It depends on what would be the application of the newly isolates microorganisms... To isolate plant growth promoting strains, you should use soil around (and) the roots. To use microorganisms for environmental purposes (bioremediation for example) test also other points close to the contaminated soil.
Everything depends upon homogeneity of the soil matrix and microbial distribution in a saline environment. Dr. Vassilev is right, but the best way would be to perform sampling from large area and preparation of composite samples of soil for microbe isolation.