Abstract
Microorganisms found in plants exist as epiphytes or endophytes. Most
epiphytes remain on plant surfaces and the latter may be intracellular pathogens,
opportunistic and adapted microbial colonisers that originate from the surrounding
environment. The main purpose of agricultural practices is thus, to develop disease-free
varieties by propagating plants under controlled environmental conditions. Such
conditions should be optimal for plant production and reduce disease development. The
former requires strict certification schemes via several routes that include (i) indexing
with subsequent removal of infected or contaminated materials from the production
chain (ii) meristem and other tissue culture production systems and (iii) the use of
thermo or chemotherapy for phytosanitation. Other methods also require balancing and
proper adjustments in fertilizer usage and crop rotation. Therefore, this chapter reviews
the role of microbial pathogen indexing as a means of controlling bacterial, fungal, and
viral diseases that have a significant role to play in agriculture.