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Efremenko E, Stepanov N, Senko O, Maslova O, Lyagin I, Domnin M, Aslanli A. "Stop, Little Pot" as the Motto of Suppressive Management of Various Microbial Consortia. Microorganisms 2024; 12:1650. [PMID: 39203492 PMCID: PMC11356704 DOI: 10.3390/microorganisms12081650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 08/07/2024] [Accepted: 08/10/2024] [Indexed: 09/03/2024] Open
Abstract
The unresolved challenges in the development of highly efficient, stable and controlled synthetic microbial consortia, as well as the use of natural consortia, are very attractive for science and technology. However, the consortia management should be done with the knowledge of how not only to accelerate but also stop the action of such "little pots". Moreover, there are a lot of microbial consortia, the activity of which should be suppressively controlled. The processes, catalyzed by various microorganisms being in complex consortia which should be slowed down or completely cancelled, are typical for the environment (biocorrosion, landfill gas accumulation, biodegradation of building materials, water sources deterioration etc.), industry (food and biotechnological production), medical practice (vaginitis, cystitis, intestinal dysbiosis, etc.). The search for ways to suppress the functioning of heterogeneous consortia in each of these areas is relevant. The purpose of this review is to summarize the general trends in these studies regarding the targets and new means of influence used. The analysis of the features of the applied approaches to solving the main problem confirms the possibility of obtaining a combined effect, as well as selective influence on individual components of the consortia. Of particular interest is the role of viruses in suppressing the functioning of microbial consortia of different compositions.
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Affiliation(s)
- Elena Efremenko
- Faculty of Chemistry, Lomonosov Moscow State University, Lenin Hills 1/3, Moscow 119991, Russia (O.S.)
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Çelik A, Çakar D, Derviş S, Morca AF, Akıllı Şimşek S, Romon-Ochoa P, Özer G. New Detection Methods for Cryphonectria Hypovirus 1 (CHV1) through SYBR Green-Based Real-Time PCR and Loop-Mediated Isothermal Amplification (LAMP). Viruses 2024; 16:1203. [PMID: 39205177 PMCID: PMC11360611 DOI: 10.3390/v16081203] [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: 07/01/2024] [Revised: 07/16/2024] [Accepted: 07/24/2024] [Indexed: 09/04/2024] Open
Abstract
Some mycoviruses can be considered as effective biocontrol agents, mitigating the impact of phytopathogenic fungi and consequently reducing disease outbreaks while promoting plant health. Cryphonectria parasitica, the causal agent of chestnut blight and a highly destructive pathogen, experienced a notable decrease in its virulence with the identification of cryphonectria hypovirus 1 (CHV1), a naturally occurring biocontrol agent. In this study, two innovative diagnostic protocols designed for the accurate and efficient detection of CHV1 are introduced. The ORF A and ORF B regions of CHV1 are targeted by these techniques, which employ colorimetric loop-mediated isothermal amplification (LAMP) with 2 Colorimetric LAMP Master Mix and real-time quantitative PCR (qPCR) with SYBR Green chemistry, respectively. The LAMP assay presents a discernible color transition, changing from pink to yellow after a 35 min incubation period. Comparative analysis, when assessed against two established reverse transcription-PCR (RT-PCR) techniques, reveals a significant enhancement in sensitivity for both the LAMP approach, which offers a tenfold increase, and the qPCR method, which showcases a remarkable 100-fold sensitivity improvement. Throughout the comparison phase, it was evident that the RT-PCR, LAMP, and qPCR procedures displayed superior performance compared to the Bavendamm test, relying on phenol oxidase activity, effectively distinguishing hypovirulent strains. Consequently, this study introduces two pioneer diagnostic assays for highly sensitive CHV1 detection, representing a substantial advancement in the realm of CHV1 surveillance techniques. These methodologies hold significant promise for enhancing research endeavors in the domain of the biological control of C. parasitica.
