Metabarcoding of the rhizosphere microbiome of perennial ryegrass in response to Epichloë festucae var. lolii infection : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Microbiology at Massey University, Palmerston North, New Zealand
Loading...
Date
2017
DOI
Open Access Location
Authors
Journal Title
Journal ISSN
Volume Title
Publisher
Massey University
Rights
The Author
Abstract
Epichloë endophytes inhabit the intercellular spaces of cool-season pasture grasses, and
can confer upon their hosts agriculturally desirable benefits such as heightened resistance
to biotic and abiotic stresses. The mechanisms underlying many of these benefits are not
well understood. Previously observed Epichloë-associated impacts towards the rhizosphere
microbiome of their hosts could be a contributing factor, however the overall extent to
which specific taxa in the rhizosphere microbiome of perennial ryegrass are affected by
Epichloë festucae var. lolii infection remains to be elucidated. To assess this, two
independent experiments were carried out in which clonal perennial ryegrass (NuiD) plants
inoculated or uninoculated with E. festucae var. lolii (Lp19) originating from sterile tissue
culture were grown in soil collected from a natural ryegrass pasture. After approximately
two months of growth under controlled conditions in a growth cabinet, their prokaryotic
and fungal rhizosphere microbiomes were compared using high-throughput
metabarcoding.
For prokaryotes, endophyte infection had no significant impact on species richness or
evenness of the rhizosphere microbiome of their hosts in either experiment. A very minor
but significant shift in overall community composition was shown in the first experiment
but not the second. At the level of phyla, aside from a minor 1.1% increase in the relative
abundances of Bacteroidetes in the rhizosphere of infected compared with uninfected
plants in the first experiment but not the second, there were no other significantly
differentially abundant prokaryotic phyla due to endophyte infection. At the genus level
rhizospheres of infected and uninfected plants showed a high degree of similarity in both
experiments, with little variability between replicates within treatments. At the level of
operational taxonomic units (OTUs), in the first experiment there was only one significantly
differentially abundant OTU in the rhizosphere depending on endophyte infection, and
nine in the second. However, all of which had relatively low abundances (<0.3%), and none
were consistently significantly differentially abundant in both experiments.
For fungi, there were no significant impacts of endophyte infection on species richness or
evenness of the rhizosphere in either experiment, nor were there any significant
endophyte-associated shifts detected in overall rhizosphere community composition.
Taxonomic analyses found that in both experiments endophyte infected plants had
decreased abundances of a single abundant OTU compared with uninfected plants, which
was found to be significant across both experiments (P= 0.026). The OTU sequence mapped
with moderate (76-90%) homology to a number of reference sequences assigned as
belonging to the class Sordariomycetes. Given previously observed endophyte-associated
effects on arbuscular mycorrhizal (AM) fungi, reads assigned as belonging to AM were
filtered and analysed separately. This showed that there were no significant effects of
endophyte infection towards AM diversity nor overall community composition in both
experiments, although there was an endophyte-associated increase in the abundance of
the AM family Acaulosporaceae in the first experiment but not the second.
Thus, aside from an endophyte-associated antagonism towards an abundant OTU in the
rhizosphere likely of the class Sordariomycetes, E. festucae var. lolii had an otherwise minor
impact on the prokaryotic and fungal rhizosphere microbiome of their perennial ryegrass
hosts. The minor magnitude of endophyte-associated effects was further emphasized by
analyses consistently showing that both prokaryotic and fungal rhizosphere community
composition differed to a greater extent between plants of each experiment irrespective
of endophyte infection than between plants of differing endophyte status within each
experiment- at least in this cultivar-endophyte strain interaction under the conditions of
this study.
Description
Keywords
Lolium perenne, Rhizosphere, Epichloë, Plant-fungus relationships, Research Subject Categories::NATURAL SCIENCES::Biology::Organism biology::Microbiology