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Wolfgang A, Temme N, Tilcher R, Berg G. Understanding the sugar beet holobiont for sustainable agriculture. Front Microbiol 2023; 14:1151052. [PMID: 37138624 PMCID: PMC10149816 DOI: 10.3389/fmicb.2023.1151052] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/31/2023] [Indexed: 05/05/2023] Open
Abstract
The importance of crop-associated microbiomes for the health and field performance of plants has been demonstrated in the last decades. Sugar beet is the most important source of sucrose in temperate climates, and-as a root crop-yield heavily depends on genetics as well as on the soil and rhizosphere microbiomes. Bacteria, fungi, and archaea are found in all organs and life stages of the plant, and research on sugar beet microbiomes contributed to our understanding of the plant microbiome in general, especially of microbiome-based control strategies against phytopathogens. Attempts to make sugar beet cultivation more sustainable are increasing, raising the interest in biocontrol of plant pathogens and pests, biofertilization and -stimulation as well as microbiome-assisted breeding. This review first summarizes already achieved results on sugar beet-associated microbiomes and their unique traits, correlating to their physical, chemical, and biological peculiarities. Temporal and spatial microbiome dynamics during sugar beet ontogenesis are discussed, emphasizing the rhizosphere formation and highlighting knowledge gaps. Secondly, potential or already tested biocontrol agents and application strategies are discussed, providing an overview of how microbiome-based sugar beet farming could be performed in the future. Thus, this review is intended as a reference and baseline for further sugar beet-microbiome research, aiming to promote investigations in rhizosphere modulation-based biocontrol options.
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Affiliation(s)
- Adrian Wolfgang
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Nora Temme
- KWS SAAT SE & Co. KGaA, Einbeck, Germany
| | | | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Microbiome Biotechnology Department, Leibniz-Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- *Correspondence: Gabriele Berg
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2
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Kottara A, Carrilero L, Harrison E, Hall JPJ, Brockhurst MA. The dilution effect limits plasmid horizontal transmission in multispecies bacterial communities. MICROBIOLOGY-SGM 2021; 167. [PMID: 34494951 PMCID: PMC8549239 DOI: 10.1099/mic.0.001086] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
By transferring ecologically important traits between species, plasmids drive genomic divergence and evolutionary innovation in their bacterial hosts. Bacterial communities are often diverse and contain multiple coexisting plasmids, but the dynamics of plasmids in multi-species communities are poorly understood. Here, we show, using experimental multi-species communities containing two plasmids, that bacterial diversity limits the horizontal transmission of plasmids due to the ‘dilution effect’; this is an epidemiological phenomenon whereby living alongside less proficient host species reduces the expected infection risk for a focal host species. In addition, plasmid horizontal transmission was also affected by plasmid diversity, such that the rate of plasmid conjugation was reduced from co-infected host cells carrying both plasmids. In diverse microbial communities, plasmid spread may be limited by the dilution effect and plasmid–plasmid interactions, reducing the rate of horizontal transmission.
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Affiliation(s)
- Anastasia Kottara
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Laura Carrilero
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Ellie Harrison
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - James P J Hall
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Michael A Brockhurst
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
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3
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Kottara A, Hall JPJ, Brockhurst MA. The proficiency of the original host species determines community-level plasmid dynamics. FEMS Microbiol Ecol 2021; 97:6134752. [PMID: 33580956 DOI: 10.1093/femsec/fiab026] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/11/2021] [Indexed: 11/13/2022] Open
Abstract
Plasmids are common in natural bacterial communities, facilitating bacterial evolution via horizontal gene transfer. Bacterial species vary in their proficiency to host plasmids: whereas plasmids are stably maintained in some species regardless of selection for plasmid-encoded genes, in other species, even beneficial plasmids are rapidly lost. It is, however, unclear how this variation in host proficiency affects plasmid persistence in communities. Here, we test this using multispecies bacterial soil communities comprising species varying in their proficiency to host a large conjugative mercury resistance plasmid, pQBR103. The plasmid reached higher community-level abundance where beneficial and when introduced to the community in a more proficient host species. Proficient plasmid host species were also better able to disseminate the plasmid to a wider diversity of host species. These findings suggest that the dynamics of plasmids in natural bacterial communities depend not only upon the plasmid's attributes and the selective environment but also upon the proficiency of their host species.
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Affiliation(s)
- Anastasia Kottara
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - James P J Hall
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Michael A Brockhurst
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
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4
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Zhang X, Ritchie SR, Chang H, Arnold DL, Jackson RW, Rainey PB. Genotypic and phenotypic analyses reveal distinct population structures and ecotypes for sugar beet-associated Pseudomonas in Oxford and Auckland. Ecol Evol 2020; 10:5963-5975. [PMID: 32607204 PMCID: PMC7319117 DOI: 10.1002/ece3.6334] [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: 02/18/2020] [Revised: 04/09/2020] [Accepted: 04/14/2020] [Indexed: 01/02/2023] Open
Abstract
Fluorescent pseudomonads represent one of the largest groups of bacteria inhabiting the surfaces of plants, but their genetic composition in planta is poorly understood. Here, we examined the population structure and diversity of fluorescent pseudomonads isolated from sugar beet grown at two geographic locations (Oxford, United Kingdom and Auckland, New Zealand). To seek evidence for niche adaptation, bacteria were sampled from three types of leaves (immature, mature, and senescent) and then characterized using a combination of genotypic and phenotypic analysis. We first performed multilocus sequence analysis (MLSA) of three housekeeping genes (gapA, gltA, and acnB) in a total of 152 isolates (96 from Oxford, 56 from Auckland). The concatenated sequences were grouped into 81 sequence types and 22 distinct operational taxonomic units (OTUs). Significant levels of recombination were detected, particularly for the Oxford isolates (rate of recombination to mutation (r/m) = 5.23 for the whole population). Subsequent ancestral analysis performed in STRUCTURE found evidence of six ancestral populations, and their distributions significantly differed between Oxford and Auckland. Next, their ability to grow on 95 carbon sources was assessed using the Biolog™ GN2 microtiter plates. A distance matrix was generated from the raw growth data (A 660) and subjected to multidimensional scaling (MDS) analysis. There was a significant correlation between substrate utilization profiles and MLSA genotypes. Both phenotypic and genotypic analyses indicated presence of a geographic structure for strains from Oxford and Auckland. Significant differences were also detected for MLSA genotypes between strains isolated from immature versus mature/senescent leaves. The fluorescent pseudomonads thus showed an ecotypic population structure, suggestive of adaptation to both geographic conditions and local plant niches.
