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  1. Abstract

    Corals and sponges harbor diverse microbial communities that are integral to the functioning of the host. While the taxonomic diversity of their microbiomes has been well-established for corals and sponges, their functional roles are less well-understood. It is unclear if the similarities of symbiosis in an invertebrate host would result in functionally similar microbiomes, or if differences in host phylogeny and environmentally driven microhabitats within each host would shape functionally distinct communities. Here we addressed this question, using metatranscriptomic and 16S rRNA gene profiling techniques to compare the microbiomes of two host organisms from different phyla. Our results indicate functional similarity in carbon, nitrogen, and sulfur assimilation, and aerobic nitrogen cycling. Additionally, there were few statistical differences in pathway coverage or abundance between the two hosts. For example, we observed higher coverage of phosphonate and siderophore metabolic pathways in the star coral,Montastraea cavernosa, while there was higher coverage of chloroalkane metabolism in the giant barrel sponge,Xestospongia muta. Higher abundance of genes associated with carbon fixation pathways was also observed inM. cavernosa, while inX. mutathere was higher abundance of fatty acid metabolic pathways. Metagenomic predictions based on 16S rRNA gene profiling analysis were similar, and there was high correlation betweenmore »the metatranscriptome and metagenome predictions for both hosts. Our results highlight several metabolic pathways that exhibit functional similarity in these coral and sponge microbiomes despite the taxonomic differences between the two microbiomes, as well as potential specialization of some microbially based metabolism within each host.

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  2. Abstract Background The importance of symbiosis has long been recognized on coral reefs, where the photosynthetic dinoflagellates of corals (Symbiodiniaceae) are the primary symbiont. Numerous studies have now shown that a diverse assemblage of prokaryotes also make-up part of the microbiome of corals. A subset of these prokaryotes is capable of fixing nitrogen, known as diazotrophs, and is also present in the microbiome of scleractinian corals where they have been shown to supplement the holobiont nitrogen budget. Here, an analysis of the microbiomes of 16 coral species collected from Australia, Curaçao, and Hawai’i using three different marker genes (16S rRNA, nif H, and ITS2) is presented. These data were used to examine the effects of biogeography, coral traits, and ecological life history characteristics on the composition and diversity of the microbiome in corals and their diazotrophic communities. Results The prokaryotic microbiome community composition (i.e., beta diversity) based on the 16S rRNA gene varied between sites and ecological life history characteristics, but coral morphology was the most significant factor affecting the microbiome of the corals studied. For 15 of the corals studied, only two species Pocillopora acuta and Seriotopora hystrix , both brooders, showed a weak relationship between the 16S rRNAmore »gene community structure and the diazotrophic members of the microbiome using the nif H marker gene, suggesting that many corals support a microbiome with diazotrophic capabilities. The order Rhizobiales , a taxon that contains primarily diazotrophs, are common members of the coral microbiome and were eight times greater in relative abundances in Hawai’i compared to corals from either Curacao or Australia. However, for the diazotrophic component of the coral microbiome, only host species significantly influenced the composition and diversity of the community. Conclusions The roles and interactions between members of the coral holobiont are still not well understood, especially critical functions provided by the coral microbiome (e.g., nitrogen fixation), and the variation of these functions across species. The findings presented here show the significant effect of morphology, a coral “super trait,” on the overall community structure of the microbiome in corals and that there is a strong association of the diazotrophic community within the microbiome of corals. However, the underlying coral traits linking the effects of host species on diazotrophic communities remain unknown.« less
    Free, publicly-accessible full text available December 1, 2023
  3. Sponges in the genus Agelas produce a diversity of bromopyrrole alkaloid secondary metabolites, some of which are known to inhibit predators and pathogens. Selective pressures on sponges to produce chemical defenses vary in time and space, often resulting in differences in the production of secondary metabolites. To characterize intraspecific variation in these compounds, we generated metabolomic profiles of the Caribbean sponge A. tubulata across spatial gradients, including multiple sites in Belize and Grand Cayman, and depths ranging from 15 to 61 m in Grand Cayman. Samples were also analyzed from a reciprocal transplant experiment across shallow (22 m) to mesophotic (61 m) reefs. We found quantitative, but not qualitative, differences in metabolite profiles across sites and depths, with 9 metabolites contributing to that variation. In