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Wu D, Dolfing J, Xie B. Bacterial perspectives on the dissemination of antibiotic resistance genes in domestic wastewater bio-treatment systems: beneficiary to victim. Appl Microbiol Biotechnol 2017; 102:597-604. [DOI: 10.1007/s00253-017-8665-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/16/2017] [Accepted: 11/17/2017] [Indexed: 11/24/2022]
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52
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Lood R, Ertürk G, Mattiasson B. Revisiting Antibiotic Resistance Spreading in Wastewater Treatment Plants - Bacteriophages as a Much Neglected Potential Transmission Vehicle. Front Microbiol 2017; 8:2298. [PMID: 29209304 PMCID: PMC5702337 DOI: 10.3389/fmicb.2017.02298] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 11/07/2017] [Indexed: 12/28/2022] Open
Abstract
The spread of antibiotic resistance is currently a major threat to health that humanity is facing today. Novel multidrug and pandrug resistant bacteria are reported on a yearly basis, while the development of novel antibiotics is lacking. Focus to limit the spread of antibiotic resistance by reducing the usage of antibiotics in health care, veterinary applications, and meat production, have been implemented, limiting the exposure of pathogens to antibiotics, thus lowering the selection of resistant strains. Despite these attempts, the global resistance has increased significantly. A recent area of focus has been to limit the spread of resistance through wastewater treatment plants (WWTPs), serving as huge reservoirs of microbes and resistance genes. While being able to quite efficiently reduce the presence of resistant bacteria entering any of the final products of WWTPs (e.g., effluent water and sludge), the presence of resistance genes in other formats (mobile genetic elements, bacteriophages) has mainly been ignored. Recent data stress the importance of transduction in WWTPs as a mediator of resistance spread. Here we examine the current literature in the role of WWTPs as reservoirs and hotspots of antibiotic resistance with a specific focus on bacteriophages as mediators of genetic exchange.
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Affiliation(s)
- Rolf Lood
- Department of Clinical Sciences, Division of Infection Medicine, Lund University, Lund, Sweden
| | - Gizem Ertürk
- Department of Clinical Sciences, Division of Infection Medicine, Lund University, Lund, Sweden
| | - Bo Mattiasson
- Department of Biotechnology, Lund University, Lund, Sweden
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53
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Potential Dissemination of ARB and ARGs into Soil Through the Use of Treated Wastewater for Agricultural Irrigation: Is It a True Cause for Concern? ACTA ACUST UNITED AC 2017. [DOI: 10.1007/978-3-319-66260-2_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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54
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Liu W, Li C, Qiu ZG, Jin M, Wang JF, Yang D, Xiao ZH, Yuan ZK, Li JW, Xu QY, Shen ZQ. Development of a novel and highly efficient method of isolating bacteriophages from water. J Microbiol Methods 2017; 139:143-149. [DOI: 10.1016/j.mimet.2017.05.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Revised: 05/27/2017] [Accepted: 05/30/2017] [Indexed: 12/13/2022]
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Sidhu C, Vikram S, Pinnaka AK. Unraveling the Microbial Interactions and Metabolic Potentials in Pre- and Post-treated Sludge from a Wastewater Treatment Plant Using Metagenomic Studies. Front Microbiol 2017; 8:1382. [PMID: 28769920 PMCID: PMC5515832 DOI: 10.3389/fmicb.2017.01382] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 07/07/2017] [Indexed: 01/06/2023] Open
Abstract
Sewage waste represents an ecosystem of complex and interactive microbial consortia which proliferate with different kinetics according to their individual genetic as well as metabolic potential. We performed metagenomic shotgun sequencing on Ion-Torrent platform, to explore the microbial community structure, their biological interactions and associated functional capacity of pre-treated/raw sludge (RS) and post-treated/dried sludge (DS) of wastewater treatment plant. Bacterial phylotypes belonging to Epsilonproteobacteria (∼45.80%) dominated the RS with relatively few Archaea (∼1.94%) whereas DS has the dominance of beta- (30.23%) and delta- (13.38%) classes of Proteobacteria with relatively greater abundance of Archaea (∼7.18%). In particular, Epsilonproteobacteria appears as a primary energy source in RS and sulfur-reducing bacteria with methanogens seems to be in the potential syntrophic association in DS. These interactions could be ultimately responsible for carrying out amino-acid degradation, aromatic compound degradation and degradation of propionate and butyrate in DS. Our data also reveal the presence of key genes in the sludge microbial community responsible for degradation of polycyclic aromatic hydrocarbons. Potential pathogenic microbes and genes for the virulence factors were found to be relatively abundant in RS which clearly reflect the necessity of treatment of RS. After treatment, potential pathogens load was reduced, indicating the sludge hygienisation in DS. Additionally, the interactions found in this study would reveal the biological and environmental cooperation among microbial communities for domestic wastewater treatment.
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Affiliation(s)
- Chandni Sidhu
- Microbial Type Culture Collection and Gene Bank, Council of Scientific and Industrial Research-Institute of Microbial TechnologyChandigarh, India
| | - Surendra Vikram
- Microbial Type Culture Collection and Gene Bank, Council of Scientific and Industrial Research-Institute of Microbial TechnologyChandigarh, India.,Centre for Microbial Ecology and Genomics, Department of Genetics, University of PretoriaPretoria, South Africa
| | - Anil Kumar Pinnaka
- Microbial Type Culture Collection and Gene Bank, Council of Scientific and Industrial Research-Institute of Microbial TechnologyChandigarh, India
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Fan N, Qi R, Yang M. Isolation and characterization of a virulent bacteriophage infecting Acinetobacter johnsonii from activated sludge. Res Microbiol 2017; 168:472-481. [DOI: 10.1016/j.resmic.2017.01.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 01/17/2017] [Accepted: 01/31/2017] [Indexed: 11/26/2022]
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57
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Simulation of phage dynamics in multi-reactor models of complex wastewater treatment systems. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2016.10.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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58
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Pajdak-Stós A, Kocerba-Soroka W, Fyda J, Sobczyk M, Fiałkowska E. Foam-forming bacteria in activated sludge effectively reduced by rotifers in laboratory- and real-scale wastewater treatment plant experiments. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:13004-13011. [PMID: 28378311 PMCID: PMC5418312 DOI: 10.1007/s11356-017-8890-z] [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: 10/11/2016] [Accepted: 03/20/2017] [Indexed: 05/05/2023]
Abstract
Lecane inermis rotifers were shown to diminish sludge bulking due to their ability to ingest the filamentous bacteria in activated sludge. To determine if rotifers are also able to control branched actinomycetes, we investigated three other Lecane species (Monogononta). In a week-long experiment, only Lecane tenuiseta significantly reduced the density of Microthrix parvicella and Type 0092 filaments, but in a 2-week experiment, actinomycetes were significantly reduced by most of the tested monogonont rotifers: L. inermis, Lecane decipiens and Lecane pyriformis. Rotifers L. inermis originating from the mass culture were artificially introduced into real-scale wastewater treatment plant (WWTP) in two series. The WWTP was monitored for 1 year. Rotifer inoculation resulted in diminishing of M. parvicella and actinomycete abundance. The experiments showed that different species of rotifers vary in their effectiveness at limiting various types of filamentous organisms. This is the first report demonstrating that one of the most troublesome bacteria, branched actinomycetes, which cause heavy foaming in bioreactors, can be controlled by rotifers. Knowledge of the consumers of filamentous bacteria that inhabit activated sludge could help WWTP operators overcome bulking and foaming through environmentally friendly methods.
