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Khilyas IV, Markelova MI, Valeeva LR, Gritseva AS, Sorokina AV, Shafigullina LT, Tukhbatova RI, Shagimardanova EI, Berkutova ES, Sharipova MR, Lochnit G, Cohen MF. Genomic and metabolomic profiling of endolithic Rhodococcus fascians strain S11 isolated from an arid serpentine environment. Arch Microbiol 2022; 204:336. [PMID: 35587838 DOI: 10.1007/s00203-022-02955-1] [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: 01/17/2022] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 11/29/2022]
Abstract
Genomic and metabolomic studies of endolithic bacteria are essential for understanding their adaptations to extreme conditions of the rock environment and their contributions to mineralization and weathering processes. The endoliths of arid serpentine rocks are exposed to different environmental stresses, including desiccation and re-hydration, temperature fluctuations, oligotrophy, and high concentrations of heavy metals. Bacteria of the genus Rhodococcus commonly inhabit endolithic environments. Here, we describe genomic and metabolomic analyses of the non-pathogenic wild-type Rhodococcus fascians strain S11, isolated from weathered serpentine rock at the arid Khalilovsky massif, Russia. We found that strain S11 lacks the virulence plasmid that functions in the phytopathogenecity of some R. fascians strains. Phenotypic profiling revealed a high pH tolerance, phytase activity and siderophore production. A widely untargeted metabolome analysis performed using an Orbitrap LC-MS/MS method demonstrated the presence of chrysobactin-type siderophores in the culture medium of strain S11. The natural variation of secondary metabolites produced by strain S11 might provide a practical basis for revealing antibacterial, fungicide or insecticidal activities. Finally, plant infection and plant growth stimulation studies showed no observable effect of exposure strain S11 bacteria on the aerial and root parts of Arabidopsis thaliana plants. Based on our findings, R. fascians strain S11 might be promising tool for investigations of organo-mineral interactions, heavy metal bioremediation, and mechanisms of bacterial mediated weathering of plant-free serpentine rock to soil.
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Affiliation(s)
- Irina V Khilyas
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation.
| | - Maria I Markelova
- Laboratory of Omics Technologies, Institute Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Lia R Valeeva
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Anastasia S Gritseva
- Department of Genetics, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Alyona V Sorokina
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Lilia T Shafigullina
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Rezeda I Tukhbatova
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region), Federal University, Kazan, Russian Federation
| | - Elena I Shagimardanova
- Laboratory of Extreme Biology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Ekaterina S Berkutova
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Margarita R Sharipova
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation
| | - Guenter Lochnit
- Faculty of Medicine Protein Analytics, Institute of Biochemistry, Justus Liebig University Giessen, Giessen, Germany
| | - Michael F Cohen
- Department of Biology, Sonoma State University, Rohnert Park, CA, USA
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Endophytic PGPR from Tomato Roots: Isolation, In Vitro Characterization and In Vivo Evaluation of Treated Tomatoes (Solanum lycopersicum L.). Microorganisms 2022; 10:microorganisms10040765. [PMID: 35456815 PMCID: PMC9031218 DOI: 10.3390/microorganisms10040765] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/17/2022] [Accepted: 03/29/2022] [Indexed: 12/10/2022] Open
Abstract
Plant-growth-promoting rhizobacteria (PGPR) are soil bacteria colonizing the rhizosphere and the rhizoplane which have an effect on plant growth through multiple chemical compounds. Rhizobacteria with beneficial effects for plants could therefore be used to reduce the dependence on synthetic chemical fertilizers in conventional agriculture. Within this study, 67 endophytic fungi and 49 bacteria were isolated from root samples from 3 different commercial productions: an off-ground tomato production in a greenhouse, an organic production and a conventional production, both in a soil tunnel. Following morphological selection, 12 fungal and 33 bacterial isolates were genetically identified. Thirteen bacterial isolates belonging to nine potential PGPR species were then applied to tomato seedlings established in sterile substrate. The ability of these bacteria to produce indole acetic acid (IAA) and solubilize phosphate was also evaluated. They all were IAA producers and solubilized phosphate. The most interesting strains for growth promotion were found to be the isolates Pseudomonas palleroniana B10, Bacillus subtilis B25, Bacillus aryabhattai B29 and Pseudomonas fluorescens B17. The isolates P. fluorescens B17, B. aryabhattai B29, B. subtilis B18 and Pseudomonas moraviensis B6 also increased root growth. This study proposed a quick protocol for isolating and testing potential endophytic PGPR that should be characterized further for the direct and indirect mechanisms of growth promotion.
