A better understanding of functional roles of fungi in the decomposition process: using precursor rRNA containing ITS regions as a marker for the active fungal community

Abstract

Decomposition and biogeochemical cycling are important ecosystem services provided by fungi (Kulhankova et al. 2006; Gange et al. 2007; Trap et al. 2011). Hitherto, different approaches have been used to examine the fungal community and its functional role in the decomposition process. Culture-dependent approaches have limitations because most fungi in environmental samples are likely to be uncultivable or difficult to isolate and such approaches are biased towards fast-growing fungi and affected by media selection (Anderson and Cairney 2004). On the other hand, cultureindependent molecular approaches are used routinely for fungal diversity and community assessment. The main targets of these approaches are the rRNA genes and spacer regions of the RNA operon (rDNA), thus basing diversity and community composition on DNA content. However, some studies show that DNA may have a long life span in the environment (Nielsen et al. 2004; Levy-Booth et al. 2007; Corinaldesi et al. 2008; Pietramellara et al. 2009). DNA can stem from fungal resting structures and spores or even senescent mycelium, all of which would be metabolically inactive at a given sampling time and even permanently. Consequently, fungal community details from DNA carry some memories about the previous community composition, and may poorly reflect the fungi that are active in decomposition processes at the time of sample collection. Additionally, it is possible that dispersed propagules leave their DNA signatures when they are carried there by wind or animals (Stenlid and Gustafsson 2001). The operational taxonomic unit (OTU) richness of decomposer fungal communities revealed by DNA-based community assessment is usually higher than that based on RNA because of the inclusion of dead or inactive fungal DNA (Anderson and Parkin 2007; Rajala et al. 2011). However, there were few cases reported vice versa or no significant differences between OTU richness of the fungal decomposers derived either by DNAor RNA-based approaches (Bastias et al. 2007; Baldrian et al. 2012). These are because some fungal OTUs are only detected using RNA and they compensate the inactive fungi detected by DNA. Nevertheless, we suggest caution that the presence of background communities of dormant or senescent fungi in environmental samples as an artifact is a potentially major hindrance to unbiased interpretation of real functional roles and correlations with enzyme production and environmental parameters. A DNAbased study (Kulhankova et al. 2006; Kubartova et al. 2009) has revealed that a large proportion of ascomycetes produce few oxidative enzymes and so are restricted in their ability to digest complex substances in the late stages of decomposition. Inactive or dead Ascomycota may be remnants of earlier stages of decomposition (Purahong and Hyde 2011; Rajala et al. 2011), which strongly supports the suggestion that there is an inert background fungal community, and that Handling Editor: Ana Rincon