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Affiliation(s)
- Agnieszka Pajdak-Stós
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland.
| | - Wioleta Kocerba-Soroka
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Janusz Fyda
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Mateusz Sobczyk
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Edyta Fiałkowska
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
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59
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Yang Q, Zhao H, Du B. Bacteria and bacteriophage communities in bulking and non-bulking activated sludge in full-scale municipal wastewater treatment systems. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2016.12.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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60
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Genome Analysis of a Novel Broad Host Range Proteobacteria Phage Isolated from a Bioreactor Treating Industrial Wastewater. Genes (Basel) 2017; 8:genes8010040. [PMID: 28106814 PMCID: PMC5295034 DOI: 10.3390/genes8010040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Revised: 12/27/2016] [Accepted: 01/11/2017] [Indexed: 01/18/2023] Open
Abstract
Bacteriophages are viruses that infect bacteria, and consequently they have a major impact on the development of a microbial population. In this study, the genome of a novel broad host range bacteriophage, Aquamicrobium phage P14, isolated from a wastewater treatment plant, was analyzed. The Aquamicrobium phage P14 was found to infect members of different Proteobacteria classes (Alphaproteobacteria and Betaproteobacteria). This phage contains a 40,551 bp long genome and 60% of its genes had blastx hits. Furthermore, the bacteriophage was found to share more than 50% of its genes with several podoviruses and has the same gene order as other polyvalent bacteriophages. The results obtained in this study led to the conclusion that indeed general features of the genome of the Aquamicrobium phage P14 are shared with other broad host range bacteriophages, however further analysis of the genome is needed in order to identify the specific mechanisms which enable the bacteriophage to infect both Alphaproteobacteria and Betaproteobacteria.
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61
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Karimi M, Mirshekari H, Moosavi Basri SM, Bahrami S, Moghoofei M, Hamblin MR. Bacteriophages and phage-inspired nanocarriers for targeted delivery of therapeutic cargos. Adv Drug Deliv Rev 2016; 106:45-62. [PMID: 26994592 PMCID: PMC5026880 DOI: 10.1016/j.addr.2016.03.003] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 03/04/2016] [Accepted: 03/08/2016] [Indexed: 02/08/2023]
Abstract
The main goal of drug delivery systems is to target therapeutic cargoes to desired cells and to ensure their efficient uptake. Recently a number of studies have focused on designing bio-inspired nanocarriers, such as bacteriophages, and synthetic carriers based on the bacteriophage structure. Bacteriophages are viruses that specifically recognize their bacterial hosts. They can replicate only inside their host cell and can act as natural gene carriers. Each type of phage has a particular shape, a different capacity for loading cargo, a specific production time, and their own mechanisms of supramolecular assembly, that have enabled them to act as tunable carriers. New phage-based technologies have led to the construction of different peptide libraries, and recognition abilities provided by novel targeting ligands. Phage hybridization with non-organic compounds introduces new properties to phages and could be a suitable strategy for construction of bio-inorganic carriers. In this review we try to cover the major phage species that have been used in drug and gene delivery systems, and the biological application of phages as novel targeting ligands and targeted therapeutics.
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Affiliation(s)
- Mahdi Karimi
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hamed Mirshekari
- Advanced Nanobiotechnology & Nanomedicine Research Group [ANNRG], Iran University of Medical Sciences, Tehran, Iran
| | - Seyed Masoud Moosavi Basri
- Drug Design and Bioinformatics Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran; Civil & Environmental Engineering Department, Shahid Beheshti University, Tehran, Iran
| | - Sajad Bahrami
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran; Student Research Committee, Iran University of Medical Sciences, Tehran, IR, Iran
| | - Mohsen Moghoofei
- Student Research Committee, Iran University of Medical Sciences, Tehran, IR, Iran; Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Michael R Hamblin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Dermatology, Harvard Medical School, Boston, MA 02115, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA.
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62
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Sharma S, Chatterjee S, Datta S, Prasad R, Dubey D, Prasad RK, Vairale MG. Bacteriophages and its applications: an overview. Folia Microbiol (Praha) 2016; 62:17-55. [PMID: 27718043 DOI: 10.1007/s12223-016-0471-x] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 09/12/2016] [Indexed: 01/21/2023]
Abstract
Bacteriophages (or phages), the most abundant viral entity of the planet, are omni-present in all the ecosystems. On the basis of their unique characteristics and anti-bacterial property, phages are being freshly evaluated taxonomically. Phages replicate inside the host either by lytic or lysogenic mode after infecting and using the cellular machinery of a bacterium. Since their discovery by Twort and d'Herelle in the early 1900s, phage became an important agent for combating pathogenic bacteria in clinical treatments and its related research gained momentum. However, due to recent emergence of bacterial resistance on antibiotics, applications of phage (phage therapy) become an inevitable option of research. Phage particles become popular as a biotechnological tool and treatment of pathogenic bacteria in a range of applied areas. However, there are few concerns over the application of phage-based solutions. This review deals with the updated phage taxonomy (ICTV 2015 Release and subsequent revision) and phage biology and the recent development of its application in the areas of biotechnology, biosensor, therapeutic medicine, food preservation, aquaculture diseases, pollution remediation, and wastewater treatment and issues related with limitations of phage-based remedy.
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Affiliation(s)
- Sonika Sharma
- Defence Research Laboratory, DRDO, Tezpur, Assam, 784001, India
| | | | | | - Rishika Prasad
- Defence Research Laboratory, DRDO, Tezpur, Assam, 784001, India
- School of Biomedical Engineering, Cornell University, Ithaca, NY, 14850, USA
| | | | | | - Mohan G Vairale
- Defence Research Laboratory, DRDO, Tezpur, Assam, 784001, India
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63
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Locating and Activating Molecular 'Time Bombs': Induction of Mycolata Prophages. PLoS One 2016; 11:e0159957. [PMID: 27487243 PMCID: PMC4972346 DOI: 10.1371/journal.pone.0159957] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 07/11/2016] [Indexed: 11/23/2022] Open
Abstract
Little is known about the prevalence, functionality and ecological roles of temperate phages for members of the mycolic acid producing bacteria, the Mycolata. While many lytic phages infective for these organisms have been isolated, and assessed for their suitability for use as biological control agents of activated sludge foaming, no studies have investigated how temperate phages might be induced for this purpose. Bioinformatic analysis using the PHAge Search Tool (PHAST) on Mycolata whole genome sequence data in GenBank for members of the genera Gordonia, Mycobacterium, Nocardia, Rhodococcus, and Tsukamurella revealed 83% contained putative prophage DNA sequences. Subsequent prophage inductions using mitomycin C were conducted on 17 Mycolata strains. This led to the isolation and genome characterization of three novel Caudovirales temperate phages, namely GAL1, GMA1, and TPA4, induced from Gordonia alkanivorans, Gordonia malaquae, and Tsukamurella paurometabola, respectively. All possessed highly distinctive dsDNA genome sequences.