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Yang J, Fu Y, Liu H. Microbiomes of air dust collected during the ground-based closed bioregenerative life support experiment "Lunar Palace 365". ENVIRONMENTAL MICROBIOME 2022; 17:4. [PMID: 35081988 PMCID: PMC8793263 DOI: 10.1186/s40793-022-00399-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/07/2022] [Indexed: 05/07/2023]
Abstract
BACKGROUND Understanding the dynamics of airborne microbial communities and antibiotic resistance genes (ARGs) in space life support systems is important because potential pathogens and antibiotic resistance pose a health risk to crew that can lead to mission failure. There have been few reports on the distribution patterns of microbiomes and ARGs in space life support systems. In particular, there have been no detailed investigations of microbiomes and/or antibiotic resistance based on molecular methods in long-term confined bioregenerative life support systems (BLSSs). Therefore, in the present study, we collected air dust samples from two crew shifts, different areas, and different time points in the "Lunar Palace 365" experiment. We evaluated microbial diversity, species composition, functional potential, and antibiotic resistance by combining cultivation-independent analyses (amplicon, shot-gun sequencing, and qPCR). RESULTS We found that the bacterial community diversity in the Lunar Palace1 (LP1) system was higher than that in a controlled environment but lower than that in an open environment. Personnel exchange led to significant differences in bacterial community diversity, and source tracking analysis revealed that most bacteria in the air derived from the cabin crew and plants, but no differences in microbial function or antibiotic resistance were observed. Thus, human presence had the strongest effect on the succession of microbial diversity in the BLSSs. CONCLUSIONS Our results highlight that microbial diversity in BLSSs is heavily influenced by changes in crew and is unique from other open and controlled environments. Our findings can be used to help develop safe, enclosed BLSS that meet the requirements of human survival and habitation in outer space. In addition, our results can further enhance our understanding of the indoor air microbial community and effectively maintain a safe working and living environment, including plant growth.
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Affiliation(s)
- Jianlou Yang
- Key Laboratory for Biomechanics and Mechanobiology of the Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, No. 37 Xueyuan Road, Beijing, 100191, China
| | - Yuming Fu
- Key Laboratory for Biomechanics and Mechanobiology of the Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, No. 37 Xueyuan Road, Beijing, 100191, China.
- State Key Laboratory of Virtual Reality Technology and Systems, School of Computer Science and Engineering, Beihang University, Beijing, 100191, China.
- International Joint Research Center of Aerospace Biotechnology and Medical Engineering, Beihang University, Beijing, 100191, China.
| | - Hong Liu
- Key Laboratory for Biomechanics and Mechanobiology of the Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, No. 37 Xueyuan Road, Beijing, 100191, China.
- State Key Laboratory of Virtual Reality Technology and Systems, School of Computer Science and Engineering, Beihang University, Beijing, 100191, China.
- International Joint Research Center of Aerospace Biotechnology and Medical Engineering, Beihang University, Beijing, 100191, China.
