Largely invariant communities of bacterial endophytes in the nonphotosynthetic mycoheterotrophic plant Pterospora andromedea

PREMISE

Mycoheterotrophic plants rely on fungi to obtain their carbon requirements. Recent experiments demonstrated the presence of endophytic bacteria associated with mycoheterotrophs. Although mycoheterotrophs show high specificity for their fungal partners, it is not known whether they also show high specificity for associated bacteria or whether the bacteria have a definite function in the symbiosis.

METHODS

Two 16S rRNA sequencing experiments were designed to explore endophytic microbial community composition and function in root ball fractions of the mycoheterotroph Pterospora andromedea (Ericaceae), and rhizosphere soil and control soil 5 m away from each plant. One experiment compared microbial assemblages in fractions of six plants to those in rhizosphere and control soil samples. Another experiment documented bacterial endophyte diversity in root balls of 97 plants from across North America.

RESULTS

Soil samples were similar in bacterial community structure but were significantly more diverse and less consistently structured than were bacterial communities within root balls. The proportion of endophytic bacterial species varied slightly but not their community composition despite differences in P. andromedea lineage, geography, conifer species, and fungi. Predictive metagenomic profiling of the endophytes in P. andromedea-only root ball fractions showed many of the bacterial endophytes likely function in N-metabolism and N-fixation.

CONCLUSIONS

Our results document a consistent and largely invariant community of endophytic bacteria in P. andromedea across biotic and abiotic environmental conditions at a continental scale. It is unknown what role these bacteria may play in the quad-partite symbiotic network centered on P. andromedea; however, the predictive metagenomic profiling suggests a possible function in N-metabolism or N-fixation. Discovery of a ubiquitous community of endophytic bacteria with a putative function centered on N-metabolism or N-fixation could have a previously unrecognized impact on understanding of mycoheterotroph ecophysiology.

Increased phylogenetic resolution within the ecologically important Rhizopogon subgenus Amylopogon using 10 anonymous nuclear loci

Rhizopogon species are ecologically significant ectomycorrhizal fungi in conifer ecosystems. The importance of this system merits the development and utilization of a more robust set of molecular markers specifically designed to evaluate their evolutionary ecology. Anonymous nuclear loci (ANL) were developed for R. subgenus Amylopogon. Members of this subgenus occur throughout the United States and are exclusive fungal symbionts associated with Pterospora andromedea, a threatened mycoheterotrophic plant endemic to disjunct eastern and western regions of North America. Candidate ANL were developed from 454 shotgun pyrosequencing and assessed for positive amplification across targeted species, sequencing success, and recovery of phylogenetically informative sites. Ten ANL were successfully developed and were subsequently used to sequence representative taxa, herbaria holotype and paratype specimens in R. subgenus Amylopogon. Phylogenetic reconstructions were performed on individual and concatenated data sets by Bayesian inference and maximum likelihood methods. Phylogenetic analyses of these 10 ANL were compared with a phylogeny traditionally constructed using the universal fungal barcode nuc rDNA ITS1-5.8S-ITS2 region (ITS). The resulting ANL phylogeny was consistent with most of the species designations delineated by ITS. However, the ANL phylogeny provided much greater phylogenetic resolution, yielding new evidence for cryptic species within previously defined species of R. subgenus Amylopogon. Additionally, the rooted ANL phylogeny provided an alternate topology to the ITS phylogeny, which inferred a novel set of evolutionary relationships not identified in prior phylogenetic studies.

Characterization of microsatellite markers for pinedrops, Pterospora andromedea (Ericaceae), from Illumina MiSeq sequencing

PREMISE OF THE STUDY

Pterospora andromedea (Ericaceae) is a mycoheterotrophic plant endemic to North America with a disjunct distribution. Eastern populations are in decline compared to western populations. Microsatellite loci will allow comparison of genetic diversity in endangered to nonthreatened populations. •

METHODS AND RESULTS

Illumina MiSeq sequencing resulted in development of 12 polymorphic microsatellite loci from 63 perfect microsatellite loci tested. One polymorphic locus was obtained from a traditional enrichment method. These 13 loci were screened across two western and two eastern populations. For western and eastern populations, respectively, number of alleles ranged from one to 10 and one to four, and observed heterozygosity ranged from 0.000 to 0.389 and 0.000 to 0.143. •

CONCLUSIONS

These are the first microsatellite loci developed for Pterospora. They will be useful in conservation efforts of the eastern populations and for examination of population genetic parameters at different geographic scales and comparison with mycorrhizal fungal hosts.