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64
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Young P, Buchanan N, Fallowfield HJ. Inactivation of indicator organisms in wastewater treated by a high rate algal pond system. J Appl Microbiol 2016; 121:577-86. [DOI: 10.1111/jam.13180] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 05/06/2016] [Indexed: 10/21/2022]
Affiliation(s)
- P. Young
- Health & the Environment Group; School of the Environment; Flinders University; Adelaide SA Australia
| | - N. Buchanan
- Health & the Environment Group; School of the Environment; Flinders University; Adelaide SA Australia
| | - H. J. Fallowfield
- Health & the Environment Group; School of the Environment; Flinders University; Adelaide SA Australia
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65
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Bacteriophage biocontrol in wastewater treatment. World J Microbiol Biotechnol 2016; 32:70. [DOI: 10.1007/s11274-016-2028-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 02/10/2016] [Indexed: 10/22/2022]
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66
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Biofilm control with natural and genetically-modified phages. World J Microbiol Biotechnol 2016; 32:67. [PMID: 26931607 DOI: 10.1007/s11274-016-2009-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Accepted: 01/07/2016] [Indexed: 01/11/2023]
Abstract
Bacteriophages, as the most dominant and diverse entities in the universe, have the potential to be one of the most promising therapeutic agents. The emergence of multidrug-resistant bacteria and the antibiotic crisis in the last few decades have resulted in a renewed interest in phage therapy. Furthermore, bacteriophages, with the capacity to rapidly infect and overcome bacterial resistance, have demonstrated a sustainable approach against bacterial pathogens-particularly in biofilm. Biofilm, as complex microbial communities located at interphases embedded in a matrix of bacterial extracellular polysaccharide substances (EPS), is involved in health issues such as infections associated with the use of biomaterials and chronic infections by multidrug resistant bacteria, as well as industrial issues such as biofilm formation on stainless steel surfaces in food industry and membrane biofouling in water and wastewater treatment processes. In this paper, the most recent studies on the potential of phage therapy using natural and genetically-modified lytic phages and their associated enzymes in fighting biofilm development in various fields including engineering, industry, and medical applications are reviewed. Phage-mediated prevention approaches as an indirect phage therapy strategy are also explored in this review. In addition, the limitations of these approaches and suggestions to overcome these constraints are discussed to enhance the efficiency of phage therapy process. Finally, future perspectives and directions for further research towards a better understanding of phage therapy to control biofilm are recommended.
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67
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Khairnar K, Chandekar R, Nair A, Pal P, Paunikar WN. Novel application of bacteriophage for controlling foaming in wastewater treatment plant- an eco-friendly approach. Bioengineered 2016; 7:46-9. [PMID: 26890996 DOI: 10.1080/21655979.2015.1134066] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
This addendum to "Novel application of bacteriophage for controlling foaming in wastewater treatment plant- an eco-friendly approach " includes characteristics of the phages NOC1, NOC2 and NOC3 not discussed in the previous paper. The phage adsorption and host interaction properties, their sensitivity to pH and temperature are inferred. NOC2 is seen to be more temperature resistant while others are not. All the phages show pH sensitivity. There is a variance observed in the behavior of these phages. Also, applicability of the phage based system to large scale reactors is studied and discussed here.
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Affiliation(s)
- Krishna Khairnar
- a Environmental Virology Cell , Council for Scientific and Industrial Research - National Environmental Engineering Research Institute (CSIR-NEERI) , Nehru Marg, Nagpur , Maharashtra , India
| | - Rajshree Chandekar
- a Environmental Virology Cell , Council for Scientific and Industrial Research - National Environmental Engineering Research Institute (CSIR-NEERI) , Nehru Marg, Nagpur , Maharashtra , India
| | - Aparna Nair
- a Environmental Virology Cell , Council for Scientific and Industrial Research - National Environmental Engineering Research Institute (CSIR-NEERI) , Nehru Marg, Nagpur , Maharashtra , India
| | - Preeti Pal
- a Environmental Virology Cell , Council for Scientific and Industrial Research - National Environmental Engineering Research Institute (CSIR-NEERI) , Nehru Marg, Nagpur , Maharashtra , India
| | - Waman N Paunikar
- a Environmental Virology Cell , Council for Scientific and Industrial Research - National Environmental Engineering Research Institute (CSIR-NEERI) , Nehru Marg, Nagpur , Maharashtra , India
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68
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Schmidt M, de Lorenzo V. Synthetic bugs on the loose: containment options for deeply engineered (micro)organisms. Curr Opin Biotechnol 2016; 38:90-6. [PMID: 26874261 DOI: 10.1016/j.copbio.2016.01.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 01/11/2016] [Accepted: 01/12/2016] [Indexed: 12/14/2022]
Abstract
Synthetic Biology (SynBio) has brought up again questions on the environmental fate of microorganisms carrying genetic modifications. The growing capacity of editing genomes for deployment of man-made programs opens unprecedented biotechnological opportunities. But the same exacerbate concerns regarding fortuitous or deliberate releases to the natural medium. Most approaches to tackle these worries involve endowing SynBio agents with containment devices for halting horizontal gene transfer and survival of the live agents only at given times and places. Genetic circuits and trophic restraint schemes have been proposed to this end in the pursuit of complete containment. The most promising include adoption of alternative genetic codes and/or dependency on xenobiotic amino acids and nucleotides. But the field has to still overcome serious bottlenecks.
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Affiliation(s)
| | - Víctor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain.
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69
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Krysiak-Baltyn K, Martin GJO, Stickland AD, Scales PJ, Gras SL. Computational models of populations of bacteria and lytic phage. Crit Rev Microbiol 2016; 42:942-68. [PMID: 26828960 DOI: 10.3109/1040841x.2015.1114466] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The use of phages to control and reduce numbers of unwanted bacteria can be traced back to the early 1900s, when phages were explored as a tool to treat infections before the wide scale use of antibiotics. Recently, phage therapy has received renewed interest as a method to treat multiresistant bacteria. Phages are also widely used in the food industry to prevent the growth of certain bacteria in foods, and are currently being explored as a tool for use in bioremediation and wastewater treatment. Despite the large body of biological research on phages, relatively little attention has been given to computational modeling of the population dynamics of phage and bacterial interactions. The earliest model was described by Campbell in the 1960s. Subsequent modifications to this model include partial or complete resistance, multiple phage binding sites, and spatial heterogeneity. This review provides a general introduction to modeling of the population dynamics of bacteria and phage. The review introduces the basic model and relevant concepts and evaluates more complex variations of the basic model published to date, including a model of disease epidemics caused by infectious bacteria. Finally, the shortcomings and potential ways to improve the models are discussed.
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Affiliation(s)
- Konrad Krysiak-Baltyn
- a Department of Chemical and Biomolecular Engineering , University of Melbourne , Parkville , Australia
| | - Gregory J O Martin
- a Department of Chemical and Biomolecular Engineering , University of Melbourne , Parkville , Australia
| | - Anthony D Stickland
- a Department of Chemical and Biomolecular Engineering , University of Melbourne , Parkville , Australia
| | - Peter J Scales
- a Department of Chemical and Biomolecular Engineering , University of Melbourne , Parkville , Australia
| | - Sally L Gras
- a Department of Chemical and Biomolecular Engineering , University of Melbourne , Parkville , Australia
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70
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Calusinska M, Marynowska M, Goux X, Lentzen E, Delfosse P. Analysis of dsDNA and RNA viromes in methanogenic digesters reveals novel viral genetic diversity. Environ Microbiol 2016; 18:1162-75. [PMID: 26568175 PMCID: PMC7163765 DOI: 10.1111/1462-2920.13127] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 08/17/2015] [Accepted: 11/06/2015] [Indexed: 01/08/2023]
Abstract
Although viruses are not the key players of the anaerobic digestion process, they may affect the dynamics of bacterial and archaeal populations involved in biogas production. Until now viruses have received very little attention in this specific habitat; therefore, as a first step towards their characterization, we optimized a virus filtration protocol from anaerobic sludge. Afterwards, to assess dsDNA and RNA viral diversity in sludge samples from nine different reactors fed either with waste water, agricultural residues or solid municipal waste plus agro‐food residues, we performed metagenomic analyses. As a result we showed that, while the dsDNA viromes (21 assigned families in total) were dominated by dsDNA phages of the order Caudovirales, RNA viruses (14 assigned families in total) were less diverse and were for the main part plant‐infecting viruses. Interestingly, less than 2% of annotated contigs were assigned as putative human and animal pathogens. Our study greatly extends the existing view of viral genetic diversity in methanogenic reactors and shows that these viral assemblages are distinct not only among the reactor types but also from nearly 30 other environments already studied, including the human gut, fermented food, deep sea sediments and other aquatic habitats.
