Systematic review of cnidarian microbiomes reveals insights into the structure, specificity, and fidelity of marine associations

Microorganisms play essential roles in the health and resilience of cnidarians. Understanding the factors influencing cnidarian microbiomes requires cross study comparisons, yet the plethora of protocols used hampers dataset integration. We unify 16S rRNA gene sequences from cnidarian microbiome studies under a single analysis pipeline. We reprocess 12,010 cnidarian microbiome samples from 186 studies, alongside 3,388 poriferan, 370 seawater samples, and 245 cultured Symbiodiniaceae, unifying ~6.5 billion sequence reads. Samples are partitioned by hypervariable region and sequencing platform to reduce sequencing variability. This systematic review uncovers an incredible diversity of 86 archaeal and bacterial phyla associated with Cnidaria, and highlights key bacteria hosted across host sub-phylum, depth, and microhabitat. Shallow (< 30 m) water Alcyonacea and Actinaria are characterized by highly shared and relatively abundant microbial communities, unlike Scleractinia and most deeper cnidarians. Utilizing the V4 region, we find that cnidarian microbial composition, richness, diversity, and structure are primarily influenced by host phylogeny, sampling depth, and ocean body, followed by microhabitat and sampling date. We identify host and geographical generalist and specific Endozoicomonas clades within Cnidaria and Porifera. This systematic review forms a framework for understanding factors governing cnidarian microbiomes and creates a baseline for assessing stress associated dysbiosis.

Building consensus around the assessment and interpretation of Symbiodiniaceae diversity

Within microeukaryotes, genetic variation and functional variation sometimes accumulate more quickly than morphological differences. To understand the evolutionary history and ecology of such lineages, it is key to examine diversity at multiple levels of organization. In the dinoflagellate family Symbiodiniaceae, which can form endosymbioses with cnidarians (e.g., corals, octocorals, sea anemones, jellyfish), other marine invertebrates (e.g., sponges, molluscs, flatworms), and protists (e.g., foraminifera), molecular data have been used extensively over the past three decades to describe phenotypes and to make evolutionary and ecological inferences. Despite advances in Symbiodiniaceae genomics, a lack of consensus among researchers with respect to interpreting genetic data has slowed progress in the field and acted as a barrier to reconciling observations. Here, we identify key challenges regarding the assessment and interpretation of Symbiodiniaceae genetic diversity across three levels: species, populations, and communities. We summarize areas of agreement and highlight techniques and approaches that are broadly accepted. In areas where debate remains, we identify unresolved issues and discuss technologies and approaches that can help to fill knowledge gaps related to genetic and phenotypic diversity. We also discuss ways to stimulate progress, in particular by fostering a more inclusive and collaborative research community. We hope that this perspective will inspire and accelerate coral reef science by serving as a resource to those designing experiments, publishing research, and applying for funding related to Symbiodiniaceae and their symbiotic partnerships.

Spatial distribution of conspecific genotypes within chimeras of the branching coral Stylophora pistillata

Chimerism is a coalescence of conspecific genotypes. Although common in nature, fundamental knowledge, such as the spatial distribution of the genotypes within chimeras, is lacking. Hence, we investigated the spatial distribution of conspecific genotypes within the brooding coral Stylophora pistillata, a common species throughout the Indo-Pacific and Red Sea. From eight gravid colonies, we collected planula larvae that settled in aggregates, forming 2–3 partner chimeras. Coral chimeras grew in situ for up to 25 months. Nine chimeras (8 kin, 1 non-related genotypes) were sectioned into 7–17 fragments (6–26 polyps/fragment), and genotyped using eight microsatellite loci. The discrimination power of each microsatellite-locus was evaluated with 330 ‘artificial chimeras,’ made by mixing DNA from three different S. pistillata genotypes in pairwise combinations. In 68% of ‘artificial chimeras,’ the second genotype was detected if it constituted 5–30% of the chimera. Analyses of S. pistillata chimeras revealed that: (a) chimerism is a long-term state; (b) conspecifics were intermixed (not separate from one another); (c) disproportionate distribution of the conspecifics occurred; (d) cryptic chimerism (chimerism not detected via a given microsatellite) existed, alluding to the underestimation of chimerism in nature. Mixed chimerism may affect ecological/physiological outcomes for a chimera, especially in clonal organisms, and challenges the concept of individuality, affecting our understanding of the unit of selection.