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Hwang IS, Oh EJ, Song E, Park IW, Lee Y, Sohn KH, Choi D, Oh CS. An Apoplastic Effector Pat-1 Cm of the Gram-Positive Bacterium Clavibacter michiganensis Acts as Both a Pathogenicity Factor and an Immunity Elicitor in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:888290. [PMID: 35432427 PMCID: PMC9006514 DOI: 10.3389/fpls.2022.888290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/14/2022] [Indexed: 05/09/2023]
Abstract
Clavibacter michiganensis, a Gram-positive plant-pathogenic bacterium, utilizes apoplastic effectors for disease development in host plants. Here, we determine the roles of Pat-1Cm (a putative serine protease) in pathogenicity and plant immunity. Pat-1Cm was found to be a genuine secreted protein, and the secreted mature form did not carry the first 33 amino acids predicted to be a signal peptide (SP). The pat-1Cm mutant impaired to cause wilting, but still caused canker symptom in tomato. Moreover, this mutant failed to trigger the hypersensitive response (HR) in a nonhost Nicotiana tabacum. Among orthologs and paralogs of pat-1Cm , only chp-7Cs from Clavibacter sepedonicus, a potato pathogen, successfully complemented pat-1Cm function in pathogenicity in tomato, whereas all failed to complement pat-1Cm function in HR induction in N. tabacum. Based on the structural prediction, Pat-1Cm carried a catalytic triad for putative serine protease, and alanine substitution of any amino acids in the triad abolished both pathogenicity and HR-inducing activities of Pat-1Cm in C. michiganensis. Ectopic expression of pat-1Cm with an SP from tobacco secreted protein triggered HR in N. tabacum, but not in tomato, whereas a catalytic triad mutant failed to induce HR. Inoculation of the pat-1Cm mutant mixed with the mutant of another apoplastic effector CelA (cellulase) caused severe wilting in tomato, indicating that these two apoplastic effectors can functionally cooperate in pathogenicity. Overall, these results indicate that Pat-1Cm is a distinct secreted protein carrying a functional catalytic triad for serine protease and this enzymatic activity might be critical for both pathogenicity and HR-eliciting activities of Pat-1Cm in plants.
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Affiliation(s)
- In Sun Hwang
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin, South Korea
| | - Eom-Ji Oh
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin, South Korea
| | - Eunbee Song
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin, South Korea
| | - In Woong Park
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin, South Korea
| | - Yoonyoung Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea
| | - Kee Hoon Sohn
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, South Korea
| | - Doil Choi
- Department of Plant Science, Plant Immunity Research Center, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Chang-Sik Oh
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin, South Korea
- Graduate School of Biotechnology, Kyung Hee University, Yongin, South Korea
- *Correspondence: Chang-Sik Oh,
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Frébortová J, Frébort I. Biochemical and Structural Aspects of Cytokinin Biosynthesis and Degradation in Bacteria. Microorganisms 2021; 9:microorganisms9061314. [PMID: 34208724 PMCID: PMC8234997 DOI: 10.3390/microorganisms9061314] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 11/16/2022] Open
Abstract
It has been known for quite some time that cytokinins, hormones typical of plants, are also produced and metabolized in bacteria. Most bacteria can only form the tRNA-bound cytokinins, but there are examples of plant-associated bacteria, both pathogenic and beneficial, that actively synthesize cytokinins to interact with their host. Similar to plants, bacteria produce diverse cytokinin metabolites, employing corresponding metabolic pathways. The identification of genes encoding the enzymes involved in cytokinin biosynthesis and metabolism facilitated their detailed characterization based on both classical enzyme assays and structural approaches. This review summarizes the present knowledge on key enzymes involved in cytokinin biosynthesis, modifications, and degradation in bacteria, and discusses their catalytic properties in relation to the presence of specific amino acid residues and protein structure.
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Legein M, Smets W, Vandenheuvel D, Eilers T, Muyshondt B, Prinsen E, Samson R, Lebeer S. Modes of Action of Microbial Biocontrol in the Phyllosphere. Front Microbiol 2020; 11:1619. [PMID: 32760378 PMCID: PMC7372246 DOI: 10.3389/fmicb.2020.01619] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022] Open
Abstract
A fast-growing field of research focuses on microbial biocontrol in the phyllosphere. Phyllosphere microorganisms possess a wide range of adaptation and biocontrol factors, which allow them to adapt to the phyllosphere environment and inhibit the growth of microbial pathogens, thus sustaining plant health. These biocontrol factors can be categorized in direct, microbe-microbe, and indirect, host-microbe, interactions. This review gives an overview of the modes of action of microbial adaptation and biocontrol in the phyllosphere, the genetic basis of the mechanisms, and examples of experiments that can detect these mechanisms in laboratory and field experiments. Detailed insights in such mechanisms are key for the rational design of novel microbial biocontrol strategies and increase crop protection and production. Such novel biocontrol strategies are much needed, as ensuring sufficient and consistent food production for a growing world population, while protecting our environment, is one of the biggest challenges of our time.