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Affiliation(s)
- Ali Çelik
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant İzzet Baysal University, Bolu 14030, Türkiye
| | - Deniz Çakar
- Central Research Laboratory Application and Research Center, Çankırı Karatekin University, Çankırı 18100, Türkiye
| | - Sibel Derviş
- Department of Plant Protection, Faculty of Kızıltepe Agricultural Sciences and Technologies, Mardin Artuklu University, Mardin 47000, Türkiye
- Department of Plant and Animal Production, Vocational School of Kızıltepe, Mardin Artuklu University, Mardin 47000, Türkiye
| | - Ali Ferhan Morca
- Directorate of Plant Protection Central Research Institute, Gayret Mah. Fatih Sultan Mehmet Bulv., Yenimahalle, Ankara 06172, Türkiye
| | - Seçil Akıllı Şimşek
- Department of Biology, Faculty of Sciences, Çankırı Karatekin University, Çankırı 18100, Türkiye
| | - Pedro Romon-Ochoa
- Forest Research, Plant Pathology Department, Alice Holt Research Station, Farnham GU10 4LH, UK
| | - Göksel Özer
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant İzzet Baysal University, Bolu 14030, Türkiye
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Ahmad F, Tomada S, Poonsiri T, Baric S. Molecular genetic variability of Cryphonectria hypovirus 1 associated with Cryphonectria parasitica in South Tyrol (northern Italy). Front Microbiol 2024; 15:1291542. [PMID: 38476955 PMCID: PMC10927965 DOI: 10.3389/fmicb.2024.1291542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 01/25/2024] [Indexed: 03/14/2024] Open
Abstract
Cryphonectria hypovirus 1 (CHV-1) has been widely studied and used as a biocontrol agent because of its ability to infect the chestnut blight fungus, Cryphonectria parasitica, and to reduce its virulence. Knowledge about the hypovirus, its presence, and diversity is completely lacking in South Tyrol (northern Italy), which may obstruct biocontrol measures for chestnut blight based on CHV-1. This work aimed to study the occurrence of CHV-1 infecting C. parasitica in South Tyrol and to perform a genetic characterization of the hypovirus. In South Tyrol, CHV-1 was found to occur in 29.2% of the fungal isolates investigated, varying in frequency between different regions and chestnut stands. Twenty-three haplotypes based on partial cDNA (complementary DNA) sequences of open reading frame (ORF)-A and 30 haplotypes based on partial cDNA sequences of ORF-B were identified among 47 and 56 hypovirulent fungal isolates, respectively. Phylogenetic analysis showed that all the haplotypes belonged to the Italian subtype of CHV-1 and that they were closely related to the populations of Italy, Switzerland, Croatia and Slovenia. Evidence of recombination was not found in the sequences and point mutations were the main source of diversity. Overall, this study indicated that the prevalence of CHV-1 in South Tyrol is low compared to many other central and western European populations and determined a need to actively impose biocontrol measures. Using sequence analysis, we identified some variants of interest of CHV-1 that should be studied in detail for their potential use in biocontrol.
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Affiliation(s)
- Farooq Ahmad
- Laboratory for Phytopathology, Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, Bolzano, Italy
| | - Selena Tomada
- Laboratory for Phytopathology, Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, Bolzano, Italy
| | - Thanalai Poonsiri
- Department of Pathobiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Sanja Baric
- Laboratory for Phytopathology, Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, Bolzano, Italy
- Competence Centre for Plant Health, Free University of Bozen-Bolzano, Bolzano, Italy
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Romon-Ochoa P, Samal P, Gorton C, Lewis A, Chitty R, Eacock A, Krzywinska E, Crampton M, Pérez-Sierra A, Biddle M, Jones B, Ward L. Cryphonectria parasitica Detections in England, Jersey, and Guernsey during 2020-2023 Reveal Newly Affected Areas and Infections by the CHV1 Mycovirus. J Fungi (Basel) 2023; 9:1036. [PMID: 37888292 PMCID: PMC10607933 DOI: 10.3390/jof9101036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/08/2023] [Accepted: 10/09/2023] [Indexed: 10/28/2023] Open
Abstract
In England, Cryphonectria parasitica was detected for the first time in 2011 in a nursery and in 2016 in the wider environment. Surveys between 2017 and 2020 identified the disease at different sites in Berkshire, Buckinghamshire, Cornwall, Derbyshire, Devon, Dorset, London, West Sussex, and the island of Jersey, while the present study comprises the results of the 2020-2023 survey with findings in Derbyshire, Devon, Kent, Nottinghamshire, Herefordshire, Leicestershire, London, West Sussex, and the islands of Jersey and Guernsey. A total of 226 suspected samples were collected from 72 surveyed sites, as far north as Edinburgh and as far west as Plymouth (both of which were negative), and 112 samples tested positive by real-time PCR and isolation from 35 sites. The 112 isolates were tested for the vegetative compatibility group (VCG), mating type, and Cryphonectria hypovirus 1 (CHV1). Twelve VCGs were identified, with two of them (EU-5 and EU-22) being the first records in the UK. Both mating types were present (37% MAT-1 and 63% MAT-2), but only one mating type was present per site and VCG, and perithecia were never observed. Cryphonectria hypovirus 1 (CHV1), consistently subtype-I haplotype E-5, was detected in three isolates at a low concentration (5.9, 21.1, and 33.0 ng/µL) from locations in London, Nottinghamshire, and Devon.