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Affiliation(s)
- Magdalena Calusinska
- Luxembourg Institute of Science and Technology, Environmental Research and Innovation (ERIN), 41 rue du Brill, L-4422, Belvaux, Luxembourg
| | - Martyna Marynowska
- Luxembourg Institute of Science and Technology, Environmental Research and Innovation (ERIN), 41 rue du Brill, L-4422, Belvaux, Luxembourg.,Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, ul. Kladki 24, 80-822, Gdansk, Poland
| | - Xavier Goux
- Luxembourg Institute of Science and Technology, Environmental Research and Innovation (ERIN), 41 rue du Brill, L-4422, Belvaux, Luxembourg
| | - Esther Lentzen
- Luxembourg Institute of Science and Technology, Materials Research and Technology (MRT), 41 rue du Brill, L-4422, Belvaux, Luxembourg
| | - Philippe Delfosse
- Luxembourg Institute of Science and Technology, Environmental Research and Innovation (ERIN), 41 rue du Brill, L-4422, Belvaux, Luxembourg
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71
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Lee YD, Park JH. Genome Analysis of Phage SMSAP5 as Candidate of Biocontrol for Staphylococcus aureus. Korean J Food Sci Anim Resour 2016; 35:86-90. [PMID: 26761804 PMCID: PMC4682501 DOI: 10.5851/kosfa.2015.35.1.86] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 12/15/2014] [Accepted: 12/16/2014] [Indexed: 11/06/2022] Open
Abstract
In this study, we reported the morphogenetic analysis and genome sequence by genomic analysis of the newly isolated staphylococcal phage SMSAP5 from soil of slaughterhouses for cattle. Based on transmission electron microscopy evident morphology, phage SMSAP5 belonged to the Siphoviridae family. Phage SMSAP5 had a double-stranded DNA genome with a length of 45,552 bp and 33 % G+C content. Bioinformatics analysis of the phage genome revealed 43 open reading frames. A blastn search revealed that its nucleotide sequence shared a high degree of similarity with that of the Staphylococcus phage tp310-2. In conclusion, this study is the first report to show the morphological features and the complete genome sequence of the phage SMSAP5 from soil of slaughterhouses for cattle.
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Affiliation(s)
- Young-Duck Lee
- Department of Food Science and Engineering, Seowon University, Cheongju 361-742, Korea
| | - Jong-Hyun Park
- Department of Food Science and Biotechnology, Gachon University, Sungnam 461-701, Korea
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72
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Bacteriophages of wastewater foaming-associated filamentous Gordonia reduce host levels in raw activated sludge. Sci Rep 2015; 5:13754. [PMID: 26349678 PMCID: PMC4563357 DOI: 10.1038/srep13754] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 08/04/2015] [Indexed: 12/03/2022] Open
Abstract
Filamentous bacteria are a normal and necessary component of the activated sludge wastewater treatment process, but the overgrowth of filamentous bacteria results in foaming and bulking associated disruptions. Bacteriophages, or phages, were investigated for their potential to reduce the titer of foaming bacteria in a mixed-microbial activated sludge matrix. Foaming-associated filamentous bacteria were isolated from activated sludge of a commercial wastewater treatment plan and identified as Gordonia species by 16S rDNA sequencing. Four representative phages were isolated that target G. malaquae and two un-named Gordonia species isolates. Electron microscopy revealed the phages to be siphophages with long tails. Three of the phages - GordTnk2, Gmala1, and GordDuk1 - had very similar ~76 kb genomes, with >93% DNA identity. These genomes shared limited synteny with Rhodococcus equi phage ReqiDocB7 and Gordonia phage GTE7. In contrast, the genome of phage Gsput1 was smaller (43 kb) and was not similar enough to any known phage to be placed within an established phage type. Application of these four phages at MOIs of 5–15 significantly reduced Gordonia host levels in a wastewater sludge model by approximately 10-fold as compared to non-phage treated reactors. Phage control was observed for nine days after treatment.
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73
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Aracic S, Manna S, Petrovski S, Wiltshire JL, Mann G, Franks AE. Innovative biological approaches for monitoring and improving water quality. Front Microbiol 2015; 6:826. [PMID: 26322034 PMCID: PMC4532924 DOI: 10.3389/fmicb.2015.00826] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 07/27/2015] [Indexed: 12/20/2022] Open
Abstract
Water quality is largely influenced by the abundance and diversity of indigenous microbes present within an aquatic environment. Physical, chemical and biological contaminants from anthropogenic activities can accumulate in aquatic systems causing detrimental ecological consequences. Approaches exploiting microbial processes are now being utilized for the detection, and removal or reduction of contaminants. Contaminants can be identified and quantified in situ using microbial whole-cell biosensors, negating the need for water samples to be tested off-site. Similarly, the innate biodegradative processes can be enhanced through manipulation of the composition and/or function of the indigenous microbial communities present within the contaminated environments. Biological contaminants, such as detrimental/pathogenic bacteria, can be specifically targeted and reduced in number using bacteriophages. This mini-review discusses the potential application of whole-cell microbial biosensors for the detection of contaminants, the exploitation of microbial biodegradative processes for environmental restoration and the manipulation of microbial communities using phages.
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Affiliation(s)
- Sanja Aracic
- Applied and Environmental Microbiology Laboratory, Department of Physiology, Anatomy and Microbiology, La Trobe University , Melbourne, VIC, Australia
| | - Sam Manna
- Applied and Environmental Microbiology Laboratory, Department of Physiology, Anatomy and Microbiology, La Trobe University , Melbourne, VIC, Australia
| | - Steve Petrovski
- Applied and Environmental Microbiology Laboratory, Department of Physiology, Anatomy and Microbiology, La Trobe University , Melbourne, VIC, Australia
| | - Jennifer L Wiltshire
- Applied and Environmental Microbiology Laboratory, Department of Physiology, Anatomy and Microbiology, La Trobe University , Melbourne, VIC, Australia
| | - Gülay Mann
- Land Division, Defence Science and Technology Organisation , Melbourne, VIC, Australia
| | - Ashley E Franks
- Applied and Environmental Microbiology Laboratory, Department of Physiology, Anatomy and Microbiology, La Trobe University , Melbourne, VIC, Australia
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74
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Beheshti Maal K, Soleimani Delfan A, Salmanizadeh S. Isolation and Identification of Two Novel Escherichia coli Bacteriophages and Their Application in Wastewater Treatment and Coliform's Phage Therapy. Jundishapur J Microbiol 2015; 8:e14945. [PMID: 25834715 PMCID: PMC4377173 DOI: 10.5812/jjm.14945] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 06/03/2014] [Accepted: 11/25/2014] [Indexed: 11/17/2022] Open
Abstract
Background: Phage therapy or use of lytic bacteriophages for eliminating bacterial populations has been developed for several aspects of human affairs such as medicine, agriculture and food industries. Objectives: The high load of coliforms of treated wastewater effluents that are discharged into the rivers or agricultural lands is a serious concern of the Iran Department of Environment and the reduction of coliforms using phages to overcome this problem is an asset. This research aimed to isolate and identify specific lytic coliphages and investigate their effects on native and standard Escherichia coli strains as well as coliform populations in municipal wastewater. Materials and Methods: The wastewater sample was cultured on selective culture media to isolate a native coliform strain and characterized using molecular methods. River water was centrifuged and passed through a 0.45 μm filter and its lytic coliphages were enriched and purified against a native E. coli as well as a standard E. coli strain. Municipal wastewater was treated with isolated lytic coliphages and most probable number (MPN) reduction was examined. Results: E. coli SBSWF27, which is a native strain of E. coli from Isfahan municipal wastewater treatment plant, was isolated and characterized. Also two novel bacteriophages related to Myoviridae and Podoviridae families of bacteriophages from Zayandehrood River (Isfahan, Iran) were isolated. These coliphages had lytic effects on E. coli PTCC1399 and E. coli SBSWF27 as coliform's index. The myovirus had a hexagonal head measuring 27.28 nm and a noncontractile tail measuring 204.5 × 13.63 nm. The podovirus had an oval head measuring 98 × 35 nm and a tail, 14 nm in diameter. The treatment of municipal sewage with the coliphage mixture resulted in a 22-fold decrease of the coliform's MPN from 2400 to 110 after two hours of incubation. Conclusions: This is the first report on isolation and identification of two novel lytic myovirus and podovirus from Zayandehrood River in Isfahan that had lytic effects on E. coli PTCC1399 and E. coli SBSWF27 strains as well as coliform's population of Isfahan municipal wastewater. We suggest that the use of these lytic coliphages for reduction of coliform's population in sewage could be considered as an effective and simple alternative for costly replacement of instruments and establishments of the old wastewater treatment plants.
