to nitrate reduction under hypoxia by the Gammaproteobacterium Methylomonas denitrificans, sp. nov. type strain FJG1. Environ Microbiol 2015; 17:3219-32. [PMID: 25580993 DOI: 10.1111/1462-2920.12772] [Citation(s) in RCA: 175] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 12/31/2014] [Indexed: 02/02/2023]
Abstract
Obligate methanotrophs belonging to the Phyla Proteobacteria and Verrucomicrobia require oxygen for respiration and methane oxidation; nevertheless, aerobic methanotrophs are abundant and active in low oxygen environments. While genomes of some aerobic methanotrophs encode putative nitrogen oxide reductases, it is not understood whether these metabolic modules are used for NOx detoxification, denitrification or other purposes. Here we demonstrate using microsensor measurements that a gammaproteobacterial methanotroph Methylomonas denitrificans sp. nov. strain FJG1(T) couples methane oxidation to nitrate reduction under oxygen limitation, releasing nitrous oxide as a terminal product. Illumina RNA-Seq data revealed differential expression of genes encoding a denitrification pathway previously unknown to methanotrophs as well as the pxmABC operon in M. denitrificans sp. nov. strain FJG1(T) in response to hypoxia. Physiological and transcriptome data indicate that genetic inventory encoding the denitrification pathway is upregulated only upon availability of nitrate under oxygen limitation. In addition, quantitation of ATP levels demonstrates that the denitrification pathway employs inventory such as nitrate reductase NarGH serving M. denitrificans sp. nov. strain FJG1(T) to conserve energy during oxygen limitation. This study unravelled an unexpected metabolic flexibility of aerobic methanotrophs, thereby assigning these bacteria a new role at the metabolic intersection of the carbon and nitrogen cycles.
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Affiliation(s)
- K Dimitri Kits
- Department of Biological Sciences, University of Alberta, CW405, Biological Sciences Building, Edmonton, AB, T6G 2E9, Canada
| | - Martin G Klotz
- Department of Biological Sciences, University of North Carolina, 9201 University City Boulevard, Charlotte, NC, 28223, USA.,Institute of Marine Microbes and Ecospheres and State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361005, China
| | - Lisa Y Stein
- Department of Biological Sciences, University of Alberta, CW405, Biological Sciences Building, Edmonton, AB, T6G 2E9, Canada
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Aas FE, Li X, Edwards J, Hongrø Solbakken M, Deeudom M, Vik Å, Moir J, Koomey M, Aspholm M. Cytochrome c-based domain modularity governs genus-level diversification of electron transfer to dissimilatory nitrite reduction. Environ Microbiol 2014; 17:2114-32. [PMID: 25330335 DOI: 10.1111/1462-2920.12661] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 10/04/2014] [Indexed: 12/19/2022]
Abstract
The genus Neisseria contains two pathogenic species (N. meningitidis and N. gonorrhoeae) in addition to a number of commensal species that primarily colonize mucosal surfaces in man. Within the genus, there is considerable diversity and apparent redundancy in the components involved in respiration. Here, we identify a unique c-type cytochrome (cN ) that is broadly distributed among commensal Neisseria, but absent in the pathogenic species. Specifically, cN supports nitrite reduction in N. gonorrhoeae strains lacking the cytochromes c5 and CcoP established to be critical to NirK nitrite reductase activity. The c-type cytochrome domain of cN shares high sequence identity with those localized c-terminally in c5 and CcoP and all three domains were shown to donate electrons directly to NirK. Thus, we identify three distinct but paralogous proteins that donate electrons to NirK. We also demonstrate functionality for a N. weaverii NirK variant with a C-terminal c-type heme extension. Taken together, modular domain distribution and gene rearrangement events related to these respiratory electron carriers within Neisseria are concordant with major transitions in the macroevolutionary history of the genus. This work emphasizes the importance of denitrification as a selectable trait that may influence speciation and adaptive diversification within this largely host-restricted bacterial genus.