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Affiliation(s)
- Marie Legein
- Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Wenke Smets
- Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Dieter Vandenheuvel
- Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Tom Eilers
- Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Babette Muyshondt
- Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Els Prinsen
- Laboratory for Integrated Molecular Plant Physiology Research, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Roeland Samson
- Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Sarah Lebeer
- Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
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Savory EA, Weisberg AJ, Stevens DM, Creason AL, Fuller SL, Pearce EM, Chang JH. Phytopathogenic Rhodococcus Have Diverse Plasmids With Few Conserved Virulence Functions. Front Microbiol 2020; 11:1022. [PMID: 32523572 PMCID: PMC7261884 DOI: 10.3389/fmicb.2020.01022] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 04/27/2020] [Indexed: 11/13/2022] Open
Abstract
Rhodococcus is a genus of Gram-positive bacteria with species that can cause growth deformations to a large number of plant species. This ability to cause disease is hypothesized to be dependent on a cluster of three gene loci on an almost 200 kb-sized linear plasmid. To reevaluate the roles of some of the genes in pathogenicity, we constructed and characterized deletion mutants of fasR and four fas genes. Findings confirmed that fasR, which encodes a putative transcriptional regulator, is necessary for pathogenesis. However, three of the fas genes, implicated in the metabolism of plant growth promoting cytokinins, are dispensable for the ability of the pathogen to cause disease. We also used long-read sequencing technology to generate high quality genome sequences for two phytopathogenic strains in which virulence genes are diverged in sequence and/or hypothesized to have recombined into the chromosome. Surprisingly, findings showed that the two strains carry extremely diverse virulence plasmids. Ortholog clustering identified only 12 genes present on all three virulence plasmids. Rhodococcus requires a small number of horizontally acquired traits to be pathogenic and the transmission of the corresponding genes, via recombination and conjugation, has the potential to rapidly diversify plasmids and bacterial populations.
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Affiliation(s)
- Elizabeth A Savory
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Danielle M Stevens
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Allison L Creason
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Skylar L Fuller
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Emma M Pearce
- 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.,Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, United States
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Harris MO, Pitzschke A. Plants make galls to accommodate foreigners: some are friends, most are foes. THE NEW PHYTOLOGIST 2020; 225:1852-1872. [PMID: 31774564 DOI: 10.1111/nph.16340] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 07/24/2019] [Indexed: 06/10/2023]
Abstract
At the colonization site of a foreign entity, plant cells alter their trajectory of growth and development. The resulting structure - a plant gall - accommodates various needs of the foreigner, which are phylogenetically diverse: viruses, bacteria, protozoa, oomycetes, true fungi, parasitic plants, and many types of animals, including rotifers, nematodes, insects, and mites. The plant species that make galls also are diverse. We assume gall production costs the plant. All is well if the foreigner provides a gift that makes up for the cost. Nitrogen-fixing nodule-inducing bacteria provide nutritional services. Gall wasps pollinate fig trees. Unfortunately for plants, most galls are made for foes, some of which are deeply studied pathogens and pests: Agrobacterium tumefaciens, Rhodococcus fascians, Xanthomonas citri, Pseudomonas savastanoi, Pantoea agglomerans, 'Candidatus' phytoplasma, rust fungi, Ustilago smuts, root knot and cyst nematodes, and gall midges. Galls are an understudied phenomenon in plant developmental biology. We propose gall inception for discovering unifying features of the galls that plants make for friends and foes, talk about molecules that plants and gall-inducers use to get what they want from each other, raise the question of whether plants colonized by arbuscular mycorrhizal fungi respond in a gall-like manner, and present a research agenda.
