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Plants are in constant interaction with microorganisms (Fig. 1). Their surfaces and surroundings form nutrient-rich habitats for complex microbial populations that can positively or negatively influence plant health and growth. Of these interactions, the detrimental effect that microbes can have on plant health is probably best known as every year an enormous amount of food gets lost due to plant diseases. Although actual numbers are hard to find, researchers estimate crop losses as high as 30 to 40 % of annual crop production which not only translates in less food but also the loss of hundreds of billions of dollars for the agricultural industry. Knowledge about these microbes, about their behavior, their interactions, metabolism and specialized traits will help us to find ways to control and prevent the diseases they cause.

I am fascinated by soil-borne plant pathogenic bacteria, and more specifically, how they interact with their surroundings and how they evolved to become successful pathogens. In order to gain access to a unique habitat, pathogens must overcome several challenging steps from surviving the often harsh soil conditions, competing with other microbes, identification of a suitable host, attachment, penetration and colonization of plant tissue, to escaping or protecting themselves against the defense mechanisms of the plant. It is clear that plant pathogenic bacteria are highly specialized microorganisms able to sense and adequately respond to their changing environment.

Fig. 1. Schematic representation of the diversity of potential plant interactions with bacteria. Adapted from Francis et al., 2010.

Streptomyces scabies

The large genus Streptomyces consists of Gram-positive, high G+C content bacteria that are mostly soil saprophytes. They are best known for the production of pharmaceutically and agriculturally important secondary metabolites, and are characterized by a complex life cycle involving the production of aerial hyphae and the subsequent differentiation into spore chains (Fig. 2; Flardh & Buttner, 2009). Although several hundred species are known to date, only a handful seem to be pathogenic. The best-studied phytopathogens are S. scabies, S. acidiscabies, S. turgidiscabies and S. ipomoeae. They cause raised or pitted scab lesions on economically-important root and tuber crops like potato (Fig. 3), radish, beet, turnip and sweet potato (Loria et al., 2006).

The primary virulence determinant of S. scabies, the oldest and best-characterized species, is the phytotoxin thaxtomin A. It is part of a family of nitrated dipeptides formed by nonribosomal peptide synthases out of the main components tryptophan, phenylalanine and nitric oxide derived from arginine (Fig. 4; Barry et al., 2012; Loria et al., 2008). Its main target is the cellulose synthase complex active in dividing and expanding plant cell tissue. Within the thaxtomin biosynthetic gene cluster lies the gene txtR that encodes a pathway-specific transcriptional activator. TxtR is triggered by cellobiose, the smallest subunit of cellulose, and induces the expression of the thaxtomin biosynthetic genes (Joshi et al., 2007).

Since the production of thaxtomin A is energetically very costly for the bacterium, it is under strict control involving several layers of regulation. We demonstrated that toxin production is controlled by at least five additional regulatory genes belonging to the bld gene family of global regulators involved in secondary metabolism and/or morphological differentiation of Streptomyces (Bignell et al., 2014). Our work is the first to demonstrate the involvement of global regulators in addition to the pathway-specific activator, TxtR, in controlling thaxtomin A production and therefore virulence in S. scabies. Moreover, recently we made major progress by uncovering another layer of regulation: a regulator that acts as the gatekeeper of pathogenicity in thaxtomin A-producing streptomycetes. More info to come in the near future!

Fig. 2. Growth, sporulation and toxin production of Streptomyces scabies.

Fig. 3. Potato tubers showing scab lesions caused by Streptomyces scabies.

Fig. 4. Structure of the phytotoxin thaxtomin A.

Our scientific contributions to the topic:

Our review paper on the topic:

Rhodococcus fascians

Rhodococcus species are common throughout nature and have been isolated from very diverse habitats. This widespread occurrence reflects their unique enzymatic capabilities and extensive catabolic diversity, which contribute to their significant ecological and biotechnological importance, such as their use in biodegradation of hydrophobic natural compounds and xenobiotics, including polychlorinated biphenyls. These characteristic metabolic functions are often encoded by genes located on plasmids (Francis et al., 2007).

The only plant pathogen within the genus, R. fascians (Fig. 5), is a biotrophic phytopathogen that infects an exceptionally broad range of both monocotyledonous and dicotyledonous plants, woody as well as herbaceous species. It causes persistent problems in the ornamentals industry, creating significant losses in nursery production systems due to growth abnormalities and malformations (Putnam & Miller, 2007). Secretion of cytokinins interferes with the hormone balance of the plant host and, hence, with its development. Morphological changes range from leaf deformation, witches' broom formation, fasciation, abnormal flowers, and overall stunted growth of the aerial plant parts, to the most typical symptom, the leafy gall (Fig.6). These galls are formed at the site of bacterial inoculation by the activation of existing meristems and the formation of new meristems from cortical plant cells that are re-activated to divide. Shortly after the initiation of numerous shoots, their outgrowth is inhibited, generating a densely packed leafy gall (Stes et al., 2013).