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Affiliation(s)
- Finn Erik Aas
- Department of Biosciences, University of Oslo, Oslo, N-0316, Norway
| | - Xi Li
- Department of Biology, University of York, York, YO10 5DD, UK
| | - James Edwards
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Monica Hongrø Solbakken
- Department of Biosciences, University of Oslo, Oslo, N-0316, Norway.,Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, N-0316, Norway
| | - Manu Deeudom
- Department of Biology, University of York, York, YO10 5DD, UK.,Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Åshild Vik
- Department of Biosciences, University of Oslo, Oslo, N-0316, Norway
| | - James Moir
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Michael Koomey
- Department of Biosciences, University of Oslo, Oslo, N-0316, Norway.,Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, N-0316, Norway
| | - Marina Aspholm
- Department of Biosciences, University of Oslo, Oslo, N-0316, Norway
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239
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Wan R, Zheng X, Chen Y, Wang H. Using cassava distiller’s dried grains as carbon and microbe sources to enhance denitrification of nitrate-contaminated groundwater. Appl Microbiol Biotechnol 2014; 99:2839-47. [DOI: 10.1007/s00253-014-6155-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 10/07/2014] [Accepted: 10/12/2014] [Indexed: 10/24/2022]
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240
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Line L, Alhede M, Kolpen M, Kühl M, Ciofu O, Bjarnsholt T, Moser C, Toyofuku M, Nomura N, Høiby N, Jensen PØ. Physiological levels of nitrate support anoxic growth by denitrification of Pseudomonas aeruginosa at growth rates reported in cystic fibrosis lungs and sputum. Front Microbiol 2014; 5:554. [PMID: 25386171 PMCID: PMC4208399 DOI: 10.3389/fmicb.2014.00554] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 10/03/2014] [Indexed: 12/13/2022] Open
Abstract
Chronic Pseudomonas aeruginosa lung infection is the most severe complication in patients with cystic fibrosis (CF). The infection is characterized by the formation of biofilm surrounded by numerous polymorphonuclear leukocytes (PMNs) and strong O2 depletion in the endobronchial mucus. We have reported that O2 is mainly consumed by the activated PMNs, while O2 consumption by aerobic respiration is diminutive and nitrous oxide (N2O) is produced in infected CF sputum. This suggests that the reported growth rates of P. aeruginosa in lungs and sputum may result from anaerobic respiration using denitrification. The growth rate of P. aeruginosa achieved by denitrification at physiological levels (~400 μM) of nitrate (NO(-) 3) is however, not known. Therefore, we have measured growth rates of anoxic cultures of PAO1 and clinical isolates (n = 12) in LB media supplemented with NO(-) 3 and found a significant increase of growth when supplementing PAO1 and clinical isolates with ≥150 μM NO(-) 3 and 100 μM NO(-) 3, respectively. An essential contribution to growth by denitrification was demonstrated by the inability to establish a significantly increased growth rate by a denitrification deficient ΔnirS-N mutant at <1 mM of NO(-) 3. Activation of denitrification could be achieved by supplementation with as little as 62.5 μM of NO(-) 3 according to the significant production of N2O by the nitrous oxide reductase deficient ΔnosZ mutant. Studies of the promoter activity, gene transcripts, and enzyme activity of the four N-oxide reductases in PAO1 (Nar, Nir, Nor, Nos) further verified the engagement of denitrification, showing a transient increase in activation and expression and rapid consumption of NO(-) 3 followed by a transient increase of NO(-) 2. Growth rates obtained by denitrification in this study were comparable to our reported growth rates in the majority of P. aeruginosa cells in CF lungs and sputum. Thus, we have demonstrated that denitrification is required for P. aeruginosa growth in infected endobronchial CF mucus.
