Plant-associated fungal communities in the light of meta’omics

Abstract

Approaches for the cultivation-independent analysis of microbial communities are summarized as meta’omics, which predominantly includes metagenomic, -transcriptomic, -proteomic and -metabolomic studies. These have shown that endophytic, root-associated and soil fungal communities are strongly shaped by associated plant species. The impact of plant identity on the composition of its litter-associated fungal community remains to be disentangled from the impact of litter chemistry. The composition of the plant community also shapes the fungal community. Most strikingly, adjacent plant species may share mycorrhizal symbionts even if the plants usually have different types of mycorrhizal fungi associated with them (ectomycorrhizal, ericoid and arbuscular mycorrhizal fungi). Environmental parameters weakly explain fungal community composition globally, and their effect is inconsistent at local and regional scales. Decrease in similarity among communities with increasing distance (i.e. distance decay) has been reported from local to global scales. This pattern is only exceptionally caused by spatial dispersal limitation of fungal propagules, but mostly due to the inability of the fungi to establish at the particular locality (i.e. environmental filtering or competitive exclusion). Fungal communities usually undergo pronounced seasonal changes and also differ between consecutive years. This indicates that development of the communities is usually not solely cyclic. Meta’omic studies challenge the classical view of plant litter decomposition. They show that mycorrhizal and (previously) endophytic fungi may be involved in plant litter decomposition and only partly support the idea of a succession from an Ascomycota to a Basidiomycota-dominated community. Furthermore, vertical separation of saprotrophic and mycorrhizal species in soil and sequential degradation from easily accessible to ‘recalcitrant’ plant compounds, such as lignin, can probably not be generalized. The current models of litter decomposition may therefore have to be eventually refined for certain ecosystems and environmental conditions. To gain deeper insights into fungal ecology, a meta’omic study design is outlined which focuses on environmental processes, because fungal communities are usually taxonomically diverse, but functionally redundant. This approach would initially identify dynamics of chemical shifts in the host and/or substrate by metametabolomics. Detected shifts would be subsequently linked to microbial activity by correlation with metatranscriptomic and/or metaproteomic data. A holistic trait-based approach might finally identify factors shaping taxonomic composition in communities against the dynamics of the environmental process(es) they are involved in.