Welcome to the POTNIS LAB Molecular Ecology of Plant-Pathogen Interactions

Our research program is exploring the dynamics of host-pathogen arms-race by studying multi-trophic interactions of a pathogen with the resident microflora, the environment and the host.  Our overall goal is to develop a mechanistic understanding of biological response of a pathogen to such dynamic environment and leverage these concepts for proposing novel/ altering current disease management strategies.

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Towards this goal, we have been working on following research areas:

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Ecological and evolutionary dynamics of plant pathogens 

 

We are studying bacterial spot xanthomonads as a model system to understand the extent of diversity in pathogen, factors involved in generating this diversity and adaptive potential of the pathogen using various omics approaches. We have recently identified novel lineages of bacterial spot xanthomonads with novel virulence factors in Alabama, not reported so far in the southeastern US. Interestingly, one of these novel lineages is aggressive on pepper, while other novel lineage seems to have acquired a novel transcription-activator-like effector (TALE). We are continuing to monitor abundance of these lineages in the tomato/pepper fields with the help of extension agents and growers.

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Another pathosystem that we are investigating for studying outbreak potential of pathogen is Xylella fastidiosa, a naturally competent, xylem-limited pathogen. We have assessed recombination patterns across different subspecies of X. fastidiosa and have identified importance of recombination hotspots in shaping ecology and evolution of this pathogen. These results were recently published in the ISME Journal.

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Unraveling the diversity of plant-associated saprophytic/non-pathogenic bacteria and their role in plant health and plant-pathogen interactions

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This is a JGI-Community Science Program funded project in collaboration with Marie-Agnès Jacques (INRA) and Jeffrey Jones. Non-pathogenic/saprophytic xanthomonads represent an important component of the host microbiome given their sympatric association with pathogenic xanthomonads from symptomatic (infected with pathogenic xanthomonads) as well as asymptomatic host tissues. In addition, these non-pathogenic xanthomonads also have a varied lifestyle in a wide range of environments, including a variety of plant species, plant debris, rain, and aerosols. These non-pathogenic strains, which cause no apparent symptoms on hosts from which they are isolated, have been characterized phenotypically and more recently, a portion of these strains were found to be phylogenetically divergent based on multi-locus sequence typing. Non-pathogenic bacteria with sympatric association with pathogenic relatives provide a classical system to explore the tripartite interactions among non-pathogens, pathogens and the host/non-host plant. A large collection of saprophytic strains is currently being sequenced and expected to improve our understanding niche specialization and epiphytic survival strategies of plant-associated microbes. 

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Understanding patho-adaptation strategies of a bacterial pathogen

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Xanthomonas genus comprises of strains capable of infecting a wide range of diverse dicots and monocots, yet, each species is often restricted to a very narrow host range. My previous post-doctoral research indicated that Xanthomonas perforans has undergone rapid evolution on tomato in a period of two decades in Florida, and that strains belonging to one of the lineages, although isolated from tomato, also had ability to cause disease on pepper, when tested with artificial inoculation under the greenhouse conditions. In our recent sampling in Alabama, we isolated strains belonging to the novel lineage of Xanthomonas perforans, from infected pepper, confirming host range expansion of X. perforans under field conditions. We have used genome-wide association analyses to identify candidate host specificity factors on pepper and are currently testing their role using functional in planta assays. We are also exploring role of emerging type III effectors, or their variants and their importance in pathogen fitness. Among other virulence factors, we are investigating the role of type VI secretion system in pathogenesis of xanthomonads. This secretion system, although being extensively studied in animal/human pathogenic bacteria, is an understudied system in plant pathogenic bacteria. Presence of multiple, large clusters of this system warrant our attention to their importance in overall host-associated life of a pathogen either through direct interaction with the host or through indirect influence on host by shaping microbial interactions in plant associated environments. 

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Microbial community interactions in the rhizosphere and/phyllosphere

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Host-associated microbiome is integral to the overall health of the host in presence of biotic or abiotic stress conditions. Our goal for the currently ongoing microbiome projects is to understand community level interactions and associated microbial taxa that contribute towards disease tolerance. Some of the recent projects include effect of cover crops on cotton/soybean rhizosphere microbiome, understanding the principles of community assembly in rhizosphere/phyllosphere and how shift in the community interactions influences pathogen persistence. 

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