addition, transplanting sponges across depths resulted in significant changes in concentrations of the metabolite sceptrin. Sponge extracts exhibited antibacterial activity against a panel of marine and human pathogens. Multiple regression analyses showed that different metabolites were associated with antibacterial activity against different pathogens. The strongest compound-specific relationship was a negative effect of oroidin on the growth of Serratia marcescens, and purified oroidin was found to inhibit S. marcescens growth in a dose-dependent manner. Overall, A.more »tubulata exhibits intraspecific variability in the production of antibacterial secondary metabolites across sites and depths that signals selective responses to its environment. Given the current increase in sponge densities, and incidence of disease on coral reefs, these data have implications for disease resistance and resilience of sponges in the Anthropocene.« less
    Free, publicly-accessible full text available June 2, 2023
  4. Abstract Background Phylogenomic approaches have great power to reconstruct evolutionary histories, however they rely on multi-step processes in which each stage has the potential to affect the accuracy of the final result. Many studies have empirically tested and established methodology for resolving robust phylogenies, including selecting appropriate evolutionary models, identifying orthologs, or isolating partitions with strong phylogenetic signal. However, few have investigated errors that may be initiated at earlier stages of the analysis. Biases introduced during the generation of the phylogenomic dataset itself could produce downstream effects on analyses of evolutionary history. Transcriptomes are widely used in phylogenomics studies, though there is little understanding of how a poor-quality assembly of these datasets could impact the accuracy of phylogenomic hypotheses. Here we examined how transcriptome assembly quality affects phylogenomic inferences by creating independent datasets from the same input data representing high-quality and low-quality transcriptome assembly outcomes. Results By studying the performance of phylogenomic datasets derived from alternative high- and low-quality assembly inputs in a controlled experiment, we show that high-quality transcriptomes produce richer phylogenomic datasets with a greater number of unique partitions than low-quality assemblies. High-quality assemblies also give rise to partitions that have lower alignment ambiguity and less compositional bias.more »In addition, high-quality partitions hold stronger phylogenetic signal than their low-quality transcriptome assembly counterparts in both concatenation- and coalescent-based analyses. Conclusions Our findings demonstrate the importance of transcriptome assembly quality in phylogenomic analyses and suggest that a portion of the uncertainty observed in such studies could be alleviated at the assembly stage.« less
  5. Abstract Coral reefs continue to experience extreme environmental pressure from climate change stressors, but many coral reefs are also exposed to eutrophication. It has been proposed that changes in the stoichiometry of ambient nutrients increase the mortality of corals, whereas eutrophication may facilitate phase shifts to macroalgae-dominated coral reefs when herbivory is low or absent. But are corals ever nutrient limited, and can eutrophication destabilize the coral symbiosis making it more sensitive to environmental stress because of climate change? The effects of eutrophication are confounded not just by the effects of climate change but by the presence of chemical pollutants in industrial, urban, and agricultural wastes. Because of these confounding effects, the increases in nutrients or changes in their stoichiometry in coastal environments, although they are important at the organismal and community level, cannot currently be disentangled from each other or from the more significant effects of climate change stressors on coral reefs.
  6. Schaack, Sarah (Ed.)
    Abstract Apoptosis is a fundamental feature of multicellular animals and is best understood in mammals, flies, and nematodes, with the invertebrate models being thought to represent a condition of ancestral simplicity. However, the existence of a leukemia-like cancer in the softshell clam Mya arenaria provides an opportunity to re-evaluate the evolution of the genetic machinery of apoptosis. Here, we report the whole-genome sequence for M. arenaria which we leverage with existing data to test evolutionary hypotheses on the origins of apoptosis in animals. We show that the ancestral bilaterian p53 locus, a master regulator of apoptosis, possessed a complex domain structure, in contrast to that of extant ecdysozoan p53s. Further, ecdysozoan taxa, but not chordates or lophotrochozoans like M. arenaria, show a widespread reduction in apoptosis gene copy number. Finally, phylogenetic exploration of apoptosis gene copy number reveals a striking linkage with p53 domain complexity across species. Our results challenge the current understanding of the evolution of apoptosis and highlight the ancestral complexity of the bilaterian apoptotic tool kit and its subsequent dismantlement during the ecdysozoan radiation.
  7. van Oppen M.J.H ; Lough, J.M. (Ed.)
    A review paper on the role of the coral microbiome in the coral bleaching phenomenon.