Size does matter: Application-driven approaches for soil metagenomics

Abstract

Metagenomic analyses can provide extensive information on the structure, composition, and predicted gene functions of diverse environmental microbial assemblages. Each environment presents its own unique challenges to metagenomic investigation and requires a specifically designed approach to accommodate physicochemical and biotic factors unique to each environment that can pose technical hurdles and/or bias the metagenomic analyses. In particular, soils harbor an exceptional diversity of prokaryotes that are largely undescribed beyond the level of ribotype and are a potentially vast resource for natural product discovery. The successful application of a soil metagenomic approach depends on selecting the appropriate DNA extraction, purification, and if necessary, cloning methods for the intended downstream analyses. The most important technical considerations in a metagenomic study include obtaining a sufficient yield of high-purity DNA representing the targeted microorganisms within an environmental sample or enrichment and (if required) constructing a metagenomic library in a suitable vector and host. Size does matter in the context of the average insert size within a clone library or the sequence read length for a highthroughput sequencing approach. It is also imperative to select the appropriate metagenomic screening strategy to address the specific question(s) of interest, which should drive the selection of methods used in the earlier stages of a metagenomic project (e.g., DNA size, to clone or not to clone). Here, we present both the promising and problematic nature of soil metagenomics and discuss the factors that should be considered when selecting soil sampling, DNA extraction, purification, and cloning methods to implement based on the ultimate study objectives.

A Short Review on Various Screening Methods to Isolate Potential Lipase Producers: Lipases-the Present and Future Enzymes of Biotech Industry

“…Meta genomics approach, a molecular genomics approach was employed for the screening of non cultivated microbes (Steele et al, 2009;Lammle et al, 2007;Rondon et al, 2000;Henne et al, 2000;Yun and Ryu, 2005). This approach is now being widely employed to search novel industrial enzymes because of the availability of genetic material of most of the organisms (Lorenz and Eck, 2005;Kakirde et al, 2010;Kennedy et al, 2008;Jiang et al, 2010). This approach also overcomes the problem of cultivation of microbes as majority of the micro organisms are not to cultivation (Handelsman et al, 1998).…”

The impact of physico-chemical water quality parameters on bacterial diversity in the Vaal River, South Africa

“…Currently, metagenomic analysis of microbial ecology, such as highthroughput sequencing (HTS), has been the focus of several environmental studies such as soil, (Lemos et al, 2011), freshwater lakes (Marshall et al, 2008) and deep sea microbiota (Sogin et al, 2006). Metagenomic analysis provides extensive information on community structure and composition (Kakirde et al, 2010). In addition, phylogenetic and functional analyses of microorganisms can be determined at community level (Cowan et al, 2005).…”

An introduction to and a reflection on the “ecogenomics promise”

“…Metagenomics can thus help to obtain a more holistic image of the microbial biodiversity at a certain site (e.g. DeLong 2004;Ward 2006;Torsten et al 2007;Kakirde et al 2010).…”

“…Shortly thereafter, Rondon demonstrated how to realise this in practice: they constructed metagenomic libraries of DNA isolated directly from soil (using BAC vectors) (Rondon et al 2000). Since then several scientists have researched the soil's microbial diversity and its capabilities (Tringe et al 2005;Leveau 2007;Kakirde et al 2010). In the Netherlands, between 2004 and 2010 a large, public-private research collaboration -the Ecogenomics Consortiumfocused (among others) on identification of the soil's hidden microbial diversity (e.g.…”

“…(Pettit 2004;Riesenfeld et al 2004;Langer et al 2006;Schmeisser et al 2007;Demain and Adrio 2008;Oh et al 2009;Barke et al 2010;Kakirde et al 2010). Sixty per cent of the drugs that became commercially available over the past 20 years originate from existing natural compounds, and not directly from the chemical industry (Lefevre et al 2008).…”