Soft-rot Enterobacteriaceae (SRE), which belong to the genera Pectobacterium and Dickeya, consist mainly of broad host-range pathogens that cause wilt, rot, and blackleg diseases on a wide range of plants. They are found in plants, insects, soil, and water in agricultural regions worldwide. SRE encode all six known protein secretion systems present in gram-negative bacteria, and these systems are involved in attacking host plants and competing bacteria. They also produce and detect multiple types of small molecules to coordinate pathogenesis, modify the plant environment, attack competing microbes, and perhaps to attract insect vectors. This review integrates new information about the role protein secretion and detection and production of ions and small molecules play in soft-rot pathogenicity.

Pectobacterium atrosepticum, P. carotovorum subsp. brasiliensis, and Dickeya spp. cause soft rot of potato (Solanum tuberosum) worldwide. Plants respond to bacterial invasion by activating defense responses associated with accumulation of several enzymes and inhibitors, which prevent pathogen infection. This study focused on the role of polyphenol oxidase (PPO), peroxidase (POD), phenylalanine ammonia lyase (PAL), chlorogenic acid, and total soluble phenols in imparting resistance to soft rot pathogens. Seven and 11 varieties grown by farmers in South Africa and Zimbabwe, respectively, were used in the study. The results showed significantly higher (P < 0.001) enzyme activity of PPO and PAL as well as higher concentrations of chlorogenic acid and total soluble phenols in Vanderplank, Pentland Dell, M69/11, Romano, M59/20, and Mondial_Zw. PAL activity increased significantly with time in all varieties, and the highest activity was recorded 8 h after cutting. The resistance of the varieties was correlated with high PPO and PAL enzyme activity as well as increased concentrations of chlorogenic acid and total soluble phenols. PPO, POD, and PAL activities increased significantly in wounded and inoculated tubers. These findings show that PAL, PPO, POD, chlorogenic acid, and total soluble phenols play a role in imparting resistance to potato soft rot infection.

Genetic diversity among isolates of Alternaria solani, the causal agent of early blight of potato, from various potato-growing regions in South Africa (SA), was determined using virulence assays, vegetative compatibility (VC) tests, and random amplified microsatellite (RAMS) primers. The virulence assays showed low virulence levels for the largest part of the population, but failed to otherwise characterize the population diversity. The VC tests revealed 19 VC groups (VCGs), indicating a relatively high level of diversity among the isolates. There was little correlation between geographic origin of isolates and VCGs. Analysis of RAMS profiles revealed 27% genetic diversity among 46 isolates. This value is relatively high for an asexually reproducing fungus, but is similar to values obtained previously by authors studying A. solani. Distance analysis of the RAMS profiles also provided no evidence for geographical clustering of isolates. VCG and RAMS profiles indicated that isolates are randomly spread across SA. This fact, together with the high diversity of A. solani in SA, indicates that the fungus has a high potential to adapt to resistant cultivars or fungicides. This information can aid in the breeding and deployment of A. solani-resistant potato varieties, and in early blight disease management in SA.

Land-use change from natural to managed agricultural ecosystems significantly impacts soil bacterial diversity and function. The Eastern Free State (EFS) is one of the most productive agricultural regions in South Africa. However, no studies aiming to understand the changes in bacterial diversity, composition and function due to land-use change in this area have been conducted. This study investigated, using high-throughput 16S rRNA gene amplicon sequencing, the effects of long-term agriculture on bacterial diversity, composition and putative function in the EFS by comparing microbiomes from lands that have been under agronomic activity for over 50 years to those from uncultivated land. Results indicate that agriculture increased bacterial diversity. Soil chemical analysis showed that land-use shifted soils from being oligotrophic to copiotrophic, which changed bacterial communities from being Actinobacteria dominated to Proteobacteria dominated. Predictive functional analysis using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) suggested that agricultural soil was abundant in genes associated with plant fitness and plant growth promotion, while non-agricultural soil was abundant in genes related to organic matter degradation. Together, these results suggest that edaphic factors induced by long-term agriculture resulted in shifts in bacterial diversity and putative function in the EFS.

A set of daily weather data simulations for 1961 to 2050 were used to calculate past and future trends in pest and disease pressure in potato cropping systems at three agro-ecologically distinct sites in South Africa: the Sandveld, the Eastern Free State and Limpopo. The diseases and pests modelled were late blight, early blight and brown spot, blackleg and soft rot, root-knot nematodes and the peach-potato aphid Myzus persicae (as indicator of Potato virus Y and Potato leaf roll virus). The effects of climate on trends in relative development rates of these pathogens and pests were modelled for each pathogen and pest using a set of quantitative parameters, which included specific temperature and moisture requirements for population growth, compiled from literature. Results showed that the cumulative relative development rate (cRDR) of soft rot and blackleg, root-knot nematodes and M. persicae will increase over the 90-year period in the areas under consideration. The cRDR of early blight and brown spot is likely to increase in the wet winter and wet summer crops of the Sandveld and Eastern Free State, respectively, but remains unchanged in the dry summer and dry winter crops of the Sandveld and Limpopo, respectively. Climate change will decrease the cRDR of late blight in all of the cropping systems modelled, except in the wet winter crop of the Sandveld. These results help to set priorities in research and breeding, specifically in relation to management strategies for diseases and pests.