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Affiliation(s)
- Xue‐Xian Zhang
- New Zealand Institute for Advanced StudyMassey UniversityAucklandNew Zealand
- School of Natural and Computational SciencesMassey UniversityAucklandNew Zealand
| | - Stephen R. Ritchie
- New Zealand Institute for Advanced StudyMassey UniversityAucklandNew Zealand
- Faculty of Medical and Health SciencesUniversity of AucklandAucklandNew Zealand
| | - Hao Chang
- New Zealand Institute for Advanced StudyMassey UniversityAucklandNew Zealand
| | - Dawn L. Arnold
- Centre for Research in BioscienceUniversity of the West of EnglandBristolUK
| | - Robert W. Jackson
- School of Biosciences and Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Paul B. Rainey
- New Zealand Institute for Advanced StudyMassey UniversityAucklandNew Zealand
- Department of Microbial Population BiologyMax Planck Institute for Evolutionary BiologyPlönGermany
- Laboratoire de Génétique de l'Evolution, Chemistry, Biology and Innovation (CBI)UMR8231ESPCI ParisCNRSPSL Research UniversityParisFrance
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5
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Kottara A, Hall JPJ, Harrison E, Brockhurst MA. Variable plasmid fitness effects and mobile genetic element dynamics across Pseudomonas species. FEMS Microbiol Ecol 2019; 94:4689093. [PMID: 29228229 PMCID: PMC5812508 DOI: 10.1093/femsec/fix172] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 11/30/2017] [Indexed: 11/28/2022] Open
Abstract
Mobile genetic elements (MGE) such as plasmids and transposons mobilise genes within and between species, playing a crucial role in bacterial evolution via horizontal gene transfer (HGT). Currently, we lack data on variation in MGE dynamics across bacterial host species. We tracked the dynamics of a large conjugative plasmid, pQBR103, and its Tn5042 mercury resistance transposon, in five diverse Pseudomonas species in environments with and without mercury selection. Plasmid fitness effects and stability varied extensively between host species and environments, as did the propensity for chromosomal capture of the Tn5042 mercury resistance transposon associated with loss of the plasmid. Whereas Pseudomonas fluorescens and Pseudomonas savastanoi stably maintained the plasmid in both environments, the plasmid was highly unstable in Pseudomonas aeruginosa and Pseudomonas putida, where plasmid-free genotypes with Tn5042 captured to the chromosome invaded to higher frequency under mercury selection. These data confirm that plasmid stability is dependent upon the specific genetic interaction of the plasmid and host chromosome rather than being a property of plasmids alone, and moreover imply that MGE dynamics in diverse natural communities are likely to be complex and driven by a subset of species capable of stably maintaining plasmids that would then act as hubs of HGT.
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Affiliation(s)
- Anastasia Kottara
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - James P J Hall
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Ellie Harrison
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Michael A Brockhurst
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
- Corresponding author: Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK. Tel: +44 (0)1142220051; E-mail:
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6
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Kottara A, Hall JPJ, Harrison E, Brockhurst MA. Multi-host environments select for host-generalist conjugative plasmids. BMC Evol Biol 2016; 16:70. [PMID: 27039285 PMCID: PMC4818893 DOI: 10.1186/s12862-016-0642-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 03/22/2016] [Indexed: 11/26/2022] Open
Abstract
Background Conjugative plasmids play an important role in bacterial evolution by transferring ecologically important genes within and between species. A key limit on interspecific horizontal gene transfer is plasmid host range. Here, we experimentally test the effect of single and multi-host environments on the host-range evolution of a large conjugative mercury resistance plasmid, pQBR57. Specifically, pQBR57 was conjugated between strains of a single host species, either P. fluorescens or P. putida, or alternating between P. fluorescens and P. putida. Crucially, the bacterial hosts were not permitted to evolve allowing us to observe plasmid evolutionary responses in isolation. Results In all treatments plasmids evolved higher conjugation rates over time. Plasmids evolved in single-host environments adapted to their host bacterial species becoming less costly, but in the case of P. fluorescens-adapted plasmids, became costlier in P. putida, suggesting an evolutionary trade-off. When evolved in the multi-host environment plasmids adapted to P. fluorescens without a higher cost in P. putida. Conclusion Whereas evolution in a single-host environment selected for host-specialist plasmids due to a fitness trade-off, this trade-off could be circumvented in the multi-host environment, leading to the evolution of host-generalist plasmids.
