A new programme of research within the Plant Pathology programme aims to use comparative genomics to identify genes and investigate mechanisms involved in the persistence of enterobacterial plant and animal pathogens in the environment.  There are now many hundreds of bacterial genomes fully sequenced, and comparative genomics tools developed at SCRI are being used to investigate the relationships between these genomes. One important new advance has been our ability to compare the genome of the enterobacterial plant pathogen Pectobacterium atrosepticum (Pba) with other plant-associated bacteria, and enterobacterial animal pathogens such as E. coli and Salmonella spp. Such comparisons have led to the discovery of many unexpected traits in Pba, such as the presence of genes involved in nitrogen fixation and root binding, which suggest that this pathogen may live in the environment for prolonged periods even in the absence of its disease host potato. Our comparisons have also clearly identified genomic islands in the enterobacterial human pathogens with similarity to genes in Pba and other plant-associated bacteria.

Food poisoning outbreaks are increasingly associated with fruit and vegetables and genomic comparisons have highlighted shared features that may be important for persistence in the environment. Many of the so-called virulence features that are known to be required for infection of either plant or animal hosts are shared by both Pba and human pathogens. Examples include flagella, type three secretion systems and fimbriae.  The work carried out here aims to characterise more of the shared features to define their roles in the interaction of human pathogenic bacteria with plants.

Soil viruses

Although viruses infect organisms belonging to all the domains of life: Bacteria, Archaea and Eukarya the central focus of virus research has concerned their roles as infectious agents and as tools for understanding molecular biology. Viruses from the natural environment and from soils in particular, are extremely understudied. Taking into account their potential role in ecology, exobiology and evolution we aim to establish a new scientific area to study viruses in soils, their structure, functions and role in structure and composition of soil microbial communities.

We have isolated and characterised some virus-like particles from soils from a temperate environment (that is, the Dundee area of Scotland) and Antarctica. Different virus morphotypes including tailed, polyhedral (spherical), rod-shaped, filamentous and bacilliform virions were detected in the soil samples. Although many of these morphotypes were essentially similar to previously identified and classified viruses, some novel morphotypes, represented by particles with flexible tails and strongly elongated heads and small spherical particles with obvious spikes, were also found. We are also analysing viruses in different soil functional domains surrounding plant roots: rhizosphere, rhizosheath and bulk soil.

Image of E.coli showing flagella

Tailed bacteriophages found in soils in Antarctica. Bar, 100 nm