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Affiliation(s)
- Keivan Beheshti Maal
- Department of Microbiology, Faculty of Biological Sciences, Falavarjan Branch, Islamic Azad University, Isfahan, IR Iran
- Corresponding author: Keivan Beheshti Maal, Department of Microbiology, Faculty of Biological Sciences, Falavarjan Branch, Islamic Azad University, Falavarjan, Isfahan, IR Iran. Tel/Fax: +98-3137420136, E-mail:
| | - Abbas Soleimani Delfan
- Department of Microbiology, Faculty of Biological Sciences, Falavarjan Branch, Islamic Azad University, Isfahan, IR Iran
| | - Sharareh Salmanizadeh
- Department of Microbiology, Faculty of Biological Sciences, Falavarjan Branch, Islamic Azad University, Isfahan, IR Iran
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75
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Haig SJ, Schirmer M, D'Amore R, Gibbs J, Davies RL, Collins G, Quince C. Stable-isotope probing and metagenomics reveal predation by protozoa drives E. coli removal in slow sand filters. THE ISME JOURNAL 2015; 9:797-808. [PMID: 25279786 PMCID: PMC4817707 DOI: 10.1038/ismej.2014.175] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 07/15/2014] [Accepted: 08/17/2014] [Indexed: 11/09/2022]
Abstract
Stable-isotope probing and metagenomics were applied to study samples taken from laboratory-scale slow sand filters 0.5, 1, 2, 3 and 4 h after challenging with (13)C-labelled Escherichia coli to determine the mechanisms and organisms responsible for coliform removal. Before spiking, the filters had been continuously operated for 7 weeks using water from the River Kelvin, Glasgow as their influent source. Direct counts and quantitative PCR assays revealed a clear predator-prey response between protozoa and E. coli. The importance of top-down trophic-interactions was confirmed by metagenomic analysis, identifying several protozoan and viral species connected to E. coli attrition, with protozoan grazing responsible for the majority of the removal. In addition to top-down mechanisms, indirect mechanisms, such as algal reactive oxygen species-induced lysis, and mutualistic interactions between algae and fungi, were also associated with coliform removal. The findings significantly further our understanding of the processes and trophic interactions underpinning E. coli removal. This study provides an example for similar studies, and the opportunity to better understand, manage and enhance E. coli removal by allowing the creation of more complex trophic interaction models.
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Affiliation(s)
| | | | - Rosalinda D'Amore
- School of Biological Sciences, University of Liverpool, Liverpool, UK
| | - Joseph Gibbs
- Microbial Ecophysiology Laboratory, School of Natural Sciences and Ryan Institute, National University of Ireland, Galway, Ireland
| | - Robert L Davies
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Gavin Collins
- School of Engineering, University of Glasgow, Glasgow, UK
- Microbial Ecophysiology Laboratory, School of Natural Sciences and Ryan Institute, National University of Ireland, Galway, Ireland
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76
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Dias E, Ebdon J, Taylor H. The application of removal coefficients for viruses in different wastewater treatment processes calculated using stochastic modelling. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2015; 71:1382-1388. [PMID: 25945856 DOI: 10.2166/wst.2015.086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
This study proposes that calculating and interpreting removal coefficients (K20) for bacteriophages in activated sludge (AS) and trickling filter (TF) systems using stochastic modelling may provide important information that may be used to estimate the removal of phages in such systems using simplified models. In order to achieve this, 14 samples of settled wastewater and post-secondary sedimentation wastewater were collected every 2 weeks, over a 6-month period (May to November), from two AS and two TF systems situated in southern England. Initial results have demonstrated that the removal of somatic coliphages in both AS and TF systems is considerably higher than that of F-RNA coliphages, and that AS more effectively removes both phage groups than TF. The results have also demonstrated that K20 values for phages in AS are higher than in TF, which could be justified by the higher removal rates observed in AS and the models assumed for both systems. The research provides a suggested framework for calculating and predicting removal rates of pathogens and indicator organisms in wastewater treatment systems using simplified models in order to support integrated water and sanitation safety planning approaches to human health risk management.
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Affiliation(s)
- Edgard Dias
- The Environment and Public Health Research Group (EPHReG), School of Environment and Technology, University of Brighton, Lewes Road, Brighton, BN2 4GJ, UK E-mail:
| | - James Ebdon
- The Environment and Public Health Research Group (EPHReG), School of Environment and Technology, University of Brighton, Lewes Road, Brighton, BN2 4GJ, UK E-mail:
| | - Huw Taylor
- The Environment and Public Health Research Group (EPHReG), School of Environment and Technology, University of Brighton, Lewes Road, Brighton, BN2 4GJ, UK E-mail:
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77
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Characterization and application of phages isolated from sewage for reduction of Escherichia coli O157:H7 in biofilm. Lebensm Wiss Technol 2015. [DOI: 10.1016/j.lwt.2014.09.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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78
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Aw TG, Howe A, Rose JB. Metagenomic approaches for direct and cell culture evaluation of the virological quality of wastewater. J Virol Methods 2014; 210:15-21. [DOI: 10.1016/j.jviromet.2014.09.017] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 09/15/2014] [Accepted: 09/16/2014] [Indexed: 10/24/2022]
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79
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80
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Saleem M, Moe LA. Multitrophic microbial interactions for eco- and agro-biotechnological processes: theory and practice. Trends Biotechnol 2014; 32:529-37. [PMID: 25192971 DOI: 10.1016/j.tibtech.2014.08.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 07/16/2014] [Accepted: 08/05/2014] [Indexed: 10/24/2022]
Abstract
Multitrophic level microbial loop interactions mediated by protist predators, bacteria, and viruses drive eco- and agro-biotechnological processes such as bioremediation, wastewater treatment, plant growth promotion, and ecosystem functioning. To what extent these microbial interactions are context-dependent in performing biotechnological and ecosystem processes remains largely unstudied. Theory-driven research may advance the understanding of eco-evolutionary processes underlying the patterns and functioning of microbial interactions for successful development of microbe-based biotechnologies for real world applications. This could also be a great avenue to test the validity or limitations of ecology theory for managing diverse microbial resources in an era of altering microbial niches, multitrophic interactions, and microbial diversity loss caused by climate and land use changes.