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Affiliation(s)
- Anastasia Kottara
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - James P J Hall
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Ellie Harrison
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
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Type III secretion system and virulence markers highlight similarities and differences between human- and plant-associated pseudomonads related to Pseudomonas fluorescens and P. putida. Appl Environ Microbiol 2015; 81:2579-90. [PMID: 25636837 DOI: 10.1128/aem.04160-14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Pseudomonas fluorescens is commonly considered a saprophytic rhizobacterium devoid of pathogenic potential. Nevertheless, the recurrent isolation of strains from clinical human cases could indicate the emergence of novel strains originating from the rhizosphere reservoir, which could be particularly resistant to the immune system and clinical treatment. The importance of type three secretion systems (T3SSs) in the related Pseudomonas aeruginosa nosocomial species and the occurrence of this secretion system in plant-associated P. fluorescens raise the question of whether clinical isolates may also harbor T3SSs. In this study, isolates associated with clinical infections and identified in hospitals as belonging to P. fluorescens were compared with fluorescent pseudomonads harboring T3SSs isolated from plants. Bacterial isolates were tested for (i) their genetic relationships based on their 16S rRNA phylogeny, (ii) the presence of T3SS genes by PCR, and (iii) their infectious potential on animals and plants under environmental or physiological temperature conditions. Two groups of bacteria were delineated among the clinical isolates. The first group encompassed thermotolerant (41°C) isolates from patients suffering from blood infections; these isolates were finally found to not belong to P. fluorescens but were closely related and harbored highly conserved T3SS genes belonging to the Ysc-T3SS family, like the T3SSs from P. aeruginosa. The second group encompassed isolates from patients suffering from cystic fibrosis; these isolates belonged to P. fluorescens and harbored T3SS genes belonging to the Hrp1-T3SS family found commonly in plant-associated P. fluorescens.
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Nogarol C, Acutis PL, Bianchi DM, Maurella C, Peletto S, Gallina S, Adriano D, Zuccon F, Borrello S, Caramelli M, Decastelli L. Molecular characterization of Pseudomonas fluorescens isolates involved in the Italian "blue mozzarella" event. J Food Prot 2013; 76:500-4. [PMID: 23462088 DOI: 10.4315/0362-028x.jfp-12-312] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Between June and September 2010, widespread Italian consumer reports of unusual blue spoilage on fresh dairy products were publicized, resulting in the so-called blue mozzarella event. An inordinately high number of samples from mozzarella and whey cheese products of Italian and German production subsequently tested positive for Pseudomonas fluorescens. The aim of this study was to verify whether a selected P. fluorescens strain was responsible for this apparently unusual event. Molecular characterization of 181 isolated P. fluorescens strains was conducted using a newly optimized pulsed-field gel electrophoresis protocol. Although a high number of pulsotypes was found (132), only four pulsotypes were associated with more than one production plant, and only one German isolate had the same pulsotype as was detected in two Italian plants. This is the only evidence of possible cross-contamination among cheeses from the two countries. The overall results did not support the spread of contamination from German to Italian plants or the presence of one environmental strain that spread in both countries.
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Affiliation(s)
- C Nogarol
- S.C. Controllo Alimenti e Igiene delle Produzioni, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, via Bologna, 148-10154 Torino, Italy.
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Zhang XX, Chang H, Tran SL, Gauntlett JC, Cook GM, Rainey PB. Variation in transport explains polymorphism of histidine and urocanate utilization in a natural Pseudomonas population. Environ Microbiol 2012; 14:1941-51. [PMID: 22225938 DOI: 10.1111/j.1462-2920.2011.02692.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Phenotypic variation is a fundamental requirement for evolution by natural selection. While evidence of phenotypic variation in natural populations abounds, its genetic basis is rarely understood. Here we report variation in the ability of plant-colonizing Pseudomonas to utilize histidine, and its derivative, urocanate, as sole sources of carbon and nitrogen. From a population of 164 phyllosphere-colonizing Pseudomonas strains, 77% were able to utilize both histidine and urocanate (His(+) , Uro(+) ) as growth substrates, whereas the remainder could utilize histidine, but not urocanate (His(+) , Uro(-) ), or vice versa (His(-) , Uro(+) ). An in silico analysis of the hut locus, which determines capacity to utilize both histidine and urocanate, from genome-sequenced Pseudomonas strains, showed significant variation in the number of putative transporters. To identify transporter genes specific for histidine and urocanate, we focused on a single genotype of Pseudomonas fluorescens, strain SBW25, which is capable of utilizing both substrates. Site-directed mutagenesis, combined with [(3) H]histidine transport assays, shows that hutT(u) encodes a urocanate-specific transporter; hutT(h) encodes the major high-affinity histidine transporter; and hutXWV encodes an ABC-type transporter that plays a minor role in histidine uptake. Introduction of cloned copies of hutT(h) and hutT(u) from SBW25 into strains incapable of utilizing either histidine, or urocanate, complemented the defect, demonstrating a lack of functional transporters in these strains. Taken together our data show that variation in transport systems, and not in metabolic genes, explains a naturally occurring phenotypic polymorphism.
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Affiliation(s)
- Xue-Xian Zhang
- NZ Institute for Advanced Study, Massey University, Auckland 0745, New Zealand.
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Lovell HC, Jackson RW, Mansfield JW, Godfrey SAC, Hancock JT, Desikan R, Arnold DL. In planta conditions induce genomic changes in Pseudomonas syringae pv. phaseolicola. MOLECULAR PLANT PATHOLOGY 2011; 12:167-76. [PMID: 21199566 PMCID: PMC6640216 DOI: 10.1111/j.1364-3703.2010.00658.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The co-evolution of bacterial plant pathogens and their hosts is a complex and dynamic process. Plant resistance can impose stress on invading pathogens that can lead to, and select for, beneficial changes in the bacterial genome. The Pseudomonas syringae pv. phaseolicola (Pph) genomic island PPHGI-1 carries an effector gene, avrPphB (hopAR1), which triggers the hypersensitive reaction in bean plants carrying the R3 resistance gene. Interaction between avrPphB and R3 generates an antimicrobial environment within the plant, resulting in the excision of PPHGI-1 and its loss from the genome. The loss of PPHGI-1 leads to the generation of a Pph strain able to cause disease in the plant. In this study, we observed that lower bacterial densities inoculated into resistant bean (Phaseolus vulgaris) plants resulted in quicker PPHGI-1 loss from the population, and that loss of the island was strongly influenced by the type of plant resistance encountered by the bacteria. In addition, we found that a number of changes occurred in the bacterial genome during growth in the plant, whether or not PPHGI-1 was lost. We also present evidence that the circular PPHGI-1 episome is able to replicate autonomously when excised from the genome. These results shed more light onto the plasticity of the bacterial genome as it is influenced by in planta conditions.
