Soil-specific limitations for access and analysis of soil microbial communities by metagenomics

Abstract

Metagenomics approaches represent an important way to acquire information on the microbial communities present in complex environments like soil. However, to what extent do these approaches provide us with a true picture of soil microbial diversity? Soil is a challenging environment to work with. Its physicochemical properties affect microbial distributions inside the soil matrix, metagenome extraction and its subsequent analyses. To better understand the bias inherent to soil metagenome 'processing', we focus on soil physicochemical properties and their effects on the perceived bacterial distribution. In the light of this information, each step of soil metagenome processing is then discussed, with an emphasis on strategies for optimal soil sampling. Then, the interaction of cells and DNA with the soil matrix and the consequences for microbial DNA extraction are examined. Soil DNA extraction methods are compared and the veracity of the microbial profiles obtained is discussed. Finally, soil metagenomic sequence analysis and exploitation methods are reviewed.

The Potential of Metagenomic Approaches for Understanding Soil Microbial Processes

“…Often stratified sampling, taking composite samples, and the use of replicated designs can help in obtaining representative samples appropriate for addressing the objective of an experiment, at least when the cost of analyses is not a major limitation (Prosser, 2010;Wollum, 1994). Although some level of replication in soil metagenomic studies is now financially feasible, other issues remain (Knight et al, 2012;Lombard et al, 2011). Working with a soil from a single location, Delmont et al (2012a) found that DNA extraction protocols displayed greater variation in metagenomic composition than either soil depth or season of sampling, which was perhaps a surprising result but is consistent with their earlier observation using other molecular methods (Delmont et al, 2011).…”

The role of microorganisms at different stages of ecosystem development for soil formation

“…Vice versa, the soil matrix as well as chemical and physical properties of soils, like quality and amount of soil organic matter, pH, and redox conditions, have a pronounced influence on the dynamics of the microbial community structure and function in soils (Lombard et al, 2011). This close interplay between abiotic conditions and the soil biosphere is one of the most fascinating issues as far as earth sciences are concerned, with huge implications on environmental as well as human health (van Elsas et al, 2008).…”

Fungal Community Structure as an Indicator of Soil Agricultural Management Effects in the Cerrado

“…The OM and microorganism relation has a fundamental role in soil -changes in soil microbial diversity over time have been related to changes in environmental conditions, such as soil moisture and OM (Lombard et al, 2011). Soil moisture affects the physiological state of the microbial community, as well as soil physicochemical properties and plant yield.…”