1
|
Maciag T, Kozieł E, Otulak-Kozieł K, Jafra S, Czajkowski R. Looking for Resistance to Soft Rot Disease of Potatoes Facing Environmental Hypoxia. Int J Mol Sci 2024; 25:3757. [PMID: 38612570 PMCID: PMC11011919 DOI: 10.3390/ijms25073757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/21/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
Plants are exposed to various stressors, including pathogens, requiring specific environmental conditions to provoke/induce plant disease. This phenomenon is called the "disease triangle" and is directly connected with a particular plant-pathogen interaction. Only a virulent pathogen interacting with a susceptible plant cultivar will lead to disease under specific environmental conditions. This may seem difficult to accomplish, but soft rot Pectobacteriaceae (SRPs) is a group virulent of pathogenic bacteria with a broad host range. Additionally, waterlogging (and, resulting from it, hypoxia), which is becoming a frequent problem in farming, is a favoring condition for this group of pathogens. Waterlogging by itself is an important source of abiotic stress for plants due to lowered gas exchange. Therefore, plants have evolved an ethylene-based system for hypoxia sensing. Plant response is coordinated by hormonal changes which induce metabolic and physiological adjustment to the environmental conditions. Wetland species such as rice (Oryza sativa L.), and bittersweet nightshade (Solanum dulcamara L.) have developed adaptations enabling them to withstand prolonged periods of decreased oxygen availability. On the other hand, potato (Solanum tuberosum L.), although able to sense and response to hypoxia, is sensitive to this environmental stress. This situation is exploited by SRPs which in response to hypoxia induce the production of virulence factors with the use of cyclic diguanylate (c-di-GMP). Potato tubers in turn reduce their defenses to preserve energy to prevent the negative effects of reactive oxygen species and acidification, making them prone to soft rot disease. To reduce the losses caused by the soft rot disease we need sensitive and reliable methods for the detection of the pathogens, to isolate infected plant material. However, due to the high prevalence of SRPs in the environment, we also need to create new potato varieties more resistant to the disease. To reach that goal, we can look to wild potatoes and other Solanum species for mechanisms of resistance to waterlogging. Potato resistance can also be aided by beneficial microorganisms which can induce the plant's natural defenses to bacterial infections but also waterlogging. However, most of the known plant-beneficial microorganisms suffer from hypoxia and can be outcompeted by plant pathogens. Therefore, it is important to look for microorganisms that can withstand hypoxia or alleviate its effects on the plant, e.g., by improving soil structure. Therefore, this review aims to present crucial elements of potato response to hypoxia and SRP infection and future outlooks for the prevention of soft rot disease considering the influence of environmental conditions.
Collapse
Affiliation(s)
- Tomasz Maciag
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences—SGGW, Nowoursynowska Street 159, 02-776 Warsaw, Poland;
| | - Edmund Kozieł
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences—SGGW, Nowoursynowska Street 159, 02-776 Warsaw, Poland;
| | - Katarzyna Otulak-Kozieł
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences—SGGW, Nowoursynowska Street 159, 02-776 Warsaw, Poland;
| | - Sylwia Jafra
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Antoniego Abrahama Street 58, 80-307 Gdansk, Poland;
| | - Robert Czajkowski
- Laboratory of Biologically Active Compounds, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Antoniego Abrahama Street 58, 80-307 Gdansk, Poland;
| |
Collapse
|
2
|
Sanmukh SG, Admella J, Moya-Andérico L, Fehér T, Arévalo-Jaimes BV, Blanco-Cabra N, Torrents E. Accessing the In Vivo Efficiency of Clinically Isolated Phages against Uropathogenic and Invasive Biofilm-Forming Escherichia coli Strains for Phage Therapy. Cells 2023; 12:cells12030344. [PMID: 36766686 PMCID: PMC9913540 DOI: 10.3390/cells12030344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/09/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
Escherichia coli is one of the most common members of the intestinal microbiota. Many of its strains are associated with various inflammatory infections, including urinary or gut infections, especially when displaying antibiotic resistance or in patients with suppressed immune systems. According to recent reports, the biofilm-forming potential of E. coli is a crucial factor for its increased resistance against antibiotics. To overcome the limitations of using antibiotics against resistant E. coli strains, the world is turning once more towards bacteriophage therapy, which is becoming a promising candidate amongst the current personalized approaches to target different bacterial infections. Although matured and persistent biofilms pose a serious challenge to phage therapy, they can still become an effective alternative to antibiotic treatment. Here, we assess the efficiency of clinically isolated phages in phage therapy against representative clinical uropathogenic and invasive biofilm-forming E. coli strains. Our results demonstrate that irrespective of host specificity, bacteriophages producing clear plaques with a high burst size, and exhibiting depolymerizing activity, are good candidates against biofilm-producing E. coli pathogens as verified from our in vitro and in vivo experiments using Galleria mellonella where survival was significantly increased for phage-therapy-treated larvae.
Collapse
Affiliation(s)
- Swapnil Ganesh Sanmukh
- Bacterial Infections: Antimicrobial Therapies Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 15-21, 08028 Barcelona, Spain
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Eötvös Lóránd Research Network, H-6726 Szeged, Hungary
- Correspondence: or (S.G.S.); or (E.T.)
| | - Joana Admella
- Bacterial Infections: Antimicrobial Therapies Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 15-21, 08028 Barcelona, Spain
| | - Laura Moya-Andérico
- Bacterial Infections: Antimicrobial Therapies Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 15-21, 08028 Barcelona, Spain
| | - Tamás Fehér
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Eötvös Lóránd Research Network, H-6726 Szeged, Hungary
| | - Betsy Verónica Arévalo-Jaimes
- Bacterial Infections: Antimicrobial Therapies Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 15-21, 08028 Barcelona, Spain
| | - Núria Blanco-Cabra
- Bacterial Infections: Antimicrobial Therapies Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 15-21, 08028 Barcelona, Spain
- Microbiology Section, Department of Genetics, Microbiology, and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Eduard Torrents
- Bacterial Infections: Antimicrobial Therapies Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 15-21, 08028 Barcelona, Spain
- Microbiology Section, Department of Genetics, Microbiology, and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
- Correspondence: or (S.G.S.); or (E.T.)
| |
Collapse
|
3
|
Naligama KN, Halmillawewa AP. Pectobacterium carotovorum Phage vB_PcaM_P7_Pc Is a New Member of the Genus Certrevirus. Microbiol Spectr 2022; 10:e0312622. [PMID: 36346243 PMCID: PMC9769974 DOI: 10.1128/spectrum.03126-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/14/2022] [Indexed: 11/09/2022] Open
Abstract
Pectobacterium carotovorum is an economically important phytopathogen and has been identified as the major causative agent of bacterial soft rot in carrots. Control of this phytopathogen is vital to minimizing carrot harvest losses. As fully efficient control measures to successfully avoid the disease are unavailable, the phage-mediated biocontrol of the pathogen has recently gained scientific attention. In this study, we present a comprehensive characterization of the P. carotovorum phage vB_PcaM_P7_Pc (abbreviated as P7_Pc) that was isolated from infected carrot samples with characteristic soft rot symptoms, which were obtained from storage facilities at market places in Gampaha District, Sri Lanka. P7_Pc is a myovirus, and it exhibits growth characteristics of an exclusively lytic life cycle. It showed visible lysis against four of the tested P. carotovorum strains and one Pectobacterium aroidearum strain. This phage also showed a longer latent period (125 min) than other related phages; however, this did not affect its high phage titter (>1010 PFU/mL). The final assembled genome of P7_Pc is 147,299 bp in length with a G+C content of 50.34%. Of the 298 predicted open reading frames (ORFs) of the genome of P7_Pc, putative functions were assigned to 53 ORFs. Seven tRNA-coding genes were predicted in the genome, while the genome lacked any major genes coding for lysogeny-related products, confirming its virulent nature. The P7_Pc genome shares 96.12% and 95.74% average nucleotide identities with Cronobacter phages CR8 and PBES02, respectively. Phylogenetic and phylogenomic analyses of the genome revealed that P7_Pc clusters well within the clade with the members representing the genus Certrevirus. Currently, there are only 4 characterized Pectobacterium phages (P. atrosepticum phages phiTE and CB7 and Pectobacterium phages DU_PP_I and DU_PP_IV) that are classified under the genus, making the phage P7_Pc the first reported member of the genus isolated using the host bacterium P. carotovorum. The results of this study provide a detailed characterization of the phage P7_Pc, enabling its careful classification into the genus Certrevirus. The knowledge gathered on the phage based on the shared biology of the genus will further aid in the future selection of phage P7_Pc as a biocontrol agent. IMPORTANCE Bacterial soft rot disease, caused by Pectobacterium spp., can lead to significant losses in carrot yields. As current control measures involving the use of chemicals or antibiotics are not recommended in many countries, bacteriophage-mediated biocontrol strategies are being explored for the successful control of these phytopathogens. The successful implementation of such biocontrol strategies relies heavily upon the proper understanding of the growth characteristics and genomic properties of the phage. Further, the selection of taxonomically different phages for the formulation of phage cocktails in biocontrol applications is critical to combat potential bacterial resistance development. This study was conducted to carefully characterize and resolve the phylogenetic placement of the P. carotovorum phage vB_PcaM_P7_Pc by using its biological and genomic properties. Phage P7_Pc has a myovirus morphotype with an exclusively lytic life cycle, and the absence of genes related to lysogeny, toxin production, and antibiotic resistance in its genome confirmed its suitability to be used in environmental applications. Furthermore, P7_Pc is classified under the genus Certrevirus, making it the first reported phage of the genus of the host species, P. carotovorum.