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Affiliation(s)
- Marion O Harris
- Department of Entomology, North Dakota State University, Fargo, ND, 58014, USA
| | - Andrea Pitzschke
- Department of Biosciences, Salzburg University, Hellbrunner Strasse 34, A-5020, Salzburg, Austria
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Vereecke D, Zhang Y, Francis IM, Lambert PQ, Venneman J, Stamler RA, Kilcrease J, Randall JJ. Functional Genomics Insights Into the Pathogenicity, Habitat Fitness, and Mechanisms Modifying Plant Development of Rhodococcus sp. PBTS1 and PBTS2. Front Microbiol 2020; 11:14. [PMID: 32082278 PMCID: PMC7002392 DOI: 10.3389/fmicb.2020.00014] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 01/06/2020] [Indexed: 01/05/2023] Open
Abstract
Pistachio Bushy Top Syndrome (PBTS) is a recently emerged disease that has strongly impacted the pistachio industry in California, Arizona, and New Mexico. The disease is caused by two bacteria, designated PBTS1 that is related to Rhodococcus corynebacterioides and PBTS2 that belongs to the species R. fascians. Here, we assessed the pathogenic character of the causative agents and examined their chromosomal sequences to predict the presence of particular functions that might contribute to the observed co-occurrence and their effect on plant hosts. In diverse assays, we confirmed the pathogenicity of the strains on "UCB-1" pistachio rootstock and showed that they can also impact the development of tobacco species, but concurrently inconsistencies in the ability to induce symptoms were revealed. We additionally evidence that fas genes are present only in a subpopulation of pure PBTS1 and PBTS2 cultures after growth on synthetic media, that these genes are easily lost upon cultivation in rich media, and that they are enriched for in an in planta environment. Analysis of the chromosomal sequences indicated that PBTS1 and PBTS2 might have complementary activities that would support niche partitioning. Growth experiments showed that the nutrient utilization pattern of both PBTS bacteria was not identical, thus avoiding co-inhabitant competition. PBTS2 appeared to have the potential to positively affect the habitat fitness of PBTS1 by improving its resistance against increased concentrations of copper and penicillins. Finally, mining the chromosomes of PBTS1 and PBTS2 suggested that the bacteria could produce cytokinins, auxins, and plant growth-stimulating volatiles and that PBTS2 might interfere with ethylene levels, in support of their impact on plant development. Subsequent experimentation supported these in silico predictions. Altogether, our data provide an explanation for the observed pathogenic behavior and unveil part of the strategies used by PBTS1 and PBTS2 to interact with plants.
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Affiliation(s)
- Danny Vereecke
- Entomology, Plant Pathology, and Weed Science, New Mexico State University, Las Cruces, NM, United States
| | - Yucheng Zhang
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
| | - Isolde M Francis
- Department of Biology, California State University, Bakersfield, CA, United States
| | - Paul Q Lambert
- Entomology, Plant Pathology, and Weed Science, New Mexico State University, Las Cruces, NM, United States
| | - Jolien Venneman
- Department of Plants and Crops, Ghent University, Ghent, Belgium
| | - Rio A Stamler
- Entomology, Plant Pathology, and Weed Science, New Mexico State University, Las Cruces, NM, United States
| | - James Kilcrease
- Entomology, Plant Pathology, and Weed Science, New Mexico State University, Las Cruces, NM, United States
| | - Jennifer J Randall
- Entomology, Plant Pathology, and Weed Science, New Mexico State University, Las Cruces, NM, United States
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10
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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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11
