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Beattie GA, Bayliss KL, Jacobson DA, Broglie R, Burkett-Cadena M, Sessitsch A, Kankanala P, Stein J, Eversole K, Lichens-Park A. From Microbes to Microbiomes: Applications for Plant Health and Sustainable Agriculture. PHYTOPATHOLOGY 2024; 114:1742-1752. [PMID: 38776137 DOI: 10.1094/phyto-02-24-0054-kc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/22/2024]
Abstract
Plant-microbe interaction research has had a transformative trajectory, from individual microbial isolate studies to comprehensive analyses of plant microbiomes within the broader phytobiome framework. Acknowledging the indispensable role of plant microbiomes in shaping plant health, agriculture, and ecosystem resilience, we underscore the urgent need for sustainable crop production strategies in the face of contemporary challenges. We discuss how the synergies between advancements in 'omics technologies and artificial intelligence can help advance the profound potential of plant microbiomes. Furthermore, we propose a multifaceted approach encompassing translational considerations, transdisciplinary research initiatives, public-private partnerships, regulatory policy development, and pragmatic expectations for the practical application of plant microbiome knowledge across diverse agricultural landscapes. We advocate for strategic collaboration and intentional transdisciplinary efforts to unlock the benefits offered by plant microbiomes and address pressing global issues in food security. By emphasizing a nuanced understanding of plant microbiome complexities and fostering realistic expectations, we encourage the scientific community to navigate the transformative journey from discoveries in the laboratory to field applications. As companies specializing in agricultural microbes and microbiomes undergo shifts, we highlight the necessity of understanding how to approach sustainable agriculture with site-specific management solutions. While cautioning against overpromising, we underscore the excitement of exploring the many impacts of microbiome-plant interactions. We emphasize the importance of collaborative endeavors with societal partners to accelerate our collective capacity to harness the diverse and yet-to-be-discovered beneficial activities of plant microbiomes.
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Affiliation(s)
- Gwyn A Beattie
- International Alliance for Phytobiomes Research, Eau Claire, WI 54701, U.S.A
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA 50014, U.S.A
| | - Kirsty L Bayliss
- Food Futures Institute, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Daniel A Jacobson
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN 37830, U.S.A
| | - Richard Broglie
- International Alliance for Phytobiomes Research, Eau Claire, WI 54701, U.S.A
| | | | - Angela Sessitsch
- International Alliance for Phytobiomes Research, Eau Claire, WI 54701, U.S.A
- Bioresources Unit, AIT Austrian Institute of Technology, 3430 Tulln, Austria
| | | | - Joshua Stein
- International Alliance for Phytobiomes Research, Eau Claire, WI 54701, U.S.A
- Eversole Associates, Arlington, MA 02476, U.S.A
| | - Kellye Eversole
- International Alliance for Phytobiomes Research, Eau Claire, WI 54701, U.S.A
- Eversole Associates, Arlington, MA 02476, U.S.A
| | - Ann Lichens-Park
- International Alliance for Phytobiomes Research, Eau Claire, WI 54701, U.S.A
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Starodumova IP, Dorofeeva LV, Prisyazhnaya NV, Tarlachkov SV, Vasilenko OV, Avtukh AN, Ospennikov YV, Subbotin SA, Evtushenko LI. Rathayibacter tanaceti sp. nov., a Novel Actinobacterium from Tanacetum vulgare Infested by Foliar Nematode Aphelenchoides sp. Curr Microbiol 2024; 81:123. [PMID: 38538917 DOI: 10.1007/s00284-024-03643-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 02/17/2024] [Indexed: 04/23/2024]
Abstract
Two novel yellow-pigmented, rod-shaped and non-motile coryneform actinobacteria, strains VKM Ac-2596T and VKM Ac-2761, were isolated from a plant Tanacetum vulgare (Asteraceae) infested by foliar nematode Aphelenchoides sp. The strains exhibited the highest 16S rRNA gene sequence similarities to Rathayibacter agropyri CA4T (99.71%), Rathayibacter rathayi DSM 7485T (99.65%) and Rathayibacter iranicus VKM Ac-1602T (99.65%). The pairwise average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between VKM Ac-2596T and VKM Ac-2671 towards the type strains of Rathayibacter species did not exceed 85.24% and 29.40%, respectively, that are well below the thresholds for species delineation. The target strains had key chemotaxonomic properties typical of the genus Rathayibacter, namely, the DAB-based peptidoglycan, rhamnose and mannose as the predominant sugars and a rhamnomannan in the cell, the major menaquinone MK-10 and fatty acids of iso-anteiso type, with a large proportion of anteiso-15:0. The strains showed clear differences from the recognized Rathayibacter species in several phenotypic characteristics, including the difference in the composition of cell wall glycopolymers. Based on the results obtained in this study and the data published previously, we provide a description of a new species, Rathayibacter tanaceti sp. nov., with DL-642T (= VKM Ac-2596T = LMG 33114T) as the type strain.
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Affiliation(s)
- Irina P Starodumova
- All-Russian Collection of Microorganisms (VKM), G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Russia, 142290.
| | - Lubov V Dorofeeva
- All-Russian Collection of Microorganisms (VKM), G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Russia, 142290
| | - Natalia V Prisyazhnaya
- All-Russian Collection of Microorganisms (VKM), G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Russia, 142290
| | - Sergey V Tarlachkov
- All-Russian Collection of Microorganisms (VKM), G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Russia, 142290
| | - Oleg V Vasilenko
- All-Russian Collection of Microorganisms (VKM), G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Russia, 142290
| | - Alexander N Avtukh
- All-Russian Collection of Microorganisms (VKM), G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Russia, 142290
| | - Yury V Ospennikov
- All-Russian Collection of Microorganisms (VKM), G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Russia, 142290
| | - Sergei A Subbotin
- Center of Parasitology, A.N. Severtsov Institute of Ecology and Evolution, Moscow, Russia, 119071
- California Department of Food and Agriculture, Sacramento, CA, 95832, USA
| | - Lyudmila I Evtushenko
- All-Russian Collection of Microorganisms (VKM), G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Russia, 142290
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3
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Rivedal HM, Zasada IA, Temple TN, Peetz AB, Núñez-Rodríguez LA, Starchvick RJ, Braithwaite ET. Plant-parasitic Nematodes Associated with Grasses Grown for Seed in the Willamette Valley of Oregon. J Nematol 2024; 56:20240020. [PMID: 38737094 PMCID: PMC11086743 DOI: 10.2478/jofnem-2024-0020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Indexed: 05/14/2024] Open
Abstract
Plant-parasitic nematodes (PPN) are an understudied pathogen group in the Oregon cool-season grass seed cropping system. In this survey, the PPN associated with annual ryegrass, bentgrass, fine fescue, orchardgrass, perennial ryegrass, and tall fescue were determined. Thirty-seven fields were sampled in the 2022 or 2023 growing season by collecting 10 soil cores in each of six 100-m transects for nematode extraction and visual identification. PerMANOVA testing indicated significant differences in PPN community composition across grass host and sampling time. Pratylenchus and Meloidogyne were the most commonly encountered nematodes, with maximum population densities of 1,984 and 2,496 nematodes/100 g soil, respectively. Sequencing of the COX1 gene region indicated the presence of P. crenatus, P. fallax, P. neglectus, P. penetrans, and P. thornei, with some of these species being detected for the first time on these grass hosts. The only Meloidogyne sp. found in these grasses was M. nassi, based upon sequencing of the ITS gene region. This first-of-its-kind survey indicates the need for further assessment of the impact of these PPNs on yield and stand longevity in cool-season grass seed fields in Oregon.