Collapse
Affiliation(s)
- Kishani N. Naligama
- Department of Microbiology, Faculty of Science, University of Kelaniya, Kelaniya, Sri Lanka
| | | |
Collapse
|
4
|
Pectobacterium versatile Bacteriophage Possum: A Complex Polysaccharide-Deacetylating Tail Fiber as a Tool for Host Recognition in Pectobacterial Schitoviridae. Int J Mol Sci 2022; 23:ijms231911043. [PMID: 36232343 PMCID: PMC9569702 DOI: 10.3390/ijms231911043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/11/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Novel, closely related phages Possum and Horatius infect Pectobacterium versatile, a phytopathogen causing soft rot in potatoes and other essential plants. Their properties and genomic composition define them as N4-like bacteriophages of the genus Cbunavirus, a part of a recently formed family Schitoviridae. It is proposed that the adsorption apparatus of these phages consists of tail fibers connected to the virion through an adapter protein. Tail fibers possess an enzymatic domain. Phage Possum uses it to deacetylate O-polysaccharide on the surface of the host strain to provide viral attachment. Such an infection mechanism is supposed to be common for all Cbunavirus phages and this feature should be considered when designing cocktails for phage control of soft rot.
Collapse
|
5
|
Mousa S, Magdy M, Xiong D, Nyaruabaa R, Rizk SM, Yu J, Wei H. Microbial Profiling of Potato-Associated Rhizosphere Bacteria under Bacteriophage Therapy. Antibiotics (Basel) 2022; 11:antibiotics11081117. [PMID: 36009986 PMCID: PMC9405460 DOI: 10.3390/antibiotics11081117] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022] Open
Abstract
Potato soft rot and wilt are economically problematic diseases due to the lack of effective bactericides. Bacteriophages have been studied as a novel and environment-friendly alternative to control plant diseases. However, few experiments have been conducted to study the changes in plants and soil microbiomes after bacteriophage therapy. In this study, rhizosphere microbiomes were examined after potatoes were separately infected with three bacteria (Ralstonia solanacearum, Pectobacterium carotovorum, Pectobacterium atrosepticum) and subsequently treated with a single phage or a phage cocktail consisting of three phages each. Results showed that using the phage cocktails had better efficacy in reducing the disease incidence and disease symptoms’ levels when compared to the application of a single phage under greenhouse conditions. At the same time, the rhizosphere microbiota in the soil was affected by the changes in micro-organisms’ richness and counts. In conclusion, the explicit phage mixers have the potential to control plant pathogenic bacteria and cause changes in the rhizosphere bacteria, but not affect the beneficial rhizosphere microbes.
Collapse
Affiliation(s)
- Samar Mousa
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- International College, University of Chinese Academy of Sciences, Beijing 101408, China
- Agricultural Botany Department, Faculty of Agriculture, Suez Canal University, Ismailia 41522, Egypt
| | - Mahmoud Magdy
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
| | - Dongyan Xiong
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Raphael Nyaruabaa
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- International College, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Samah Mohamed Rizk
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
| | - Junping Yu
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Hongping Wei
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- Correspondence:
| |
Collapse
|
6
|
Farooq T, Hussain MD, Shakeel MT, Tariqjaveed M, Aslam MN, Naqvi SAH, Amjad R, Tang Y, She X, He Z. Deploying Viruses against Phytobacteria: Potential Use of Phage Cocktails as a Multifaceted Approach to Combat Resistant Bacterial Plant Pathogens. Viruses 2022; 14:171. [PMID: 35215763 PMCID: PMC8879233 DOI: 10.3390/v14020171] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/13/2022] [Accepted: 01/14/2022] [Indexed: 02/05/2023] Open
Abstract
Plants in nature are under the persistent intimidation of severe microbial diseases, threatening a sustainable food production system. Plant-bacterial pathogens are a major concern in the contemporary era, resulting in reduced plant growth and productivity. Plant antibiotics and chemical-based bactericides have been extensively used to evade plant bacterial diseases. To counteract this pressure, bacteria have evolved an array of resistance mechanisms, including innate and adaptive immune systems. The emergence of resistant bacteria and detrimental consequences of antimicrobial compounds on the environment and human health, accentuates the development of an alternative disease evacuation strategy. The phage cocktail therapy is a multidimensional approach effectively employed for the biocontrol of diverse resistant bacterial infections without affecting the fauna and flora. Phages engage a diverse set of counter defense strategies to undermine wide-ranging anti-phage defense mechanisms of bacterial pathogens. Microbial ecology, evolution, and dynamics of the interactions between phage and plant-bacterial pathogens lead to the engineering of robust phage cocktail therapeutics for the mitigation of devastating phytobacterial diseases. In this review, we highlight the concrete and fundamental determinants in the development and application of phage cocktails and their underlying mechanism, combating resistant plant-bacterial pathogens. Additionally, we provide recent advances in the use of phage cocktail therapy against phytobacteria for the biocontrol of devastating plant diseases.
Collapse
Affiliation(s)
- Tahir Farooq
- Plant Protection Research Institute and Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (T.F.); (Y.T.)
| | - Muhammad Dilshad Hussain
- State Key Laboratory for Agro-Biotechnology, and Ministry of Agriculture and Rural Affairs, Key Laboratory for Pest Monitoring and Green Management, Department of Plant Pathology, China Agricultural University, Beijing 100193, China;
| | - Muhammad Taimoor Shakeel
- Department of Plant Pathology, Faculty of Agriculture & Environment, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan; (M.T.S.); (M.N.A.)
| | - Muhammad Tariqjaveed
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China;
| | - Muhammad Naveed Aslam
- Department of Plant Pathology, Faculty of Agriculture & Environment, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan; (M.T.S.); (M.N.A.)
| | - Syed Atif Hasan Naqvi
- Department of Plant Pathology, Faculty of Agriculture Science and Technology, Bahauddin Zakariya University, Multan 60800, Pakistan;
| | - Rizwa Amjad
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan;
| | - Yafei Tang
- Plant Protection Research Institute and Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (T.F.); (Y.T.)
| | - Xiaoman She
- Plant Protection Research Institute and Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (T.F.); (Y.T.)
| | - Zifu He
- Plant Protection Research Institute and Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (T.F.); (Y.T.)
| |
Collapse
|
7
|
Nwokolo NL, Enebe MC. Shotgun metagenomics evaluation of soil fertilization effect on the rhizosphere viral community of maize plants. Antonie van Leeuwenhoek 2021; 115:69-78. [PMID: 34762236 DOI: 10.1007/s10482-021-01679-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 10/19/2021] [Indexed: 11/30/2022]
Abstract
The need for sustainability in food supply has led to progressive increase in soil nutrient enrichment. Fertilizer application effects both biological and abiotic processes in the soil, of which the bacterial community that support viral multiplication are equally influenced. Nevertheless, little is known on the effect of soil fertilization on the Soil viral community composition and dynamics. In this study, we evaluated the influence of soil fertilization on the maize rhizosphere viral community growing in Luvisolic soil. The highest abundance of bacteriophages were detected in soil treated with 8 tons/ha compost manure (Cp8), 60 kg/ha inorganic fertilizer (N1), 4 tons/ha compost manure (Cp4) and the unfertilized control (Cn0). Our result showed higher relative abundance of Myoviridae, Podoviridae and Siphoviridae in 8 tons/ha organic manure (Cp8) fertilized compared to others. While Inoviridae and Microviridae were the most relative abundant phage families in 4 tons/ha organic manure (Cp4) fertilized soil. This demonstrate that soil fertilization with organic manure increases the abundance and diversity of viruses in the soil due to its soil conditioning effects.
