Stable mucus-associated bacterial communities in bleached and healthy corals of Porites lobata from the Arabian Seas

Coral reefs are subject to coral bleaching manifested by the loss of endosymbiotic algae from coral host tissue. Besides algae, corals associate with bacteria. In particular, bacteria residing in the surface mucus layer are thought to mediate coral health, but their role in coral bleaching is unknown. We collected mucus from bleached and healthy Porites lobata colonies in the Persian/Arabian Gulf (PAG) and the Red Sea (RS) to investigate bacterial microbiome composition using 16S rRNA gene amplicon sequencing. We found that bacterial community structure was notably similar in bleached and healthy corals, and the most abundant bacterial taxa were identical. However, fine-scale differences in bacterial community composition between the PAG and RS were present and aligned with predicted differences in sulfur- and nitrogen-cycling processes. Based on our data, we argue that bleached corals benefit from the stable composition of mucus bacteria that resemble their healthy coral counterparts and presumably provide a conserved suite of protective functions, but monitoring of post-bleaching survival is needed to further confirm this assumption. Conversely, fine-scale site-specific differences highlight flexibility of the bacterial microbiome that may underlie adjustment to local environmental conditions and contribute to the widespread success of Porites lobata.This publication is based upon work supported by the King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) under Award Nos FCC/1/1973-21-01 and FCC/1/1973-22-01

Metatranscriptome analysis of the reef-building coral Orbicella faveolata indicates holobiont response to coral disease

White Plague Disease (WPD) is implicated in coral reef decline in the Caribbean and is characterized by microbial community shifts in coral mucus and tissue. Studies thus far have focused on assessing microbial communities or the identification of specific pathogens, yet few have addressed holobiont response across metaorganism compartments in coral disease. Here, we report on the first metatranscriptomic assessment of the coral host, algal symbiont, and microbial compartment in order to survey holobiont structure and function in healthy and diseased samples from Orbicella faveolata collected at reef sites off Puerto Rico. Our data indicate holobiont-wide as well as compartment-specific responses to WPD. Gene expression changes in the diseased coral host involved proteins playing a role in innate immunity, cytoskeletal integrity, cell adhesion, oxidative stress, chemical defense, and retroelements. In contrast, the algal symbiont showed comparatively few expression changes, but of large magnitude, of genes related to stress, photosynthesis, and metal transport. Concordant with the coral host response, the bacterial compartment showed increased abundance of heat shock proteins, genes related to oxidative stress, DNA repair, and potential retroelement activity. Importantly, analysis of the expressed bacterial gene functions establishes the participation of multiple bacterial families in WPD pathogenesis and also suggests a possible involvement of viruses and/or phages in structuring the bacterial assemblage. In this study, we implement an experimental approach to partition the coral holobiont and resolve compartment- and taxa-specific responses in order to understand metaorganism function in coral disease

Symbiodinium Transcriptomes: Genome Insights into the Dinoflagellate Symbionts of Reef-Building Corals

Dinoflagellates are unicellular algae that are ubiquitously abundant in aquatic environments. Species of the genus Symbiodinium form symbiotic relationships with reef-building corals and other marine invertebrates. Despite their ecologic importance, little is known about the genetics of dinoflagellates in general and Symbiodinium in particular. Here, we used 454 sequencing to generate transcriptome data from two Symbiodinium species from different clades (clade A and clade B). With more than 56,000 assembled sequences per species, these data represent the largest transcriptomic resource for dinoflagellates to date. Our results corroborate previous observations that dinoflagellates possess the complete nucleosome machinery. We found a complete set of core histones as well as several H3 variants and H2A.Z in one species. Furthermore, transcriptome analysis points toward a low number of transcription factors in Symbiodinium spp. that also differ in the distribution of DNA-binding domains relative to other eukaryotes. In particular the cold shock domain was predominant among transcription factors. Additionally, we found a high number of antioxidative genes in comparison to non-symbiotic but evolutionary related organisms. These findings might be of relevance in the context of the role that Symbiodinium spp. play as coral symbionts

Bacterial community dynamics are linked to patterns of coral heat tolerance

Ocean warming threatens corals and the coral reef ecosystem. Nevertheless, corals can be adapted to their thermal environment and inherit heat tolerance across generations. In addition, the diverse microbes that associate with corals have the capacity for more rapid change, potentially aiding the adaptation of long-lived corals. Here, we show that the microbiome of reef corals is different across thermally variable habitats and changes over time when corals are reciprocally transplanted. Exposing these corals to thermal bleaching conditions changes the microbiome for heat-sensitive corals, but not for heat-tolerant corals growing in habitats with natural high heat extremes. Importantly, particular bacterial taxa predict the coral host response in a short-term heat stress experiment. Such associations could result from parallel responses of the coral and the microbial community to living at high natural temperatures. A competing hypothesis is that the microbial community and coral heat tolerance are causally linked.publishe

Comparison of the antioxidant gene repertoire between <i>Arabidopsis thaliana</i>, <i>Phycomitrella patens</i>, <i>Symbiodinium</i> sp. CassKB8, <i>Symbiodinium</i> sp. Mf1.05b, <i>Thalassosira pseudonana</i>, and <i>Phaeodactylum tricornutum</i> based on Pfam domains associated with antioxidant function.

<p>Comparison of the antioxidant gene repertoire between <i>Arabidopsis thaliana</i>, <i>Phycomitrella patens</i>, <i>Symbiodinium</i> sp. CassKB8, <i>Symbiodinium</i> sp. Mf1.05b, <i>Thalassosira pseudonana</i>, and <i>Phaeodactylum tricornutum</i> based on Pfam domains associated with antioxidant function.</p

Genes that are outliers in the correspondence analysis of codon usage (red points in Fig. 1).

<p>The assumed cellular location is noted as follows: C, chloroplast minicircles; M, mitochrondrium; N, nucleus. All genes were grouped according to their BLASTX annotation and the number of genes for each annotation is shown for both species. Genes with less than 100 analyzed codons were not included.</p

Comparison of histones and nucleosome-associated proteins from this and previous studies (DinoEST).

*<p>Subtype not specified.</p

Nc and correspondence analysis of codon usage plots.

<p>(A, B) Plots of the effective number of codons (Nc) plotted versus third codon position GC content (GC3) in CassKB8 and Mf1.5b respectively. The red points are the same genes as in C and D, respectively. The yellow line represents the neutral expectation for Nc. (C, D) Correspondence analysis of codon usage. The genes separated from the main cloud are marked red.</p

Phylogenetic analysis of histone sequences.

<p>H2A- and H3-like sequences from <i>Symbiodinium</i> sp. CassKB8, Mf1.05b, and other organisms were used to calculate phylogenetic trees. The trees were inferred using contigs and singlets with full-length amino acid sequences of (A) H2A and (B) H3-like genes using Maximum-Likelihood and Bayesian analysis. Bootstrap values and posterior probabilities are provided as ML/MB for nodes with support above 50% or 0.5. The singlet and contig names are provided for <i>Symbiodinium</i> sp. CassKB8 and Mf1.05b sequences (in bold), other taxa are shown as species name followed by GenBank accession number. The H2 tree was rooted for H2A.Bbd sequences whereas the H3 tree was rooted for <i>Homo sapiens</i> H3.</p