Frontiers for research on the ecology of plant‐pathogenic bacteria: fundamentals for sustainability

Morris, Cindy E.; Barny, Marie Anne; Berge, Odile; Kinkel, Linda L.; Lacroix, Catherine

doi:10.1111/mpp.12508

Cited by 18 publications

(8 citation statements)

References 43 publications

(48 reference statements)

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“…However, the obstacles to changing the vocabulary for P. syringae can be overcome. As pointed out previously, although pathovars are named in legislation to control the emergence and movement of various strains of phytopathogenic bacteria, in reality the directives are implemented in the form of standard diagnostic procedures that correspond to approved techniques (Morris et al 2017). Clear description of the techniques and their proper implementation-and not a description of the pathovar-are what assure the efficacy of quarantine and the accuracy of the diagnostics.…”

Section: Discussionmentioning

confidence: 99%

The overlapping continuum of host range among strains in the Pseudomonas syringae complex

et al. 2019

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Pseudomonas syringae is the most frequently emerging group of plant pathogenic bacteria. Because this bacterium is ubiquitous as an epiphyte and on various substrates in non-agricultural settings, there are many questions about how to assess the risk for plant disease posed by strains in the environment. Although P. syringae is considered to have discrete host ranges in defined pathovars, there have been few reports of comprehensive comparisons of host range potential. Here we present results of host range tests for 134 strains, representing eight phylogroups, from epidemics and environmental reservoirs on 15 to 22 plant species per test conducted in four separate tests to determine the patterns and extent of host range. We sought to identify trends that are indicative of distinct pathotypes and to assess if strains in the P. syringae complex are indeed restricted in their host range. We show that for each test, strains display a diversity of host ranges from very restricted to very broad regardless of the gamut of phylogroups used in the test. Overall, strains form an overlapping continuum of host range potential with equal representation of narrow, moderate and broad host ranges. Groups of distinct pathotypes, including strains with currently the same pathovar name, could not be identified. The absence of groupings was validated with statistical tests for pattern recognition. The extent of host range was positively correlated with the capacity of strains to swarm on semi-solid agar medium and with the abundance of genes in biosynthetic clusters and was inversely correlated with the abundance of genes for proteins with transmembrane domains in their genomes. Our results are consistent with the current paradigm that disease symptoms are the result of multiple molecular interactions between P. syringae and its plant host that are modulated by abiotic and biotic conditions. This leads us to propose that pathovar denominations do not correspond to the underlying biology of P. syringae. A new concept of pathogenicity that accounts for the continuum of pathogenic potential in P. syringae would open new perspectives to understand the evolution of pathogenicity in this bacterium and new insights to anticipate disease and to manage plant health.

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Section: Discussionmentioning

confidence: 99%

The overlapping continuum of host range among strains in the Pseudomonas syringae complex

et al. 2019

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“…In most cases, culture‐based methods are not quantitative and often result in selection of the dominant pathogenic species or genotype. Where in reality, disease outbreaks may be incited by a mixture of strains that exhibit a spatially aggregated distribution within agricultural fields, with patch‐to‐patch migration events that link these groups into a so‐called metapopulation (Burdon, ; Morris et al ., ).…”

Section: Introductionmentioning

confidence: 97%

Genome‐resolved metagenomics to study co‐occurrence patterns and intraspecific heterogeneity among plant pathogen metapopulations

Newberry

Bhandari

Kemble

et al. 2020

Environmental Microbiology

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Summary Assessment of pathogen diversity in agricultural fields is essential for informing management decisions and the development of resistant plant varieties. However, many population genomic studies have relied on culture‐based approaches that do not provide quantitative assessment of pathogen populations at the field‐level or the associated host microbiome. Here, we applied whole‐genome shotgun sequencing of microbial DNA extracted directly from the washings of pooled leaf samples, collected from individual tomato and pepper fields in Alabama that displayed the classical symptoms of bacterial spot disease caused by Xanthomonas spp. Our results revealed that while the occurrence of both X. perforans and X. euvesicatoria within fields was limited, evidence of co‐occurrence of up to three distinct X. perforans genotypes was obtained in 7 of 10 tomato fields sampled. These population dynamics were accompanied by the corresponding type 3 secreted effector repertoires associated with the co‐occurring X. perforans genotypes, indicating that metapopulation structure within fields should be considered when assessing the adaptive potential of X. perforans. Finally, analysis of microbial community composition revealed that co‐occurrence of the bacterial spot pathogens Pseudomonas cichorii and Xanthomonas spp. is common in Alabama fields and provided evidence for the non‐random association of several other human and plant opportunists.

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“…As noted by Morris et al ( 2017 ), “delineation of pertinent phylogenetic contours of plant pathogenic bacteria and naming of strains independent of their presumed life style is one of the five challenges for understanding the ecology of plant pathogenic bacteria.” With the goal of clarifying the taxonomic delineation of species in the P. syringae phylogenetic group, 139 genomes of the 15 recognized species assigned to this group that are available in public databases have been analyzed by a phylogenomic approach. At least one member of each phylogroup described in the P. syringae phylogenetic branch by Berge et al ( 2014 ) was included in the analyses if it was available in the public databases.…”

Section: Introductionmentioning

confidence: 99%

Clarification of Taxonomic Status within the Pseudomonas syringae Species Group Based on a Phylogenomic Analysis

et al. 2017

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The Pseudomonas syringae phylogenetic group comprises 15 recognized bacterial species and more than 60 pathovars. The classification and identification of strains is relevant for practical reasons but also for understanding the epidemiology and ecology of this group of plant pathogenic bacteria. Genome-based taxonomic analyses have been introduced recently to clarify the taxonomy of the whole genus. A set of 139 draft and complete genome sequences of strains belonging to all species of the P. syringae group available in public databases were analyzed, together with the genomes of closely related species used as outgroups. Comparative genomics based on the genome sequences of the species type strains in the group allowed the delineation of phylogenomic species and demonstrated that a high proportion of strains included in the study are misclassified. Furthermore, representatives of at least 7 putative novel species were detected. It was also confirmed that P. ficuserectae, P. meliae, and P. savastanoi are later synonyms of P. amygdali and that “P. coronafaciens” should be revived as a nomenspecies.

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Frontiers for research on the ecology of plant‐pathogenic bacteria: fundamentals for sustainability

Cited by 18 publications

References 43 publications

The overlapping continuum of host range among strains in the Pseudomonas syringae complex

The overlapping continuum of host range among strains in the Pseudomonas syringae complex

Genome‐resolved metagenomics to study co‐occurrence patterns and intraspecific heterogeneity among plant pathogen metapopulations

Clarification of Taxonomic Status within the Pseudomonas syringae Species Group Based on a Phylogenomic Analysis

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