Collapse
Affiliation(s)
| | - Matthew Chekwube Enebe
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa.
| |
Collapse
|
8
|
Bonilla E, Costa AR, van den Berg DF, van Rossum T, Hagedoorn S, Walinga H, Xiao M, Song W, Haas PJ, Nobrega FL, Brouns SJJ. Genomic characterization of four novel bacteriophages infecting the clinical pathogen Klebsiella pneumoniae. DNA Res 2021; 28:6352498. [PMID: 34390569 PMCID: PMC8386662 DOI: 10.1093/dnares/dsab013] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 08/12/2021] [Indexed: 12/19/2022] Open
Abstract
Bacteriophages are an invaluable source of novel genetic diversity. Sequencing of phage genomes can reveal new proteins with potential uses as biotechnological and medical tools, and help unravel the diversity of biological mechanisms employed by phages to take over the host during viral infection. Aiming to expand the available collection of phage genomes, we have isolated, sequenced, and assembled the genome sequences of four phages that infect the clinical pathogen Klebsiella pneumoniae: vB_KpnP_FBKp16, vB_KpnP_FBKp27, vB_KpnM_FBKp34, and Jumbo phage vB_KpnM_FBKp24. The four phages show very low (0–13%) identity to genomic phage sequences deposited in the GenBank database. Three of the four phages encode tRNAs and have a GC content very dissimilar to that of the host. Importantly, the genome sequences of the phages reveal potentially novel DNA packaging mechanisms as well as distinct clades of tubulin spindle and nucleus shell proteins that some phages use to compartmentalize viral replication. Overall, this study contributes to uncovering previously unknown virus diversity, and provides novel candidates for phage therapy applications against antibiotic-resistant K. pneumoniae infections.
Collapse
Affiliation(s)
- Estrada Bonilla
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands.,Kavli Institute of Nanoscience, Delft, The Netherlands.,Fagenbank, Delft, The Netherlands
| | - Ana Rita Costa
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands.,Kavli Institute of Nanoscience, Delft, The Netherlands.,Fagenbank, Delft, The Netherlands
| | - Daan F van den Berg
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands.,Kavli Institute of Nanoscience, Delft, The Netherlands
| | - Teunke van Rossum
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands.,Kavli Institute of Nanoscience, Delft, The Netherlands.,Fagenbank, Delft, The Netherlands
| | - Stefan Hagedoorn
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands
| | - Hielke Walinga
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands
| | - Minfeng Xiao
- BGI-Shenzhen, Shenzhen 518083, China.,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
| | - Wenchen Song
- BGI-Shenzhen, Shenzhen 518083, China.,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
| | - Pieter-Jan Haas
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Franklin L Nobrega
- Fagenbank, Delft, The Netherlands.,School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK
| | - Stan J J Brouns
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands.,Kavli Institute of Nanoscience, Delft, The Netherlands.,Fagenbank, Delft, The Netherlands
| |
Collapse
|
9
|
Miroshnikov KA, Evseev PV, Lukianova AA, Ignatov AN. Tailed Lytic Bacteriophages of Soft Rot Pectobacteriaceae. Microorganisms 2021; 9:1819. [PMID: 34576713 PMCID: PMC8472413 DOI: 10.3390/microorganisms9091819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 02/07/2023] Open
Abstract
The study of the ecological and evolutionary traits of Soft Rot Pectobacteriaceae (SRP) comprising genera Pectobacterium and Dickeya often involves bacterial viruses (bacteriophages). Bacteriophages are considered to be a prospective tool for the ecologically safe and highly specific protection of plants and harvests from bacterial diseases. Information concerning bacteriophages has been growing rapidly in recent years, and this has included new genomics-based principles of taxonomic distribution. In this review, we summarise the data on phages infecting Pectobacterium and Dickeya that are available in publications and genomic databases. The analysis highlights not only major genomic properties that assign phages to taxonomic families and genera, but also the features that make them potentially suitable for phage control applications. Specifically, there is a discussion of the molecular mechanisms of receptor recognition by the phages and problems concerning the evolution of phage-resistant mutants.
Collapse
Affiliation(s)
- Konstantin A Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
- Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Str., 49, 127434 Moscow, Russia
| | - Peter V Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
| | - Anna A Lukianova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
- Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Str., 49, 127434 Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory, 1, bldg. 12, 119234 Moscow, Russia
| | - Alexander N Ignatov
- Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Str., 49, 127434 Moscow, Russia
- Agrobiotechnology Department, Agrarian and Technological Institute, RUDN University, Miklukho-Maklaya Str., 6, 117198 Moscow, Russia
| |
Collapse
|
10
|
Bartnik P, Jafra S, Narajczyk M, Czaplewska P, Czajkowski R. Pectobacterium parmentieri SCC 3193 Mutants with Altered Synthesis of Cell Surface Polysaccharides Are Resistant to N4-Like Lytic Bacteriophage ϕA38 (vB_Ppp_A38) but Express Decreased Virulence in Potato ( Solanum tuberosum L.) Plants. Int J Mol Sci 2021; 22:7346. [PMID: 34298965 PMCID: PMC8304393 DOI: 10.3390/ijms22147346] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/02/2021] [Accepted: 07/06/2021] [Indexed: 01/15/2023] Open
Abstract
Pectobacterium parmentieri is a Gram-negative plant-pathogenic bacterium able to infect potato (Solanum tuberosum L.). Little is known about lytic bacteriophages infecting P. parmentieri and how phage-resistance influences the environmental fitness and virulence of this species. A lytic phage vB_Ppp_A38 (ϕA38) has been previously isolated and characterized as a potential biological control agent for the management of P. parmentieri. In this study, seven P. parmentieri SCC 3193 Tn5 mutants were identified that exhibited resistance to infection caused by vB_Ppp_A38 (ϕA38). The genes disrupted in these seven mutants encoded proteins involved in the assembly of O-antigen, sugar metabolism, and the production of bacterial capsule exopolysaccharides. The potential of A38-resistant P. parmentieri mutants for plant colonization and pathogenicity as well as other phenotypes expected to contribute to the ecological fitness of P. parmentieri, including growth rate, use of carbon and nitrogen sources, production of pectinolytic enzymes, proteases, cellulases, and siderophores, swimming and swarming motility, presence of capsule and flagella as well as the ability to form biofilm were assessed. Compared to the wild-type P. parmentieri strain, all phage-resistant mutants exhibited a reduced ability to colonize and to cause symptoms in growing potato (S. tuberosum L.) plants. The implications of bacteriophage resistance on the ecological fitness of P. parmentieri are discussed.
Collapse
Affiliation(s)
- Przemyslaw Bartnik
- Laboratory of Biologically Active Compounds, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Antoniego Abrahama 58, 80-307 Gdansk, Poland;
| | - Sylwia Jafra
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Antoniego Abrahama 58, 80-307 Gdansk, Poland;
| | - Magdalena Narajczyk
- Laboratory of Electron Microscopy, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland;
| | - Paulina Czaplewska
- Laboratory of Mass Spectrometry-Core Facility Laboratories, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Antoniego Abrahama 58, 80-307 Gdansk, Poland;
| | - Robert Czajkowski
- Laboratory of Biologically Active Compounds, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Antoniego Abrahama 58, 80-307 Gdansk, Poland;
| |
Collapse
|
11
|
Phages in Food Industry Biocontrol and Bioremediation. Antibiotics (Basel) 2021; 10:antibiotics10070786. [PMID: 34203362 PMCID: PMC8300737 DOI: 10.3390/antibiotics10070786] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 12/25/2022] Open
Abstract
Bacteriophages are ubiquitous in nature and their use is a current promising alternative in biological control. Multidrug resistant (MDR) bacterial strains are present in the livestock industry and phages are attractive candidates to eliminate them and their biofilms. This alternative therapy also reduces the non-desirable effects produced by chemicals on food. The World Health Organization (WHO) estimates that around 420,000 people die due to a foodborne illness annually, suggesting that an improvement in food biocontrol is desirable. This review summarizes relevant studies of phage use in biocontrol focusing on treatments in live animals, plants, surfaces, foods, wastewaters and bioremediation.