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Affiliation(s)
- Muhammad Saleem
- Department of Plant and Soil Sciences, 311 Plant Science Building, University of Kentucky, Lexington, KY 40546-0312, USA.
| | - Luke A Moe
- Department of Plant and Soil Sciences, 311 Plant Science Building, University of Kentucky, Lexington, KY 40546-0312, USA
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81
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Characterization of the morphology and genome of an Escherichia coli podovirus. Arch Virol 2014; 159:3249-56. [PMID: 25163858 DOI: 10.1007/s00705-014-2189-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 07/18/2014] [Indexed: 01/20/2023]
Abstract
Escherichia coli is an important opportunistic pathogen. It can cause sepsis and severe infection. The application of lytic bacteriophages to treat infectious diseases is an alternative to antibiotics. A lytic Escherichia coli phage, designated IME-EC2, was isolated from hospital sewage. Transmission electron microscopy revealed that IME-EC2 to be a member of the family Podoviridae. It had a 60-nm head and a 15-nm tail. Here, we present the complete genome sequence of this phage, which consists of 41,510 bp with an overall G+C content of 59.2 %. A total of 60 coding sequences (CDS) were identified, and the phage genome does not contain any tRNA genes. Forty percent of the unknown CDSs are unique to IME-EC2. This phage does not show significant similarity to other phages at the DNA level, which suggests that IME-EC2 could be a novel phage. One of the unique features identified in the IME-EC2 genome was a gene coding for a putative colanic-acid-degrading protein, which could allow the phage to degrade bacterial capsule and biofilms. Another unique feature is that IME-EC2 does not contain a terminase small subunit, which suggests that this phage may have a unique packaging mechanism. The present work provides novel information on phages and shows that this lytic phage or its products could be exploited to destroy bacterial biofilms and pathogenic E. coli.
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82
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Isolation and characterization of bacteriophages infecting nocardioforms in wastewater treatment plant. BIOTECHNOLOGY RESEARCH INTERNATIONAL 2014; 2014:151952. [PMID: 25140256 PMCID: PMC4129933 DOI: 10.1155/2014/151952] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 07/08/2014] [Indexed: 11/17/2022]
Abstract
Activated sludge plants (ASP) are associated with the stable foaming problem worldwide. Apart from the physical and chemical treatment methods, biological treatment method has been least explored and may prove to be a novel and ecofriendly approach to tackle the problem of stable foam formation. In ASP Nocardia species are commonly found and are one of the major causes for forming sticky and stable foam. This study describes the isolation and characterization of three Nocardia bacteriophages NOC1, NOC2, and NOC3 for the control of Nocardia species. The bacteriophages isolated in this study have shown promising results in controlling foam producing bacterial growth under laboratory conditions, suggesting that it may prove useful in the field as an alternative biocontrol agent to reduce the foaming problem. To the best of our knowledge to date no work has been published from India related to biological approach for the control of foaming.
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83
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Orruño M, Garaizabal I, Bravo Z, Parada C, Barcina I, Arana I. Mechanisms involved in Escherichia coli and Serratia marcescens removal during activated sludge wastewater treatment. Microbiologyopen 2014; 3:657-67. [PMID: 25044599 PMCID: PMC4234258 DOI: 10.1002/mbo3.196] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 06/06/2014] [Accepted: 06/17/2014] [Indexed: 11/10/2022] Open
Abstract
Wastewater treatment reduces environmental contamination by removing gross solids and mitigating the effects of pollution. Treatment also reduces the number of indicator organisms and pathogens. In this work, the fates of two coliform bacteria, Escherichia coli and Serratia marcescens, were analyzed in an activated sludge process to determine the main mechanisms involved in the reduction of pathogenic microorganisms during wastewater treatment. These bacteria, modified to express green fluorescent protein, were inoculated in an activated sludge unit and in batch systems containing wastewater. The results suggested that, among the different biological factors implied in bacterial removal, bacterivorous protozoa play a key role. Moreover, a representative number of bacteria persisted in the system as free-living or embedded cells, but their distribution into liquid or solid fractions varied depending on the bacterium tested, questioning the real value of bacterial indicators for the control of wastewater treatment process. Additionally, viable but nonculturable cells constituted an important part of the bacterial population adhered to solid fractions, what can be derived from the competition relationships with native bacteria, present in high densities in this environment. These facts, taken together, emphasize the need for reliable quantitative and qualitative analysis tools for the evaluation of pathogenic microbial composition in sludge, which could represent an undefined risk to public health and ecosystem functions when considering its recycling.
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Affiliation(s)
- Maite Orruño
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country UPV/EHU, Barrio Sarriena s/n, E-48940, Leioa, Spain
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84
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Lee YD, Kim JY, Park JH. Characteristics of coliphage ECP4 and potential use as a sanitizing agent for biocontrol of Escherichia coli O157:H7. Food Control 2013. [DOI: 10.1016/j.foodcont.2013.04.043] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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85
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Petrovski S, Seviour RJ, Tillett D. Genome sequence of the Nocardia bacteriophage NBR1. Arch Virol 2013; 159:167-73. [PMID: 23913189 DOI: 10.1007/s00705-013-1799-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 06/17/2013] [Indexed: 11/28/2022]
Abstract
We here characterize a novel bacteriophage (NBR1) that is lytic for Nocardia otitidiscaviarum and N. brasiliensis. NBR1 is a member of the family Siphoviridae and appears to have a structurally more complex tail than previously reported Siphoviridae phages. NBR1 has a linear genome of 46,140 bp and a sequence that appears novel when compared to those of other phage sequences in GenBank. Annotation of the genome reveals 68 putative open reading frames. The phage genome organization appears to be similar to other Siphoviridae phage genomes in that it has a modular arrangement.
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Affiliation(s)
- Steve Petrovski
- La Trobe Institute for Molecular Sciences, La Trobe University, Bendigo, Australia,
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86
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Dias RS, Eller MR, Duarte VS, Pereira ÂL, Silva CC, Mantovani HC, Oliveira LL, de A. M Silva E, De Paula SO. Use of phages against antibiotic-resistant Staphylococcus aureus isolated from bovine mastitis1. J Anim Sci 2013; 91:3930-9. [DOI: 10.2527/jas.2012-5884] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- R. S. Dias
- Laboratory of Molecular Immunovirology, Department of General Biology, Federal University of Viçosa, Viçosa, Brazil
| | - M. R. Eller
- Laboratory of Molecular Immunovirology, Department of General Biology, Federal University of Viçosa, Viçosa, Brazil
| | - V. S. Duarte
- Laboratory of Molecular Immunovirology, Department of General Biology, Federal University of Viçosa, Viçosa, Brazil
| | - Â. L. Pereira
- Laboratory of Molecular Immunovirology, Department of General Biology, Federal University of Viçosa, Viçosa, Brazil
| | - C. C. Silva
- Department of Microbiology, Federal University of Viçosa, Viçosa, Brazil
| | - H. C. Mantovani
- Laboratory of Anaerobic Microorganisms, Department of Microbiology, Federal University of Viçosa, Viçosa, Brazil
| | - L. L. Oliveira
- Laboratory of Molecular Immunovirology, Department of General Biology, Federal University of Viçosa, Viçosa, Brazil
| | - E. de A. M Silva
- Laboratory of Molecular Immunovirology, Department of General Biology, Federal University of Viçosa, Viçosa, Brazil
| | - S. O. De Paula
- Laboratory of Molecular Immunovirology, Department of General Biology, Federal University of Viçosa, Viçosa, Brazil
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87
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Kęsik-Szeloch A, Drulis-Kawa Z, Weber-Dąbrowska B, Kassner J, Majkowska-Skrobek G, Augustyniak D, Lusiak-Szelachowska M, Zaczek M, Górski A, Kropinski AM. Characterising the biology of novel lytic bacteriophages infecting multidrug resistant Klebsiella pneumoniae. Virol J 2013; 10:100. [PMID: 23537199 PMCID: PMC3620542 DOI: 10.1186/1743-422x-10-100] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 03/25/2013] [Indexed: 01/21/2023] Open
Abstract
Background Members of the genus Klebsiella are among the leading microbial pathogens associated with nosocomial infection. The increased incidence of antimicrobial resistance in these species has propelled the need for alternate/combination therapeutic regimens to aid clinical treatment. Bacteriophage therapy forms one of these alternate strategies. Methods Electron microscopy, burst size, host range, sensitivity of phage particles to temperature, chloroform, pH, and restriction digestion of phage DNA were used to characterize Klebsiella phages. Results and conclusions Of the 32 isolated phages eight belonged to the family Myoviridae, eight to the Siphoviridae whilst the remaining 16 belonged to the Podoviridae. The host range of these phages was characterised against 254 clinical Enterobacteriaceae strains including multidrug resistant Klebsiella isolates producing extended-spectrum beta-lactamases (ESBLs). Based on their lytic potential, six of the phages were further characterised for burst size, physicochemical properties and sensitivity to restriction endonuclease digestion. In addition, five were fully sequenced. Multiple phage-encoded host resistance mechanisms were identified. The Siphoviridae phage genomes (KP16 and KP36) contained low numbers of host restriction sites similar to the strategy found in T7-like phages (KP32). In addition, phage KP36 encoded its own DNA adenine methyltransferase. The φKMV-like KP34 phage was sensitive to all endonucleases used in this study. Dam methylation of KP34 DNA was detected although this was in the absence of an identifiable phage encoded methyltransferase. The Myoviridae phages KP15 and KP27 both carried Dam and Dcm methyltransferase genes and other anti-restriction mechanisms elucidated in previous studies. No other anti-restriction mechanisms were found, e.g. atypical nucleotides (hmC or glucosyl hmC), although Myoviridae phage KP27 encodes an unknown anti-restriction mechanism that needs further investigation.
