Total bacterial diversity in soil and sediment communities—A review

Abstract

Advances in microbial methods have demonstrated that microorganisms globally are the dominating organisms both concerning biomass and diversity. Their functional and genetic potential may exceed that of higher organisms. Studies of bacterial diversity have been hampered by their dependence on phenotypic characterization of bacterial isolates. Molecular techniques have provided the tools for analyzing the entire bacterial community including those which we are not able to grow in the laboratory. Reassociation analysis of DNA isolated directly from the bacteria in pristine soil and marine sediment samples revealed that such environments contained in the order of 10 000 bacterial types. The diversity of the total bacterial community was approximately 170 times higher than the diversity of the collection of bacterial isolates from the same soil. The culturing conditions therefore select for a small and probably skewed fraction of the organisms present in the environment. Environmental stress and agricultural management reduce the bacterial diversity. With the reassociation technique it was demonstrated that in heavily polluted fish farm sediments the diversity was reduced by a factor of 200 as compared to pristine sediments. Here we discuss some molecular mechanisms and environmental factors controlling the bacterial diversity in soil and sediments.