Insights into the Cultured Bacterial Fraction of Corals

Abstract

Our paper is the first study to synthesize currently available but decentralized data of cultured microbes associated with corals. We were able to collate 3,055 isolates across a number of published studies and unpublished collections from various laboratories and researchers around the world.

Intracellular Bacterial Symbionts in Corals: Challenges and Future Directions

“…The latter was hypothesized to participate in the bacterium's ability to reduce coral health when nitrogen is in excess. Meta-omics data would provide insight into designing suitable culture conditions, including specific metabolites that are needed to obtain pure cultures of coral intracellular symbionts [158]. Obtaining endosymbionts in pure culture could be challenging but not unfeasible.…”

Consensus Guidelines for Advancing Coral Holobiont Genome and Specimen Voucher Deposition

“…For coral-associated prokaryotes, much work remains to be done (Supplementary Table 5), but the recent assembly and genome-level description of bacteria associated with Porites lutea Milne Edwards and Haime, 1851 (Robbins et al, 2019) and the cataloging of cultured bacterial coral isolates (Sweet et al, 2021) provide a groundwork to build upon. Given that coral genomics is a nascent field, any guidelines put forward here must be considered provisional, and indeed current limitations should be a motivation rather than a barrier to begin to work on formulating the types of information that are most important to provide alongside sequencing data.…”

“…Coral-associated bacterial communities are complex and highly variable, which must be considered in the implementation of consensus guideline approaches (Roder et al, 2015;Williams et al, 2015;Röthig et al, 2017;Sweet et al, 2017;Vohsen et al, 2020b;Voolstra and Ziegler, 2020). While historically bacteria (host-associated and free-living) were characterized employing culturing methods, this has been largely replaced by sequencing-based approaches that are more affordable and higher throughput, although the two different approaches are complementary in scope and insight (Sweet et al, 2021). Here, we discuss methods best suited to characterize prokaryotic associates and provide suggestions to "standardize" coral microbiome work for enhanced comparability and meta-analysis.…”

“…Fewer studies have utilized shotgun metagenomic sequencing to obtain prokaryotic genomes via metagenome-assembled genomes (MAGs) (Neave et al, 2017a;Cárdenas et al, 2018;Robbins et al, 2019). As outlined above, it is desirable to provide both the raw sequencing data and the assembled genomes, as well as the bioinformatic pipelines used for assembly and annotation (Mende et al, 2020;Sweet et al, 2021;Cardénas and Voolstra, 2021). If available, culture-based methods are valuable because they directly align a 16S rRNA gene sequence or genome with a cultured isolate that can then be subjected to further study and experimental investigation (Neave et al, 2014(Neave et al, , 2017a.…”

“…We aim to provide consensus guidelines on the "minimal taxonomic information" that should be provided to maximize the utility of the generated sequence data. We further expand these guidelines to also include coral-associated prokaryotic genomes due to recent efforts in describing and collating the culturable fraction of the prokaryotic community of the coral holobiont (Sweet et al, 2021). We advocate for the provision of taxonomic information for the most important (i.e., best understood, most commonly researched) coral holobiont entities: the coral animal host, the Symbiodiniaceae microalgae, and the associated prokaryotes (bacteria and archaea).…”