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Affiliation(s)
- H. M. Rivedal
- USDA-ARS Forage Seed and Cereal Research Unit, 3450 SW Campus Way, Corvallis, OR97331
| | - I. A. Zasada
- USDA-ARS Horticultural Crops Disease and Pest Management Unit, 3420 Orchard Ave., Corvallis, OR97330
| | - T. N. Temple
- USDA-ARS Forage Seed and Cereal Research Unit, 3450 SW Campus Way, Corvallis, OR97331
| | - A. B. Peetz
- USDA-ARS Horticultural Crops Disease and Pest Management Unit, 3420 Orchard Ave., Corvallis, OR97330
| | - L. A. Núñez-Rodríguez
- Oregon State University, Department of Botany and Plant Pathology, 2072 Cordley Hall, Corvallis, OR97331
| | - R. J. Starchvick
- Oregon State University, Department of Horticulture, 4017 Agriculture and Life Sciences Building, Corvallis, OR97331
| | - E. T. Braithwaite
- Oregon State University, Department of Horticulture, 4017 Agriculture and Life Sciences Building, Corvallis, OR97331
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Li Y, Tao S, Liang Y. Time-Course Responses of Apple Leaf Endophytes to the Infection of Gymnosporangium yamadae. J Fungi (Basel) 2024; 10:128. [PMID: 38392801 PMCID: PMC10890309 DOI: 10.3390/jof10020128] [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: 12/26/2023] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 02/24/2024] Open
Abstract
Apple rust, caused by Gymnosporangium yamadae, poses a significant challenge to apple production. Prior studies have underscored the pivotal role played by endophytic microbial communities, intimately linked with the host, in influencing plant diseases and their pathogenic outcomes. The objective of this study is to scrutinize alternations in endophytic microbial communities within apple leaves at different stages of apple rust using high-throughput sequencing technology. The findings revealed a discernible pattern characterized by an initial increase and subsequent decrease in the alpha diversity of microbial communities in diseased leaves. A microbial co-occurrence network analysis revealed that the complexity of the bacterial community in diseased leaves diminished initially and then rebounded during the progression of the disease. Additionally, employing the PICRUSt2 platform, this study provided preliminary insights into the functions of microbial communities at specific disease timepoints. During the spermogonial stage, endophytic bacteria particularly exhibited heightened activity in genetic information processing, metabolism, and environmental information processing pathways. Endophytic fungi also significantly enriched a large number of metabolic pathways during the spermogonial stage and aecial stage, exhibiting abnormally active life activities. These findings establish a foundation for comprehending the role of host endophytes in the interaction between pathogens and hosts. Furthermore, they offer valuable insights for the development and exploitation of plant endophytic resources, thereby contributing to enhanced strategies for managing apple rust.
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Affiliation(s)
- Yunfan Li
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing 100083, China
| | - Siqi Tao
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing 100083, China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan 518000, China
| | - Yingmei Liang
- Museum of Beijing Forestry University, Beijing Forestry University, Beijing 100083, China
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Vieira P, Kantor MR, Jansen A, Handoo ZA, Eisenback JD. Cellular insights of beech leaf disease reveal abnormal ectopic cell division of symptomatic interveinal leaf areas. PLoS One 2023; 18:e0292588. [PMID: 37797062 PMCID: PMC10553357 DOI: 10.1371/journal.pone.0292588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 09/25/2023] [Indexed: 10/07/2023] Open
Abstract
The beech leaf disease nematode, Litylenchus crenatae subsp. mccannii, is recognized as a newly emergent nematode species that causes beech leaf disease (BLD) in beech trees (Fagus spp.) in North America. Changes of leaf morphology before emergence from the bud induced by BLD can provoke dramatic effects on the leaf architecture and consequently to tree performance and development. The initial symptoms of BLD appear as dark green, interveinal banding patterns of the leaf. Despite the fast progression of this disease, the cellular mechanisms leading to the formation of such aberrant leaf phenotype remains totally unknown. To understand the cellular basis of BLD, we employed several types of microscopy to provide an exhaustive characterization of nematode-infected buds and leaves. Histological sections revealed a dramatic cell change composition of these nematode-infected tissues. Diseased bud scale cells were typically hypertrophied and showed a high variability of size. Moreover, while altered cell division had no influence on leaf organogenesis, induction of cell proliferation on young leaf primordia led to a dramatic change in cell layer architecture. Hyperplasia and hypertrophy of the different leaf cell layers, coupled with an abnormal proliferation of chloroplasts especially in the mesophyll cell layers, resulted in the typical interveinal leaf banding. These discrepancies in leaf cell structure were depicted by an abnormal rate of cellular division of the leaf interveinal areas infected by the nematode, promoting significant increase of cell size and leaf thickness. The formation of symptomatic BLD leaves is therefore orchestrated by distinct cellular processes, to enhance the value of these feeding sites and to improve their nutrition status for the nematode. Our findings thus uncover relevant cellular events and provide a structural framework to understand this important disease.
