Life in leaf litter: novel insights into community dynamics of bacteria and fungi during litter decomposition

Abstract

Microorganisms play a crucial role in the biological decomposition of plant litter in terrestrial ecosystems. Due to the permanently changing litter quality during decomposition, studies of both fungi and bacteria at a fine taxonomic resolution are required during the whole process. Here we investigated microbial community succession in decomposing leaf litter of temperate beech forest using pyrotag sequencing of the bacterial 16S and the fungal internal transcribed spacer (ITS) rRNA genes. Our results reveal that both communities underwent rapid changes. Proteobacteria, Actinobacteria and Bacteroidetes dominated over the entire study period, but their taxonomic composition and abundances changed markedly among sampling dates. The fungal community also changed dynamically as decomposition progressed, with ascomycete fungi being increasingly replaced by basidiomycetes. We found a consistent and highly significant correlation between bacterial richness and fungal richness (R = 0.76, P< 0.001) and community structure (RM antel = 0.85, P < 0.001), providing evidence of coupled dynamics in the fungal and bacterial communities. A network analysis highlighted nonrandom co-occurrences among bacterial and fungal taxa as well as a shift in the cross-kingdom co-occurrence pattern of their communities from the early to the later stages of decomposition. During this process, macronutrients, micronutrients, C:N ratio and pH were significantly correlated with the fungal and bacterial communities, while bacterial richness positively correlated with three hydrolytic enzymes important for C, N and P acquisition. Overall, we provide evidence that the complex litter decay is the result of a dynamic cross-kingdom functional succession.

Can we use environmental DNA as holotypes?

“…NGS consistently confirmed that Ascomycota have highest relative abundances in the early stages of litter decomposition in temperate forests, and then there is a clear shift from Ascomycota to Basidiomycota in the later stages (Voříšková and Baldrian 2013;Purahong et al 2016). However, the presence/absence data show that Ascomycota (66-82%) are much more frequently detected as compared with Basidiomycota (18-33%) across different sampling times during 473 days .…”

Microbial community composition is related to soil biological and chemical properties and bacterial wilt outbreak

“…In addition, the abundance of Ascomycota was higher in the healthy soils than the bacterial wilt infected soils from 0 d to 60 d, which can enhance soil C cycle and plant nutrient uptake 49, 50 . The abundance of Basidiomycota decreased at 30 d and then increased at 60 d and 90 d in the healthy soils, while it decreased both at 30 and 60 d in the bacterial wilt infected soils.…”

Characterization of Unexplored Deadwood Mycobiome in Highly Diverse Subtropical Forests Using Culture-independent Molecular Technique

“…Thus we used the abundant OTUs (OTUs with > 3 reads) for further statistical analysis. To assess the role of the omitted rare OTUs, a Mantel test based on a Bray–Curtis distance measure with 999 permutations was applied to both the full matrix and the one excluding the rare OTUs (Hammer et al, 2001; Hoppe et al, 2016; Purahong et al, 2016b). The result indicated that the removal of rare OTUs from the WIF communities had no effect on community composition ( R Mantel = 0.999, P = 0.001).…”