Fungal endophytes in aboveground tissues of desert plants: infrequent in culture, but highly diverse and distinctive symbionts

Abstract

In hot deserts, plants cope with aridity, high temperatures, and nutrient-poor soils with morphological and biochemical adaptations that encompass intimate microbial symbioses. Whereas the root microbiomes of arid-land plants have received increasing attention, factors influencing assemblages of symbionts in aboveground tissues have not been evaluated for many woody plants that flourish in desert environments. We evaluated the diversity, host affiliations, and distributions of endophytic fungi associated with photosynthetic tissues of desert trees and shrubs, focusing on nonsucculent woody plants in the species-rich Sonoran Desert. To inform our strength of inference, we evaluated the effects of two different nutrient media, incubation temperatures, and collection seasons on the apparent structure of endophyte assemblages. Analysis of >22,000 tissue segments revealed that endophytes were isolated four times more frequently from photosynthetic stems than leaves. Isolation frequency was lower than expected given the latitude of the study region and varied among species a function of sampling site and abiotic factors. However, endophytes were very species-rich and phylogenetically diverse, consistent with less arid sites of a similar latitudinal position. Community composition differed among host species, but not as a function of tissue type, sampling site, sampling month, or exposure. Estimates of abundance, diversity, and composition were not influenced by isolation medium or incubation temperature. Phylogenetic analyses of the most commonly isolated genus (Preussia) revealed multiple evolutionary origins of desert-plant endophytism and little phylogenetic structure with regard to seasonality, tissue preference, or optimal temperatures and nutrients for growth in vitro. Together, these results provide insight into endophytic symbioses in desert-plant communities and can be used to optimize strategies for capturing endophyte biodiversity at regional scales.

Fig. 1

Isolation frequency for endophytes from leaves of Sonoran Desert plants reflects a site × species × sampling month interaction (see Table 2). Data indicate the percent of tissue segments from leaves of Larrea tridentata and Simmondsia chinensis that yielded endophytes in culture as a function of sampling site (A, King Canyon; B, Red Hills Visitor Center) and sampling month (October vs. February).

Fig. 2

Isolation frequency for endophytes from photosynthetic stems of Sonoran Desert plants reflects a site × species × sampling month × exposure interaction (see Table 2). Data indicate the percent of tissue segments from stems of Larrea tridentata, Parkinsonia microphylla, and Simmondsia chinensis that yielded endophytes in culture, as a function of sampling site (A, King Canyon; B, Red Hills), sampling month (October vs. February), and exposure (flat, exposed; south- or west-facing, highly exposed; or north-facing, protected).

Fig. 3

Species accumulation curve reveals high richness of cultivable fungal endophytes in leaves and stems of four common species of non-succulent woody plants in two collection sites in the Sonoran Desert (Tucson Mountain District, Saguaro National Park). Solid black line: number of observed OTU (Sobs, based on 95% sequence similarity); grey lines: upper and lower bounds of the 95% confidence interval around observed richness; dashed line: bootstrap estimate of total species richness.

Fig. 4

Community-level analyses reveal significant structuring of endophyte communities by host species. (A) Non-metric multidimensional scaling of endophyte communities and ANOSIM results based on the Morisita index, calculated using nonsingleton OTU. (B) mean pairwise similarity values for endophyte communities in conspecific vs. heterospecific hosts, calculated using Jaccard's index and the Morisita-Horn index (nonsingletons only, and only including host individuals for which ≥4 endophytes were obtained in culture). Annotations on the y-axis indicate mean values (dots) and ranges (bars) expected for temperate comparisons using Jaccard's index (J) and the Morisita-Horn index (M) (values obtained from [9]).

Fig. 5

Phylogenetic analysis of Preussia endophytes obtained from Sonoran Desert plants reveals high phylogenetic diversity, congruence of clades with OTU, and a lack of structure with regard to ecological and methodological factors. Terminal taxa in bold were isolated in this study and are annotated to indicate isolate number, host, tissue of origin, site and transect, sampling month, isolation medium and temperature, and OTU group, here listed such that shared letters indicate membership in the same OTU. Tree depicts the results of maximum likelihood (ML) analysis of ITSrDNA data; support values are ML bootstrap values (before slash; values ≥60% are shown) and Bayesian posterior probabilities (after slash; values ≥ 90% are shown).