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Affiliation(s)
- Paulo Vieira
- Mycology and Nematology Genetic Diversity and Biology Laboratory, United States Department of Agriculture—Agricultural Research Service, Beltsville, Maryland, United States of America
| | - Mihail R. Kantor
- Plant Pathology & Environmental Microbiology Department, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Andrew Jansen
- Electron and Confocal Microscopy Unit, United States Department of Agriculture–Agricultural Research Service, Beltsville, Maryland, United States of America
| | - Zafar A. Handoo
- Mycology and Nematology Genetic Diversity and Biology Laboratory, United States Department of Agriculture—Agricultural Research Service, Beltsville, Maryland, United States of America
| | - Jonathan D. Eisenback
- School of Plant and Environmental Science, Virginia Tech, Blacksburg, Virginia, United States of America
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6
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Draft Genome Sequences of 9 Actinobacteria from the Family
Microbacteriaceae
Associated with Insect- and Nematode-Damaged Plants. Microbiol Resour Announc 2022; 11:e0048722. [PMID: 36043868 PMCID: PMC9584284 DOI: 10.1128/mra.00487-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Draft genome sequences of 9 strains of known and putative new species of Microbacteriaceae isolated from insect- and nematode-damaged plants were generated using Illumina technology. The data obtained will contribute to the development of the genome-based prokaryote taxonomy and the knowledge on the biology of the microbial group investigated.
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7
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Tancos MA, McMahon MB, Garrett WM, Luster DG, Rogers EE. Comparative Secretome Analyses of Toxigenic and Atoxigenic Rathayibacter Species. PHYTOPATHOLOGY 2021; 111:1530-1540. [PMID: 33499664 DOI: 10.1094/phyto-11-20-0495-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Phytopathogenic Rathayibacter species are unique bacterial plant pathogens because they are obligately vectored by plant parasitic anguinid nematodes to the developing seedheads of forage grasses and cereals. This understudied group of plant-associated Actinomycetes includes the neurotoxigenic plant pathogen R. toxicus, which causes annual ryegrass toxicity in grazing livestock. R. toxicus is currently endemic to Australia and is listed as a plant pathogen select agent by the U.S. Department of Agriculture-Animal and Plant Health Inspection Service. The complex Rathayibacter disease cycle requires intimate interactions with the nematode vector and plant hosts, which warrants an increased understanding of the secretory and surface-associated proteins that mediate these diverse eukaryotic interactions. Here we present the first comparative secretome analysis for this complex, nematode-vectored Rathayibacter genus that compares the three agronomically damaging toxigenic and atoxigenic Rathayibacter species, R. toxicus, R. iranicus, and R. tritici. The exoproteomic comparison identified 1,423 unique proteins between the three species via liquid chromatography-tandem mass spectrometry, leading to the identification of putative pathogenicity-related proteins and proteins that may mediate nematode attachment. Of the uniquely identified proteins, 94 homologous proteins were conserved between the three Rathayibacter exoproteomes and comprised between 43.4 and 58.6% of total protein abundance. Comparative analyses revealed both conserved and uniquely expressed extracellular proteins, which, interestingly, had more similarities to extracellular proteins commonly associated with bacterial animal pathogens than classic plant pathogens. This comparative exoproteome analysis will facilitate the characterization of proteins essential for vector attachment and host colonization and assist in the development of serological diagnostic assays.
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Affiliation(s)
- Matthew A Tancos
- Foreign Disease-Weed Science Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Frederick, MD
| | - Michael B McMahon
- Foreign Disease-Weed Science Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Frederick, MD
| | - Wesley M Garrett
- Animal Biosciences and Biotechnology Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD
| | - Douglas G Luster
- Foreign Disease-Weed Science Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Frederick, MD
| | - Elizabeth E Rogers
- Foreign Disease-Weed Science Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Frederick, MD
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Shashkov AS, Tul'skaya EM, Potekhina NV, Dmitrenok AS, Senchenkova SN, Zaychikov VA, Dorofeeva LV, Evtushenko LI. D-Rhamnan and Pyruvate-Containing Teichuronic Acid from the Cell Wall of Rathayibacter sp. VKM Ac-2759. BIOCHEMISTRY (MOSCOW) 2021; 86:506-516. [PMID: 33941071 DOI: 10.1134/s0006297921040118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Rathayibacter sp. VKM Ac-2759 (family Microbacteriaceae, class Actinobacteria) contains two glycopolymers in the cell wall. The main chain of rhamnan, glycopolymer 1, is built from the repeating tetrasaccharide units carrying terminal arabinofuranose residues at the non-reducing end, →3)-α-[α-D-Araf-(1→2)]-D-Rhap-(1→2)-α-D-Rhap-(1→3)-α-D-Rhap-(1→2)-α-D-Rhap-(1→. Similar to other described Rathayibacter species, rhamnose in the neutral glycopolymer of the VKM Ac-2759 strain is present in the D-configuration. Acetalated with pyruvic acid teichuronic acid, glycopolymer 2, is composed of the repeating tetrasaccharide units, →4)-β-D-GlcpA-(1→4)-β-D-Galp-(1→4)-β-D-Glcp-(1→3)-β-[4,6-S-Pyr]-D-Manp-(1→. Glycopolymers 1 and 2 were identified in prokaryotic microorganisms for the first time and their structures were established by chemical analysis and NMR spectroscopy. The obtained data can be used in taxonomic research, as well as for elucidating the mechanisms of plant colonization and infection by bacteria of the Rathayibacter genus.