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Affiliation(s)
- Agata Kęsik-Szeloch
- Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, Wroclaw, Poland
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88
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Al-Manasra AM, Al-Razem F. Cloning and expression of a new bacteriophage (SHPh) DNA ligase isolated from sewage. J Genet Eng Biotechnol 2012. [DOI: 10.1016/j.jgeb.2012.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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89
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Zhang Y, Hu Z. Combined treatment ofPseudomonas aeruginosabiofilms with bacteriophages and chlorine. Biotechnol Bioeng 2012; 110:286-95. [DOI: 10.1002/bit.24630] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 07/14/2012] [Accepted: 07/26/2012] [Indexed: 11/12/2022]
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90
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Singh A, Arutyunov D, Szymanski CM, Evoy S. Bacteriophage based probes for pathogen detection. Analyst 2012; 137:3405-21. [PMID: 22724121 DOI: 10.1039/c2an35371g] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Rapid and specific detection of pathogenic bacteria is important for the proper treatment, containment and prevention of human, animal and plant diseases. Identifying unique biological probes to achieve a high degree of specificity and minimize false positives has therefore garnered much interest in recent years. Bacteriophages are obligate intracellular parasites that subvert bacterial cell resources for their own multiplication and production of disseminative new virions, which repeat the cycle by binding specifically to the host surface receptors and injecting genetic material into the bacterial cells. The precision of host recognition in phages is imparted by the receptor binding proteins (RBPs) that are often located in the tail-spike or tail fiber protein assemblies of the virions. Phage host recognition specificity has been traditionally exploited for bacterial typing using laborious and time consuming bacterial growth assays. At the same time this feature makes phage virions or RBPs an excellent choice for the development of probes capable of selectively capturing bacteria on solid surfaces with subsequent quick and automatic detection of the binding event. This review focuses on the description of pathogen detection approaches based on immobilized phage virions as well as pure recombinant RBPs. Specific advantages of RBP-based molecular probes are also discussed.
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Affiliation(s)
- Amit Singh
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB T6G 2V4, Canada.
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91
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Abstract
Enterococcus faecalis is an important bacterium for use as a probiotic and is an opportunistic pathogen in human beings. The antibiotic resistance acquired by E. faecalis is restricted to antibiotics used in the clinical setting. While screening for alternative antibiotics for use against multidrug-resistant E. faecalis, we isolated a virulent enterococcal bacteriophage, SAP6, belonging to the family Siphoviridae. To our knowledge, this study is the first to report the complete genome sequence of bacteriophage SAP6, which might be used as a therapeutic agent in combination with alternative antibiotics for multidrug-resistant E. faecalis.
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92
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Rogers GB, Carroll MP, Bruce KD. Enhancing the utility of existing antibiotics by targeting bacterial behaviour? Br J Pharmacol 2012; 165:845-57. [PMID: 21864314 DOI: 10.1111/j.1476-5381.2011.01643.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The discovery of novel classes of antibiotics has slowed dramatically. This has occurred during a time when the appearance of resistant strains of bacteria has shown a substantial increase. Concern is therefore mounting over our ability to continue to treat infections in an effective manner using the antibiotics that are currently available. While ongoing efforts to discover new antibiotics are important, these must be coupled with strategies that aim to maintain as far as possible the spectrum of activity of existing antibiotics. In many instances, the resistance to antibiotics exhibited by bacteria in chronic infections is mediated not by direct resistance mechanisms, but by the adoption of modes of growth that confer reduced susceptibility. These include the formation of biofilms and the occurrence of subpopulations of 'persister' cells. As our understanding of these processes has increased, a number of new potential drug targets have been revealed. Here, advances in our ability to disrupt these systems that confer reduced susceptibility, and in turn increase the efficacy of antibiotic therapy, are discussed.
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Affiliation(s)
- Geraint B Rogers
- Molecular Microbiology Research Laboratory, Institute of Pharmaceutical Sciences, King's College London, London, UK.
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93
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Vítor JMB, Vale FF. Alternative therapies for Helicobacter pylori: probiotics and phytomedicine. ACTA ACUST UNITED AC 2012; 63:153-64. [PMID: 22077218 DOI: 10.1111/j.1574-695x.2011.00865.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Helicobacter pylori is a common human pathogen infecting about 30% of children and 60% of adults worldwide and is responsible for diseases such as gastritis, peptic ulcer and gastric cancer. Treatment against H. pylori is based on the use of antibiotics, but therapy failure can be higher than 20% and is essentially due to an increase in the prevalence of antibiotic-resistant bacteria, which has led to the search for alternative therapies. In this review, we discuss alternative therapies for H. pylori, mainly phytotherapy and probiotics. Probiotics are live organisms or produced substances that are orally administrated, usually in addition to conventional antibiotic therapy. They may modulate the human microbiota and promote health, prevent antibiotic side effects, stimulate the immune response and directly compete with pathogenic bacteria. Phytomedicine consists of the use of plant extracts as medicines or health-promoting agents, but in most cases the molecular mode of action of the active ingredients of these herbal extracts is unknown. Possible mechanisms include inhibition of H. pylori urease enzyme, disruption of bacterial cell membrane, and modulation of the host immune system. Other alternative therapies are also reviewed.
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Affiliation(s)
- Jorge M B Vítor
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
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94
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Genome sequences and characterization of the related Gordonia phages GTE5 and GRU1 and their use as potential biocontrol agents. Appl Environ Microbiol 2011; 78:42-7. [PMID: 22038604 DOI: 10.1128/aem.05584-11] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Activated sludge plants suffer frequently from the operational problem of stable foam formation on aerobic reactor surfaces, which can be difficult to prevent. Many foams are stabilized by mycolic acid-containing Actinobacteria, the mycolata. The in situ biocontrol of foaming using phages is an attractive strategy. We describe two polyvalent phages, GTE5 and GRU1, targeting Gordonia terrae and Gordonia rubrupertincta, respectively, isolated from activated sludge. Phage GRU1 also propagates on Nocardia nova. Both phages belong to the family Siphoviridae and have similar-size icosahedral heads that encapsulate double-stranded DNA genomes (∼65 kb). Their genome sequences are similar to each other but markedly different from those of other sequenced phages. Both are arranged in a modular fashion. These phages can reduce or eliminate foam formation by their host cells under laboratory conditions.
