The metagenomics of soil

Abstract

Phylogenetic surveys of soil ecosystems have shown that the number of prokaryotic species found in a single sample exceeds that of known cultured prokaryotes. Soil metagenomics, which comprises isolation of soil DNA and the production and screening of clone libraries, can provide a cultivation-independent assessment of the largely untapped genetic reservoir of soil microbial communities. This approach has already led to the identification of novel biomolecules. However, owing to the complexity and heterogeneity of the biotic and abiotic components of soil ecosystems, the construction and screening of soil-based libraries is difficult and challenging. This review describes how to construct complex libraries from soil samples, and how to use these libraries to unravel functions of soil microbial communities.

Isolation and characterization of bacteria from soil contaminated with diesel oil and the possible use of these in autochthonous bioaugmentation

“…Among these, only isolate J was isolated using nutrient media such as LB and soil extracted media. This difficulty in isolating soil intrinsic bacteria coincides with the general finding that most soil intrinsic bacteria are hard to cultivate in ordinary nutrient media (Daniel 2005). However, bacterial strains corresponding to DGGE bands E to J were surely "cultivated" in soils supplanted with LB medium.…”

Phylogeny, classification and metagenomic bioprospecting of microbial acetyl xylan esterases

“…For identification of AcXE-encoding genes from metagenomic sequence data, it is generally recommended to conduct searches based on conserved AcXE domains [26,38,86,111]. However, the prediction of AcXE genes based on CE family sequence homologies from the CAZy database is complex and unreliable without confirmatory functional studies, since individual CE families include non-AcXE members and members of different CAZy classes may be grouped into a similar Protein Family (PFAM) class.…”

Protein function space: viewing the limits or limited by our view?

“…Although these could be linked to technical issues, such as sequencing depth (leading to more assembly and larger contigs, which, in turn, improve ORF calling), they could also be due to biological factors, such as ecological complexity (e.g. most novelty is in functionally complex habitats, such as soil [68]) or average genome size per sample (larger genomes harbor a smaller relative fraction of universal and housekeeping genes, and thus a greater chance of novelty [69,70]; (Fig.3). Indeed, there seems to be a weakly significant positive correlation between the effective genome size (EGS) and the potential for novelty (Spearmans rho = 1, p = 0.08; Fig.3).…”