Primer Sets Developed for Functional Genes Reveal Shifts in Functionality of Fungal Community in Soils.

S Emilia Hannula,Johannes A Van Veen

doi:10.3389/fmicb.2016.01897

Abstract

Phylogenetic diversity of soil microbes is a hot topic at the moment. However, the molecular tools for the assessment of functional diversity in the fungal community are less developed than tools based on genes encoding the ribosomal operon. Here 20 sets of primers targeting genes involved mainly in carbon cycling were designed and/or validated and the functioning of soil fungal communities along a chronosequence of land abandonment from agriculture was evaluated using them. We hypothesized that changes in fungal community structure during secondary succession would lead to difference in the types of genes present in soils and that these changes would be directional. We expected an increase in genes involved in degradation of recalcitrant organic matter in time since agriculture. Out of the investigated genes, the richness of the genes related to carbon cycling was significantly higher in fields abandoned for longer time. The composition of six of the genes analyzed revealed significant differences between fields abandoned for shorter and longer time. However, all genes revealed significant variance over the fields studied, and this could be related to other parameters than the time since agriculture such as pH, organic matter, and the amount of available nitrogen. Contrary to our initial hypothesis, the genes significantly different between fields were not related to the decomposition of more recalcitrant matter but rather involved in degradation of cellulose and hemicellulose.

Highlights

Fungi are ubiquitous and diverse; the global number of fungal species has been estimated to be more than 1.5 million species (Hawksworth and Rossman, 1997; Hawksworth, 2001)
From the well-studied wooddecaying systems it is known that fungal species differ markedly in the way they decompose wood (Worrall et al, 1997), with the decomposition rates depending on the fungal community structure (Boddy et al, 1989)
The primers in this study were designed to catch as broad spectrum of fungi as possible

Summary

Introduction

Fungi are ubiquitous and diverse; the global number of fungal species has been estimated to be more than 1.5 million species (Hawksworth and Rossman, 1997; Hawksworth, 2001). Fungal diversity is thought to have important consequences for ecosystem functioning through their contribution to nutrient cycling and transport, moisture retention, and plant growth (van der Heijden et al, 1998; Setälä and McLean, 2004). Despite the presumptive great importance of the relationship between fungal diversity and ecosystem function (Nielsen et al, 2011), little is known about extent of the diversity even at the local scale and about the factors generating and maintaining it mainly because the majority of the species are not yet been described and are potentially unculturable. From the well-studied wooddecaying systems it is known that fungal species differ markedly in the way they decompose wood (Worrall et al, 1997), with the decomposition rates depending on the fungal community structure (Boddy et al, 1989). Every ecosystem has many fungal types with overlapping functions (Liers et al, 2011)

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