Cryptic functional diversity within a grass mycobiome

Abstract

Eukaryotic hosts harbor tremendously diverse microbiomes that affect host fitness and response to environmental challenges. Fungal endophytes are prominent members of plant microbiomes, but we lack information on the diversity in functional traits affecting their interactions with their host and environment. We used two culturing approaches to isolate fungal endophytes associated with the widespread, dominant prairie grass Andropogon gerardii and characterized their taxonomic diversity using rDNA barcode sequencing. A randomly chosen subset of fungi representing the diversity of each leaf was then evaluated for their use of different carbon compound resources and growth on those resources. Applying community phylogenetic analyses, we discovered that these fungal endophyte communities are comprised of phylogenetically distinct assemblages of slow- and fast-growing fungi that differ in their use and growth on differing carbon substrates. Our results demonstrate previously undescribed and cryptic functional diversity in carbon resource use and growth in fungal endophyte communities of A. gerardii.

Fig 1. Distribution of mean standardized growth values among fungal isolates obtained by leaf sectioning and maceration.

Mean standardized growth = mean (measured OD₅₉₀ –water control OD₅₉₀) on 62 Biolog carbon resources after 3 days (see Materials and Methods). Slower-growing fungi (blue bars) were primarily obtained by leaf sectioning (top panel) and faster-growing fungi (gold bars) were primarily obtained by leaf maceration. We fit a finite mixture model to derive the cut-off value of 0.12 OD₅₉₀(black arrow) to distinguish the distributions of slow- (< 0.12 OD₅₉₀) and fast- growing (> 0.12 OD₅₉₀) fungi.

Fig 2. Distribution of niche widths in slow- and fast-growing assemblages.

Slow-growing fungi (blue bars) had lower mean but higher variance in niche width (mean = 46, sd = 25) than did fast-growing fungi (gold bars; mean = 82, sd = 12). Niche width is the number of resources used by an isolate (standardized growth > 0.005 OD₅₉₀ after 3 days). Arrows show mean niche width of slow- (blue) or fast- (gold) growing assemblages.

Fig 3. Phylogenetic structure of resource use.

The OTU labels are color-coded (slow: blue; fast: gold) for each isolate evaluated on Biolog C resource plates. Columns represent fungal class and order (“Other” represents classes or orders with a relative abundance ≤2%). Resource use (standardized growth > 0.005 OD₅₉₀) is shown in the grid to the right (used: dark orange, not used: blue). Within the class Sordariomycetes, taxa in the orders Diaporthales and Xylariales are most often slow-growing whereas taxa in order Hypocreales are often fast-growing. Taxa in the Eurotiales (class Eurotiomycetes) are often fast-growing. Both assemblages have members in the class Dothidiomycetes (see S3 Table).