Defining a microbial species: implications for plant biosecurity

22 - 24 September 2009

The genomics revolution is changing our thinking of the microbiological world. Only 15 years have passed since the first bacterial genome was sequenced and novel species are now being identified at a rapid rate. Doubt has been cast on the existence of microbial species among environmental isolates and this problem is particularly acute as millions of microbial species are thought to exist that have not yet been cultivated. Possibly the greatest challenge to the species concept for bacteria has been driven by the recognition that lateral gene transfer (LGT) or horizontal gene transfer, has occurred on innumerable occasions. Evidence is emerging that the rate of LGT is far higher than previously thought and that the role of the ‘mobilome’ in defining the phenotype of a bacterial species has been underestimated.

Next generation sequencing technologies have produced the most accurate estimate on the abundance and variability of the virosphere. It has been estimated that on average, there are 50 million virus particles per ml of costal seawater with the total number of viruses in the ocean now estimated at greater than 10³⁰. A recent study in the Costa Rican rainforest identified thousands of plant viral ‘sequence tags’ from the rainforest canopy. It is also becoming more evident that viruses are not just pathogens (parasites) but can also be commensal agents (neither host nor virus benefits or is harmed) and mutualists (both virus and host benefit). These findings are in stark contrast to the known plant viruses (less than 2,000 viral species) of which, only six per cent have been isolated from plants in the wild.

Plant viruses and bacteria have recently been identified as the cause of more than two thirds of the emerging infectious diseases of plants during the period of 1996 – 2002 and it is likely that this trend will continue. The emergence of a global community and an increase in plant microbial discovery in the last 15 years has increased the requirement for countries and regions to protect their farming systems from exotic pests. In addressing plant biosecurity requirements countries need to comply with its international obligations as defined by the World Trade Organization Agreement on the application of Sanitary and Phytosanitary measures and protect crops from emergency plant pests (EPPs) at national, regional and individual farm levels. Currently plant quarantine is based on the presence of the pathogen and not the disease. Trade can also be disrupted by the ‘presence of the pathogen’, or lack of evidence that a pest or pathogen is ‘known not to occur’.

It is becoming increasingly unreliable to base the identification of a microbial pathogen on genome sequence data alone. Accurate definitions and identification of microbial species, pathovars and strains are crucial and demonstration of their pathogenicity is required. It is critical that we only quarantine microbial species that have been shown to cause, or be associated with disease.