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95
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Hao X, Wang Q, Cao Y, van Loosdrecht MCM. Evaluating sludge minimization caused by predation and viral infection based on the extended activated sludge model No. 2d. WATER RESEARCH 2011; 45:5130-5140. [PMID: 21821271 DOI: 10.1016/j.watres.2011.07.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 07/11/2011] [Accepted: 07/12/2011] [Indexed: 05/31/2023]
Abstract
The Activated Sludge Model No. 2d (ASM2d) was extended to incorporate the processes of both predation and viral infection. The extended model was used to evaluate the contributions of predation and viral infection to sludge minimization in a sequencing batch reactor (SBR) system enriching polyphosphate-accumulating organisms (PAOs). Three individual decay processes formulated according to the general model rules were used in the extended model. The model was firstly calibrated and validated by different experimental results. It was used to evaluate the potential extent of predation and viral infection on sludge minimization. Simulations indicate that predation contributes roughly two times more to sludge minimization than viral infection in the SBR system enriching PAOs. The sensitivity analyses of the selected key parameters reveal that there are thresholds on both predation and viral infection rates, if they are too large a minimal sludge retention time is obtained and the effluent quality is deteriorating. Due to the thresholds, the contributions of predation and viral infection to sludge minimization are limited to a maximal extent of about 21% and 9%, respectively. However, it should be noted that the parameters concerning predation and viral infection were not calibrated separately by independent experiment in our study due to the lack of an effective method, especially for the parameters regarding viral infection. Therefore, it is essential to better evaluate these parameters in the future.
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Affiliation(s)
- Xiaodi Hao
- Key Laboratory of Urban Stormwater System and Water Environment/R & D Centre for Sustainable Environmental Biotechnology, Beijing University of Civil Engineering and Architecture, Ministry of Education, 1 Zhanlanguan Road, Xicheng District, Beijing 100044, PR China.
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96
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Genomic sequence analysis of virulent Cronobacter sakazakii bacteriophage ES2. Arch Virol 2011; 156:2105-8. [PMID: 21931999 DOI: 10.1007/s00705-011-1096-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Accepted: 08/21/2011] [Indexed: 10/17/2022]
Abstract
Virulent Cronobacter sakazakii bacteriophage ES2 was isolated from swine fecal samples, and the genome sequence by was determined GS-Flx. Bacteriophage ES2 had a double-stranded DNA genome with a length of 22,162 bp and a G+C content of 50.08%. The morphological characteristics under a transmission electron microscope indicated that bacteriophage ES2 belongs to the family Myoviridae. The structural proteins, including the phage coat protein, were separated by SDS-PAGE and identified by Q-TOF. Bioinformatics analysis of the bacteriophage genome revealed 30 putative open reading frames (ORFs). The predicted protein products of the ORFs were determined and described. To our knowledge, the genome of the newly isolated bacteriophage ES2 was not significantly similar to that of any previously reported bacteriophages of members of the family Enterobacteriaceae.
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97
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Prevention of Gordonia and Nocardia stabilized foam formation by using bacteriophage GTE7. Appl Environ Microbiol 2011; 77:7864-7. [PMID: 21926218 DOI: 10.1128/aem.05692-11] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Most activated sludge treatment plants suffer from the presence of foams on the surfaces of their aeration reactors. These are often stabilized by hydrophobic mycolic acid-synthesizing actinobacterial species. A polyvalent Siphoviridae phage, GTE7, which lysed several Gordonia and Nocardia species, is described here. Its genome has a modular structure similar to that described for Rhodococcus phage ReqiDocB7. In laboratory-scale experiments, we showed that GTE7 prevents stabilization of foams by these Gordonia and Nocardia species.
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98
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Rosenberg E, Bittan-Banin G, Sharon G, Shon A, Hershko G, Levy I, Ron EZ. The phage-driven microbial loop in petroleum bioremediation. Microb Biotechnol 2011; 3:467-72. [PMID: 21255344 PMCID: PMC3815812 DOI: 10.1111/j.1751-7915.2010.00182.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
During the drilling process and transport of crude oil, water mixes with the petroleum. At oil terminals, the water settles to the bottom of storage tanks. This drainage water is contaminated with emulsified oil and water‐soluble hydrocarbons and must be treated before it can be released into the environment. In this study, we tested the efficiency of a continuous flow, two‐stage bioreactor for treating drainage water from an Israeli oil terminal. The bioreactor removed all of the ammonia, 93% of the sulfide and converted 90% of the total organic carbon (TOC) into carbon dioxide. SYBR Gold staining indicated that reactor 1 contained 1.7 × 108 bacteria and 3.7 × 108 phages per millilitre, and reactor 2 contained 1.3 × 108 bacteria and 1.7 × 109 phages per millilitre. The unexpectedly high mineralization of TOC and high concentration of phage in reactor 2 support the concept of a phage‐driven microbial loop in the bioremediation of the drainage water. In general, application of this concept in bioremediation of contaminated water has the potential to increase the efficiency of processes.
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Affiliation(s)
- Eugene Rosenberg
- Department of Molecular Microbiology & Biotechnology, Tel Aviv University, Ramat Aviv, Israel.
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99
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Characterization of the genome of the polyvalent lytic bacteriophage GTE2, which has potential for biocontrol of Gordonia-, Rhodococcus-, and Nocardia-stabilized foams in activated sludge plants. Appl Environ Microbiol 2011; 77:3923-9. [PMID: 21498753 DOI: 10.1128/aem.00025-11] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Hydrophobic Actinobacteria are commonly associated with the stabilization of foams in activated sludge systems. One possible attractive approach to control these foam-stabilizing organisms is the use of specific bacteriophages. We describe the genome characterization of a novel polyvalent DNA phage, GTE2, isolated from activated sludge. This phage is lytic for Gordonia terrae, Rhodococcus globerulus, Rhodococcus erythropolis, Rhodococcus erythropolis, Nocardia otitidiscaviarum, and Nocardia brasiliensis. Phage GTE2 belongs to the family Siphoviridae, possessing a characteristic icosahedral head encapsulating a double-stranded DNA linear genome (45,530 bp) having 10-bp 3'-protruding cohesive ends. The genome sequence is 98% unique at the DNA level and contains 57 putative genes. The genome can be divided into two components, where the first is modular and encodes phage structural proteins and lysis genes. The second is not modular, and the genes harbored there are involved in DNA replication, repair, and metabolism. Some have no known function. GTE2 shows promising results in controlling stable foam production by its host bacteria under laboratory conditions, suggesting that it may prove useful in the field as a biocontrol agent.
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100
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Shapiro OH, Kushmaro A. Bacteriophage ecology in environmental biotechnology processes. Curr Opin Biotechnol 2011; 22:449-55. [PMID: 21354780 DOI: 10.1016/j.copbio.2011.01.012] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 01/17/2011] [Accepted: 01/28/2011] [Indexed: 11/18/2022]
Abstract
Heterotrophic bacteria are an integral part of any environmental biotechnology process (EBP). Therefore, factors controlling bacterial abundance, activity, and community composition are central to the understanding of such processes. Among these factors, top-down control by bacteriophage predation has so far received very limited attention. With over 10(8) particles per ml, phage appear to be the most numerous biological entities in EBP. Phage populations in EBP appear to be highly dynamic and to correlate with the population dynamics of their hosts and genomic evidence suggests bacteria evolve to avoid phage predation. Clearly, there is much to learn regarding bacteriophage in EBP before we can truly understand the microbial ecology of these globally important systems.
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Affiliation(s)
- Orr H Shapiro
- Ben Gurion University of the Negev, Biotechnology Engineering, POb 653, Beer sheva 84105, Israel.
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