Collapse
|
12
|
Cristobal-Cueto P, García-Quintanilla A, Esteban J, García-Quintanilla M. Phages in Food Industry Biocontrol and Bioremediation. Antibiotics (Basel) 2021; 10:antibiotics10070786. [PMID: 34203362 DOI: 10.3390/antibiotic6as10070786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 05/28/2023] Open
Abstract
Bacteriophages are ubiquitous in nature and their use is a current promising alternative in biological control. Multidrug resistant (MDR) bacterial strains are present in the livestock industry and phages are attractive candidates to eliminate them and their biofilms. This alternative therapy also reduces the non-desirable effects produced by chemicals on food. The World Health Organization (WHO) estimates that around 420,000 people die due to a foodborne illness annually, suggesting that an improvement in food biocontrol is desirable. This review summarizes relevant studies of phage use in biocontrol focusing on treatments in live animals, plants, surfaces, foods, wastewaters and bioremediation.
Collapse
Affiliation(s)
- Pablo Cristobal-Cueto
- Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, Av. Reyes Católicos, 2, 28040 Madrid, Spain
| | - Alberto García-Quintanilla
- Department of Biochemistry and Molecular Biology, School of Pharmacy, University of Seville, Calle Profesor García Gonzalez, 2, 41012 Seville, Spain
| | - Jaime Esteban
- Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, Av. Reyes Católicos, 2, 28040 Madrid, Spain
| | | |
Collapse
|
13
|
Alanin KWS, Junco LMF, Jørgensen JB, Nielsen TK, Rasmussen MA, Kot W, Hansen LH. Metaviromes Reveal the Dynamics of Pseudomonas Host-Specific Phages Cultured and Uncultured by Plaque Assay. Viruses 2021; 13:959. [PMID: 34064231 PMCID: PMC8224292 DOI: 10.3390/v13060959] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/14/2021] [Accepted: 05/18/2021] [Indexed: 12/17/2022] Open
Abstract
Isolating single phages using plaque assays is a laborious and time-consuming process. Whether single isolated phages are the most lyse-effective, the most abundant in viromes, or those with the highest ability to make plaques in solid media is not well known. With the increasing accessibility of high-throughput sequencing, metaviromics is often used to describe viruses in environmental samples. By extracting and sequencing metaviromes from organic waste with and without exposure to a host-of-interest, we show a host-related phage community's shift, as well as identify the most enriched phages. Moreover, we isolated plaque-forming single phages using the same virome-host matrix to observe how enrichments in liquid media correspond to the metaviromic data. In this study, we observed a significant shift (p = 0.015) of the 47 identified putative Pseudomonas phages with a minimum twofold change above zero in read abundance when adding a Pseudomonas syringae DC3000 host. Surprisingly, it appears that only two out of five plaque-forming phages from the same organic waste sample, targeting the Pseudomonas strain, were highly abundant in the metavirome, while the other three were almost absent despite host exposure. Lastly, our sequencing results highlight how long reads from Oxford Nanopore elevates the assembly quality of metaviromes, compared to short reads alone.
Collapse
Affiliation(s)
- Katrine Wacenius Skov Alanin
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; (K.W.S.A.); (L.M.F.J.); (J.B.J.); (T.K.N.)
- Department of Environmental Science, Aarhus University, 4000 Roskilde, Denmark
| | - Laura Milena Forero Junco
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; (K.W.S.A.); (L.M.F.J.); (J.B.J.); (T.K.N.)
| | - Jacob Bruun Jørgensen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; (K.W.S.A.); (L.M.F.J.); (J.B.J.); (T.K.N.)
| | - Tue Kjærgaard Nielsen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; (K.W.S.A.); (L.M.F.J.); (J.B.J.); (T.K.N.)
| | - Morten Arendt Rasmussen
- Department of Food Science, University of Copenhagen, 1958 Frederiksberg C, Denmark;
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, 2820 Gentofte, Denmark
| | - Witold Kot
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; (K.W.S.A.); (L.M.F.J.); (J.B.J.); (T.K.N.)
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; (K.W.S.A.); (L.M.F.J.); (J.B.J.); (T.K.N.)
| |
Collapse
|
14
|
Oulghazi S, Sarfraz S, Zaczek-Moczydłowska MA, Khayi S, Ed-Dra A, Lekbach Y, Campbell K, Novungayo Moleleki L, O’Hanlon R, Faure D. Pectobacterium brasiliense: Genomics, Host Range and Disease Management. Microorganisms 2021; 9:E106. [PMID: 33466309 PMCID: PMC7824751 DOI: 10.3390/microorganisms9010106] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 12/29/2020] [Accepted: 12/30/2020] [Indexed: 12/13/2022] Open
Abstract
Pectobacterium brasiliense (Pbr) is considered as one of the most virulent species among the Pectobacteriaceae. This species has a broad host range within horticulture crops and is well distributed elsewhere. It has been found to be pathogenic not only in the field causing blackleg and soft rot of potato, but it is also transmitted via storage causing soft rot of other vegetables. Genomic analysis and other cost-effective molecular detection methods such as a quantitative polymerase chain reaction (qPCR) are essential to investigate the ecology and pathogenesis of the Pbr. The lack of fast, field deployable point-of-care testing (POCT) methods, specific control strategies and current limited genomic knowledge make management of this species difficult. Thus far, no comprehensive review exists about Pbr, however there is an intense need to research the biology, detection, pathogenicity and management of Pbr, not only because of its fast distribution across Europe and other countries but also due to its increased survival to various climatic conditions. This review outlines the information available in peer-reviewed literature regarding host range, detection methods, genomics, geographical distribution, nomenclature and taxonomical evolution along with some of the possible management and control strategies. In summary, the conclusions and a further directions highlight the management of this species.
Collapse
Affiliation(s)
- Said Oulghazi
- Department of Biology, Faculty of Sciences, Moulay Ismaïl University, BP.11201, Zitoune Meknes 50000, Morocco; (S.O.); (A.E.-D.)
- Institute for Integrative Biology of the Cell (I2BC), CEA CNRS University Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Sohaib Sarfraz
- Department of Plant Pathology, Faculty of Agriculture, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan;
| | - Maja A. Zaczek-Moczydłowska
- Institute for Global Food Security, School of Biological Sciences, Queen’s University, Belfast BT9 5DL, UK; (M.A.Z.-M.); (K.C.)
| | - Slimane Khayi
- Biotechnology Research Unit, CRRA-Rabat, National Institute for Agricultural Research (INRA), Rabat 10101, Morocco;
| | - Abdelaziz Ed-Dra
- Department of Biology, Faculty of Sciences, Moulay Ismaïl University, BP.11201, Zitoune Meknes 50000, Morocco; (S.O.); (A.E.-D.)
| | - Yassir Lekbach
- Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang 110819, China;
| | - Katrina Campbell
- Institute for Global Food Security, School of Biological Sciences, Queen’s University, Belfast BT9 5DL, UK; (M.A.Z.-M.); (K.C.)
