Maple and hickory leaf litter fungal communities reflect pre-senescent leaf communities

Abstract

Fungal communities are known to contribute to the functioning of living plant microbiomes as well as to the decay of dead plant material and affect vital ecosystem services, such as pathogen resistance and nutrient cycling. Yet, factors that drive structure and function of phyllosphere mycobiomes and their fate in leaf litter are often ignored. We sought to determine the factors contributing to the composition of communities in temperate forest substrates, with culture-independent amplicon sequencing of fungal communities of pre-senescent leaf surfaces, internal tissues, leaf litter, underlying humus soil of co-occurring red maple (Acer rubrum) and shagbark hickory (Carya ovata). Paired samples were taken at five sites within a temperate forest in southern Michigan, USA. Fungal communities were differentiable based on substrate, host species, and site, as well as all two-way and three-way interactions of these variables. PERMANOVA analyses and co-occurrence of taxa indicate that soil communities are unique from both phyllosphere and leaf litter communities. Correspondence of endophyte, epiphyte, and litter communities suggests dispersal plays an important role in structuring fungal communities. Future work will be needed to assess how this dispersal changes microbial community functioning in these niches.

Keywords: Acer rubrum; Carya ovata; Endophyte; Epiphyte; Fungal Ecology; Leaf Litter; Metabarcoding; Phyllosphere Mycobiome; Plant-Microbe Interactions; Soil.

Figure 1. Heatmap of OTU abundance by substrate.

A total of 42 OTUs were included in the heatmap, all which were significant indicator taxa as determined using the multipatt function in the indicspecies package. Taxa names were determined using the CONSTAX2 classifier. Sample names are included beneath each column, with host species as either Acer rubrum (Acer) and Carya ovata (Carya) and site number designated in the name.

Figure 2. Venn diagram of shared OTUs by substrate.

A total of 657 OTUs were included which had substrate-weighted abundance greater than 0.01%. Overlapping regions indicate OTUs with at least one read in each of the substrates.

Figure 3. Comparison of community composition by substrate, host species, site, and swab material.

(A) The most abundant 30 genera, determined by substrate-weighted abundance and CONSTAX2 classification, are displayed by the proportion of the community composed of OTUs classified within each genus. “Other” includes all OTUs not in the top 30, regardless of abundance. Samples are labeled by host species (genus name) and site with each substrate. (B) Communities were ordinated using non-metric multidimensional scaling (NMDS) and Bray-Curtis distance, with ellipses representing 97% confidence interval estimates of centroids. (C) Epiphyte communities were re-ordinated separately from the remaining samples. Ellipses show 97% confidence interval estimates of centroids of each swab material.

Figure 4. Richness and within-sample diversity of fungal communities by swab material.

Epiphyte communities sampled with swabs were compared by observed richness, Shannon, and Inverse Simpson estimates of within-sample (alpha) diversity. Diversity estimates were determined using the phyloseq package. Test stastistic F and p-values are derived from linear mixed models with swab material as a fixed effect and leaf sampled as a random intercept effect.