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Affiliation(s)
- Alexander S Shashkov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Elena M Tul'skaya
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
| | - Natalia V Potekhina
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Andrey S Dmitrenok
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Sofia N Senchenkova
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Vlad A Zaychikov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Lubov V Dorofeeva
- All-Russian Collection of Microorganisms (VKM), Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Lyudmila I Evtushenko
- All-Russian Collection of Microorganisms (VKM), Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
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9
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Field-Deployable Recombinase Polymerase Amplification Assay for Specific, Sensitive and Rapid Detection of the US Select Agent and Toxigenic Bacterium, Rathayibacter toxicus. BIOLOGY 2021; 10:biology10070620. [PMID: 34356474 PMCID: PMC8301136 DOI: 10.3390/biology10070620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/15/2021] [Accepted: 06/30/2021] [Indexed: 11/17/2022]
Abstract
Simple Summary Early, accurate, and rapid detection of R. toxicus is extremely important to improve inspections of imported annual ryegrass hay and seed at ports of entry and enhance in-field detection. RPA is a comparatively new, easy to use, and robust technology that can be performed in the palm of the hand without losing specificity. The RPA assay was more sensitive than endpoint PCR and did not require lab equipment in the field. The developed assay has tremendous applications for in-field plant diagnostics and biosecurity surveillance. Abstract Rathayibacter toxicus is a toxigenic bacterial pathogen of several grass species and is responsible for massive livestock deaths in Australia and South Africa. Due to concern for animal health and livestock industries, it was designated a U.S. Select Agent. A rapid, accurate, and sensitive in-field detection method was designed to assist biosecurity surveillance surveys and to support export certification of annual ryegrass hay and seed. Complete genomes from all known R. toxicus populations were explored, unique diagnostic sequences identified, and target-specific primers and a probe for recombinase polymerase amplification (RPA) and endpoint PCR were designed. The RPA reaction ran at 37 °C and a lateral flow device (LFD) was used to visualize the amplified products. To enhance reliability and accuracy, primers and probes were also designed to detect portions of host ITS regions. RPA assay specificity and sensitivity were compared to endpoint PCR using appropriate inclusivity and exclusivity panels. The RPA assay sensitivity (10 fg) was 10 times more sensitive than endpoint PCR with and without a host DNA background. In comparative tests, the RPA assay was unaffected by plant-derived amplification inhibitors, unlike the LAMP and end-point PCR assays. In-field validation of the RPA assay at multiple sites in South Australia confirmed the efficiency, specificity, and applicability of the RPA assay. The RPA assay will support disease management and evidence-based in-field biosecurity decisions.
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10
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Arif M, Busot GY, Mann R, Rodoni B, Stack JP. Multiple internal controls enhance reliability for PCR and real time PCR detection of Rathayibacter toxicus. Sci Rep 2021; 11:8365. [PMID: 33863977 PMCID: PMC8052354 DOI: 10.1038/s41598-021-87815-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/26/2021] [Indexed: 01/05/2023] Open
Abstract
Rathayibacter toxicus is a toxigenic bacterial plant pathogen indigenous to Australia and South Africa. A threat to livestock industries globally, the bacterium was designated a U.S. Select Agent. Biosecurity and phytosanitary concerns arise due to the international trade of seed and hay that harbor the bacterium. Accurate diagnostic protocols to support phytosanitary decisions, delineate areas of freedom, and to support research are required to address those concerns. Whole genomes of three genetic populations of R. toxicus were sequenced (Illumina MiSeq platforms), assembled and genomic regions unique to each population identified. Highly sensitive and specific TaqMan qPCR and multiplex endpoint PCR assays were developed for the detection and identification of R. toxicus to the population level of discrimination. Specificity was confirmed with appropriate inclusivity and exclusivity panels; no cross reactivity was observed. The endpoint multiplex PCR and TaqMan qPCR assays detected 10 fg and 1 fg of genomic DNA, respectively. To enhance reliability and increase confidence in results, three types of internal controls with no or one extra primer were developed and incorporated into each assay to detect both plant and artificial internal controls. Assays were validated by blind ring tests with multiple operators in three international laboratories.
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Affiliation(s)
- Mohammad Arif
- Department of Plant and Environmental Protection Sciences, University of Hawaii At Manoa, Honolulu, HI, USA.,Department of Plant Pathology, Great Plains Diagnostic Network, Kansas State University, 4024 Throckmorton Plant Sciences Center, Manhattan, KS, 66506-5502, USA.,Plant Biosecurity Cooperative Research Centre, Canberra, Australia
| | - Grethel Y Busot
- Department of Plant Pathology, Great Plains Diagnostic Network, Kansas State University, 4024 Throckmorton Plant Sciences Center, Manhattan, KS, 66506-5502, USA.,Plant Biosecurity Cooperative Research Centre, Canberra, Australia.,Inari Agricultural Inc., One Kendall Square, Cambridge, MA, USA
| | - Rachel Mann
- Department of Economic Development, Jobs, Transport and Resources, Biosciences Research Division, Bundoora, VIC, Australia.,Plant Biosecurity Cooperative Research Centre, Canberra, Australia
| | - Brendan Rodoni
- Department of Economic Development, Jobs, Transport and Resources, Biosciences Research Division, Bundoora, VIC, Australia.,Plant Biosecurity Cooperative Research Centre, Canberra, Australia
| | - James P Stack
- Department of Plant Pathology, Great Plains Diagnostic Network, Kansas State University, 4024 Throckmorton Plant Sciences Center, Manhattan, KS, 66506-5502, USA. .,Plant Biosecurity Cooperative Research Centre, Canberra, Australia.
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11
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Draft Genome Sequences of 28 Actinobacteria of the Family Microbacteriaceae Associated with Nematode-Infected Plants. Microbiol Resour Announc 2021; 10:10/9/e01400-20. [PMID: 33664138 PMCID: PMC7936636 DOI: 10.1128/mra.01400-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Draft genome sequences of 28 strains of Microbacteriaceae from plants infested by plant-parasitic nematodes were obtained using Illumina technology. The sequence data will provide useful baseline information for the development of comparative genomics and systematics of Microbacteriaceae and facilitate understanding of molecular mechanisms involved in interactions between plants and nematode-associated bacterial complexes.
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12
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Draft Genome Sequences of 13 Plant-Associated Actinobacteria of the Family Microbacteriaceae. Microbiol Resour Announc 2020; 9:9/38/e00795-20. [PMID: 32943566 PMCID: PMC7498432 DOI: 10.1128/mra.00795-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Draft genome sequences of 13 bacterial strains from the family Microbacteriaceae were generated using Illumina technology. The genome sizes varied from 3.0 to 4.8 Mb, and the DNA G+C content was 68.1 to 72.5%. The sequences obtained will contribute to the development of genome-based taxonomy and understanding of molecular interactions between bacteria and plants.
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Complete and Draft Genome Sequences of 12 Plant-Associated Rathayibacter Strains of Known and Putative New Species. Microbiol Resour Announc 2020; 9:9/22/e00316-20. [PMID: 32467269 PMCID: PMC7256256 DOI: 10.1128/mra.00316-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Complete and draft genome sequences of 12 Rathayibacter strains were generated using Oxford Nanopore and Illumina technologies. The genome sizes of these strains are 3.21 to 4.61 Mb, with high G+C content (67.2% to 72.7%) genomic DNA. Genomic data will provide useful baseline information for natural taxonomy and comparative genomics of members of the genus Rathayibacter. Complete and draft genome sequences of 12 Rathayibacter strains were generated using Oxford Nanopore and Illumina technologies. The genome sizes of these strains are 3.21 to 4.61 Mb, with high G+C content (67.2% to 72.7%) genomic DNA. Genomic data will provide useful baseline information for natural taxonomy and comparative genomics of members of the genus Rathayibacter.
