Transcriptome analysis of Xanthomonas fragariae in strawberry leaves

Role of methylglyoxal and redox homeostasis in microbe-mediated stress mitigation in plants

One of the general consequences of stress in plants is the accumulation of reactive oxygen (ROS) and carbonyl species (like methylglyoxal) to levels that are detrimental for plant growth. These reactive species are inherently produced in all organisms and serve different physiological functions but their excessive accumulation results in cellular toxicity. It is, therefore, essential to restore equilibrium between their synthesis and breakdown to ensure normal cellular functioning. Detoxification mechanisms that scavenge these reactive species are considered important for stress mitigation as they maintain redox balance by restricting the levels of ROS, methylglyoxal and other reactive species in the cellular milieu. Stress tolerance imparted to plants by root-associated microbes involves a multitude of mechanisms, including maintenance of redox homeostasis. By improving the overall antioxidant response in plants, microbes can strengthen defense pathways and hence, the adaptive abilities of plants to sustain growth under stress. Hence, through this review we wish to highlight the contribution of root microbiota in modulating the levels of reactive species and thereby, maintaining redox homeostasis in plants as one of the important mechanisms of stress alleviation. Further, we also examine the microbial mechanisms of resistance to oxidative stress and their role in combating plant stress.

Complete genome sequence of an Israeli isolate of Xanthomonas hortorum pv. pelargonii strain 305 and novel type III effectors identified in Xanthomonas

Xanthomonas hortorum pv. pelargonii is the causative agent of bacterial blight in geranium ornamental plants, the most threatening bacterial disease of this plant worldwide. Xanthomonas fragariae is the causative agent of angular leaf spot in strawberries, where it poses a significant threat to the strawberry industry. Both pathogens rely on the type III secretion system and the translocation of effector proteins into the plant cells for their pathogenicity. Effectidor is a freely available web server we have previously developed for the prediction of type III effectors in bacterial genomes. Following a complete genome sequencing and assembly of an Israeli isolate of Xanthomonas hortorum pv. pelargonii - strain 305, we used Effectidor to predict effector encoding genes both in this newly sequenced genome, and in X. fragariae strain Fap21, and validated its predictions experimentally. Four and two genes in X. hortorum and X. fragariae, respectively, contained an active translocation signal that allowed the translocation of the reporter AvrBs2 that induced the hypersensitive response in pepper leaves, and are thus considered validated novel effectors. These newly validated effectors are XopBB, XopBC, XopBD, XopBE, XopBF, and XopBG.

Dynamic character displacement among a pair of bacterial phyllosphere commensals in situ

Differences between species promote stable coexistence in a resource-limited environment. These differences can result from interspecies competition leading to character shifts, a process referred to as character displacement. While character displacement is often interpreted as a consequence of genetically fixed trait differences between species, it can also be mediated by phenotypic plasticity in response to the presence of another species. Here, we test whether phenotypic plasticity leads to a shift in proteome allocation during co-occurrence of two bacterial species from the abundant, leaf-colonizing families Sphingomonadaceae and Rhizobiaceae in their natural habitat. Upon mono-colonizing of the phyllosphere, both species exhibit specific and shared protein functions indicating a niche overlap. During co-colonization, quantitative differences in the protein repertoire of both bacterial populations occur as a result of bacterial coexistence in planta. Specifically, the Sphingomonas strain produces enzymes for the metabolization of xylan, while the Rhizobium strain reprograms its metabolism to beta-oxidation of fatty acids fueled via the glyoxylate cycle and adapts its biotin acquisition. We demonstrate the conditional relevance of cross-species facilitation by mutagenesis leading to loss of fitness in competition in planta. Our results show that dynamic character displacement and niche facilitation mediated by phenotypic plasticity can contribute to species coexistence.

In this study, the concept of dynamic character displacement among interacting bacterial species from leaf-colonizing families was empirically tested using a proteomics approach. A phenotypic shift towards the utilization of alternative carbon sources was observed during coexistence, thereby minimizing niche overlap.

Prevalence and Specificity of Chemoreceptor Profiles in Plant-Associated Bacteria

Chemosensory pathways are among the most abundant prokaryotic signal transduction systems, allowing bacteria to sense and respond to environmental stimuli. Signaling is typically initiated by the binding of specific molecules to the ligand binding domain (LBD) of chemoreceptor proteins (CRs). Although CRs play a central role in plant-microbiome interactions such as colonization and infection, little is known about their phylogenetic and ecological specificity. Here, we analyzed 82,277 CR sequences from 11,806 representative microbial species covering the whole prokaryotic phylogeny, and we classified them according to their LBD type using a de novo homology clustering method. Through phylogenomic analysis, we identified hundreds of LBDs that are found predominantly in plant-associated bacteria, including several LBDs specific to phytopathogens and plant symbionts. Functional annotation of our catalogue showed that many of the LBD clusters identified might constitute unknown types of LBDs. Moreover, we found that the taxonomic distribution of most LBD types that are specific to plant-associated bacteria is only partially explained by phylogeny, suggesting that lifestyle and niche adaptation are important factors in their selection. Finally, our results show that the profile of LBD types in a given genome is related to the lifestyle specialization, with plant symbionts and phytopathogens showing the highest number of niche-specific LBDs. The LBD catalogue and information on how to profile novel genomes are available at https://github.com/compgenomicslab/CRs.

IMPORTANCE Considering the enormous variety of LBDs at sensor proteins, an important question resides in establishing the forces that have driven their evolution and selection. We present here the first clear demonstration that environmental factors play an important role in the selection and evolution of LBDs. We were able to demonstrate the existence of LBD families that are highly enriched in plant-associated bacteria but show a wide phylogenetic spread. These findings offer a number of research opportunities in the field of single transduction, such as the exploration of similar relationships in chemoreceptors of bacteria with a different lifestyle, like those inhabiting or infecting the human intestine. Similarly, our results raise the question whether similar LBD types might be shared by members of different sensor protein families. Lastly, we provide a comprehensive catalogue of CRs classified by their LBD region that includes a large number of putative new LBD types.