Temporal Variation in the Microbiome of Acropora Coral Species Does Not Reflect Seasonality

Abstract

The coral microbiome is known to fluctuate in response to environmental variation and has been suggested to vary seasonally. However, most studies to date, particularly studies on bacterial communities, have examined temporal variation over a time frame of less than 1 year, which is insufficient to establish if microbiome variations are indeed seasonal in nature. The present study focused on expanding our understanding of long-term variability in microbial community composition using two common coral species, Acropora hyacinthus , and Acropora spathulata , at two mid-shelf reefs on the Great Barrier Reef. By sampling over a 2-year time period, this study aimed to determine whether temporal variations reflect seasonal cycles. Community composition of both bacteria and Symbiodiniaceae was characterized through 16S rRNA gene and ITS2 rDNA metabarcoding. We observed significant variations in community composition of both bacteria and Symbiodiniaceae among time points for A. hyacinthus and A. spathulata . However, there was no evidence to suggest that temporal variations were cyclical in nature and represented seasonal variation. Clear evidence for differences in the microbial communities found between reefs suggests that reef location and coral species play a larger role than season in driving microbial community composition in corals. In order to identify the basis of temporal patterns in coral microbial community composition, future studies should employ longer time series of sampling at sufficient temporal resolution to identify the environmental correlates of microbiome variation.

Reef environments shape microbial partners in a highly connected coral population

“…21%) (electronic supplementary material, tableS4). These compositions are consistent with A. hyacinthus in Epstein et al[65] from the Great Barrier Reef. By contrast, FR A. hyacinthus collected in Mo'orea by Maher et al[66] in 2016 showed higher relative abundances of Endozoicomonas relative to our results, which may indicate shifts in microbial partners through time.…”

Insights into plastic biodegradation: community composition and functional capabilities of the superworm (Zophobas morio) microbiome in styrofoam feeding trials

“…Subsequently, GraftM results were manually curated by removing lineages identified as contamination. In brief, sample contamination is a combination of crosstalk from nearby wells and background contaminants (Minich et al, 2019), and we therefore followed an approach outlined previously (Epstein et al, 2019; Lee et al, 2015), which is based on the presumption that contaminant taxa are expected to have high relative abundances in negative controls but low relative abundances in samples. Therefore, lineages that exhibited a relative abundance of one or more orders of magnitude higher in the negative control compared to any sample were removed.…”

Inconsistent Patterns of Microbial Diversity and Composition Between Highly Similar Sequencing Protocols: A Case Study With Reef-Building Corals

“…We conducted all diversity tests on the two coral species separately due to well-established differences in both alpha and beta diversity measures across host species ( Hernandez-Agreda et al, 2017 ; Epstein et al, 2019 ; Ziegler et al, 2019 ) that could have obscured significant differences between protocols. Three alpha diversity metrics were calculated to account for richness, evenness and phylogenetic diversity: observed species richness, Shannon diversity index and Faith’s Phylogenetic Diversity (PD) were calculated on rarefied data (1000 and 998 reads/sample for ASV and OTU data, respectively; these depths were chosen for each dataset to maintain comparability using the highest sample sizes without severely compromising rarefied alpha diversity).…”