| | - Lucy Novungayo Moleleki
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa;
| | - Richard O’Hanlon
- Agri-Food and Biosciences Institute, 18a Newforge Lane, Belfast BT9 5PX, UK;
- Department of Agriculture, Food and the Marine, D02 WK12 Dublin 2, Ireland
| | - Denis Faure
- Institute for Integrative Biology of the Cell (I2BC), CEA CNRS University Paris-Saclay, 91190 Gif-sur-Yvette, France
| |
Collapse
|
15
|
Premaratne A, Zhang H, Wang R, Chinivasagam N, Billington C. Phage Biotechnology to Mitigate Antimicrobial Resistance in Agriculture. SUSTAINABLE AGRICULTURE REVIEWS 2021. [DOI: 10.1007/978-3-030-58259-3_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
|
16
|
Djurhuus AM, Carstens AB, Neve H, Kot W, Hansen LH. Two New Dickeya dadantii Phages with Odd Growth Patterns Expand the Diversity of Phages Infecting Soft Rot Pectobacteriaceae. ACTA ACUST UNITED AC 2020; 1:251-259. [DOI: 10.1089/phage.2020.0039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Amaru Miranda Djurhuus
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Alexander Byth Carstens
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Kiel, Germany
| | - Witold Kot
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| |
Collapse
|
17
|
Pedersen JS, Carstens AB, Djurhuus AM, Kot W, Neve H, Hansen LH. Pectobacterium Phage Jarilo Displays Broad Host Range and Represents a Novel Genus of Bacteriophages Within the Family Autographiviridae. PHAGE (NEW ROCHELLE, N.Y.) 2020; 1:237-244. [PMID: 36147289 DOI: 10.1089/phage.2020.0037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Background: Soft rot Pectobacteriaceae includes the genera Pectobacterium and Dickeya, which are important plant pathogens being responsible for diseases in a wide range of plant species, with potatoes as the main group. Both genera cause pre- and postharvest losses of potatoes, resulting in huge economic losses linked with the soft rot diseases. Materials and Methods: Organic waste was used to isolate phages, with Pectobacterium carotovorum subsp. carotovorum DSM 30170 as host. Complete genome sequencing, comparative genomics, and electron microscopy were used to characterize the phage. An adsorption assay was used to estimate adsorption rate. Twenty-three strains from the genera Pectobacterium and Dickeya were used to examine the host range of the phage. Results: Pectobacterium phage Jarilo represents a novel genus of bacteriophages within the family Autographiviridae, order Caudovirales. Jarilo possesses a double-stranded DNA genome of 40557 bp with a G+C% content of 50.08% and 50 predicted open reading frames. Gene synteny and products seem to be partly conserved between Pectobacterium phage Jarilo and Enterobacteria phage T7, but limited nucleotide similarity is found between Jarilo and other phages within the family Autographiviridae. The adsorption rate of phage Jarilo increased continuously for 1 h upon infection. Phage Jarilo was not able to infect any strains of P. carotovorum and Dickeya tested with the exception of the P. carotovorum strain used for isolation. However, phage Jarilo infected 10 of 16 Pectobacterium atrosepticum strains tested. Conclusion: We propose Pectobacterium phage Jarilo as the first member of a new genus of bacteriophages within the family Autographiviridae, order Caudovirales, displaying a broad host range within the genera of Pectobacterium.
Collapse
Affiliation(s)
- Julie Stenberg Pedersen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Alexander Byth Carstens
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Amaru Miranda Djurhuus
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Witold Kot
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Kiel, Germany
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| |
Collapse
|
18
|
Holtappels D, Fortuna K, Lavigne R, Wagemans J. The future of phage biocontrol in integrated plant protection for sustainable crop production. Curr Opin Biotechnol 2020; 68:60-71. [PMID: 33176252 DOI: 10.1016/j.copbio.2020.08.016] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/28/2020] [Accepted: 08/31/2020] [Indexed: 02/06/2023]
Abstract
Bacterial phytopathogens significantly reduce crop yields and hence, pose a threat to the food supply of our increasing world population. In this context, bacteriophages are investigated as potential sustainable biocontrol agents. Here, recent advances in phage biocontrol are reviewed and considered within the framework of integrated plant protection strategies. This shows that understanding the pathogen's biology is crucial to develop a targeted strategy, tailored to individual pathosystems and driven by biotechnological insights. Moreover, the potential synergy of phages in contemporary farming practices based on the Internet of Things is proposed, potentially enabling a timely and cost-efficient treatment of plants at an early stage of the disease. Finally, these prospects are placed in the regulatory context of virus-oriented integrated pest control.
Collapse
Affiliation(s)
| | - Kiandro Fortuna
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Belgium
| | - Jeroen Wagemans
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Belgium.
| |
Collapse
|
19
|
Wittmann J, Turner D, Millard AD, Mahadevan P, Kropinski AM, Adriaenssens EM. From Orphan Phage to a Proposed New Family-the Diversity of N4-Like Viruses. Antibiotics (Basel) 2020; 9:E663. [PMID: 33008130 PMCID: PMC7650795 DOI: 10.3390/antibiotics9100663] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 01/29/2023] Open
Abstract
Escherichia phage N4 was isolated in 1966 in Italy and has remained a genomic orphan for a long time. It encodes an extremely large virion-associated RNA polymerase unique for bacterial viruses that became characteristic for this group. In recent years, due to new and relatively inexpensive sequencing techniques the number of publicly available phage genome sequences expanded rapidly. This revealed new members of the N4-like phage group, from 33 members in 2015 to 115 N4-like viruses in 2020. Using new technologies and methods for classification, the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) has moved the classification and taxonomy of bacterial viruses from mere morphological approaches to genomic and proteomic methods. The analysis of 115 N4-like genomes resulted in a huge reassessment of this group and the proposal of a new family "Schitoviridae", including eight subfamilies and numerous new genera.
Collapse
Affiliation(s)
- Johannes Wittmann
- Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Dann Turner
- Department of Applied Sciences, University of the West of England, Bristol BS16 1QY, UK;
| | - Andrew D. Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH UK;
| | | | - Andrew M. Kropinski
- Department of Food Science, University of Guelph, Guelph, ON N1G 2W1, Canada;
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | | |
Collapse
|
20
|
Sieiro C, Areal-Hermida L, Pichardo-Gallardo Á, Almuiña-González R, de Miguel T, Sánchez S, Sánchez-Pérez Á, Villa TG. A Hundred Years of Bacteriophages: Can Phages Replace Antibiotics in Agriculture and Aquaculture? Antibiotics (Basel) 2020; 9:E493. [PMID: 32784768 PMCID: PMC7460141 DOI: 10.3390/antibiotics9080493] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 08/04/2020] [Accepted: 08/04/2020] [Indexed: 12/12/2022] Open
Abstract
Agriculture, together with aquaculture, supplies most of the foodstuffs required by the world human population to survive. Hence, bacterial diseases affecting either agricultural crops, fish, or shellfish not only cause large economic losses to producers but can even create food shortages, resulting in malnutrition, or even famine, in vulnerable populations. Years of antibiotic use in the prevention and the treatment of these infections have greatly contributed to the emergence and the proliferation of multidrug-resistant bacteria. This review addresses the urgent need for alternative strategies for the use of antibiotics, focusing on the use of bacteriophages (phages) as biocontrol agents. Phages are viruses that specifically infect bacteria; they are highly host-specific and represent an environmentally-friendly alternative to antibiotics to control and kill pathogenic bacteria. The information evaluated here highlights the effectiveness of phages in the control of numerous major pathogens that affect both agriculture and aquaculture, with special emphasis on scientific and technological aspects still requiring further development to establish phagotherapy as a real universal alternative to antibiotic treatment.
Collapse
Affiliation(s)
- Carmen Sieiro
- Department of Functional Biology and Health Sciences, Microbiology Area, University of Vigo, Lagoas-Marcosende, 36310 Vigo, Spain; (L.A.-H.); (Á.P.-G.); (R.A.-G.)
| | - Lara Areal-Hermida
- Department of Functional Biology and Health Sciences, Microbiology Area, University of Vigo, Lagoas-Marcosende, 36310 Vigo, Spain; (L.A.-H.); (Á.P.-G.); (R.A.-G.)
| | - Ángeles Pichardo-Gallardo
- Department of Functional Biology and Health Sciences, Microbiology Area, University of Vigo, Lagoas-Marcosende, 36310 Vigo, Spain; (L.A.-H.); (Á.P.-G.); (R.A.-G.)
| | - Raquel Almuiña-González
- Department of Functional Biology and Health Sciences, Microbiology Area, University of Vigo, Lagoas-Marcosende, 36310 Vigo, Spain; (L.A.-H.); (Á.P.-G.); (R.A.-G.)
| | - Trinidad de Miguel
- Department of Microbiology and Parasitology, University of Santiago de Compostela, 5706 Santiago de Compostela, Spain; (T.d.M.); (S.S.)