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Affiliation(s)
- Helen C Lovell
- Centre for Research in Plant Science, University of the West of England, Bristol BS16 1QY, UK
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Frey P, Smith JJ, Albar L, Prior P, Saddler GS, Trigalet-Demery D, Trigalet A. Bacteriocin Typing of Burkholderia (Pseudomonas) solanacearum Race 1 of the French West Indies and Correlation with Genomic Variation of the Pathogen. Appl Environ Microbiol 2010; 62:473-9. [PMID: 16535234 PMCID: PMC1388772 DOI: 10.1128/aem.62.2.473-479.1996] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Burkholderia solanacearum race 1 isolates indigenous to the French West Indies were characterized by bacteriocin typing and two genomic fingerprinting methods: pulsed-field gel electrophoresis of genomic DNA digested by rare-cutting restriction endonucleases (RC-PFGE) and PCR with primers corresponding to repetitive extragenic palindromic (REP), enterobacterial repetitive intergenic consensus (ERIC), and BOX elements (collectively known as rep-PCR). The survey comprised 24 reference strains and 65 isolates obtained from a field trial in Guadeloupe in 1993. Comparison of the data identified RC-PFGE as the most discriminatory method, delineating 17 pulsed-field gel profile types. rep-PCR and bacteriocin typing identified nine rep-PCR profile types and nine bacteriocin groups. Independent determination of similarity coefficients and clustering of RC-PFGE and rep-PCR data identified six groups common to both sets of data that correlated to biovar and bacteriocin groups. Further study of bacteriocin production in planta gave results consistent with in vitro bacteriocin typing. It was observed that spontaneous bacteriocin-resistant mutants exhibited a cross-resistance to other bacteriocins as identified by the typing scheme and that such mutants possessed a selective advantage for growth over isogenic nonmutants in the presence of a bacteriocin. The results are significant in the search for biological control of disease by nonpathogenic mutants of the wild-type organism.
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12
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San José M, Rodicio MR, Argudín MÁ, Mendoza MC, González AJ. Regional variations in the population structure of Pseudomonas syringae pathovar phaseolicola from Spain are revealed by typing with PmeI pulsed-field gel electrophoresis, plasmid profiling and virulence gene complement. MICROBIOLOGY-SGM 2010; 156:1795-1804. [PMID: 20167625 DOI: 10.1099/mic.0.036152-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
One hundred and twenty pathogenic isolates of Pseudomonas syringae pv. phaseolicola recovered in Spain were subjected to biochemical and genomic typing, and investigated for virulence gene complement. Fifty-six were recovered from common beans (Phaseolus vulgaris) of the type Granja Asturiana, grown in a northern Spanish region (Asturias), and 64 from other common beans cultured in the neighbouring region of Castilla y León. Typing by PmeI digestion followed by pulsed-field gel electrophoresis revealed 27 profiles, with only three being common to both regions. Relationships between profiles distributed the isolates into two clusters: A (subdivided into subclusters A1 and A2) and B. Cluster A included all isolates from Granja Asturiana and about a quarter of the isolates from Castilla y León. Isolates from cluster A were negative for mannitol utilization and hybridized to probes for the argK-tox region responsible for phaseolotoxin production. Isolates that grouped in cluster B, which were only found in Castilla y León, were able to utilize mannitol but did not hybridize to probes for the argK-tox region. Separation of the isolates into three genomic groups, subsequently termed PphA1, PphA2 and PphB, was also supported by effector gene complement and location. In PphB, all effector genes tested (hopX1, hopF1, avrB2 and avrD1) mapped on chromosomal fragments, but faint hybridization of avrB2 with plasmids of about 40 kb was also observed. In PphA hopX1 mapped on the chromosome; in PphA1 avrB2 and avrD1 were carried on virulence plasmids (most of approx. 125 kb) and hopF1 was not detected, while in PphA2 the three genes were located on plasmids (approx. 75-160 kb). These results can be used as a framework to investigate the basis of regional variation in population structure, and for further epidemiological surveillance of P. syringae pv. phaseolicola.