Summer reading 2021 , Beth Simone Noveck , Yale University Press, 2021, 448 pp. , Larissa Zimberoff , Abrams Press, 2021, 240 pp. , Elinor Cleghorn, Dutton , 2021, 400 pp. , Erik Nordman , Island Press, 2021, 256 pp. , Caleb Scharf , Riverhead Books, 2021, 352 pp. , Hakeem Oluseyi and Joshua Horwitz , Ballantine Books, 2021, 368 pp. , Kai Kupferschmidt , The Experiment, 2021, 224 pp. , Lauren Aguirre , Pegasus Books, 2021, 336 pp

A journalist probes the tech companies racing to entice consumers—and investors—with futuristic foods. An outsider documents his ascent in academia. A policy expert proposes a human-centered approach to solving society's problems. From an ode to azure to a deep dive into data, this year's summer reading picks—reviewed by alumni of the AAAS Mass Media Science & Engineering Fellows program—offer readers fresh perspectives on timely scientific topics. Confront the biases that have long imperiled women's health, probe the mysteries of memory, celebrate a prescient economist, and more, with the books reviewed below.

Climate Change Leads to a Reduction in Symbiotic Derived Cnidarian Biodiversity on Coral Reefs

Symbiotic relationships enable partners to thrive and survive in habitats where they would either not be as successful, or potentially not exist, without the symbiosis. The coral reef ecosystem, and its immense biodiversity, relies on the symbioses between cnidarians (e.g., scleractinian corals, octocorals, sea anemones, jellyfish) and multiple organisms including dinoflagellate algae (family Symbiodiniaceae), bivalves, crabs, shrimps, and fishes. In this review, we discuss the ramifications of whether coral reef cnidarian symbioses are obligatory, whereby at least one of the partners must be in the symbiosis in order to survive or are facultative. Furthermore, we cover the consequences of cnidarian symbioses exhibiting partner flexibility or fidelity. Fidelity, where a symbiotic partner can only engage in symbiosis with a subset of partners, may be absolute or context dependent. Current literature demonstrates that many cnidarian symbioses are highly obligative and appear to exhibit absolute fidelity. Consequently, for many coral reef cnidarian symbioses, surviving changing environmental conditions will depend on the robustness and potential plasticity of the existing host-symbiont(s) combination. If environmental conditions detrimentally affect even one component of this symbiotic consortium, it may lead to a cascade effect and the collapse of the entire symbiosis. Symbiosis is at the heart of the coral reef ecosystem, its existence, and its high biodiversity. Climate change may cause the demise of some of the cnidarian symbioses, leading to subsequent reduction in biodiversity on coral reefs.

Conceptualization of the Holobiont Paradigm as It Pertains to Corals

Corals' obligate association with unicellular dinoflagellates, family Symbiodiniaceae form the foundation of coral reefs. For nearly a century, researchers have delved into understanding the coral-algal mutualism from multiple levels of resolution and perspectives, and the questions and scope have evolved with each iteration of new techniques. Advances in genetic technologies not only aided in distinguishing between the multitude of Symbiodiniaceae but also illuminated the existence and diversity of other organisms constituting the coral microbiome. The coral therefore is a meta-organism, often referred to as the coral holobiont. In this review, we address the importance of including a holistic perspective to understanding the coral holobiont. We also discuss the ramifications of how different genotypic combinations of the coral consortium affect the holobiont entity. We highlight the paucity of data on most of the coral microbiome. Using Symbiodiniaceae data, we present evidence that the holobiont properties are not necessarily the sum of its parts. We then discuss the consequences of the holobiont attributes to the fitness of the holobiont and the myriad of organisms that contribute to it. Considering the complexity of host-symbiont genotypic combinations will aid in our understanding of coral resilience, robustness, acclimation, and/or adaptation in the face of environmental change and increasing perturbations.

