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Zhang S, Zhang C, Wu J, Liu S, Zhang R, Handique U. Isolation, characterization and application of noble bacteriophages targeting potato common scab pathogen Streptomyces stelliscabiei. Microbiol Res 2024; 283:127699. [PMID: 38520838 DOI: 10.1016/j.micres.2024.127699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 03/16/2024] [Accepted: 03/18/2024] [Indexed: 03/25/2024]
Abstract
Bacteriophages have emerged as promising alternatives to pesticides for controlling bacterial pathogens in crops. Among these pathogens, Streptomyces stelliscabiei (syn. S. stelliscabiei) is a primary causative agent of potato common scab (PCS), resulting in substantial global economic losses. The traditional management methods for PCS face numerous challenges, highlighting the need for effective and environmentally friendly control strategies. In this study, we successfully isolated three novel bacteriophages, namely Psst1, Psst2, and Psst4, which exhibited a broad host range encompassing seven S. stelliscabiei strains. Morphological analysis revealed their distinct features, including an icosahedral head and a non-contractile tail. These phages demonstrated stability across a broad range of temperatures (20-50°C), pH (pH 3-11), and UV exposure time (80 min). Genome sequencing revealed double-stranded DNA phage with open reading frames encoding genes for phage structure, DNA packaging and replication, host lysis and other essential functions. These phages lacked genes for antibiotic resistance, virulence, and toxicity. Average nucleotide identity, phylogenetic, and comparative genomic analyses classified the three phages as members of the Rimavirus genus, with Psst1 and Psst2 representing novel species. All three phages efficiently lysed S. stelliscabiei in the liquid medium and alleviated scab symptom development and reduced pathogen abundance on potato slices. Furthermore, phage treatments of radish seedlings alleviated the growth inhibition caused by S. stelliscabiei with no disease symptoms. In soil potted experiments, phages significantly reduced disease incidence by 40%. This decrease is attributed to a reduction in pathogen density and the selection of S. stelliscabiei strains with reduced virulence and slower growth rates in natural environments. Our study is the first to report the isolation of three novel phages that infect S. stelliscabiei as a host bacterium. These phages exhibit a broad host range, and demonstrate stability under a variety of environmental conditions. Additionally, they demonstrate biocontrol efficacy against bacterial infections in potato slices, radish seedlings, and potted experiments, underscoring their significant potential as biocontrol agents for the effective management of PCS.
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Affiliation(s)
- Shihe Zhang
- Inner Mongolia Potato Engineering and Technology Research Center, Inner Mongolia University, Hohhot 010021, China
| | - Cheligeer Zhang
- Inner Mongolia Potato Engineering and Technology Research Center, Inner Mongolia University, Hohhot 010021, China
| | - Jian Wu
- Inner Mongolia Potato Engineering and Technology Research Center, Inner Mongolia University, Hohhot 010021, China
| | - Simiao Liu
- Inner Mongolia Potato Engineering and Technology Research Center, Inner Mongolia University, Hohhot 010021, China
| | - Ruofang Zhang
- Inner Mongolia Potato Engineering and Technology Research Center, Inner Mongolia University, Hohhot 010021, China
| | - Utpal Handique
- Inner Mongolia Potato Engineering and Technology Research Center, Inner Mongolia University, Hohhot 010021, China.
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Vincent CV, Bignell DRD. Regulation of virulence mechanisms in plant-pathogenic Streptomyces. Can J Microbiol 2024; 70:199-212. [PMID: 38190652 DOI: 10.1139/cjm-2023-0171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Streptomyces have a uniquely complex developmental life cycle that involves the coordination of morphological differentiation with the production of numerous bioactive specialized metabolites. The majority of Streptomyces spp. are soil-dwelling saprophytes, while plant pathogenicity is a rare attribute among members of this genus. Phytopathogenic Streptomyces are responsible for economically important diseases such as common scab, which affects potato and other root crops. Following the acquisition of genes encoding virulence factors, Streptomyces pathogens are expected to have specifically adapted their regulatory pathways to enable transition from a primarily saprophytic to a pathogenic lifestyle. Investigations of the regulation of pathogenesis have primarily focused on Streptomyces scabiei and the principal pathogenicity determinant thaxtomin A. The coordination of growth and thaxtomin A production in this species is controlled in a hierarchical manner by cluster-situated regulators, pleiotropic regulators, signalling and plant-derived molecules, and nutrients. Although the majority of phytopathogenic Streptomyces produce thaxtomins, many also produce additional virulence factors, and there are scab-causing pathogens that do not produce thaxtomins. The development of effective control strategies for common scab and other Streptomyces plant diseases requires a more in-depth understanding of the genetic and environmental factors that modulate the plant pathogenic lifestyle of these organisms.
