Metagenomic analysis of bacterial assemblages from Sardinian soils

The soil microbiota is investigated by technical approaches that are usually grouped in two main categories i) cultivation-based and ii) cultivation independent techniques. Only 0,1 to 1% of known soil bacteria species are today “culturable”.Most of soil species are not tractable using conventional cultivation methods and therefore these must be studied by cultivation independent techniques.The taxonomic composition of the bacterial fractions of soil has been recently investigated by employing the so called “omic” approaches. Deep sequencing of 16S rRNA based libraries have demonstrated an enormous diversities of bacteria inhabiting the soils.In the first chapter of this work we applied pyrosequencing of 16S rRNA libraries to analyze richness and diversity of bacterial communities of Sardinian soils managed with different grazing intensity. Our data indicated that grazing is associated to a dramatic shift of community structure with Firmicutes being positively associated to grazing intensity and becoming the dominant phylum in intensively grazed soils. No significant shifts were noted in the relative abundance at class, order or family taxonomic levels suggesting no drastic changes within phyla. Correlation analysis of bacterial communities composition and physical-chemical properties of soils highlighted significant associations between soil pH or C/N ratio and Firmicutes and Verrucomicrobia relative abundance. In second chapter of the present work we analyzed the effects of organic and mineral fertilization on soil microbiota communities. The organic fertilization source was cattle manure and slurry, while the mineral was represented by ENTEC.The experimental setup was designed to represent a typical land management system of a nitrogen vulnerable zone of central Sadinia. Our results indicated that systems receiving manure are characterized by a bacteria community enriched for species able to degrade complex organic compounds.On the contrary, systems receiving mineral fertilization were enriched for oligotrophic species adapter to nutrients limited environments.