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Shashkov AS, Tul’skaya EM, Streshinskaya GM, Dmitrenok AS, Potekhina NV, Senchenkova SN, Piskunkova NF, Dorofeeva LV, Evtushenko LI. Rhamnomannans and Teichuronic Acid from the Cell Wall of Rathayibacter tritici VKM Ac-1603T. BIOCHEMISTRY (MOSCOW) 2020; 85:369-377. [DOI: 10.1134/s0006297920030128] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Yasuhara-Bell J, Arif M, Busot GY, Mann R, Rodoni B, Stack JP. Comparative Genomic Analysis Confirms Five Genetic Populations of the Select Agent, Rathayibacter toxicus. Microorganisms 2020; 8:E366. [PMID: 32150860 PMCID: PMC7143919 DOI: 10.3390/microorganisms8030366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/24/2020] [Accepted: 03/03/2020] [Indexed: 02/01/2023] Open
Abstract
Rathayibacter toxicus is a Gram-positive, nematode-vectored bacterium that infects several grass species in the family Poaceae. Unique in its genus, R. toxicus has the smallest genome, possesses a complete CRISPR-Cas system, a vancomycin-resistance cassette, produces tunicamycin, a corynetoxin responsible for livestock deaths in Australia, and is designated a Select Agent in the United States. In-depth, genome-wide analyses performed in this study support the previously designated five genetic populations, with a core genome comprising approximately 80% of the genome for all populations. Results varied as a function of the type of analysis and when using different bioinformatics tools for the same analysis; e.g., some programs failed to identify specific genomic regions that were actually present. The software variance highlights the need to verify bioinformatics results by additional methods; e.g., PCR, mapping genes to genomes, use of multiple algorithms). These analyses suggest the following relationships among populations: RT-IV ↔ RT-I ↔ RT-II ↔ RT-III ↔ RT-V, with RT-IV and RT-V being the most unrelated. This is the most comprehensive analysis of R. toxicus that included populations RT-I and RT-V. Future studies require underrepresented populations and more recent isolates from varied hosts and geographic locations.
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Affiliation(s)
- Jarred Yasuhara-Bell
- Department of Plant Pathology, Kansas State University, 1712 Claflin Road, 4024 Throckmorton Plant Science Center, Manhattan, KS 66506, USA; (J.Y.-B.); (G.Y.B.)
- Plant Biosecurity Cooperative Research Centre, CRC for National Plant Biosecurity, Level 2, Building 22, Innovation Centre, University Drive, University of Canberra, Bruce, Australian Capital Territory, Canberra 2617, Australia; (M.A.); (R.M.); (B.R.)
| | - Mohammad Arif
- Plant Biosecurity Cooperative Research Centre, CRC for National Plant Biosecurity, Level 2, Building 22, Innovation Centre, University Drive, University of Canberra, Bruce, Australian Capital Territory, Canberra 2617, Australia; (M.A.); (R.M.); (B.R.)
- Department of Plant and Environmental Protection Sciences, University of Hawai`i at Mānoa, Honolulu, HI 96822, USA
| | - Grethel Y. Busot
- Department of Plant Pathology, Kansas State University, 1712 Claflin Road, 4024 Throckmorton Plant Science Center, Manhattan, KS 66506, USA; (J.Y.-B.); (G.Y.B.)
- Plant Biosecurity Cooperative Research Centre, CRC for National Plant Biosecurity, Level 2, Building 22, Innovation Centre, University Drive, University of Canberra, Bruce, Australian Capital Territory, Canberra 2617, Australia; (M.A.); (R.M.); (B.R.)
| | - Rachel Mann
- Plant Biosecurity Cooperative Research Centre, CRC for National Plant Biosecurity, Level 2, Building 22, Innovation Centre, University Drive, University of Canberra, Bruce, Australian Capital Territory, Canberra 2617, Australia; (M.A.); (R.M.); (B.R.)
- Department of Jobs, Precincts and Regions, Microbial Sciences, Pests & Diseases, Agriculture Victoria, AgriBio Centre, La Trobe University, 5 Ring Rd, Bundoora, Victoria 3083, Australia
| | - Brendan Rodoni
- Plant Biosecurity Cooperative Research Centre, CRC for National Plant Biosecurity, Level 2, Building 22, Innovation Centre, University Drive, University of Canberra, Bruce, Australian Capital Territory, Canberra 2617, Australia; (M.A.); (R.M.); (B.R.)
- Department of Jobs, Precincts and Regions, Microbial Sciences, Pests & Diseases, Agriculture Victoria, AgriBio Centre, La Trobe University, 5 Ring Rd, Bundoora, Victoria 3083, Australia
| | - James P. Stack
- Department of Plant Pathology, Kansas State University, 1712 Claflin Road, 4024 Throckmorton Plant Science Center, Manhattan, KS 66506, USA; (J.Y.-B.); (G.Y.B.)
- Plant Biosecurity Cooperative Research Centre, CRC for National Plant Biosecurity, Level 2, Building 22, Innovation Centre, University Drive, University of Canberra, Bruce, Australian Capital Territory, Canberra 2617, Australia; (M.A.); (R.M.); (B.R.)
