Coral SML microbiome
The metagenomes associated with the coral SML of P. strigosa were
sequenced at high coverage, ranging from 356,426 to 1,296,198 sequence
counts (Supplemental Tab. 1). Principal Component Analyses of bacterial
genera and genes related to stress response, nitrogen metabolism, and
sulfur metabolism (Fig.1), showed that dispersion (β-diversity) was
lower among metagenomes from heat-stressed corals than from
pre-treatment and control groups. Pairwise PERMANOVAs concluded that
relative abundances of microbial genera (t = 2.62, P(perm) <
0.03), nitrogen metabolism genes (t = 2.52, P(perm) = 0.03), and sulfur
metabolism genes (t = 3.14, P(perm) = 0.03) were significantly different
between pre-treatment and heat-stressed microbiomes. Metagenomes from
corals at ambient conditions did not significantly change when compared
to pre-experiment or heat treatments. Relative abundances of microbial
stress response genes showed no significant change across treatments.
Heat exposure led to a significant increase in the relative abundances
of Ruegeria (t = - 2.38, corrected p-value < 0.02),Roseobacter (t = - 2.15, corrected p-value < 0.001),Oceanibulbus (t = - 1.58 corrected p-value < 0.03),Chromohalobacter (t = - 0.84, corrected p-value <
0.02), and Halomonas (t = - 0.87, corrected p-value <
0.02), according to Welch’s pairwise comparisons among the top 20 most
abundant taxa in the coral microbiome (Fig. 2). In contrast, there was a
significant decrease in the relative abundances of Shewanella (t
= 0.82 corrected p-value < 0.001), Synechococcus (t =
0.88, corrected p-value < 0.04), and Vibrio (t = 0.284,
p-value < 0.02) in the microbiome of corals exposed to heat
treatment (Fig. 2). Heat-stressed coral SML metagenomes analyzed at the
level of bacterial genera formed a cluster with the greatest similarity
(Bray-Curtis index > 95%) across all samples (Supplemental
Fig. 2). Microbial richness (S, number of genera) ranged from 578 to 587
genera and did not significantly change between microbiome samples
collected in situ and across the experimental treatments
(Supplemental Tab. 2). Diversity (H’) was highest in situ due a
decrease in evenness (J’) under experimental conditions.
Within nitrogen metabolism, the relative abundances of microbial gene
pathways related to amidase with urea and nitrile hydratase (t = -
0.363, corrected p-value < 0.0001), allantoin utilization (t =
- 1.079, corrected p-value = 0.042), and nitrogen fixation (t = - 0.130,
corrected p-value = 0.049) increased in the coral microbiome under heat
stress, while nitrosative stress (t = 1.628, corrected p-value = 0.033),
and ammonia assimilation (t = 4.51 corrected p-value = 0.037) decreased
(Fig. 4.B).
Sulfur metabolism microbial genes also changed in relative abundance
after heat exposure of corals. There was an increase in glutathione
utilization (t = - 1.70, corrected p-value < 0.0001), sulfur
oxidation (t = - 8.08, corrected p-value < 0.0001), and
taurine utilization (t = - 1.44, corrected p-value < 0.0001),
and a decrease in inorganic sulfur assimilation (t = 8.04, corrected
p-value < 0.0001) (Fig. 4.C).