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Affiliation(s)
- Pedro Romon-Ochoa
- Forest Research, Plant Pathology Department, Alice Holt Research Station, Farnham, Surrey GU10 4LH, UK; (P.S.); (M.B.); (L.W.)
| | - Pankajini Samal
- Forest Research, Plant Pathology Department, Alice Holt Research Station, Farnham, Surrey GU10 4LH, UK; (P.S.); (M.B.); (L.W.)
| | - Caroline Gorton
- Forest Research, THDAS-Tree Health Diagnostics and Advisory Service, Alice Holt Research Station, Farnham, Surrey GU10 4LH, UK; (C.G.); (A.L.); (R.C.); (A.E.); (E.K.); (M.C.); (A.P.-S.)
| | - Alex Lewis
- Forest Research, THDAS-Tree Health Diagnostics and Advisory Service, Alice Holt Research Station, Farnham, Surrey GU10 4LH, UK; (C.G.); (A.L.); (R.C.); (A.E.); (E.K.); (M.C.); (A.P.-S.)
| | - Ruth Chitty
- Forest Research, THDAS-Tree Health Diagnostics and Advisory Service, Alice Holt Research Station, Farnham, Surrey GU10 4LH, UK; (C.G.); (A.L.); (R.C.); (A.E.); (E.K.); (M.C.); (A.P.-S.)
| | - Amy Eacock
- Forest Research, THDAS-Tree Health Diagnostics and Advisory Service, Alice Holt Research Station, Farnham, Surrey GU10 4LH, UK; (C.G.); (A.L.); (R.C.); (A.E.); (E.K.); (M.C.); (A.P.-S.)
| | - Elzbieta Krzywinska
- Forest Research, THDAS-Tree Health Diagnostics and Advisory Service, Alice Holt Research Station, Farnham, Surrey GU10 4LH, UK; (C.G.); (A.L.); (R.C.); (A.E.); (E.K.); (M.C.); (A.P.-S.)
| | - Michael Crampton
- Forest Research, THDAS-Tree Health Diagnostics and Advisory Service, Alice Holt Research Station, Farnham, Surrey GU10 4LH, UK; (C.G.); (A.L.); (R.C.); (A.E.); (E.K.); (M.C.); (A.P.-S.)
| | - Ana Pérez-Sierra
- Forest Research, THDAS-Tree Health Diagnostics and Advisory Service, Alice Holt Research Station, Farnham, Surrey GU10 4LH, UK; (C.G.); (A.L.); (R.C.); (A.E.); (E.K.); (M.C.); (A.P.-S.)
| | - Mick Biddle
- Forest Research, Plant Pathology Department, Alice Holt Research Station, Farnham, Surrey GU10 4LH, UK; (P.S.); (M.B.); (L.W.)
| | - Ben Jones
- Forestry Commission, 620 Bristol Business Park, Bristol BS16 1EJ, UK;
| | - Lisa Ward
- Forest Research, Plant Pathology Department, Alice Holt Research Station, Farnham, Surrey GU10 4LH, UK; (P.S.); (M.B.); (L.W.)
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Romon-Ochoa P, Smith O, Lewis A, Kupper Q, Shamsi W, Rigling D, Pérez-Sierra A, Ward L. Temperature Effects on the Cryphonectria hypovirus 1 Accumulation and Recovery within Its Fungal Host, the Chestnut Blight Pathogen Cryphonectria parasitica. Viruses 2023; 15:1260. [PMID: 37376560 DOI: 10.3390/v15061260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
Biological control of Cryphonectria parasitica fungus, the causal agent of chestnut blight, by virus infection (hypovirulence) is an effective control strategy against chestnut blight in Europe and some parts of North America. The most studied mycovirus is the Cryphonectria hypovirus 1 (CHV1) type species of the Hypoviridae family. In this study, the CHV1 virus was studied within some highly infected British isolates of Cryphonectria parasitica, gained in the past through co-culture transmissions. The effects of six temperatures (5-30 °C, in 5 °C steps) on six infected isolates (three with viral strain E-5, and other three with viral strain L-18) and their respective negative non-infected controls, three isogenic virulent fungal isolates, were examined. Experiments were performed with the nine isolate types with three replicates on potato dextrose agar (PDA) with cellophane sheets per isolate and temperature. A recently developed rapid, specific, quantitative reverse transcription PCR (RT-qPCR) screening method was used. This enabled quantifying the concentration (nanograms per microliter or copy numbers) of the virus within each isolate repetition. The presence of the virus had a significant negative effect between 20 and 25 °C on the C. parasitica growth rate, which was anyway highly influenced by and positively correlated with the temperature. The temperature clearly determined the virus accumulation and its recovery from cold or heat, and the virus optimum temperature was estimated at 15-25 °C.
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Affiliation(s)
- Pedro Romon-Ochoa
- Forest Research, Plant Pathology Department, Alice Holt Research Station, Surrey GU104LH, UK
| | - Olivia Smith
- Forest Research, Plant Pathology Department, Alice Holt Research Station, Surrey GU104LH, UK
| | - Alex Lewis
- Forest Research, Tree Health Diagnostics and Advisory Service (THDAS), Alice Holt, Surrey GU104LH, UK
| | - Quirin Kupper
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zuercherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Wajeeha Shamsi
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zuercherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Daniel Rigling
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zuercherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Ana Pérez-Sierra
- Forest Research, Tree Health Diagnostics and Advisory Service (THDAS), Alice Holt, Surrey GU104LH, UK
| | - Lisa Ward
- Forest Research, Plant Pathology Department, Alice Holt Research Station, Surrey GU104LH, UK
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