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Affiliation(s)
- Mateo San José
- Departamento de Biología Funcional (área de Microbiología) and Instituto Universitario de Biotecnología de Asturias (IUBA), Universidad de Oviedo, 33006 Oviedo, Spain
| | - M Rosario Rodicio
- Departamento de Biología Funcional (área de Microbiología) and Instituto Universitario de Biotecnología de Asturias (IUBA), Universidad de Oviedo, 33006 Oviedo, Spain
| | - M Ángeles Argudín
- Departamento de Biología Funcional (área de Microbiología) and Instituto Universitario de Biotecnología de Asturias (IUBA), Universidad de Oviedo, 33006 Oviedo, Spain
| | - M Carmen Mendoza
- Departamento de Biología Funcional (área de Microbiología) and Instituto Universitario de Biotecnología de Asturias (IUBA), Universidad de Oviedo, 33006 Oviedo, Spain
| | - Ana J González
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Principado de Asturias, 33300 Villaviciosa, Spain
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13
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Silby MW, Cerdeño-Tárraga AM, Vernikos GS, Giddens SR, Jackson RW, Preston GM, Zhang XX, Moon CD, Gehrig SM, Godfrey SAC, Knight CG, Malone JG, Robinson Z, Spiers AJ, Harris S, Challis GL, Yaxley AM, Harris D, Seeger K, Murphy L, Rutter S, Squares R, Quail MA, Saunders E, Mavromatis K, Brettin TS, Bentley SD, Hothersall J, Stephens E, Thomas CM, Parkhill J, Levy SB, Rainey PB, Thomson NR. Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens. Genome Biol 2009; 10:R51. [PMID: 19432983 PMCID: PMC2718517 DOI: 10.1186/gb-2009-10-5-r51] [Citation(s) in RCA: 283] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Revised: 04/21/2009] [Accepted: 05/11/2009] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Pseudomonas fluorescens are common soil bacteria that can improve plant health through nutrient cycling, pathogen antagonism and induction of plant defenses. The genome sequences of strains SBW25 and Pf0-1 were determined and compared to each other and with P. fluorescens Pf-5. A functional genomic in vivo expression technology (IVET) screen provided insight into genes used by P. fluorescens in its natural environment and an improved understanding of the ecological significance of diversity within this species. RESULTS Comparisons of three P. fluorescens genomes (SBW25, Pf0-1, Pf-5) revealed considerable divergence: 61% of genes are shared, the majority located near the replication origin. Phylogenetic and average amino acid identity analyses showed a low overall relationship. A functional screen of SBW25 defined 125 plant-induced genes including a range of functions specific to the plant environment. Orthologues of 83 of these exist in Pf0-1 and Pf-5, with 73 shared by both strains. The P. fluorescens genomes carry numerous complex repetitive DNA sequences, some resembling Miniature Inverted-repeat Transposable Elements (MITEs). In SBW25, repeat density and distribution revealed 'repeat deserts' lacking repeats, covering approximately 40% of the genome. CONCLUSIONS P. fluorescens genomes are highly diverse. Strain-specific regions around the replication terminus suggest genome compartmentalization. The genomic heterogeneity among the three strains is reminiscent of a species complex rather than a single species. That 42% of plant-inducible genes were not shared by all strains reinforces this conclusion and shows that ecological success requires specialized and core functions. The diversity also indicates the significant size of genetic information within the Pseudomonas pan genome.
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Affiliation(s)
- Mark W Silby
- Centre for Adaptation Genetics and Drug Resistance and Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA 02111, USA
| | - Ana M Cerdeño-Tárraga
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Georgios S Vernikos
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Stephen R Giddens
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Robert W Jackson
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
- School of Biological Sciences, The University of Reading, Whiteknights, Reading RG6 6AJ, UK
| | - Gail M Preston
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Xue-Xian Zhang
- New Zealand Institute for Advanced Study, Massey University, Private Bag 102 904, North Shore Mail Centre, Auckland, New Zealand
| | - Christina D Moon
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
- Current address: AgResearch Limited, Grasslands Research Centre, Private Bag 11008, Palmerston North, New Zealand
| | - Stefanie M Gehrig
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Scott AC Godfrey
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
- Current address: School of Life Sciences, University of the West of England, Bristol, Frenchay Campus, Coldharbour Lane, Bristol BS16 1QY, UK
| | - Christopher G Knight
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
- Current address: Faculty of Life Sciences, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Jacob G Malone
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
- Current address: Biozentrum, University of Basel, Klingelbergstrasse 50-70, 4056 Basel, Switzerland
| | - Zena Robinson
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Andrew J Spiers
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
- Current address: SIMBIOS Centre, Level 5, Kydd Building, University of Abertay Dundee, Bell Street, Dundee DD1 1HG, UK
| | - Simon Harris
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Gregory L Challis
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Alice M Yaxley
- Department of Biological Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - David Harris
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Kathy Seeger
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Lee Murphy
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Simon Rutter
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Rob Squares
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Michael A Quail
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Elizabeth Saunders
- DOE Joint Genome Institute, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Konstantinos Mavromatis
- Genome Biology Program, Department of Energy's Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Thomas S Brettin
- DOE Joint Genome Institute, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Stephen D Bentley
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Joanne Hothersall
- Department of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Elton Stephens
- Department of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Christopher M Thomas
- Department of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Julian Parkhill
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Stuart B Levy
- Centre for Adaptation Genetics and Drug Resistance and Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA 02111, USA
| | - Paul B Rainey
- New Zealand Institute for Advanced Study, Massey University, Private Bag 102 904, North Shore Mail Centre, Auckland, New Zealand
- Allan Wilson Centre for Molecular Ecology and Evolution, Massey University Auckland, Private Bag 102 904, North Shore Mail Centre, Auckland, New Zealand
| | - Nicholas R Thomson
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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14
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. MEG, . NA. Growth Promoting of Some Ornamental Plants by Root Treatment with Specific Fluorescent Pseudomonads. ACTA ACUST UNITED AC 2006. [DOI: 10.3923/jbs.2006.610.615] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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15
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Lilley AK, Hails RS, Cory JS, Bailey MJ. The dispersal and establishment of pseudomonad populations in the phyllosphere of sugar beet by phytophagous caterpillars. FEMS Microbiol Ecol 2006. [DOI: 10.1111/j.1574-6941.1997.tb00431.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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16
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Meyer AF, Lipson DA, Martin AP, Schadt CW, Schmidt SK. Molecular and metabolic characterization of cold-tolerant alpine soil Pseudomonas sensu stricto. Appl Environ Microbiol 2004; 70:483-9. [PMID: 14711678 PMCID: PMC321299 DOI: 10.1128/aem.70.1.483-489.2004] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Alpine soils undergo dramatic temporal changes in their microclimatic properties, suggesting that the bacteria there encounter uncommon shifting selection gradients. Pseudomonads constitute important members of the alpine soil community. In order to characterize the alpine Pseudomonas community and to assess the impact of shifting selection on this community, we examined the ability of cold-tolerant Pseudomonas isolates to grow on a variety of carbon sources, and we determined their phylogenetic relationships based on 16S ribosomal DNA sequencing. We found a high prevalence of Pseudomonas in our soil samples, and isolates from these soils exhibited extensive metabolic diversity. In addition, our data revealed that many of our isolates form a unique cold-adapted clade, representatives of which are also found in the Swedish tundra and Antarctica. Our data also show a lack of concordance between the metabolic properties and 16S phylogeny, indicating that the metabolic diversity of these organisms cannot be predicted by phylogeny.