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Francis IM, Vereecke D. Plant-Associated Rhodococcus Species, for Better and for Worse. BIOLOGY OF RHODOCOCCUS 2019. [DOI: 10.1007/978-3-030-11461-9_13] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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12
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Jameson PE, Dhandapani P, Song J, Zatloukal M, Strnad M, Remus-Emsermann MNP, Schlechter RO, Novák O. The Cytokinin Complex Associated With Rhodococcus fascians: Which Compounds Are Critical for Virulence? FRONTIERS IN PLANT SCIENCE 2019; 10:674. [PMID: 31191583 PMCID: PMC6539147 DOI: 10.3389/fpls.2019.00674] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 05/03/2019] [Indexed: 05/22/2023]
Abstract
Virulent strains of Rhodococcus fascians cause a range of disease symptoms, many of which can be mimicked by application of cytokinin. Both virulent and avirulent strains produce a complex of cytokinins, most of which can be derived from tRNA degradation. To test the three current hypotheses regarding the involvement of cytokinins as virulence determinants, we used PCR to detect specific genes, previously associated with a linear virulence plasmid, including two methyl transferase genes (mt1 and mt2) and fas4 (dimethyl transferase), of multiple strains of R. fascians. We inoculated Pisum sativum (pea) seeds with virulent and avirulent strains of R. fascians, monitored the plants over time and compared these to mock-inoculated controls. We used RT-qPCR to monitor the expression of mt1, mt2, and fas4 in inoculated tissues and LC-MS/MS to obtain a comprehensive picture of the cytokinin complement of inoculated cotyledons, roots and shoots over time. The presence and expression of mt1 and mt2 was associated with those strains of R. fascians classed as virulent, and not those classed as avirulent. Expression of mt1, mt2, and fas4 peaked at 9 days post-inoculation (dpi) in cotyledons and at 15 dpi in shoots and roots developed from seeds inoculated with virulent strain 602. Pea plants inoculated with virulent and avirulent strains of R. fascians both contained cytokinins likely to have been derived from tRNA turnover including the 2-methylthio cytokinins and cis-zeatin-derivatives. Along with the isopentenyladenine-type cytokinins, the levels of these compounds did not correlate with virulence. Only the novel 1- and 2-methylated isopentenyladenine cytokinins were uniquely associated with infection by the virulent strains and are, therefore, the likely causative factors of the disease symptoms.
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Affiliation(s)
- Paula E. Jameson
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- *Correspondence: Paula E. Jameson
| | - Pragathi Dhandapani
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Jiancheng Song
- School of Life Sciences, Yantai University, Yantai, China
| | - Marek Zatloukal
- Laboratory of Growth Regulators, The Czech Academy of Sciences, Faculty of Science, Institute of Experimental Botany & Palacký University, Olomouc, Czech Republic, China
| | - Miroslav Strnad
- Laboratory of Growth Regulators, The Czech Academy of Sciences, Faculty of Science, Institute of Experimental Botany & Palacký University, Olomouc, Czech Republic, China
| | | | - Rudolf O. Schlechter
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Ondrej Novák
- Laboratory of Growth Regulators, The Czech Academy of Sciences, Faculty of Science, Institute of Experimental Botany & Palacký University, Olomouc, Czech Republic, China
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Vereecke D. Comment on "Evolutionary transitions between beneficial and phytopathogenic Rhodococcus challenge disease management". eLife 2018; 7:35238. [PMID: 29737966 PMCID: PMC5951678 DOI: 10.7554/elife.35238] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 04/13/2018] [Indexed: 02/06/2023] Open
Abstract
I would like to report significant issues of concern regarding this paper (Savory et al., 2017).