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Affiliation(s)
- Laura Line
- Department of Clinical Microbiology Rigshospitalet, Copenhagen, Denmark ; Department of International Health, Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen Copenhagen, Denmark
| | - Morten Alhede
- Department of Clinical Microbiology Rigshospitalet, Copenhagen, Denmark ; Department of International Health, Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen Copenhagen, Denmark
| | - Mette Kolpen
- Department of Clinical Microbiology Rigshospitalet, Copenhagen, Denmark ; Department of International Health, Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen Copenhagen, Denmark
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen Copenhagen, Denmark ; Plant Functional Biology and Climate Change Cluster, University of Technology Sydney Sydney, NSW, Australia ; Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University Singapore, Singapore
| | - Oana Ciofu
- Department of International Health, Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen Copenhagen, Denmark
| | - Thomas Bjarnsholt
- Department of Clinical Microbiology Rigshospitalet, Copenhagen, Denmark ; Department of International Health, Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen Copenhagen, Denmark
| | - Claus Moser
- Department of Clinical Microbiology Rigshospitalet, Copenhagen, Denmark
| | - Masanori Toyofuku
- Graduate School of Life and Environmental Sciences, University of Tsukuba Tsukuba, Japan
| | - Nobuhiko Nomura
- Graduate School of Life and Environmental Sciences, University of Tsukuba Tsukuba, Japan
| | - Niels Høiby
- Department of Clinical Microbiology Rigshospitalet, Copenhagen, Denmark ; Department of International Health, Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen Copenhagen, Denmark
| | - Peter Ø Jensen
- Department of Clinical Microbiology Rigshospitalet, Copenhagen, Denmark
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241
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Cua LS, Stein LY. Characterization of denitrifying activity by the alphaproteobacterium, Sphingomonas wittichii RW1. Front Microbiol 2014; 5:404. [PMID: 25147547 PMCID: PMC4123721 DOI: 10.3389/fmicb.2014.00404] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 07/17/2014] [Indexed: 11/13/2022] Open
Abstract
Sphingomonas wittichii RW1 has no reported denitrifying activity yet encodes nitrite and nitric oxide reductases. The aims of this study were to determine conditions under which S. wittichii RW1 consumes nitrite (NO(-) 2) and produces nitrous oxide (N2O), examine expression of putative genes for N-oxide metabolism, and determine the functionality of chromosomal (ch) and plasmid (p) encoded quinol-dependent nitric oxide reductases (NorZ). Batch cultures of wildtype (WT) and a norZ ch mutant of S. wittichii RW1 consumed NO(-) 2 and produced N2O during stationary phase. The norZ ch mutant produced N2O, although at significantly lower levels (c.a. 66-87%) relative to the WT. Rates of N2O production were 2-3 times higher in cultures initiated at low relative to atmospheric O2 per unit biomass, although rates of NO(-) 2 consumption were elevated in cultures initiated with atmospheric O2 and 1 mM NaNO2. Levels of mRNA encoding nitrite reductase (nirK), plasmid-encoded nitric oxide dioxygenase (hmp p) and plasmid-encoded nitric oxide reductase (norZ p) were significantly higher in the norZ ch mutant over a growth curve relative to WT. The presence of NO(-) 2 further increased levels of nirK and hmp p mRNA in both the WT and norZ ch mutant; levels of norZ p mRNA compensated for the loss of norZ ch expression in the norZ ch mutant. Together, the results suggest that S. wittichii RW1 denitrifies NO(-) 2 to N2O and expresses gene products predicted to detoxify N-oxides. So far, only S. wittichii strains within four closely related taxa have been observed to encode both nirK and norZ genes, indicating a species-specific lateral gene transfer that may be relevant to the niche preference of S. wittichii.
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Affiliation(s)
- Lynnie S Cua
- Department of Environmental Sciences, University of California Riverside, CA, USA
| | - Lisa Y Stein
- Department of Biological Sciences, Faculty of Science, University of Alberta Edmonton, AB, Canada
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242
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Zheng M, He D, Ma T, Chen Q, Liu S, Ahmad M, Gui M, Ni J. Reducing NO and N₂O emission during aerobic denitrification by newly isolated Pseudomonas stutzeri PCN-1. BIORESOURCE TECHNOLOGY 2014; 162:80-88. [PMID: 24747385 DOI: 10.1016/j.biortech.2014.03.125] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 03/21/2014] [Accepted: 03/23/2014] [Indexed: 06/03/2023]
Abstract
As two obligatory intermediates of denitrification, both NO and N2O had harmful environmental and biological impacts. An aerobic denitrifying bacterial strain PCN-1 was newly isolated and identified as Pseudomonas stutzeri, which was capable of high efficient nitrogen removal under aerobic condition with maximal NO and N2O accumulation as low as 0.003% and 0.33% of removed NO3(-)-N, respectively. Further experiment taking nitrite as denitrifying substrate indicated similar low NO and N2O emission of 0.006% and 0.29% of reduced NO2(-)-N, respectively. Reverse transcription-polymerase chain reaction (RT-PCR) analysis revealed that the coordinate expression of denitrification gene nirS (for cytochrome cd1 nitrite reductase), cnorB (for NO reductase) and nosZ (for N2O reductase) was the fundamental reason of low NO and N2O accumulation. Activated sludge system bioaugmented by strain PCN-1 demonstrated a significant reduction of NO and N2O emission from wastewater during aerobic denitrification, implied great potential of PCN-1 in practical applications.
