allows researchers to access the functional and metabolic diversity of microbial communities, but it cannot show which of these processes are active. The extraction and analysis of metagenomic mRNA (the metatranscriptome) provides information on the regulation and expression profiles of complex communities. Because of the technical difficulties (the short half-life of mRNA, for example) in the collection of environmental RNA there have been relatively few in situ metatranscriptomic studies of microbial communities to date. While originally limited to microarray technology, metatranscriptomics studies have made use of transcriptomics technologies to measure whole-genome expression and quantification of a microbial community, first employed in analysis of ammonia oxidation in soils. Viruses Metagenomic sequencing is particularly useful in the study of viral communities. As viruses lack a shared universal phylogenetic marker (as 16S RNA for bacteria and archaea, and 18S RNA for eukarya), the only way to access the genetic diversity of the viral community from an environmental sample is through metagenomics. Viral metagenomes (also called viromes) should thus provide more and more information about viral diversity and evolution. For example, a metagenomic pipeline called Giant Virus Finder showed the first evidence of existence of giant viruses in a saline desert and in Antarctic dry valleys. Applications Metagenomics has the potential to advance knowledge in a wide variety of fields. It can also be applied to solve practical challenges in medicine, engineering, agriculture, sustainability and ecology. Agriculture The soils in which plants grow are inhabited by microbial communities, with one gram of soil containing around 109-1010 microbial cells which comprise about one gigabase of sequence information. The microbial communities which inhabit soils are some of the most complex known to science, and remain poorly understood despite their economic importance. Microbial consortia perform a wide variety of ecosystem services necessary for plant growth, including fixing atmospheric nitrogen, nutrient cycling, disease suppression, and sequester iron and other metals. Functional metagenomics strategies are being used to explore the interactions between plants and microbes through cultivation-independent study of these microbial communities. By allowing insights into the role of previously uncultivated or rare community members in nutrient cycling and the promotion of plant growth, metagenomic approaches can contribute to improved disease detection in crops and livestock and the adaptation of enhanced farming practices which improve crop health by harnessing the relationship between microbes and plants. Biofuel Biofuels are fuels derived from biomass conversion, as in the conversion of cellulose