Metagenom – zródło nowej informacji o mikroorganizmach glebowych

Metagenome – a new source of information about soil microorganisms
J. Kozdrój

1. Wstęp. 2. Problemy z poznaniem mikrobiomu oraz próby ich przezwyciężania. 3. Metagenomika a specyficzny charakter gleby. 4. Analiza genetyczna mikrobiomu. 5. Analiza funkcjonalna metagenomu. 6. Strukturalna różnorodność mikroorganizmów w różnych środowiskach glebowych. 7. Podsumowanie

Abstract: Soil environment, due to its high heterogeneity, is considered as a major reservoir of microbial genetic and metabolic diversity in the biosphere. The knowledge on this diversity is limited, because most of the soil microorganisms cannot be cultured under the usual laboratory conditions. During the last two decades, development of methods to isolate nucleic acids from soil has opened a window to a previously unknown microbial world. In consequence, a new metagenomic approach based on the analyses of total microbial DNA has appeared in soil studies. Total microbial DNA extracted from soil by direct or indirect methods is mostly used for amplification of marker genes (e.g. SSU rRNA) which is further differentiated by fingerprinting (e.g. DGGE, T-RFLP) or sequenced directly. Until recently, sequencing was mainly performed after first cloning PCR products to produce a clone library of amplicons. Lately, another approach has been introduced to reduce costs and labour; it is commonly known as 454-pyrosequencing, the method that does not require cloning. These methods as well as DNA microarrays have demonstrated an unanticipated level of microbial diversity, especially in the newly discovered world of the biosphere. Thousands or even several hundred thousands of different bacterial phylotypes can be present in a gram of soil. They belong to dozens of phyla. The molecular approach changed the picture of structural diversity of soil microbiome, also indicating that bacteria, archaea, fungi and even viruses are diverse both globally and locally. Moreover, soil metagenomics, allows for a comprehensive search for gene expression and metabolic activity within microbiome.

1. Introduction. 2. Difficulties with microbiome analysis and attempts to overcome them. 3. Metagenomics vs. distict features of soil. 4. Genetic analysis of microbiome. 5. Functional analysis of microbiome. 6. Microbial structural diversity in different soil environments. 7. Summary