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Affiliation(s)
- Danny Vereecke
- Department of Applied Biosciences, Ghent University, Ghent, Belgium
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Savory EA, Fuller SL, Weisberg AJ, Thomas WJ, Gordon MI, Stevens DM, Creason AL, Belcher MS, Serdani M, Wiseman MS, Grünwald NJ, Putnam ML, Chang JH. Correction: Evolutionary transitions between beneficial and phytopathogenic Rhodococcus challenge disease management. eLife 2018. [PMID: 29533183 PMCID: PMC5849409 DOI: 10.7554/elife.36350] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
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Dolzblasz A, Banasiak A, Vereecke D. Neovascularization during leafy gall formation on Arabidopsis thaliana upon Rhodococcus fascians infection. PLANTA 2018; 247:215-228. [PMID: 28942496 DOI: 10.1007/s00425-017-2778-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/24/2017] [Indexed: 06/07/2023]
Abstract
Extensive de novo vascularization of leafy galls emerging upon Rhodococcus fascians infection is achieved by fascicular/interfascicular cambium activity and transdifferentiation of parenchyma cells correlated with increased auxin signaling. A leafy gall consisting of fully developed yet growth-inhibited shoots, induced by the actinomycete Rhodococcus fascians, differs in structure compared to the callus-like galls induced by other bacteria. To get insight into the vascular development accompanying the emergence of the leafy gall, the anatomy of infected axillary regions of the inflorescence stem of wild-type Arabidopsis thaliana accession Col-0 plants and the auxin response in pDR5:GUS-tagged plants were followed in time. Based on our observations, three phases can be discerned during vascularization of the symptomatic tissue. First, existing fascicular cambium becomes activated and interfascicular cambium is formed giving rise to secondary vascular elements in a basipetal direction below the infection site in the main stem and in an acropetal direction in the entire side branch. Then, parenchyma cells in the region between both stems transdifferentiate acropetally towards the surface of the developing symptomatic tissue leading to the formation of xylem and vascularize the hyperplasia as they expand. Finally, parenchyma cells in the developing gall also transdifferentiate to vascular elements without any specific direction resulting in excessive vasculature disorderly distributed in the leafy gall. Prior to any apparent anatomical changes, a strong auxin response is mounted, implying that auxin is the signal that controls the vascular differentiation induced by the infection. To conclude, we propose the "sidetracking gall hypothesis" as we discuss the mechanisms driving the formation of superfluous vasculature of the emerging leafy gall.
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Affiliation(s)
- Alicja Dolzblasz
- Department of Plant Developmental Biology, Faculty of Biological Sciences, Institute of Experimental Biology, University of Wroclaw, Wroclaw, Poland.
| | - Alicja Banasiak
- Department of Plant Developmental Biology, Faculty of Biological Sciences, Institute of Experimental Biology, University of Wroclaw, Wroclaw, Poland
| | - Danny Vereecke
- Department of Applied Biosciences, Ghent University, Ghent, Belgium.
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16
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Savory EA, Fuller SL, Weisberg AJ, Thomas WJ, Gordon MI, Stevens DM, Creason AL, Belcher MS, Serdani M, Wiseman MS, Grünwald NJ, Putnam ML, Chang JH. Evolutionary transitions between beneficial and phytopathogenic Rhodococcus challenge disease management. eLife 2017; 6:30925. [PMID: 29231813 PMCID: PMC5726852 DOI: 10.7554/elife.30925] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 11/03/2017] [Indexed: 02/02/2023] Open
Abstract
Understanding how bacteria affect plant health is crucial for developing sustainable crop production systems. We coupled ecological sampling and genome sequencing to characterize the population genetic history of Rhodococcus and the distribution patterns of virulence plasmids in isolates from nurseries. Analysis of chromosome sequences shows that plants host multiple lineages of Rhodococcus, and suggested that these bacteria are transmitted due to independent introductions, reservoir populations, and point source outbreaks. We demonstrate that isolates lacking virulence genes promote beneficial plant growth, and that the acquisition of a virulence plasmid is sufficient to transition beneficial symbionts to phytopathogens. This evolutionary transition, along with the distribution patterns of plasmids, reveals the impact of horizontal gene transfer in rapidly generating new pathogenic lineages and provides an alternative explanation for pathogen transmission patterns. Results also uncovered a misdiagnosed epidemic that implicated beneficial Rhodococcus bacteria as pathogens of pistachio. The misdiagnosis perpetuated the unnecessary removal of trees and exacerbated economic losses. All organisms live in a world teeming with bacteria. Some bacteria are beneficial and, for example, provide their hosts with nutrients. Others cause harm, for example, by stealing nutrients and causing disease. Many bacteria can also gain DNA from other bacteria, and the genes encoded within the new DNA can help them to live with other organisms. This can start the bacteria on an evolutionary path to becoming beneficial or harmful. Rhodococcus are bacteria that live in association with many species of plants, including trees. Most are harmless but some cause disease. Plants infected with harmful Rhodococcus can show deformed growth, which causes major losses to the nursery industry. Savory, Fuller, Weisberg et al. set out to understand how disease-causing Rhodococcus are introduced into nurseries, if they are transferred between nurseries, whether they persist in nurseries, and how to limit their spread. It turns out that harmless Rhodococcus are beneficial to plants. However, if these harmless bacteria gain a certain DNA molecule – called a virulence plasmid – they can convert into harmful bacteria. Further analysis showed that some nurseries repeatedly acquired the harmful bacteria. The pattern of affected nurseries suggested that some might have purchased diseased plants from a common provider. In other cases, the sources remained a mystery. Savory et al. also report that, contrary to previous findings, there is no evidence to support the diagnosis that Rhodococcus without a virulence plasmid are responsible for an unusual growth problem that has plagued the pistachio industry. In recent years, this incorrect diagnosis led to trees being unnecessarily destroyed, worsening the economic losses. These findings suggest that genes moving between bacteria can dramatically change how those bacteria interact with the organisms in which they live. It needs to be shown whether this is an exceptional process, unique to only certain groups of bacteria, or if it is more widespread in nature. These findings could inform future disease management strategies to better protect agricultural systems.
