Soil Metagenomics: Potential Applications and Methodological Problems
Jan Dirk van Elsas, Mariana Silvia Cretoiu, Anna Maria Kielak and Francisco Dini-Andreote
from: Omics in Soil Science (Edited by: Paolo Nannipieri, Giacomo Pietramellara and Giancarlo Renella). Caister Academic Press, U.K. (2014)
Metagenomics has been defined as the study of the collective genomes of the microbiota in given habitat. Soil offers a huge microbial diversity and the use of metagenomics approaches will allow a deeper understanding of soil microbial diversity and function. The two areas, phylogenetically-based diversity and functional gene based function, are complementary and may be used side-by-side in order to allow a better understanding of the living soil. Moreover, genes for relevant functions can be cloned into suitable vectors, after which they can be studied and possibly explored for biotechnological purposes. Thus, opportunities for novel product discovery via metagenomics are rapidly rising. However, there are caveats in what metagenomics techniques can tell us about the soil environment and its functioning, and also in the chances of successful exploration of soil. In this chapter, we review the developments in the metagenomics-based exploitation and exploration of soil and examine how soil metagenomics can enhance our vision about natural functioning and exploration for biotechnological novelty. One major issue, the need for advanced bioinformatics tools, is stressed. We conclude that the rich microbiota of soil offers an astonishing big playground for metagenomics, but that methodological and conceptual problems still hamper its full exploitation read more ...