Soil-borne microbial functional structure across different land uses.

Eiko E Kuramae,George A Kowalchuk,Johannes A Van Veen,Jizhong Z Zhou

doi:10.1155/2014/216071

Abstract

Land use change alters the structure and composition of microbial communities. However, the links between environmental factors and microbial functions are not well understood. Here we interrogated the functional structure of soil microbial communities across different land uses. In a multivariate regression tree analysis of soil physicochemical properties and genes detected by functional microarrays, the main factor that explained the different microbial community functional structures was C : N ratio. C : N ratio showed a significant positive correlation with clay and soil pH. Fields with low C : N ratio had an overrepresentation of genes for carbon degradation, carbon fixation, metal reductase, and organic remediation categories, while fields with high C : N ratio had an overrepresentation of genes encoding dissimilatory sulfate reductase, methane oxidation, nitrification, and nitrogen fixation. The most abundant genes related to carbon degradation comprised bacterial and fungal cellulases; bacterial and fungal chitinases; fungal laccases; and bacterial, fungal, and oomycete polygalacturonases. The high number of genes related to organic remediation was probably driven by high phosphate content, while the high number of genes for nitrification was probably explained by high total nitrogen content. The functional gene diversity found in different soils did not group the sites accordingly to land management. Rather, the soil factors, C : N ratio, phosphate, and total N, were the main factors driving the differences in functional genes across the fields examined.

Highlights

Nutrient cycling within terrestrial ecosystems is mostly performed via the activities of soil-borne microorganisms [1]
Most of the studies related to the impact of land use change on microbes have focused on the phylogenetic composition of the soil microbial community
Because the amount of DNA extracted was in most cases insufficient for direct labeling and hybridization, 30 ng of DNA per sample was amplified by whole community rolling cycle amplification (WCRCA) using a TempliPhi kit (GE Healthcare, Piscataway, NJ)

Summary

Introduction

Nutrient cycling within terrestrial ecosystems is mostly performed via the activities of soil-borne microorganisms [1]. Microarray technologies have made it possible to represent the diversity of key enzyme functions as an array of probes, which can be interrogated with DNA or RNA extracted from the environment [11,12,13] In this way, the total metagenome of an environmental sample can be examined for the presence, diversity, and activity of genes critical to the major nutrient cycles. In order to answer these questions, we used functional gene arrays (FGA), focussing on crucial steps of key nutrient cycles (C, N, P, and S) across eight fields representing five generally representative forms of land use (conventional arable field, organic arable field, pasture, natural grassland, and pine forest) in The Netherlands To our knowledge, this is one of few studies to apply functional microarray technique across a range of different land managements. This study is one of the first to include a suite of soil measurements to explore the environmental factors driving soil microbial functions under different land uses

Material and Methods

Results and Discussion

Conclusion