So far I know that the bacterium eludes the host cells intra-cellular defense mechanisms and multiplies and they started damaging the DNA of the host and leads to gene mutation. They may also cause membrane damage. They are responsible to slowed down the decomposition process which affect the soil fertility. They may damage the embryo for seed germination.

By soil fertility, you mean the ability of soil to support plant life. Fertile soil contains the sufficient minerals and nutrients needed for plant growth, and it is often composed of large amounts of topsoil. Possibly it is just a competition for the nutrient which is leading to decreasing in soil fertility. Maybe it competes with beneficial soil microflora. 

Germination of seed and crop productivity can be linked to the depletion of nutrient.

Respected Sir,

In quest to explore agricultural important microorganisms, more or less pathogenic bacteria are studied as potential contender to promote plant health and growth, but to spoor up the agriculture economy in eco-safe manner which can be accomplished by looking over few non-pathogenic strains of microorganisms. A plenty of bacteria have been reported to induce seed germination, plant growth and maintenance/mobilization of essential nutrients in soil to render soil fertility. Therefore, before to processed bacterial strain for agricultural benefits (in vivo/in vitro/ex situ), it is must to monitor pathogenic nature of bacteria by using preliminary investigations such as haemolytic activity, further phylogeny analysis with pathogenic and non-pathogenic type strains to determine its ancestry with non-pathogenic or pathogenic bacteria will help us more. Only the non-pathogenic bacteria have to be exploit for crop production or so. I strongly disagree working on pathogenic bacteria for agricultural benefits, which upon colonization in fruit and seed part harm human race in-spite of benefiting by raising crop production and productivity. I aspires that my submission would be able to fire a place in the discussion.

Regards,

Dheeman S.