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Affiliation(s)
- Elizabeth A Savory
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States
| | - Skylar L Fuller
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States.,Molecular and Cellular Biology Program, Oregon State University, Corvallis, United States
| | - Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States
| | - William J Thomas
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States
| | - Michael I Gordon
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States
| | - Danielle M Stevens
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States
| | - Allison L Creason
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States.,Molecular and Cellular Biology Program, Oregon State University, Corvallis, United States
| | - Michael S Belcher
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States
| | - Maryna Serdani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States
| | - Michele S Wiseman
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States
| | - Niklaus J Grünwald
- Horticultural Crops Research Laboratory, United States Department of Agriculture and Agricultural Research Service, Corvallis, United States
| | - Melodie L Putnam
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States.,Molecular and Cellular Biology Program, Oregon State University, Corvallis, United States.,Center for Genome Research, Oregon State University, Corvallis, United States
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17
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Dhandapani P, Song J, Novak O, Jameson PE. Infection by Rhodococcus fascians maintains cotyledons as a sink tissue for the pathogen. ANNALS OF BOTANY 2017; 119:841-852. [PMID: 27864224 PMCID: PMC5378184 DOI: 10.1093/aob/mcw202] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 07/31/2016] [Accepted: 08/05/2016] [Indexed: 05/06/2023]
Abstract
Background and Aims Pisum sativum L. (pea) seed is a source of carbohydrate and protein for the developing plant. By studying pea seeds inoculated by the cytokinin-producing bacterium, Rhodococcus fascians , we sought to determine the impact of both an epiphytic (avirulent) strain and a pathogenic strain on source-sink activity within the cotyledons during and following germination. Methods Bacterial spread was monitored microscopically, and real-time reverse transcription-quantitative PCR was used to determine the expression of cytokinin biosynthesis, degradation and response regulator gene family members, along with expression of family members of SWEET , SUT , CWINV and AAP genes - gene families identified initially in pea by transcriptomic analysis. The endogenous cytokinin content was also determined. Key Results The cotyledons infected by the virulent strain remained intact and turned green, while multiple shoots were formed and root growth was reduced. The epiphytic strain had no such marked impact. Isopentenyl adenine was elevated in the cotyledons infected by the virulent strain. Strong expression of RfIPT , RfLOG and RfCKX was detected in the cotyledons infected by the virulent strain throughout the experiment, with elevated expression also observed for PsSWEET , PsSUT and PsINV gene family members. The epiphytic strain had some impact on the expression of these genes, especially at the later stages of reserve mobilization from the cotyledons. Conclusions The pathogenic strain retained the cotyledons as a sink tissue for the pathogen rather than the cotyledon converting completely to a source tissue for the germinating plant. We suggest that the interaction of cytokinins, CWINVs and SWEETs may lead to the loss of apical dominance and the appearance of multiple shoots.
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Affiliation(s)
- Pragatheswari Dhandapani
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Jiancheng Song
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
- School of Life Sciences, Yantai University, Yantai 264005, China
| | - Ondrej Novak
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany CAS & Faculty of Science of Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Paula E. Jameson
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
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