| | - Sandra Sánchez
- Department of Microbiology and Parasitology, University of Santiago de Compostela, 5706 Santiago de Compostela, Spain; (T.d.M.); (S.S.)
| | - Ángeles Sánchez-Pérez
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydnay NSN 2006, Australia;
| | - Tomás G. Villa
- Department of Microbiology and Parasitology, University of Santiago de Compostela, 5706 Santiago de Compostela, Spain; (T.d.M.); (S.S.)
| |
Collapse
|
21
|
Carstens AB, Djurhuus AM, Kot W, Hansen LH. A novel six-phage cocktail reduces Pectobacterium atrosepticum soft rot infection in potato tubers under simulated storage conditions. FEMS Microbiol Lett 2020; 366:5490331. [PMID: 31095303 DOI: 10.1093/femsle/fnz101] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 05/14/2019] [Indexed: 01/18/2023] Open
Abstract
Pectobacterium atrosepticum is a species of plant pathogenic bacteria responsible for significant losses in potato production worldwide. Pectobacterium atrosepticum can cause blackleg disease on potato stems as well as the tuber disease termed potato soft rot. Methods for the effective control of these diseases are limited and are primarily based on good agricultural practices. Bacteriophages, viruses of bacteria, could be used as an alternative, environmentally friendly, control measure. Here, we describe the isolation and characterization of 29 phages virulent to P. atrosepticum. The phages belong to 12 different species based on a 95% sequence identity cut-off. Furthermore, based on sequence diversity and propagation results, we selected six of these phages to form a phage cocktail. The phages in the cocktail was tested on a number of P. atrosepticum strains in order to determine their host range. The phages was found to lyse 93% of the tested strains. The cocktail was subsequently tested for its effectiveness in combatting potato soft rot under simulated storage conditions. Use of the phage cocktail reduced both disease incidence and disease severity by 61% and 64%, respectively, strongly indicating that phage biocontrol has the potential to reduce the economic impact of soft rot in potato production.
Collapse
Affiliation(s)
- Alexander Byth Carstens
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, Roskilde, DK 4000, Denmark
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK 1871, Denmark
| | - Amaru Miranda Djurhuus
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, Roskilde, DK 4000, Denmark
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK 1871, Denmark
| | - Witold Kot
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, Roskilde, DK 4000, Denmark
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK 1871, Denmark
| | - Lars Hestbjerg Hansen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, Roskilde, DK 4000, Denmark
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK 1871, Denmark
| |
Collapse
|
22
|
Buttimer C, Lynch C, Hendrix H, Neve H, Noben JP, Lavigne R, Coffey A. Isolation and Characterization of Pectobacterium Phage vB_PatM_CB7: New Insights into the Genus Certrevirus. Antibiotics (Basel) 2020; 9:E352. [PMID: 32575906 PMCID: PMC7344957 DOI: 10.3390/antibiotics9060352] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 12/20/2022] Open
Abstract
To date, Certrevirus is one of two genera of bacteriophage (phage), with phages infecting Pectobacterium atrosepticum, an economically important phytopathogen that causes potato blackleg and soft rot disease. This study provides a detailed description of Pectobacterium phage CB7 (vB_PatM_CB7), which specifically infects P. atrosepticum. Host range, morphology, latent period, burst size and stability at different conditions of temperature and pH were examined. Analysis of its genome (142.8 kbp) shows that the phage forms a new species of Certrevirus, sharing sequence similarity with other members, highlighting conservation within the genus. Conserved elements include a putative early promoter like that of the Escherichia coli sigma70 promoter, which was found to be shared with other genus members. A number of dissimilarities were observed, relating to DNA methylation and nucleotide metabolism. Some members do not have homologues of a cytosine methylase and anaerobic nucleotide reductase subunits NrdD and NrdG, respectively. Furthermore, the genome of CB7 contains one of the largest numbers of homing endonucleases described in a single phage genome in the literature to date, with a total of 23 belonging to the HNH and LAGLIDADG families. Analysis by RT-PCR of the HNH homing endonuclease residing within introns of genes for the large terminase, DNA polymerase, ribonucleotide reductase subunits NrdA and NrdB show that they are splicing competent. Electrospray ionization-tandem mass spectrometry (ESI-MS/MS) was also performed on the virion of CB7, allowing the identification of 26 structural proteins-20 of which were found to be shared with the type phages of the genera of Vequintavirus and Seunavirus. The results of this study provide greater insights into the phages of the Certrevirus genus as well as the subfamily Vequintavirinae.
Collapse
Affiliation(s)
- Colin Buttimer
- Department of Biological Sciences, Cork Institute of Technology, T12 P928 Cork, Ireland; (C.B.); (C.L.)
- APC Microbiome Institute, University College, T12 YT20 Cork, Ireland
| | - Caoimhe Lynch
- Department of Biological Sciences, Cork Institute of Technology, T12 P928 Cork, Ireland; (C.B.); (C.L.)
| | - Hanne Hendrix
- Laboratory of Gene Technology, KU Leuven, 3001 Leuven, Belgium; (H.H.); (R.L.)
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, 24103 Kiel, Germany;
| | - Jean-Paul Noben
- Biomedical Research Institute and Transnational University Limburg, Hasselt University, 3590 Hasselt, Belgium;
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, 3001 Leuven, Belgium; (H.H.); (R.L.)
| | - Aidan Coffey
- Department of Biological Sciences, Cork Institute of Technology, T12 P928 Cork, Ireland; (C.B.); (C.L.)
- APC Microbiome Institute, University College, T12 YT20 Cork, Ireland
| |
Collapse
|
23
|
Thanh NC, Nagayoshi Y, Fujino Y, Iiyama K, Furuya N, Hiromasa Y, Iwamoto T, Doi K. Characterization and Genome Structure of Virulent Phage EspM4VN to Control Enterobacter sp. M4 Isolated From Plant Soft Rot. Front Microbiol 2020; 11:885. [PMID: 32582040 PMCID: PMC7283392 DOI: 10.3389/fmicb.2020.00885] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/16/2020] [Indexed: 12/22/2022] Open
Abstract
Enterobacter sp. M4 and other bacterial strains were isolated from plant soft rot disease. Virulent phages such as EspM4VN isolated from soil are trending biological controls for plant disease. This phage has an icosahedral head (100 nm in diameter), a neck, and a contractile sheath (100 nm long and 18 nm wide). It belongs to the Ackermannviridae family and resembles Shigella phage Ag3 and Dickeya phages JA15 and XF4. We report herein that EspM4VN was stable from 10°C to 50°C and pH 4 to 10 but deactivated at 70°C and pH 3 and 12. This phage formed clear plaques only on Enterobacter sp. M4 among tested bacterial strains. A one-step growth curve showed that the latent phase was 20 min, rise period was 10 min, and an average of 122 phage particles were released from each absorbed cell. We found the phage’s genome size was 160,766 bp and that it annotated 219 open reading frames. The genome organization of EspM4VN has high similarity with the Salmonella phage SKML-39; Dickeya phages Coodle, PP35, JA15, and Limestone; and Shigella phage Ag3. The phage EspM4VN has five tRNA species, four tail-spike proteins, and a thymidylate synthase. Phylogenetic analysis based on structural proteins and enzymes indicated that EspM4VN was identified as a member of the genus Agtrevirus, subfamily Aglimvirinae, family Ackermannviridae.
Collapse
Affiliation(s)
- Nguyen Cong Thanh
- Microbial Genetics Division, Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka, Japan.,Plant Protection Research Institute, Hanoi, Vietnam
| | - Yuko Nagayoshi
- Microbial Genetics Division, Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Yasuhiro Fujino
- Microbial Genetics Division, Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Kazuhiro Iiyama
- Laboratory of Plant Pathology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Naruto Furuya
- Laboratory of Plant Pathology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Yasuaki Hiromasa
- Attached Promotive Center for International Education and Research of Agriculture, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Takeo Iwamoto
- Core Research Facilities for Basic Science, Research Center for Medical Sciences, The Jikei University School of Medicine, Tokyo, Japan
| | - Katsumi Doi
- Microbial Genetics Division, Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| |
Collapse
|
24
|
Autographivirinae Bacteriophage Arno 160 Infects Pectobacterium carotovorum via Depolymerization of the Bacterial O-Polysaccharide. Int J Mol Sci 2020; 21:ijms21093170. [PMID: 32365879 PMCID: PMC7246868 DOI: 10.3390/ijms21093170] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 11/17/2022] Open
Abstract
Phytopathogenic bacteria belonging to the Pectobacterium and Dickeya genera (soft-rot Pectobacteriaceae) are in the focus of agriculture-related microbiology because of their diversity, their substantial negative impact on the production of potatoes and vegetables, and the prospects of bacteriophage applications for disease control. Because of numerous amendments in the taxonomy of P. carotovorum, there are still a few studied sequenced strains among this species. The present work reports on the isolation and characterization of the phage infectious to the type strain of P. carotovorum. The phage Arno 160 is a lytic Podovirus representing a potential new genus of the subfamily Autographivirinae. It recognizes O-polysaccahride of the host strain and depolymerizes it in the process of infection using a rhamnosidase hydrolytic mechanism. Despite the narrow host range of this phage, it is suitable for phage control application.
