A heritable symbiont and host‐associated factors shape fungal endophyte communities across spatial scales

Abstract

Microbial ecologists are intensely interested in the processes governing microbial community assembly; however, progress has been limited by a lack of studies that span multiple geographical scales and levels of biological organization. We used high throughput sequencing to characterize foliar fungal endophyte communities and host plant genetic structure both within and among 24 populations of spotted locoweed Astragalus lentiginosus across the Great Basin Desert. Across the Great Basin, both within and among populations of the host plant, fungal endophyte richness was predicted by plant size and variation in the seed‐borne, heritable fungus, Alternaria fulva, which produces the bioactive alkaloid swainsonine. The degree of between‐plant turnover in the endophyte community was inversely related to host plant inbreeding and average plant size and positively related to the relative abundance of A. fulva. Plant size was inversely related to endophyte community richness, both among and within populations. The genetic and physical distance between host populations was not predictive of differences in fungal community structure. Synthesis. Through pairing intensive local and regional sampling, we uncovered a primacy of deterministic forces imposed by a heritable symbiont on the community structure of locoweed endophytes.

Rarity does not limit genetic variation or preclude subpopulation structure in the geographically restricted desert forb Astragalus lentiginosus var. piscinensis

“…We used a previously published data set spanning A. lentiginosus varieties to examine the association between range size and genetic variation. This data set was comprised of 11,475 SNPs (for further details, see Harrison et al., , b) from 11 varieties (including var. piscinensis ) that were collected throughout the Great Basin Desert.…”

“…As per Harrison et al. (), we used BLAST (Camacho et al., ) to align contigs to the RefSeq databases for archaea, viruses, fungi, and bacteria (accessed Feb 21, 2016; https://www.ncbi.nlm.nih.gov/refseq/; Tatusova et al., ), to the 1000 Fungal Genomes Project database (accessed 7 February 2016; https://genome.jgi.doe.gov/programs/fungi/1000fungalgenomes.jsf; Grigoriev et al., ), and to all Fabaceae chloroplast DNA in the NCBI nucleotide database (accessed 9 February 2016; https://www.ncbi.nlm.nih.gov/nucleotide/). Sequences in the GBS reference that matched accessions in any of these databases at ≥97% where removed to avoid analyzing nonhost or haploid organellar DNA.…”

“…To compare genetic variation among populations of A. lentiginosus varieties differing in range size, we used previously published sequence data generated using the same GBS approach described above for an additional 458 individuals spanning 11 varieties and 25 populations (including var. piscinensis ) across the Great Basin Desert (see Harrison et al., for details). This data set was previously used to explore associations between genetic distance and fungal endophyte assemblage dissimilarity in A. lentiginosus ; all analyses presented here are novel.…”

“…Data available from the Dryad Digital Repository: https://doi.org/10.5061/dryad.tj3bd3n (Harrison et al., , b).…”

“…semotus ). Many varieties of A. lentiginosus are genetically distinct (Knaus et al., ; Harrison et al., ), but the degree of within‐variety genetic variation and structure in the complex is poorly understood.…”