Assessing the coral microbiome at the scale of tissue-specific habitats within the coral meta-organism

Abstract

As sequencing techniques have advanced and become cheaper in recent years, there has been a rapid increase in the number of studies conducted into the role of the microbiome in coral health, physiology, and response to environmental change. However, there is substantial variation in the methodological approaches applied. For example, DNA extraction protocols and the types of tissues sampled from the coral meta-organism are known to influence the downstream analyses of the amplified microbial communities and subsequently the interpretation of the microbiome diversity, stability and role. Studies have generally focused on whole organisms, in which the coral sampling steps homogenize the meta-organism microhabitats, however other studies targeting specific microhabitats have identified sources of variation specific to distinct compartments of the coral’s microbial landscape. Here we present a comparative analysis of methodologies optimized for the generation of coral microbiome data from the coral tissues and whole coral fragments of two commonly studied branching coral genera with distinct tissue structure. We investigate the microbiome of the imperforate Pocillopora, where the coral tissue does not penetrate through the calcium carbonate matrix, and the perforate Acropora, where the coral tissues and skeleton are interwoven throughout the coral branch. Through comparing data generated from different DNA extraction protocols using fixed coral tissues isolated from the coral skeletal structure with fixed whole coral fragments, we identify sources of variation inherent to microbial data generated from different sample types, species, and extraction protocols.

An Update of Knowledge of the Bacterial Assemblages Associated with the Mexican Caribbean Corals Acropora palmata, Orbicella faveolata, and Porites porites

“…Corals harbor a dynamic microbiota featuring a wide variety of taxa consisting of viruses and members of the Archaea, Eukarya, and Eubacteria domains [6,7]. Within this microbial assemblage are bacteria that can inhabit different niches within the coral, i.e., the mucopolysaccharide surface layer, skeleton, and tissues [8,9].…”

Characteristics of The Bleached Microbiome of The Generalist CoralPocillopora damicornisfrom Two Distinct Reef Habitats

“… Ricci et al. (2022) found a high abundance of Pseudoalteromonas species in the tissues and skeleton of Pocilloporidae from the GBR that was not observed in the present study, possibly due to different bacterial communities associated with different sample collection methods targeting different regions of the holobiont ( Bergman et al. 2022 ) or potentially seasonal difference in the microbiome which need to be assessed in future studies ( Sharp et al.…”

Best practices for generating and analyzing 16S rRNA amplicon data to track coral microbiome dynamics

“…Tissues can also be dissected from the skeleton with a scalpel or razor blade, although the skeleton would almost certainly be present in any sample using this method ( Littman et al, 2010 ; Kvennefors et al, 2012 ; Sudek et al, 2012 ). Another means to acquire exclusively tissue would be to add preservative and/or fixative that would allow downstream DNA extraction and then decalcify the coral using salt buffers or a mixture of formic acid and sodium nitrate ( Berzins et al, 2011 ; Hernandez-Agreda et al, 2018a ; Bergman et al, 2022 ). Tissue samples can be stored in ultra-freezers, in 100% molecular grade ethanol, or depending on the subsequent microbiological analysis, it can be fixed with 4% paraformaldehyde at 4°C for 12 h ( Staley et al, 2017 ; Hernandez-Agreda et al, 2018a ).…”

“…These studies suggest that no specific DNA extraction kit must be used with coral samples (as exists for soils and plants studies). Bergman et al (2022) also compared the output of microbial community analysis from 2 different coral species with 3 different kits (see citation for details) and found that, at least for the same coral species, each kit resulted in similar alpha and beta diversity estimates. Given these data, we recommend that research be carried out on the lysis and methods that each DNA extraction kit uses to determine the most suitable kit for a given sample type.…”