Soil is often considered to be one of the main reservoirs of microbial diversity on the planet. This diversity could provide a range of information about the origins of microbial functional diversity as well as novel genetic resources. However, our historical inability to cultivate the majority of soil bacteria has hampered our understanding and exploitation of this large diverse community (more than 95% are often considered inaccessible through traditional culture techniques). Over the last 20 years, new methods have been developed to overcome the limitations due to culture techniques and access a significantly greater soil microbial diversity through the direct extraction and exploration of DNA from soil. This metagenomic toolbox allows accessing, storing, and analyzing the DNA extracted from the quasi total microbial community and thus can provide an otherwise hard-to-attain insight into the biology and evolution of environmental micro-organisms. The limits and benefits of this approach need to be discussed before attempting to completely sequence a soil metagenome. The complete sequencing of a soil metagenome, (i.e. the genome of all bacteria inhabiting the soil environment) is now an imaginable objective that would require a strong international collaboration including soil microbiologists, geneticians, bioinformaticians etc. The establishment of a working public international consortium for the complete sequencing of the metagenome of a reference soil would provide focus for an increased effort on the barriers in accessing the entire soil metagenome. These barriers include imperfect methods of soil sampling, DNA extraction, DNA purification, cloning and sequencing. The soil system proposed for investigation, Park Grass, Rothamsted (UK), is a charismatic, internationally recognized unique resource that includes ongoing experiments that have been running for over 140 years. This unique long term ecological site (LTER) provides a history of soil biology and chemistry, as well as an archive of soil samples representing detailed studies of the impact of manipulations and its metagenome sequence could constitute the “reference” to which other soils could be compared.
« Hide