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Luster DG, McMahon MB, Carter ML, Sechler AJ, Rogers EE, Schroeder BK, Murray TD. Immunoreagents for development of a diagnostic assay specific for Rathayibacter toxicus. FOOD AGR IMMUNOL 2020. [DOI: 10.1080/09540105.2020.1714554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Affiliation(s)
- Douglas G. Luster
- United States Department of Agriculture, Agricultural Research Service, Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD, USA
| | - Michael B. McMahon
- United States Department of Agriculture, Agricultural Research Service, Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD, USA
| | - Melissa L. Carter
- United States Department of Agriculture, Agricultural Research Service, Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD, USA
| | - Aaron J. Sechler
- United States Department of Agriculture, Agricultural Research Service, Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD, USA
| | - Elizabeth E. Rogers
- United States Department of Agriculture, Agricultural Research Service, Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD, USA
| | - Brenda K. Schroeder
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID, USA
| | - Timothy D. Murray
- Department of Plant Pathology, Washington State University, Pullman, WA, USA
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Tancos MA, Sechler AJ, Davis EW, Chang JH, Schroeder BK, Murray TD, Rogers EE. The Identification and Conservation of Tunicaminyluracil-Related Biosynthetic Gene Clusters in Several Rathayibacter Species Collected From Australia, Africa, Eurasia, and North America. Front Microbiol 2020; 10:2914. [PMID: 31998251 PMCID: PMC6965331 DOI: 10.3389/fmicb.2019.02914] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 12/03/2019] [Indexed: 01/12/2023] Open
Abstract
Tunicaminyluracil antibiotics are a novel class of toxigenic glycolipids that are synthesized by several soil-associated Actinomycetes. The acquisition of a tunicaminyluracil biosynthetic gene cluster (TGC) in Rathayibacter toxicus has led to the emergence of the only described, naturally occurring tunicaminyluracil-associated mammalian disease, annual ryegrass toxicity of livestock. Endemic to Australia, R. toxicus is obligately vectored by Anguinid seed gall nematodes to the developing seedheads of forage grasses, in which the bacteria synthesize tunicaminyluracils that may subsequently be consumed by livestock and result in high rates of mortality and morbidity. The potential impact of R. toxicus on U.S. agriculture has led the U.S. Department of Agriculture - Animal and Plant Health Inspection Service to list R. toxicus as a Plant Pathogen Select Agent. R. toxicus is the only characterized phytopathogenic bacterium to produce tunicaminyluracils, but numerous R. toxicus-like livestock poisonings outside Australia suggest additional bacterial sources of tunicaminyluracils may exist. To investigate the conservation of the TGC in R. toxicus and whether the TGC is present in other Rathayibacter species, we analyzed genome sequences of members of the Rathayibacter genus. Putative TGCs were identified in genome sequences of R. toxicus, R. iranicus, R. agropyri, and an undescribed South African Rathayibacter species. In the latter three species, the putative TGCs have homologs of tunicaminyluracil-related genes essential for toxin production, but the TGCs differ in gene number and order. The TGCs appear at least partially functional because in contrast to atoxigenic species, TGC-containing Rathayibacter species were each able to tolerate exogenous applications of tunicamycin from Streptomyces chartreusis. The North American R. agropyri TGC shows extensive diversity among the sequenced isolates, with presense/absense polymorphisms in multiple genes or even the whole TGC. R. agropyri TGC structure does not appear to correlate with date or location of isolate collection. The conservation and identification of tunicaminyluracil-related gene clusters in three additional Rathayibacter species isolated from South Africa, the Middle East, and the United States, suggests a wider global distribution of potentially neurotoxigenic plant-associated bacteria. This potential for additional endemic and exotic toxigenic Rathayibacter species could have widespread and severe implications for agriculture.
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Affiliation(s)
- Matthew A. Tancos
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture-Agricultural Research Service, Frederick, MD, United States
| | - Aaron J. Sechler
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture-Agricultural Research Service, Frederick, MD, United States
| | - Edward W. Davis
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Jeff H. Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Brenda K. Schroeder
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID, United States
| | - Timothy D. Murray
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | - Elizabeth E. Rogers
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture-Agricultural Research Service, Frederick, MD, United States
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Thapa SP, Davis EW, Lyu Q, Weisberg AJ, Stevens DM, Clarke CR, Coaker G, Chang JH. The Evolution, Ecology, and Mechanisms of Infection by Gram-Positive, Plant-Associated Bacteria. ANNUAL REVIEW OF PHYTOPATHOLOGY 2019; 57:341-365. [PMID: 31283433 DOI: 10.1146/annurev-phyto-082718-100124] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Gram-positive bacteria are prominent members of plant-associated microbial communities. Although many are hypothesized to be beneficial, some are causative agents of economically important diseases of crop plants. Because the features of Gram-positive bacteria are fundamentally different relative to those of Gram-negative bacteria, the evolution and ecology as well as the mechanisms used to colonize and infect plants also differ. Here, we discuss recent advances in our understanding of Gram-positive, plant-associated bacteria and provide a framework for future research directions on these important plant symbionts.
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Affiliation(s)
- Shree P Thapa
- Department of Plant Pathology, University of California, Davis, California 95616, USA
| | - Edward W Davis
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA;
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon 97331, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USA
| | - Qingyang Lyu
- Department of Plant Pathology, University of California, Davis, California 95616, USA
| | - Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA;
| | - Danielle M Stevens
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA;
- Integrative Genetics and Genomics, University of California, Davis, California 95616, USA
| | - Christopher R Clarke
- Genetic Improvement for Fruits and Vegetables Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, Maryland 20705, USA
| | - Gitta Coaker
- Department of Plant Pathology, University of California, Davis, California 95616, USA
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA;
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon 97331, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USA
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Dmitrenok AS, Shashkov AS, Streshinskaya GM, Tul'skaya EM, Potekhina NV, Senchenkova SN, Dorofeeva LV, Evtushenko LI. New glycopolymers containing both D- and L-rhamnopyranoses from Rathayibacter iranicus VKM Ac-1602T cell wall. Carbohydr Res 2019; 482:107728. [DOI: 10.1016/j.carres.2019.06.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 06/10/2019] [Accepted: 06/12/2019] [Indexed: 10/26/2022]
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Abstract
Rathayibacter toxicus is a toxin-producing species found in Australia and is often fatal to grazing animals. The threat of introduction of the species into the United States led to its inclusion in the Federal Select Agent Program, which makes R. toxicus a highly regulated species. This work provides novel insights into the evolution of R. toxicus. R. toxicus is the only species in the genus to have acquired a CRISPR adaptive immune system to protect against bacteriophages. Results suggest that coexistence with the bacteriophage NCPPB3778 led to the massive shrinkage of the R. toxicus genome, species divergence, and the maintenance of low genetic diversity in extant bacterial groups. This work contributes to an understanding of the evolution and ecology of an agriculturally important species of bacteria. Rathayibacter toxicus is a species of Gram-positive, corynetoxin-producing bacteria that causes annual ryegrass toxicity, a disease often fatal to grazing animals. A phylogenomic approach was employed to model the evolution of R. toxicus to explain the low genetic diversity observed among isolates collected during a 30-year period of sampling in three regions of Australia, gain insight into the taxonomy of Rathayibacter, and provide a framework for studying these bacteria. Analyses of a data set of more than 100 sequenced Rathayibacter genomes indicated that Rathayibacter forms nine species-level groups. R. toxicus is the most genetically distant, and evidence suggested that this species experienced a dramatic event in its evolution. Its genome is significantly reduced in size but is colinear to those of sister species. Moreover, R. toxicus has low intergroup genomic diversity and almost no intragroup genomic diversity between ecologically separated isolates. R. toxicus is the only species of the genus that encodes a clustered regularly interspaced short palindromic repeat (CRISPR) locus and that is known to host a bacteriophage parasite. The spacers, which represent a chronological history of infections, were characterized for information on past events. We propose a three-stage process that emphasizes the importance of the bacteriophage and CRISPR in the genome reduction and low genetic diversity of the R. toxicus species.