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Affiliation(s)
- A F Meyer
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA
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17
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Dawson SL, Fry JC, Dancer BN. A comparative evaluation of five typing techniques for determining the diversity of fluorescent pseudomonads. J Microbiol Methods 2002; 50:9-22. [PMID: 11943354 DOI: 10.1016/s0167-7012(02)00003-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Five typing methods were evaluated, utilising 63 strains of fluorescent pseudomonads, to assess their usefulness as tools to study the bacterial diversity within this complex group. The methods used were Biolog metabolic profiling, restriction fragment length polymorphism ribotyping, PCR ribotyping, and repetitive element sequence-based PCR (rep-PCR) utilising BOX and enterobacterial repetitive intergenic consensus (ERIC) primers. Cluster analysis of the results clearly demonstrated the considerable homogeneity of Pseudomonas aeruginosa isolates and, conversely, the heterogeneity within the other species, in particular P. putida and P. fluorescens, which need further taxonomic investigation. Biolog metabolic profiling enabled the best differentiation among the species. Rep-PCR proved to be highly discriminatory, more so than the other DNA fingerprinting techniques, demonstrating its suitability for the analysis of highly clonal isolates. RFLP ribotyping, PCR ribotyping, and rep-PCR produced specific clusters of P. aeruginosa isolates, which corresponded to their origins of isolation, hence we recommend these methods for intraspecific typing of bacteria.
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Affiliation(s)
- Shula L Dawson
- Cardiff School of Biosciences, Main Building, Cardiff University, P.O. Box 915, CF10 3TL, UK
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18
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Braun PG, Hildebrand PD, Ells TC, Kobayashi DY. Evidence and characterization of a gene cluster required for the production of viscosin, a lipopeptide biosurfactant, by a strain ofPseudomonas fluorescens. Can J Microbiol 2001; 47:294-301. [PMID: 11358168 DOI: 10.1139/w01-017] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The genetic control of viscosin production was examined in a strain of Pseudomonas fluorescens (PfA7B) that causes broccoli head rot. Viscosin is a potent lipopeptide biosurfactant that enables the bacteria to come into intimate contact with the difficult-to-wet waxy heads of broccoli. Tn5 mutagenesis completely disrupted viscosin production as shown by HPLC analysis of the mutagenized cell lysates. The Vismutants retained their pectolytic capability and were able to decay potato slices. On broccoli, however, the Vismutants caused decay of wounded florets, but the decay failed to spread to adjacent nonwounded florets as had occurred with the wild-type PfA7B. Triparental matings of the Vismutants with their corresponding wild-type clones and the helper Escherichia coli HB101 carrying the mobilization plasmid pPK2013 resulted in three stable viscosin-producing transconjugants that caused typical decay of broccoli tissue. Linkage maps of clones and protein profiles showed that a 25-kb chromosomal DNA region of PfA7B affected the production of three high molecular mass proteins required for viscosin synthesis. These proteins, approximately 218, 215, and 137 kDa in size, likely compose a synthetase complex that assembles the nine amino acid peptide of viscosin and subsequently attaches this to the hydrophobic fatty acid component of the molecule. A probe made from this DNA region hybridized with DNA fragments of other phytopathogenic pseudomonads to varying degrees.Key words: virulence factor, head rot, broccoli.
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Affiliation(s)
- P G Braun
- Atlantic Food and Horticulture Research Centre, Agriculture and Agri-Food Canada, Kentville, NS.
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19
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Spiers AJ, Buckling A, Rainey PB. The causes of Pseudomonas diversity. MICROBIOLOGY (READING, ENGLAND) 2000; 146 ( Pt 10):2345-2350. [PMID: 11021911 DOI: 10.1099/00221287-146-10-2345] [Citation(s) in RCA: 208] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Andrew J Spiers
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK1
| | - Angus Buckling
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK1
| | - Paul B Rainey
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK1
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20
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Timms-Wilson TM, Ellis RJ, Bailey MJ. Immuno-capture differential display method (IDDM) for the detection of environmentally induced promoters in rhizobacteria. J Microbiol Methods 2000; 41:77-84. [PMID: 10856780 DOI: 10.1016/s0167-7012(00)00139-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A rapid immunological method for trapping and selection of functionally regulated prokaryotic promoters is described. The method is based on application of a novel mini-Tn5 derived promoter probe (pUTTKZY-promoterless lacZY as a reporter and kanamycin resistance) to mutagenise a plant growth promoting fluorescent pseudomonad, Pseudomonas fluorescens 54/96. The transposon allows selection of operon fusion mutants (lacZY(+)) directly on media containing lactose as a sole carbon source as well as selection for kanamycin and lacZ (beta-galactosidase) expression on X-gal indicator media. We have extended the technique to target the surface expression of the induced lactose permease gene (lacY) from mutagenised libraries and the immuno-capture of bacteria with magnetic beads and anti-LacY monospecifc antisera. The benefits of the lacZY reporter are that a library can be rapidly generated and screened in vitro to isolate non-expressed mutants for further in situ screening. Here we demonstrate the development and utility of the technique and its potential as a differential display method for the isolation of promoters that direct regulated gene expression in the phytosphere, or under other imposed conditions.