Collapse
|
25
|
Application of Adaptive Evolution to Improve the Stability of Bacteriophages during Storage. Viruses 2020; 12:v12040423. [PMID: 32283683 PMCID: PMC7232334 DOI: 10.3390/v12040423] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 04/05/2020] [Accepted: 04/06/2020] [Indexed: 02/07/2023] Open
Abstract
Phage stability is important for the successful application of bacteriophages as alternative antibacterial agents. Considering that temperature is a critical factor in phage stability, this study aimed to explore the possibility of improving long-term phage stability through adaptive evolution to elevated temperature. Evolution of three wild-type ancestral phages (Myoviridae phage Wc4 and Podoviridae phages CX5 and P-PSG-11) was induced by subjecting the phages to heat treatment at 60 °C for five cycles. The adapted phages showed better stability than the wild-type ancestral phages when subjected to heat treatment at 60 °C for 1 h and after 60 days of storage at 37 °C. However, the adapted phages could not withstand thermal treatment at 70 °C for 1 h. The infectivity and the lytic properties of the phages were not changed by the evolution process. Whole-genome sequencing revealed that single substitutions in the tail tubular proteins were the only changes observed in the genomes of the adapted phages. This study demonstrates that adaptive evolution could be used as a general method for enhancing the thermal stability of phages without affecting their lytic activity. Sequencing results showed that bacteriophages may exist as a population with minor heterogeneous mutants, which might be important to understand the ecology of phages in different environments.
Collapse
|
26
|
Zaczek-Moczydłowska MA, Young GK, Trudgett J, Plahe C, Fleming CC, Campbell K, O’ Hanlon R. Phage cocktail containing Podoviridae and Myoviridae bacteriophages inhibits the growth of Pectobacterium spp. under in vitro and in vivo conditions. PLoS One 2020; 15:e0230842. [PMID: 32240203 PMCID: PMC7117878 DOI: 10.1371/journal.pone.0230842] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 03/10/2020] [Indexed: 12/28/2022] Open
Abstract
Globally, there is a high economic burden caused by pre- and post-harvest losses in vegetables, fruits and ornamentals due to soft rot diseases. At present, the control methods for these diseases are limited, but there is some promise in developing biological control products for use in Integrated Pest Management. This study sought to formulate a phage cocktail which would be effective against soft rot Pectobacteriaceae species affecting potato (Solanum tuberosum L.), with potential methods of application in agricultural systems, including vacuum-infiltration and soil drench, also tested. Six bacteriophages were isolated and characterized using transmission electron microscopy, and tested against a range of Pectobacterium species that cause soft rot/blackleg of potato. Isolated bacteriophages of the family Podoviridae and Myoviridae were able to control isolates of the Pectobacterium species: Pectobacterium atrosepticum and Pectobacterium carotovorum subsp. carotovorum. Genomic analysis of three Podoviridae phages did not indicate host genes transcripts or proteins encoding toxin or antibiotic resistance genes. These bacteriophages were formulated as a phage cocktail and further experiments showed high activity in vitro and in vivo to suppress Pectobacterium growth, potentially indicating their efficacy in formulation as a microbial pest control agent to use in planta.
Collapse
Affiliation(s)
- Maja A. Zaczek-Moczydłowska
- Institute for Global Food Security, School of Biological Sciences, Queen's University, Belfast, Northern Ireland, United Kingdom
- * E-mail:
| | - Gillian K. Young
- Sustainable Agri-Food Sciences Division, Agri-Food and Biosciences Institute, Belfast, Northern Ireland, United Kingdom
| | - James Trudgett
- Veterinary Sciences Division, Agri-Food and Biosciences Institute, Stormont, Belfast, Northern Ireland, United Kingdom
| | - Cali Plahe
- School of Biological Sciences, Queen's University, Belfast, Northern Ireland, United Kingdom
| | - Colin C. Fleming
- Sustainable Agri-Food Sciences Division, Agri-Food and Biosciences Institute, Belfast, Northern Ireland, United Kingdom
- School of Biological Sciences, Queen's University, Belfast, Northern Ireland, United Kingdom
| | - Katrina Campbell
- Institute for Global Food Security, School of Biological Sciences, Queen's University, Belfast, Northern Ireland, United Kingdom
| | - Richard O’ Hanlon
- Sustainable Agri-Food Sciences Division, Agri-Food and Biosciences Institute, Belfast, Northern Ireland, United Kingdom
- School of Biological Sciences, Queen's University, Belfast, Northern Ireland, United Kingdom
| |
Collapse
|
27
|
Boon M, De Zitter E, De Smet J, Wagemans J, Voet M, Pennemann FL, Schalck T, Kuznedelov K, Severinov K, Van Meervelt L, De Maeyer M, Lavigne R. 'Drc', a structurally novel ssDNA-binding transcription regulator of N4-related bacterial viruses. Nucleic Acids Res 2020; 48:445-459. [PMID: 31724707 PMCID: PMC7145618 DOI: 10.1093/nar/gkz1048] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/16/2019] [Accepted: 10/23/2019] [Indexed: 12/22/2022] Open
Abstract
Bacterial viruses encode a vast number of ORFan genes that lack similarity to any other known proteins. Here, we present a 2.20 Å crystal structure of N4-related Pseudomonas virus LUZ7 ORFan gp14, and elucidate its function. We demonstrate that gp14, termed here as Drc (ssDNA-binding RNA Polymerase Cofactor), preferentially binds single-stranded DNA, yet contains a structural fold distinct from other ssDNA-binding proteins (SSBs). By comparison with other SSB folds and creation of truncation and amino acid substitution mutants, we provide the first evidence for the binding mechanism of this unique fold. From a biological perspective, Drc interacts with the phage-encoded RNA Polymerase complex (RNAPII), implying a functional role as an SSB required for the transition from early to middle gene transcription during phage infection. Similar to the coliphage N4 gp2 protein, Drc likely binds locally unwound middle promoters and recruits the phage RNA polymerase. However, unlike gp2, Drc does not seem to need an additional cofactor for promoter melting. A comparison among N4-related phage genera highlights the evolutionary diversity of SSB proteins in an otherwise conserved transcription regulation mechanism.
Collapse
Affiliation(s)
- Maarten Boon
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Elke De Zitter
- Department of Chemistry, Biomolecular Architecture, KU Leuven, Leuven 3001, Belgium
| | - Jeroen De Smet
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Jeroen Wagemans
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Marleen Voet
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Friederike L Pennemann
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Thomas Schalck
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | | | | | - Luc Van Meervelt
- Department of Chemistry, Biomolecular Architecture, KU Leuven, Leuven 3001, Belgium
| | - Marc De Maeyer
- Department of Chemistry, Laboratory of Biomolecular Modelling and Design, KU Leuven, Leuven 3001, Belgium
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| |
Collapse
|
28
|
Genomic Characterization, Formulation and Efficacy in Planta of a Siphoviridae and Podoviridae Protection Cocktail against the Bacterial Plant Pathogens Pectobacterium spp. Viruses 2020; 12:v12020150. [PMID: 32012814 PMCID: PMC7077305 DOI: 10.3390/v12020150] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/22/2020] [Accepted: 01/25/2020] [Indexed: 12/13/2022] Open
Abstract
In the face of global human population increases, there is a need for efficacious integrated pest management strategies to improve agricultural production and increase sustainable food production. To counteract significant food loses in crop production, novel, safe and efficacious measures should be tested against bacterial pathogens. Pectobacteriaceae species are one of the causative agents of the bacterial rot of onions ultimately leading to crop losses due to ineffective control measures against these pathogens. Therefore, the aim of this study was to isolate and characterize bacteriophages which could be formulated in a cocktail and implemented in planta under natural environmental conditions. Transmission electron microscopy (TEM) and genome analysis revealed Siphoviridae and Podoviridae family bacteriophages. To test the protective effect of a formulated phage cocktail against soft rot disease, three years of field trials were performed, using three different methods of treatment application. This is the first study to show the application of a phage cocktail containing Podoviridae and Siphoviridae bacteriophages capable of protecting onions against soft rot in field conditions.