Microbiomes of Caribbean Octocorals Vary Over Time but Are Resistant to Environmental Change

The bacterial microbiome is an essential component of many corals, although knowledge of the microbiomes in scleractinian corals far exceeds that for octocorals. This study characterized the bacterial communities present in shallow water Caribbean gorgonian octocorals over time and space, in addition to determining the bacterial assemblages in gorgonians exposed to environmental perturbations. We found that seven shallow water Caribbean gorgonian species maintained distinct microbiomes and predominantly harbored two bacterial genera, Mycoplasma and Endozoicomonas. Representatives of these taxa accounted for over 70% of the sequences recovered, made up the three most common operational taxonomic units (OTUs), and were present in most of the gorgonian species. Gorgonian species sampled in different seasons and/or in different years, exhibited significant shifts in the abundances of these bacterial OTUs, though there were few changes to overall bacterial diversity, or to the specific OTUs present. These shifts had minimal impact on the relative abundance of inferred functional proteins within the gorgonian corals. Sequences identified as Escherichia were ubiquitous in gorgonian colonies sampled from a lagoon but not in colonies sampled from a back reef. Exposure to increased temperature and/or ultraviolet radiation (UVR) or nutrient enrichment led to few significant changes in the gorgonian coral microbiomes. While there were some shifts in the abundance of the prevalent bacteria, more commonly observed was “microbial switching” between different OTUs identified within the same bacterial genus. The relative stability of gorgonian coral bacterial microbiome may potentially explain some of the resistance and resilience of Caribbean gorgonian corals against changing environmental conditions.

Caribbean gorgonian octocorals cope with nutrient enrichment

Corals inhabit oligotrophic waters, thriving amidst limited nutrients such as nitrogen and phosphorous. When nutrient levels increase, usually due to human activity, the symbiosis of dinoflagellates (family Symbiodiniaceae) with scleractinian corals can break down. Although gorgonian corals dominate many Caribbean reefs, the impact of enrichment on them and their algae is understudied. We exposed two gorgonian species, Pseudoplexaura porosa and Eunicea tourneforti, to elevated concentrations of either ammonium (10 μM or 50 μM) or phosphate (4 μM). Enrichment with 10 μM ammonium increased chlorophyll content and algal density in both species, whereas the host biochemical composition was unaffected. Exposure to 50 μM ammonium only reduced the quantum yield in P. porosa and mitotic indices in both species. Conversely, algal carbon and nitrogen content within E. tourneforti increased with 4 μM phosphate exposure. These gorgonian species coped with short-term nutrient enrichment, furthering our understanding of the success of Caribbean gorgonians.

Symbiodinium photosynthesis in Caribbean octocorals

Symbioses with the dinoflagellate Symbiodinium form the foundation of tropical coral reef communities. Symbiodinium photosynthesis fuels the growth of an array of marine invertebrates, including cnidarians such as scleractinian corals and octocorals (e.g., gorgonian and soft corals). Studies examining the symbioses between Caribbean gorgonian corals and Symbiodinium are sparse, even though gorgonian corals blanket the landscape of Caribbean coral reefs. The objective of this study was to compare photosynthetic characteristics of Symbiodinium in four common Caribbean gorgonian species: Pterogorgia anceps, Eunicea tourneforti, Pseudoplexaura porosa, and Pseudoplexaura wagenaari. Symbiodinium associated with these four species exhibited differences in Symbiodinium density, chlorophyll a per cell, light absorption by chlorophyll a, and rates of photosynthetic oxygen production. The two Pseudoplexaura species had higher Symbiodinium densities and chlorophyll a per Symbiodinium cell but lower chlorophyll a specific absorption compared to P. anceps and E. tourneforti. Consequently, P. porosa and P. wagenaari had the highest average photosynthetic rates per cm2 but the lowest average photosynthetic rates per Symbiodinium cell or chlorophyll a. With the exception of Symbiodinium from E. tourneforti, isolated Symbiodinium did not photosynthesize at the same rate as Symbiodinium in hospite. Differences in Symbiodinium photosynthetic performance could not be attributed to Symbiodinium type. All P. anceps (n = 9) and P. wagenaari (n = 6) colonies, in addition to one E. tourneforti and three P. porosa colonies, associated with Symbiodinium type B1. The B1 Symbiodinium from these four gorgonian species did not cluster with lineages of B1 Symbiodinium from scleractinian corals. The remaining eight E. tourneforti colonies harbored Symbiodinium type B1L, while six P. porosa colonies harbored type B1i. Understanding the symbioses between gorgonian corals and Symbiodinium will aid in deciphering why gorgonian corals dominate many Caribbean reefs.