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Affiliation(s)
- T M Timms-Wilson
- Molecular Microbial Ecology Laboratory, Natural Environment Research Council, Institute of Virology and Environmental Microbiology, Oxford, UK
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21
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Ellis RJ, Timms-Wilson TM, Bailey MJ. Identification of conserved traits in fluorescent pseudomonads with antifungal activity. Environ Microbiol 2000; 2:274-84. [PMID: 11200428 DOI: 10.1046/j.1462-2920.2000.00102.x] [Citation(s) in RCA: 94] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A collection of 29 fluorescent pseudomonads, some with known biological control activity against a range of phytopathogenic fungi, were characterized phenotypically and genotypically by comparing carbon source utilization patterns, suppression of Pythium ultimum both in planta and in vitro and the potential to produce known secondary metabolites. Fatty acid profiling and restriction fragment length polymorphism (RFLP) analysis of the ribosomal DNA operon (ribotyping) were used to determine the diversity of isolates. A small group of genetically related Pseudomonas spp. with similar properties was identified; each isolate produced a diffusible bioactive product in vitro and was active against Pythium ultimum in planta. However, other isolates that were able to suppress damping off disease but did not inhibit hyphal extension in vitro clustered outside this group. Phenotypic analyses revealed that the accumulation of C17:0 cyclopropane fatty acid (17CFA) and the production of hydrogen cyanide correlated significantly with biological control activity and with the antagonism of fungal development. The potential of 17CFA as a marker for the selection of fluorescent pseudomonads with biocontrol agent (BCA) potential was demonstrated by the isolation of a novel active strain. This was selected after the screening of 13 clonal groups of fluorescent pseudomonads identified from 500 isolates from the phytosphere of sugar beet. Levels of 17CFA synthesis possibly reflect the efficacy of the rpoS allele in particular strains.
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Affiliation(s)
- R J Ellis
- Molecular Microbial Ecology, NERC Institute of Virology and Environmental Microbiology, Oxford, UK
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22
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Truu J, Talpsep E, Heinaru E, Stottmeister U, Wand H, Heinaru A. Comparison of API 20NE and Biolog GN identification systems assessed by techniques of multivariate analyses. J Microbiol Methods 1999; 36:193-201. [PMID: 10379805 DOI: 10.1016/s0167-7012(99)00030-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The increasing use of commercial multitest systems for identification of environmental bacteria creates the problem of how to compare the identification results obtained from different systems. The limited use of species designations in such comparisons is caused by low usage of environmental bacteria in the development of commercial identification schemes. Two multivariate statistical methods, the Mantel's test and the co-inertia analysis, were applied to analyze data derived from the Biolog GN and the API 20NE systems of identification for 50 environmental bacterial strains. We found these two methods to be useful for revealing the relationship between the two sets of numerical taxonomic traits. Both of these methods showed that the distances according to the Biolog GN results between the studied strains were related to those derived from the API 20NE results, despite the differences in the test sets of the two systems. In addition, the co-inertia analysis allowed us to visualise the relationships between classifications of strains derived from the two identification systems and, simultaneously, to estimate the contribution of particular tests to the differentiation of bacterial strains.
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Affiliation(s)
- J Truu
- Institute of Molecular and Cell Biology, University of Tartu, Estonia.
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23
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Barnett SJ, Alami Y, Singleton I, Ryder MH. Diversification of Pseudomonas corrugata 2140 produces new phenotypes altered in GC-FAME, BIOLOG, and in vitro inhibition profiles and taxonomic identification. Can J Microbiol 1999; 45:287-98. [PMID: 10420580 DOI: 10.1139/w99-006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bacteria are known to rapidly produce new phenotypes, but it is unclear how phenotype "plasticity" relates to studies on the population ecology of bacteria in complex environments. We characterised a collection of 14 spontaneous phenotype variants, derived from in vitro and in vivo cultures (wheat roots) of Pseudomonas corrugata 2140, using fatty acid methyl ester profiles (GC-FAME), carbon substrate utilisation (BIOLOG), and in vitro inhibition against seven soil microorganisms. All three phenotype profiles indicated marked differences between some variants and the parent isolate. Some variant types were classified taxonomically by GC-FAME as different species to their wild-type parent, and up to a Euclidian distance of 11 from their parent. Taxonomic identification by the BIOLOG assay was more consistent; however, use of 22 carbon sources were altered (lost or gained) in one or more variants. All variant types had a reduced ability to inhibit one or more test organisms, depending on the variant and test organism. Hierarchical cluster analysis of variants using GC-FAME, BIOLOG, and inhibition profiles produced different groupings. The ability of variants to cross taxonomic boundaries specified by the GC-FAME and BIOLOG libraries at the species level has implications for both taxonomy and the ecological study of bacterial communities.
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Affiliation(s)
- S J Barnett
- Department of Crop Protection, University of Adelaide, South Australia.
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24
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Ellis RJ, Thompson IP, Bailey MJ. Temporal fluctuations in the pseudomonad population associated with sugar beet leaves. FEMS Microbiol Ecol 1999. [DOI: 10.1111/j.1574-6941.1999.tb00589.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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25
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Heuer H, Smalla K. Bacterial phyllosphere communities of Solanum tuberosum L. and T4-lysozyme-producing transgenic variants. FEMS Microbiol Ecol 1999. [DOI: 10.1111/j.1574-6941.1999.tb00590.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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26
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Lilley AK, Bailey MJ. The acquisition of indigenous plasmids by a genetically marked pseudomonad population colonizing the sugar beet phytosphere is related to local environmental conditions. Appl Environ Microbiol 1997; 63:1577-83. [PMID: 16535580 PMCID: PMC1389558 DOI: 10.1128/aem.63.4.1577-1583.1997] [Citation(s) in RCA: 102] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The transfer of naturally occurring conjugative plasmids from the indigenous microflora to a genetically modified population of bacteria colonizing the phytospheres of plants has been observed. The marked strain (Pseudomonas fluorescens SBW25EeZY6KX) was introduced as a seed dressing to sugar beets (Beta vulgaris var. Amethyst) as part of a field experiment to assess the ecology and genetic stability of deliberately released bacterial inocula. The sustained populations of the introduced strain, which colonized the phytosphere, were assessed throughout the growing season for the acquisition of plasmids conferring mercury resistance (Hg(supr)). Transconjugants were isolated only from root and leaf samples collected within a narrow temporal window coincident with the midseason maturation of the crop. Conjugal-transfer events were recorded during this defined period in two separate field release experiments conducted over consecutive years. On one occasion seven of nine individual plants sampled supported transconjugant P. fluorescens SBW25EeZY6KX, demonstrating that conjugative gene transfer between bacterial populations in the phytosphere may be a common event under specific environmental conditions. The plasmids acquired in situ by the colonizing inocula were identified as natural variants of restriction digest pattern group I, III, or IV plasmids from five genetically distinct groups of large, conjugative mercury resistance plasmids known to persist in the phytospheres of sugar beets at the field site. These data demonstrate not only that gene transfer may be a common event but also that the genetic and phenotypic stability of inocula released into the natural environment cannot be predicted.
