Uncovering unseen fungal diversity from plant DNA banks

Abstract

Throughout the world DNA banks are used as storage repositories for genetic diversity of organisms ranging from plants to insects to mammals. Designed to preserve the genetic information for organisms of interest, these banks also indirectly preserve organisms' associated microbiomes, including fungi associated with plant tissues. Studies of fungal biodiversity lag far behind those of macroorganisms, such as plants, and estimates of global fungal richness are still widely debated. Utilizing previously collected specimens to study patterns of fungal diversity could significantly increase our understanding of overall patterns of biodiversity from snapshots in time. Here, we investigated the fungi inhabiting the phylloplane among species of the endemic Hawaiian plant genus, Clermontia (Campanulaceae). Utilizing next generation DNA amplicon sequencing, we uncovered approximately 1,780 fungal operational taxonomic units from just 20 DNA bank samples collected throughout the main Hawaiian Islands. Using these historical samples, we tested the macroecological pattern of decreasing community similarity with decreasing geographic proximity. We found a significant distance decay pattern among Clermontia associated fungal communities. This study provides the first insights into elucidating patterns of microbial diversity through the use of DNA bank repository samples.

Keywords: Biobanks; Biodiversity; DNA banks; Fungi; Microbial diversity.

Figure 1. Sample interpolation (solid lines) and extrapolation (dashed lines) curves for phylloplane fungi from all ten Clermontia DNA bank samples.

Based Hill’s numbers three different diversity estimators were used (Chao1 richness, exponential of Shannon entropy, and inverse Simpson concentration indices) and are shown by the different colors with 95% confidence intervals shown by shading. Shapes represent observed phylloplane fungal OTU diversity for the ten samples of Clermontia spp.

Figure 2. Relative abundances of fungal phyla for each Clermontia DNA bank sample.

Figure 3. Relative abundances of the top ten most abundant fungal orders for each Clermontia DNA bank sample represented by color bars.

The less abundant orders are represented by grayscale bars.

Figure 4. (A) A Venn Diagram displaying the number of overlapping fungal OTUs shared between Clermontia samples from each of the five main Hawaiian Islands, represented by a different color. The number of OTUs unique to each island lie on the outermost portion of each ellipse. (B) The geographic layout of the main Hawaiian Islands.

Figure 5. Pair-wise Bray-Curtis fungal community dissimilarity plotted against corresponding pair-wise physical distances for each Clermontia plant bank sample spanning the main Hawaiian Islands.

A regression line was fit to the data, shown in blue, with 95% confidence intervals shown in grey. (Partial Mantel test: r = 0.424, p = 0.005, accounting for time between sample collection in days).