Diagnostic gene expression biomarkers of coral thermal stress

Gene expression biomarkers can enable rapid assessment of physiological conditions in situ, providing a valuable tool for reef managers interested in linking organism physiology with large-scale climatic conditions. Here, we assessed the ability of quantitative PCR (qPCR)-based gene expression biomarkers to evaluate (i) the immediate cellular stress response (CSR) of Porites astreoides to incremental thermal stress and (ii) the magnitude of CSR and cellular homeostasis response (CHR) during a natural bleaching event. Expression levels largely scaled with treatment temperature, with the strongest responses occurring in heat-shock proteins. This is the first demonstration of a 'tiered' CSR in a coral, where the magnitude of expression change is proportional to stress intensity. Analysis of a natural bleaching event revealed no signature of an acute CSR in normal or bleached corals, indicating that the bleaching stressor(s) had abated by the day of sampling. Another long-term stress CHR-based indicator assay was significantly elevated in bleached corals, although assay values overall were low, suggesting good prospects for recovery. This study represents the first step in linking variation in gene expression biomarkers to stress tolerance and bleaching thresholds in situ by quantifying the severity of ongoing thermal stress and its accumulated long-term impacts.

'Rejected' vs. 'rejecting' transcriptomes in allogeneic challenged colonial urochordates

In botryllid ascidians, allogeneic contacts between histoincompatible colonies lead to inflammatory rejection responses, which eventually separate the interacting colonies. In order to elucidate the molecular background of allogeneic rejection in the colonial ascidian Botryllus schlosseri, we performed microarray assays verified by qPCR, and employed bioinformatic analyses of the results, revealing disparate transcription profiles of the rejecting partners. While only minor expression changes were documented during rejection when both interacting genotypes were pooled together, analyses performed on each genotype separately portrayed disparate transcriptome responses. Allogeneic interacting genotypes that developed the morphological markers of rejection (points of rejection; PORs), termed 'rejected' genotypes, showed transcription inhibition of key functional gene groups, including protein biosynthesis, cell structure and motility and stress response genes. In contrast, the allogeneic partners that did not show PORs, termed 'rejecting' genotypes, showed minor expression changes that were different from those of the 'rejected' genotypes. This data demonstrates that the observed morphological changes in the 'rejected' genotypes are not due to active transcriptional response to the immune challenge but reflect transcription inhibition of response elements. Based on the morphological and molecular outcomes we suggest that the 'rejected' colony activates an injurious self-destructive mechanism in order to disconnect itself from its histoincompatible neighboring colony.

Light intensity mediated polarotaxis in Pontella karachiensis (Pontellidae, Copepoda)

Polarization sensitivity provides animals with information not available in the intensity or spectral domains. We examined the polarotaxis reactions in the epiplanktonic copepod Pontella karachiensis. Polarotaxis reactions were intensity dependent. At intensities corresponding to ambient daylight, P. karachiensis showed an attraction to a polarized light field; while at low intensities, corresponding to nighttime illumination, it showed negative polarotaxis. P. karachiensis's eye contained two classes of photoreceptors, each class with microvilli at orthogonal orientation to the other. P. karachiensis' eye structure can provide information regarding the polarization percentage but is not sufficient to calculate the exact e-vector orientation. The threshold for polarotoxisis response was 20-30%. Animals responded similarly to horizontal and vertical polarization; and also showed negative phototaxis, affected by light polarization. Results suggest that P. karachiensis responds to polarized light analogously to changes in brightness. The dynamic pattern of polarotaxis responses suggests that polarization sensitivity may enable P. karachiensis to detect other planktonic animals.