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Affiliation(s)
- Maosheng Zheng
- Department of Environmental Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Da He
- Department of Environmental Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Tao Ma
- Department of Environmental Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Qian Chen
- Department of Environmental Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Sitong Liu
- Department of Environmental Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Muhammad Ahmad
- Department of Environmental Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Mengyao Gui
- Department of Environmental Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Jinren Ni
- Department of Environmental Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China.
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243
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Nitschke W, Russell MJ. Beating the acetyl coenzyme A-pathway to the origin of life. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120258. [PMID: 23754811 DOI: 10.1098/rstb.2012.0258] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Attempts to draft plausible scenarios for the origin of life have in the past mainly built upon palaeogeochemical boundary conditions while, as detailed in a companion article in this issue, frequently neglecting to comply with fundamental thermodynamic laws. Even if demands from both palaeogeochemistry and thermodynamics are respected, then a plethora of strongly differing models are still conceivable. Although we have no guarantee that life at its origin necessarily resembled biology in extant organisms, we consider that the only empirical way to deduce how life may have emerged is by taking the stance of assuming continuity of biology from its inception to the present day. Building upon this conviction, we have assessed extant types of energy and carbon metabolism for their appropriateness to conditions probably pertaining in those settings of the Hadean planet that fulfil the thermodynamic requirements for life to come into being. Wood-Ljungdahl (WL) pathways leading to acetyl CoA formation are excellent candidates for such primordial metabolism. Based on a review of our present understanding of the biochemistry and biophysics of acetogenic, methanogenic and methanotrophic pathways and on a phylogenetic analysis of involved enzymes, we propose that a variant of modern methanotrophy is more likely than traditional WL systems to date back to the origin of life. The proposed model furthermore better fits basic thermodynamic demands and palaeogeochemical conditions suggested by recent results from extant alkaline hydrothermal seeps.
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Affiliation(s)
- Wolfgang Nitschke
- Bioénergétique et Ingénierie des Protéines UMR7281, CNRS/AMU, FR3479 Marseille, France.
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244
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Takahama U, Ansai T, Hirota S. Nitrogen Oxides Toxicology of the Aerodigestive Tract. ADVANCES IN MOLECULAR TOXICOLOGY 2013. [DOI: 10.1016/b978-0-444-62645-5.00004-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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245
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Schoepp-Cothenet B, van Lis R, Atteia A, Baymann F, Capowiez L, Ducluzeau AL, Duval S, ten Brink F, Russell MJ, Nitschke W. On the universal core of bioenergetics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:79-93. [PMID: 22982447 DOI: 10.1016/j.bbabio.2012.09.005] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 09/06/2012] [Accepted: 09/07/2012] [Indexed: 01/05/2023]
Abstract
Living cells are able to harvest energy by coupling exergonic electron transfer between reducing and oxidising substrates to the generation of chemiosmotic potential. Whereas a wide variety of redox substrates is exploited by prokaryotes resulting in very diverse layouts of electron transfer chains, the ensemble of molecular architectures of enzymes and redox cofactors employed to construct these systems is stunningly small and uniform. An overview of prominent types of electron transfer chains and of their characteristic electrochemical parameters is presented. We propose that basic thermodynamic considerations are able to rationalise the global molecular make-up and functioning of these chemiosmotic systems. Arguments from palaeogeochemistry and molecular phylogeny are employed to discuss the evolutionary history leading from putative energy metabolisms in early life to the chemiosmotic diversity of extant organisms. Following the Occam's razor principle, we only considered for this purpose origin of life scenarios which are contiguous with extant life. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.
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Affiliation(s)
- Barbara Schoepp-Cothenet
- Laboratoire de Bioénergétique et Ingénierie des Protéines UMR 7281 CNRS/AMU, FR3479, F-13402 Marseille Cedex 20, France.
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