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Affiliation(s)
- Corrie V Vincent
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Dawn R D Bignell
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
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Karagoz K, Dadasoglu F, Alaylar B, Kotan R. Evaluation of molecular typing methods for some scab-causing Streptomyces strains from Turkey. World J Microbiol Biotechnol 2024; 40:122. [PMID: 38441818 PMCID: PMC10914884 DOI: 10.1007/s11274-024-03914-2] [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: 01/03/2023] [Accepted: 01/30/2024] [Indexed: 03/07/2024]
Abstract
This study was conducted for identifying phylogenetic relationships between 15 scab-causing Streptomyces species including S. bottropensis, S. europaeiscabiei, S. scabiei, S. stelliscabiei and, other 11 Streptomyces sp. All of the strains were originally isolated from symptomatic potatoes in Erzurum Province, The Eastern Anatolia Region of Turkey. Some morphological and biochemical properties of the strains were defined in our former research. Then, 16 s rRNA regions of them were sequenced. After the sequence data assembly, phylogenetic analyzes were performed. The phylogenetic analyses revealed that the strains are involved in the same major group and, substantially similar to reference strains. Additionally, some subgroup formations were also recorded. Moreover, Repetitive element-based PCR (Rep-PCR), Enterobacterial repetitive intergenic consensus (ERIC-PCR), and BOX-PCR fingerprinting molecular typing methods were used for as molecular typing methods. According to our knowledge, this is the first report on phylogenetic relationships of scab-causing Streptomyces species from Turkey. However, the identification of most pathogenic strains remained at the species level.
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Affiliation(s)
- Kenan Karagoz
- Faculty of Science and Literature, Department of Molecular Biology and Genetics, Agri Ibrahim Cecen University, 04100, Agri, Turkey.
| | - Fatih Dadasoglu
- Agricultural Faculty, Department of Plant Protection, Ataturk University, 25240, Erzurum, Turkey
| | - Burak Alaylar
- Faculty of Science and Literature, Department of Molecular Biology and Genetics, Agri Ibrahim Cecen University, 04100, Agri, Turkey
| | - Recep Kotan
- Agricultural Faculty, Department of Plant Protection, Ataturk University, 25240, Erzurum, Turkey
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Phylogenetic analysis and characterization of arsenic (As) transforming bacterial marker proteins following isolation of As-tolerant indigenous bacteria. Arch Microbiol 2022; 204:660. [PMID: 36190579 DOI: 10.1007/s00203-022-03270-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 09/01/2022] [Accepted: 09/22/2022] [Indexed: 11/02/2022]
Abstract
Marker proteins play a significant role in bacterial arsenic (As) transformation. Phylogenetic analysis and three-dimensional (3D) characteristics of As transforming bacterial marker proteins guide the evolutionary origin and As transforming potential of the species. Indeed, As-tolerant bacteria also show a significant level of As transformation. Hence, characterization of As transforming bacterial marker proteins, isolation of As transforming bacteria, and proper integration of the findings may guide to elucidate how bacteria transform As. Therefore, phylogenetic analysis and 3D characterization of As transforming bacterial marker protein following isolation of potential indigenous As-tolerant indigenous bacteria were done to explore the mechanism of bacterial As transformation. Phylogenetic analysis of ten As transforming marker proteins (arsA, arsB, arsC, arsD, arsR, aioA, arrA, aioB, acr1, and acr3) in 20 potential bacterial genomes (except 19 for the acr3) were studied. Some bacterial genomes featured up to five marker proteins, and therefore, 3D characteristics of the marker proteins were analyzed in those genomes having three-to-five marker proteins. In phylogeny, species in close clades represent their phylogenetic resemblances and may have similar functions. P. aeruginosa, E. coli, and K. pneumonia were found to be more effective due to having the highest number (five) of marker proteins. In 3D protein modeling, most of the marker proteins were found to be active. Among 19 indigenous bacterial isolates, multiple isolates showed tolerance up to 50 mM As(III) and 250 mM As(V), which may potentially transform a significant quantities of As. Hence, integration of the results of phylogenetic analysis, 3D protein characteristics, and As tolerance in the bacterial isolates could guide to explore the mechanism of how bacteria transform As at cellular and molecular levels.
