What microbial guilds are causing PSF?
We found 66 indicator prokaryotes out of 887 OTUs and 110 indicator
fungi out of 1534 OTUs. Guild affiliation was possible for 45
prokaryotes and 33 fungi among our indicator OTUs. We found no
significant overrepresentation of fungal pathogens as indicator OTUs of
negative plant growth response (Fig. 2, χ2 =
9.79, d.f. = 10, P = 0.46, Fig. 2). Rather, only one of
the 33 indicator fungi was a pathogen (negatively affectingBromus ). All the remaining 32 indicator fungi were saprotrophs,
and either positively (9) or negatively (3) affected both plants, or
negatively affected Bromus only (20). Twelve of the 33 indicator
fungi (36%) similarly affected Bromus and Koeleria , while
the remainder (64%) had species-specific effects (a necessary condition
for microorganisms to drive species-specific PSF). Regarding the
prokaryotes, of the 66 indicator OTUs, the majority (37) were associated
with improved performance for both Bromus and Koeleria .
Conversely, 6 negatively affected Bromus growth and 23 were
detrimental to both species. Thus, as opposed to fungi, few indicator
prokaryotes (9%, 6 out of 66) had species-specific effects on plants.
Indicator prokaryotes were mostly related to N cycling (bacterial and
archaeal nitrifiers) or were primary producers (Chloroflexi
spp. ). Interestingly, while the vast majority of prokaryotic
saprotrophs were associated with positive plant growth responses (18 out
of 26 saprotrophic OTUs), fungal saprotrophs tended to be associated
with a negative rather than positive plant growth response (23 vs. 9
OTUs, respectively). This contrast between prokaryotes and fungi was
statistically significant (χ2 = 8.16,d.f. = 1, P = 0.004).
There was a surprising scarcity of symbiotic indicator OTUs. Out of the
18 arbuscular mycorrhizal fungi and the 16 fungal endophytes (mostly
dark septate endophytes) found in our dataset, none were identified as
indicator OTU. Similarly, among prokaryotes, we did not find any of the
typical plant-growth promoting lineages (e.g., Pseudomonas spp .,Burkholderia spp ., Bacillus spp .) to be associated with
consistently improved plant growth in our greenhouse assay, even though
they were present in the total microbiome.