Collapse
|
29
|
Sun X, Huang S, Long L. Characterization, complete genome and proteome of a bacteriophage infecting a coral-derived Vibrio strain. Mar Genomics 2019. [DOI: 10.1016/j.margen.2019.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
30
|
Kering KK, Kibii BJ, Wei H. Biocontrol of phytobacteria with bacteriophage cocktails. PEST MANAGEMENT SCIENCE 2019; 75:1775-1781. [PMID: 30624034 DOI: 10.1002/ps.5324] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 01/01/2019] [Accepted: 01/02/2019] [Indexed: 06/09/2023]
Abstract
Crop loss due to plant pathogens has provoked renewed interest in bacteriophages as a feasible biocontrol strategy of plant diseases. Phage cocktails in particular present a viable option for broadening the phage host range, limiting the emergence of bacterial resistance while maintaining the lytic activity of the phages. It is therefore important that the design used to formulate a phage cocktail should result in the most effective cocktail against the pathogen. It is also critical that certain factors are considered during the formulation and application of a phage cocktail: their stability, the production time and cost of complex cocktails, the potential impact on untargeted bacteria, the timing of phage application, and the persistence in the plant environment. Continuous monitoring is required to ensure that the efficacy of a cocktail is sustained due to the dynamic nature of phages. Although phage cocktails are considered as a plausible biocontrol strategy of phytobacteria, more research needs to be done to understand the complex interaction between phages and bacteria in the plant environment, and to overcome the technical obstacles. © 2019 Society of Chemical Industry.
Collapse
Affiliation(s)
- Kelvin K Kering
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Belindah J Kibii
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hongping Wei
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| |
Collapse
|
31
|
Cordova AV, Laglaguano JC. Bacteriophages applications in agriculture. BIONATURA 2019. [DOI: 10.21931/rb/cs/2019.02.01.24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The bacteriophages life cycle has two stages: a lytic stage where the phages reproduce inside the bacteria and lyse bacteria and a lysogenic stage where the phage is in a stationary stage where do not exist phage reproduction. The understanding of the life cycle of phages is fundamental to understand the advantages of phage offers as biological control applications and how engineered phages work. The bacteriophages are an alternative to fight against the antimicrobial or pesticides because phages offer advantages such as high host specificity, the ability of long term effect, are active against dividing or not dividing bacterial cells, effective elimination of biofilms and are capable vehicles for nucleic acids delivery. Phages have been isolated from water or soil samples in different parts of the world and for specific bacterial pathogens. In the following review, in the main topics in bacteriophages and its applications in agriculture: the bacteriophages life cycle, advantages of phages in biological control applications, the last isolated phages and described for different pathogens and the last advances in phage engineering applications for biological control.
Collapse
Affiliation(s)
- Airina Valentina Cordova
- School of Chemical Sciences and Engineering. Yachay Tech University, San Miguel de Urcuquí, Ecuador
| | - Juan Carlos Laglaguano
- School of Biological Sciences and Engineering, Yachay Tech University, San Miguel de Urcuquí, Ecuador
| |
Collapse
|
32
|
Carstens AB, Djurhuus AM, Kot W, Jacobs-Sera D, Hatfull GF, Hansen LH. Unlocking the Potential of 46 New Bacteriophages for Biocontrol of Dickeya Solani. Viruses 2018; 10:E621. [PMID: 30423804 PMCID: PMC6267328 DOI: 10.3390/v10110621] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/08/2018] [Accepted: 11/09/2018] [Indexed: 01/12/2023] Open
Abstract
Modern agriculture is expected to face an increasing global demand for food while also needing to comply with higher sustainability standards. Therefore, control of crop pathogens requires new, green alternatives to current methods. Potatoes are susceptible to several bacterial diseases, with infections by soft rot Enterobacteriaceae (SRE) being a significant contributor to the major annual losses. As there are currently no efficient ways of combating SRE, we sought to develop an approach that could easily be incorporated into the potato production pipeline. To this end, 46 phages infecting the emerging potato pathogen Dickeya solani were isolated and thoroughly characterized. The 46 isolated phages were grouped into three different groups based on DNA similarity, representing two distinct clusters and a singleton. One cluster showed similarity to phages previously used to successfully treat soft rot in potatoes, whereas the remaining phages were novel and showed only very limited similarity to previously isolated phages. We selected six diverse phages in order to create the hereto most complex phage cocktail against SRE. The cocktail was applied in a proof-of-principle experiment to treat soft rot in potatoes under simulated storage conditions. We show that the phage cocktail was able to significantly reduce the incidence of soft rot as well as disease severity after 5 days of storage post-infection with Dickeya solani. This confirms results from previous studies that phages represent promising biocontrol agents against SRE infection in potato.
Collapse
Affiliation(s)
- Alexander B Carstens
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark.
| | - Amaru M Djurhuus
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark.
| | - Witold Kot
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark.
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Lars H Hansen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark.
| |
Collapse
|
33
|
Buttimer C, Lucid A, Neve H, Franz CMAP, O'Mahony J, Turner D, Lavigne R, Coffey A. Pectobacterium atrosepticum Phage vB_PatP_CB5: A Member of the Proposed Genus ' Phimunavirus'. Viruses 2018; 10:E394. [PMID: 30050020 PMCID: PMC6115819 DOI: 10.3390/v10080394] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/23/2018] [Accepted: 07/24/2018] [Indexed: 11/23/2022] Open
Abstract
Pectobacterium atrosepticum is a phytopathogen of economic importance as it is the causative agent of potato blackleg and soft rot. Here we describe the Pectobacterium phage vB_PatP_CB5 (abbreviated as CB5), which specifically infects the bacterium. The bacteriophage is characterized in detail and TEM micrographs indicate that it belongs to the Podoviridae family. CB5 shares significant pairwise nucleotide identity (≥80%) with P. atrosepticum phages φM1, Peat1, and PP90 and also shares common genome organization. Phylograms constructed using conserved proteins and whole-genome comparison-based amino acid sequences show that these phages form a distinct clade within the Autographivirinae. They also possess conserved RNA polymerase recognition and specificity loop sequences. Their lysis cassette resembles that of KP34virus, containing in sequential order a U-spanin, a holin, and a signal⁻arrest⁻release (SAR) endolysin. However, they share low pairwise nucleotide identity with the type phage of the KP34virus genus, Klebsiella phage KP34. In addition, phage KP34 does not possess several conserved proteins associated with these P. atrosepticum phages. As such, we propose the allocation of phages CB5, Peat1, φM1, and PP90 to a separate new genus designated Phimunavirus.
Collapse
Affiliation(s)
- Colin Buttimer
- Department of Biological Sciences, Cork Institute of Technology, T12 P928 Cork, Ireland.
| | - Alan Lucid
- Department of Biological Sciences, Cork Institute of Technology, T12 P928 Cork, Ireland.
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, 24103 Kiel, Germany.
| | - Charles M A P Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, 24103 Kiel, Germany.
| | - Jim O'Mahony
- Department of Biological Sciences, Cork Institute of Technology, T12 P928 Cork, Ireland.
| | - Dann Turner
- Department of Applied Sciences, University of the West of England, Bristol, Frenchay Campus, Coldharbour Lane, Bristol BS16 1QY, UK.
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, 3001 Leuven, Belgium.
| | - Aidan Coffey
- Department of Biological Sciences, Cork Institute of Technology, T12 P928 Cork, Ireland.
- APC Microbiome Institute, University College, T12 YT20 Cork, Ireland.
| |
Collapse
|