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Nguyen HP, Weisberg AJ, Chang JH, Clarke CR. Streptomyces caniscabiei sp. nov., which causes potato common scab and is distributed across the world. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005225] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fourteen strains of
Streptomyces
isolated from scab lesions on potato are described as members of a novel species based on genetic distance, morphological observation and biochemical analyses. Morphological and biochemical characteristics of these strains are distinct from other described phytopathogenic species. Strain NE06-02DT has white aerial mycelium and grey, cylindrical, smooth spores on rectus-flexibilis spore chains. Members of this species group can utilize most of the International
Streptomyces
Project sugars, utilize melibiose and trehalose, produce melanin, grow on 6–7 % NaCl and pH 5–5.5 media, and are susceptible to oleandomycin (100 µg ml−1), streptomycin (20 µg ml−1) and penicillin G (30 µg ml−1). Though the 16S rRNA gene sequences from several members of this novel species are identical to the
Streptomyces bottropensis
16S rRNA gene sequence, whole-genome average nucleotide identity and multi-locus sequence analysis confirm that the strains are members of a novel species. Strains belonging to this novel species have been isolated from the United States, Egypt and China with the earliest known members being isolated in 1961 from common scab lesions of potato in both California, USA, and Maine, USA. The name Streptomyces caniscabiei sp. nov. is proposed for strain NE06-02DT (=DSM111602T=ATCC TSD-236T) and the other members of this novel species group.
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Affiliation(s)
- Hien P. Nguyen
- Genetic Improvement for Fruits and Vegetables Lab, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | | | - Jeff H. Chang
- Department of Botany and Plant Pathology, Oregon State University, OR 97331, USA
| | - Christopher R. Clarke
- Genetic Improvement for Fruits and Vegetables Lab, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
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Wei Q, Li J, Yang S, Wang W, Min F, Guo M, Zhang S, Dong X, Hu L, Li Z, Wang X. Streptomyces rhizophilus Causes Potato Common Scab Disease. PLANT DISEASE 2022; 106:266-274. [PMID: 34615364 DOI: 10.1094/pdis-09-20-1902-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Common scab (CS) caused by Streptomyces spp. is a significant soilborne potato disease that results in tremendous economic losses globally. Identification of CS-associated species of the genus Streptomyces can enhance understanding of the genetic variation of these bacterial species and is necessary for the control of this epidemic disease. The present study isolated Streptomyces strain 6-2-1(1) from scabby potatoes in Keshan County, Heilongjiang Province, China. PCR analysis confirmed that the strain harbored the characteristic Streptomyces pathogenicity island (PAI) genes (txtA, txtAB, nec1, and tomA). Pathogenicity assays proved that the strain caused typical scab lesions on potato tuber surfaces and necrosis on radish seedlings and potato slices. Subsequently, the strain was systemically characterized at morphological, physiological, biochemical, and phylogenetic levels. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 6-2-1(1) shared 99.86% sequence similarity with Streptomyces rhizophilus JR-41T, isolated initially from bamboo in rhizospheric soil in Korea. PCR amplification followed by Sanger sequencing of the 16S rRNA gene of 164 scabby potato samples collected in Heilongjiang Province from 2019 to 2020 demonstrated that approximately 2% of the tested samples were infected with S. rhizophilus. Taken together, these results demonstrate that S. rhizophilus is capable of causing potato CS disease and may pose a potential challenge to potato production in Heilongjiang Province of China.
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Affiliation(s)
- Qi Wei
- Potato Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150016, China
| | - Jie Li
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Shuai Yang
- Potato Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150016, China
| | - Wenzhong Wang
- Potato Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150016, China
| | - Fanxiang Min
- Potato Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150016, China
| | - Mei Guo
- Potato Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150016, China
| | - Shu Zhang
- Potato Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150016, China
| | - Xuezhi Dong
- Potato Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150016, China
| | - Linshuang Hu
- Potato Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150016, China
| | - Zhugang Li
- Institute of Tillage and Cultivation, Heilongjiang Academy of Agricultural Sciences, Harbin 150016, China
| | - Xiaodan Wang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
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Du J, Li Y, Yin Z, Wang H, Zhang X, Ding X. High-Throughput Customization of Plant Microbiomes for Sustainable Agriculture. FRONTIERS IN PLANT SCIENCE 2020; 11:569742. [PMID: 33013992 PMCID: PMC7505944 DOI: 10.3389/fpls.2020.569742] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/18/2020] [Indexed: 05/02/2023]
Abstract
Soil microorganisms can form a stable dynamic system with plant root systems. The composition of the soil microorganism community is related to the growth and stress resistance of plants; in turn, soil microorganisms are also regulated by plant genotypes and root exudates. Therefore, research on how to identify microorganisms that are beneficial or harmful to plants, study the interaction between microorganisms and plants, and form stable microbial communities for better plant growth plays an important role in sustainable agriculture. It is of great significance to identify and analyze rhizosphere microorganisms and plant endophytes through high-throughput methods, especially to analyze which microorganisms are beneficial to plants, which are harmful to plants, and which are opportunistic pathogens. This review provides a theoretical basis and outlook for the utilization of beneficial microbes in sustainable agriculture.
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Affiliation(s)
- Jianfeng Du
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Yang Li
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Ziyi Yin
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Hongfeng Wang
- Shandong Pengbo Biotechnology Co., Ltd., Tai’an, China
| | | | - Xinhua Ding
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai’an, China
- *Correspondence: Xinhua Ding,
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