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21
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Shashkov AS, Tul’skaya EM, Dmitrenok AS, Streshinskaya GM, Potekhina NV, Senchenkova SN, Piskunkova NF, Dorofeeva LV, Evtushenko LI. Rhamnose-Containing Cell Wall Glycopolymers from Rathayibacter toxicus VKM Ac-1600 and “Rathayibacter tanaceti” VKM Ac-2596. BIOCHEMISTRY (MOSCOW) 2018; 83:717-726. [DOI: 10.1134/s0006297918060093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Barrantes-Infante BL, Schroeder BK, Subbotin SA, Murray TD. Afrina sporoboliae sp. n. (Nematoda: Anguinidae) Associated with Sporobolus cryptandrus from Idaho, United States: Phylogenetic Relationships and Population Structure. PHYTOPATHOLOGY 2018; 108:768-779. [PMID: 29327647 DOI: 10.1094/phyto-12-17-0395-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The dropseed gall-forming nematode, Afrina sporoboliae sp. n., is described from seed galls of Sporobolus cryptandrus (Poaceae: Chloridoideae: Sporobolinae) collected in Idaho, USA. This is the third report of an Afrina species in North America and the first report of this genus in a natural plant population on this continent. Morphological, morphometric, and molecular analyses placed this nematode in genus Afrina and demonstrated that it differs from Afrina hyparrheniae and Afrina spermophaga by having longer body and stylet lengths for females and males, and from Afrina wevelli by the absence of tip irregularities on the tails of female and presence of lips noticeably protruding beyond the body contour. The new species has several characters that overlap with Afrina tumefaciens, but differs from this species by inducing seed galls, whereas Afrina tumefaciens induces ovoid galls on stems, leaves, and in flower heads. Evolutionary relationships of Afrina sporoboliae sp. n. with other representatives of the family Anguinidae are presented based on analysis of the internal transcribed spacer (ITS)1-5.8S-ITS2 rRNA and the D2-D3 regions of the rRNA genes. Analysis of 270 sequences of the cox1 gene from 25 populations of Afrina sporoboliae sp. n. revealed seven haplotypes with sequence divergence up to 5%. This study did not demonstrate a significant positive relationship between genetic difference and geographic distance. Seed gall nematodes are important quarantine pests in many countries. The association of this and other seed gall nematodes with Rathayibacter species and their ability to serve as vectors, especially of R. toxicus, is of concern for U.S. agriculture.
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Affiliation(s)
- Bianca L Barrantes-Infante
- First and fourth authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; second author: Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow 83844-2329; and third author: California Department of Food and Agriculture, Plant Pest Diagnostic Center, 3294 Meadowview Road, Sacramento 95832, and Center of Parasitology of A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Leninskii Prospect 33, Moscow, 117071, Russia
| | - Brenda K Schroeder
- First and fourth authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; second author: Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow 83844-2329; and third author: California Department of Food and Agriculture, Plant Pest Diagnostic Center, 3294 Meadowview Road, Sacramento 95832, and Center of Parasitology of A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Leninskii Prospect 33, Moscow, 117071, Russia
| | - Sergei A Subbotin
- First and fourth authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; second author: Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow 83844-2329; and third author: California Department of Food and Agriculture, Plant Pest Diagnostic Center, 3294 Meadowview Road, Sacramento 95832, and Center of Parasitology of A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Leninskii Prospect 33, Moscow, 117071, Russia
| | - Timothy D Murray
- First and fourth authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; second author: Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow 83844-2329; and third author: California Department of Food and Agriculture, Plant Pest Diagnostic Center, 3294 Meadowview Road, Sacramento 95832, and Center of Parasitology of A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Leninskii Prospect 33, Moscow, 117071, Russia
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Dorofeeva LV, Starodumova IP, Krauzova VI, Prisyazhnaya NV, Vinokurova NG, Lysanskaya VY, Tarlachkov SV, Evtushenko LI. Rathayibacter oskolensis sp. nov., a novel actinobacterium from Androsace koso-poljanskii Ovcz. (Primulaceae) endemic to the Central Russian Upland. Int J Syst Evol Microbiol 2018. [DOI: 10.1099/ijsem.0.002681] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Lubov V. Dorofeeva
- All-Russian Collection of Microorganisms (VKM), G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, 142290, Russia
| | - Irina P. Starodumova
- Pushchino State Institute of Natural Sciences, Pushchino, 142290, Russia
- All-Russian Collection of Microorganisms (VKM), G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, 142290, Russia
| | - Valentina I. Krauzova
- All-Russian Collection of Microorganisms (VKM), G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, 142290, Russia
| | - Natalia V. Prisyazhnaya
- All-Russian Collection of Microorganisms (VKM), G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, 142290, Russia
| | - Natalia G. Vinokurova
- All-Russian Collection of Microorganisms (VKM), G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, 142290, Russia
| | - Valentina Y. Lysanskaya
- All-Russian Collection of Microorganisms (VKM), G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, 142290, Russia
| | - Sergey V. Tarlachkov
- All-Russian Collection of Microorganisms (VKM), G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, 142290, Russia
- Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, 142290, Russia
| | - Lyudmila I. Evtushenko
- All-Russian Collection of Microorganisms (VKM), G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, 142290, Russia
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Baek KY, Lee HH, Son GJ, Lee PA, Roy N, Seo YS, Lee SW. Specific and Sensitive Primers Developed by Comparative Genomics to Detect Bacterial Pathogens in Grains. THE PLANT PATHOLOGY JOURNAL 2018; 34:104-112. [PMID: 29628816 PMCID: PMC5880354 DOI: 10.5423/ppj.oa.11.2017.0250] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 01/11/2018] [Accepted: 01/11/2018] [Indexed: 05/02/2023]
Abstract
Accurate and rapid detection of bacterial plant pathogen is the first step toward disease management and prevention of pathogen spread. Bacterial plant pathogens Clavibacter michiganensis subsp. nebraskensis (Cmn), Pantoea stewartii subsp. stewartii (Pss), and Rathayibacter tritici (Rt) cause Goss's bacterial wilt and blight of maize, Stewart's wilt of maize and spike blight of wheat and barley, respectively. The bacterial diseases are not globally distributed and not present in Korea. This study adopted comparative genomics approach and aimed to develop specific primer pairs to detect these three bacterial pathogens. Genome comparison among target pathogens and their closely related bacterial species generated 15-20 candidate primer pairs per bacterial pathogen. The primer pairs were assessed by a conventional PCR for specificity against 33 species of Clavibacter, Pantoea, Rathayibacter, Pectobacterium, Curtobacterium. The investigation for specificity and sensitivity of the primer pairs allowed final selection of one or two primer pairs per bacterial pathogens. In our assay condition, a detection limit of Pss and Cmn was 2 pg/μl of genomic DNA per PCR reaction, while the detection limit for Rt primers was higher. The selected primers could also detect bacterial cells up to 8.8 × 103 cfu to 7.84 × 104 cfu per gram of grain seeds artificially infected with corresponding bacterial pathogens. The primer pairs and PCR assay developed in this study provide an accurate and rapid detection method for three bacterial pathogens of grains, which can be used to investigate bacteria contamination in grain seeds and to ultimately prevent pathogen dissemination over countries.