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Abstract
Microbial population dynamics on leaves in time and space are a function of immigration, emigration, growth, and death. Insight into the relative significance of each population process to the generation of specific dynamics for individual microorganisms is necessary to understanding the ecology and life history strategy of the microorganism and to developing effective control strategies. Additionally, information on the significance of within-leaf versus extra-leaf processes to the generation of phyllosphere dynamics is important to determining the range of spatial scales over which a population should be studied. Unfortunately, such information is difficult to obtain due to the lack of effective methodologies for distinguishing these processes within phyllosphere populations. Future research efforts should focus on the quantification of immigration, emigration, growth, and death relative to the population dynamics of phyllosphere microorganisms.
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Affiliation(s)
- L L Kinkel
- Department of Plant Pathology, University of Minnesota, Saint Paul, Minnesota 55108, USA.
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29
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Torsvik V, Sørheim R, Goksøyr J. Total bacterial diversity in soil and sediment communities—A review. J Ind Microbiol Biotechnol 1996. [DOI: 10.1007/bf01574690] [Citation(s) in RCA: 134] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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30
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Smith JJ, Offord LC, Holderness M, Saddler GS. Genetic diversity of Burkholderia solanacearum (synonym Pseudomonas solanacearum) race 3 in Kenya. Appl Environ Microbiol 1995; 61:4263-8. [PMID: 8534093 PMCID: PMC167737 DOI: 10.1128/aem.61.12.4263-4268.1995] [Citation(s) in RCA: 78] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Genetic diversity among isolates of the bacterial plant pathogen Burkholderia solanacearum (synonym Pseudomonas solanacearum) race 3 biovar II of Kenya was determined by PCR with repetitive sequences (ERIC and BOX repetitive primer sets) and pulsed-field gel electrophoresis of genomic DNA digested by rare-cutting restriction endonucleases (RC-PFGE). The study comprised 46 isolates collected during 1992 from the major potato-growing regions of Kenya (45 were identified as race 3 biovar II, and 1 belonged to race 3 biovar N2) and 39 reference isolates from 19 other countries. RC-PFGE identified 10 distinct profile types among the Kenyan race 3 biovar II isolates (29 of the isolates exhibited identical profiles) and a further 27 distinct profile types among the reference isolates. ERIC and BOX primer sets were unable to differentiate race 3 biovar II isolates within the Kenyan population but differentiated a further two distinct profile types among the reference isolates. The race 3 biovar N2 isolate had a highly distinct RC-PFGE and repetitive sequence PCR profile. Statistical analysis of the data identified biogeographic trends consistent with conclusions drawn from previous studies on the origin and worldwide dissemination of race 3 biovar II isolates; however, genomic fingerprinting by RC-PFGE revealed a level of genetic diversity previously unrealized.
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Affiliation(s)
- J J Smith
- International Mycological Institute, Egham, Surrey, United Kingdom
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31
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Bailey MJ, Lilley AK, Thompson IP, Rainey PB, Ellis RJ. Site directed chromosomal marking of a fluorescent pseudomonad isolated from the phytosphere of sugar beet; stability and potential for marker gene transfer. Mol Ecol 1995; 4:755-63. [PMID: 8564013 DOI: 10.1111/j.1365-294x.1995.tb00276.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A plasmid-free, non-pathogenic, ribosomal RNA group 1 fluorescent pseudomonad, Pseudomonas fluorescens SBW25, was selected from the microflora of sugar beet (Beta vulgaris) and modified to contain constitutively expressed marker genes. By site directed homologous recombination a KX cassette [kanamycin resistance (kanr) and catechol 2,3 dioxygenase (xylE)] and a ZY cassette [lactose utilization (lacZY, beta-galactosidase, lactose permease)] were introduced at least 1 Mbp apart on the 6.6 Mbp bacterial chromosome. Separate sites were selected to provide sensitive detection methods and allow assessments of marker gene stability of the genetically modified micro-organism (GMM), SBW25EeZY6KX, when it colonized the leaves and roots of sugar beet plants following seed inoculation.
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Affiliation(s)
- M J Bailey
- Natural Environment Research Council, Institute of Virology and Environmental Microbiology, Oxford, UK
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32
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Survival, Colonization and Dispersal of Genetically Modified Pseudomonas fluorescens SBW25 in the Phytosphere of Field Grown Sugar Beet. Nat Biotechnol 1995. [DOI: 10.1038/nbt1295-1493] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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33
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Thompson IP, Bailey MJ, Ellis RJ, Lilley AK, McCormack PJ, Purdy KJ, Rainey PB. Short-term community dynamics in the phyllosphere microbiology of field-grown sugar beet. FEMS Microbiol Ecol 1995. [DOI: 10.1111/j.1574-6941.1995.tb00284.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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