In strain D188, genes implicated in leafy gall formation are located on a large conjugative linear plasmid, pFiD188 (fasciation induction). Careful annotation and sequence comparison with linear plasmids from other environmentally-important Rhododcoccus species revealed four conserved and three unique regions (Fig. 7). The conserved regions are implicated in plasmid maintenance and dispersal, whereas the unique regions are involved in virulence, interactions with the host, secondary metabolite production and ecological fitness of the bacterium (Francis et al., 2012).

Fig. 5. R. fascians D188 on plate.

Fig. 6. Leafy gall caused by R. fascians D188 on a young tobacco plant.

Fig. 7. Sequence comparison of rhodococcal linear plasmids. Similarities are plotted (tblastx) between pFiD188 (R. fascians D188), pBD2 and pREL1 (R. erythropolis BD2 and PR4, respectively), and pRHL2 (R. jostii RHA1).

Our scientific contributions to the topic:

Our review papers on the topic:

Rhizorhapis suberifaciens

Corky root of lettuce (van Bruggen and Francis, 2014) is caused by aerobic Gram-negative bacteria belonging to several genera in the Sphingomonodaceae family of the alpha-subclass of proteobacteria (van Bruggen and Francis, 2014). Pathogenic bacteria most commonly isolated from diseased tissue belong to the genus Rhizorhapis (previously known as Rhizomonas), more specifically the species R. suberifaciens. Rhizorhapis is related to the genera Sphingobium, Sphingopyxis, Rhizorhabdus and Sphingomonas, which include common soil and rhizosphere bacteria. Corky root-causing bacteria have been found within these genera with exception of Sphingomonas (Francis et al., 2014).

Typical symptoms consist of yellow bands on young roots and greenish brown, longitudinal corky ridges on the taproot and main lateral roots (Fig. 6). Affected areas of the root are swollen, and ultimately the infected root becomes brittle and breaks off easily. Severely diseased plants develop chlorotic and necrotic lower leaves, and the lettuce heads remain small. Yield losses from reduced head size may range from 30 to 70 %. Apart from direct losses in yield, lettuce corky root also results in indirect losses due to inefficient water and nutrient uptake, and a higher risk at secondary infections by root-rotting organisms (van Bruggen and Francis, 2014).

Currently there are corky root resistant cultivars available for different lettuce types, conferred by a single recessive gene called cor (Brown and Michelmore, 1988). Nevertheless, several strains have been isolated that are equally virulent on susceptible as on resistant lettuce cultivars and breeding lines (van Bruggen et al., 2014b). Moreover, a non-pathogenic strain FL11 was found to provide biological control against various pathogenic strains causing lettuc corky root (van Bruggen et al., 2014a)









Fig. 8. Typical corky root symptoms on lettuce roots (right) compared to the roots of a healthy plant (left).

Our contribution:

Francis, I.M., Jochimsen, K.N., De Vos, P., and van Bruggen, A.H.C. (2014). Reclassification of rhizosphere bacteria including strains causing corky root of lettuce as Rhizorhapis suberifaciens gen. nov., Sphingobium mellinum sp. nov., Sphingobium xanthum sp. nov., and Rhizorhabdus argentea gen. nov., sp. nov. International Journal of Systematic and Evolutionary Microbiology 64 (4): 1340-1350. (web)

van Bruggen, A.H.C., and Francis, I.M. (2014). Case investigation and forensic evidence for a new plant disease: the case of lettuce corky root. Plant Disease (accepted).

van Bruggen, A.H.C., Francis, I.M., and Jochimsen, K.N. (2014a). Non-pathogenic rhizosphere bacteria belonging to the genera Rhizorhapis and Sphingobium provide specific control of lettuce corky root disease caused by species of the same bacterial genera. Plant Pathology, doi: 10.1111/ppa.12212. (web)

van Bruggen, A.H.C., Ochoa, O., Francis, I.M., and Michelmore, R.W. (2014b). Differential interactions between strains of Rhizorhapis, Sphingobium, Sphingopyxis or Rhizorhabdus and accessions of Lactuca spp. with respect to severity of corky root disease. Plant Pathology, doi: 10.1111/ppa.12188. (web)