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Affiliation(s)
- Kwang Yeol Baek
- Department of Applied Bioscience, Dong-A University, Busan 49315,
Korea
| | - Hyun-Hee Lee
- Department of Microbiology, Pusan National University, Busan 46241,
Korea
| | - Geun Ju Son
- Department of Applied Bioscience, Dong-A University, Busan 49315,
Korea
| | - Pyeong An Lee
- Department of Applied Bioscience, Dong-A University, Busan 49315,
Korea
| | - Nazish Roy
- Department of Applied Bioscience, Dong-A University, Busan 49315,
Korea
| | - Young-Su Seo
- Department of Microbiology, Pusan National University, Busan 46241,
Korea
- Co-corresponding authors. Young-Su Seo, Phone) +82-51-510-2267, FAX) +82-51-514-1778, E-mail) . Seon-Woo Lee, Phone) +82-51-200-7551, FAX) +82-51-200-7505, E-mail)
| | - Seon-Woo Lee
- Department of Applied Bioscience, Dong-A University, Busan 49315,
Korea
- Co-corresponding authors. Young-Su Seo, Phone) +82-51-510-2267, FAX) +82-51-514-1778, E-mail) . Seon-Woo Lee, Phone) +82-51-200-7551, FAX) +82-51-200-7505, E-mail)
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25
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Fennessey CM, McMahon MB, Sechler AJ, Kaiser J, Garrett WM, Tancos MA, Luster DG, Rogers EE, Schneider WL. Partial Proteome of the Corynetoxin-Producing Gram-Positive Bacterium, Rathayibacter toxicus. Proteomics 2018; 18. [PMID: 29327412 DOI: 10.1002/pmic.201700350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/05/2017] [Indexed: 11/12/2022]
Abstract
Rathayibacter toxicus is a Gram-positive bacterium that is the causative agent of annual ryegrass toxicity (ARGT), a disease that causes devastating losses in the Australian livestock industry. R. toxicus exhibits a complex life cycle, using the nematode Anguina funesta as a physical vector to carry it up to the seed head of the host plant. ARGT is caused by a tunicamycin-like corynetoxin that is produced in R. toxicus-infected seed galls. We analyzed protein expression in R. toxicus under stationary growth phase conditions to obtain a more complete understanding of the biology of this organism and identify potential targets for immunoassay development. A total of 323 unique proteins were identified, including those with putative roles in secondary metabolism and pathogenicity. The proteome analysis for this complex phytopathogenic Gram-positive bacterium will facilitate in the characterization of proteins necessary for host colonization and toxin production, and assist in the development of diagnostic assays. Data are available via ProteomeXchange with identifier PXD004238.
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Affiliation(s)
- Christine M Fennessey
- USDA, ARS, Foreign Disease Weed Science Research Unit, Fort Detrick, MD, USA.,AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Michael B McMahon
- USDA, ARS, Foreign Disease Weed Science Research Unit, Fort Detrick, MD, USA
| | - Aaron J Sechler
- USDA, ARS, Foreign Disease Weed Science Research Unit, Fort Detrick, MD, USA
| | - Jaclyn Kaiser
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Wesley M Garrett
- USDA, ARS, Animal Biosciences and Biotechnology Laboratory, Beltsville, MD, USA
| | - Matthew A Tancos
- USDA, ARS, Foreign Disease Weed Science Research Unit, Fort Detrick, MD, USA
| | - Douglas G Luster
- USDA, ARS, Foreign Disease Weed Science Research Unit, Fort Detrick, MD, USA
| | - Elizabeth E Rogers
- USDA, ARS, Foreign Disease Weed Science Research Unit, Fort Detrick, MD, USA
| | - William L Schneider
- USDA, ARS, Foreign Disease Weed Science Research Unit, Fort Detrick, MD, USA
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Draft Genome Sequence of Rathayibacter sp. Strain VKM Ac-2630 Isolated from Leaf Gall Induced by the Knapweed Nematode Mesoanguina picridis on Acroptilon repens. GENOME ANNOUNCEMENTS 2017; 5:5/30/e00650-17. [PMID: 28751392 PMCID: PMC5532830 DOI: 10.1128/genomea.00650-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A draft genome sequence of Rathayibacter sp. strain VKM Ac-2630 was derived using Ion Torrent sequencing technology. The genome size of this strain is 3.88 Mb, with an average G+C content of 72.0%. Genomic evidence of an aerobic mode of respiration and a heterotrophic lifestyle of this bacterium was obtained.
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