Standard microorganism isolating technology applied for complex multiphase environmental samples such as soil or sediment needs pre-treatment steps to remove living cells from their mixed-phase microniche, by creating a liquid-phase sample. This process removes synergetic relationships, which help to maintain viability of yet-to-be-cultured and hard-to-culture bacteria. In this paper we demonstrate a high throughput Laser Micro-Sampling (LMS) technology for direct isolation of pure microbial cultures and microbial consortia from soil. This technology is based on laser printing of soil microparticles by focusing near-infrared laser pulses on specially prepared samples of a soil/gel mixture spread onto a gold-coated glass plate. Microsamples of soil are printed on glucose-peptone-yeast agar plates, to estimate the LMS process influence on functional and taxonomic microbial diversity, and on «Eco-log» sole carbon sources microplates, to investigate functional diversity by "metabolic fingerprinting". The obtained results are compared with traditionally treated soil samples. It was shown that LMS treatment leads to increasing of cultured biodiversity and modifies the functional diversity. The strain of rare genus Nonomuraea was isolated by LMS from complex natural environment without using media selective for this genus.