Endosymbiont diversity and community structure in Porites lutea from Southeast Asia are driven by a suite of environmental variables

Genomic data reveals habitat partitioning in massive Porites on Guam, Micronesia

Corals in marginal reef habitats generally exhibit less bleaching and associated mortality compared to nearby corals in more pristine reef environments. It is unclear, however, if these differences are due to environmental differences, including turbidity, or genomic differences between the coral hosts in these different environments. One particularly interesting case is in the coral genus Porites, which contains numerous morphologically similar massive Porites species inhabiting a wide range of reef habitats, from turbid river deltas and stagnant back reefs to high-energy fore reefs. Here, we generate ddRAD data for 172 Porites corals from river delta and adjacent (<0.5 km) fore reef populations on Guam to assess the extent of genetic differentiation among massive Porites corals in these two contrasting environments and throughout the island. Phylogenetic and population genomic analyses consistently identify seven different clades of massive Porites, with the two largest clades predominantly inhabiting either river deltas or fore reefs, respectively. No population structure was detected in the two largest clades, and Cladocopium was the dominant symbiont genus in all clades and environments. The perceived bleaching resilience of corals in marginal reefs may therefore be attributed to interspecific differences between morphologically similar species, in addition to potentially mediating environmental differences. Marginal reef environments may therefore not provide a suitable refuge for many reef corals in a heating world, but instead host additional cryptic coral diversity.

Highly Diverse Symbiodiniaceae Types Hosted by Corals in a Global Hotspot of Marine Biodiversity

Symbiotic dinoflagellates in the genus Symbiodiniaceae play vital roles in promoting resilience and increasing stress tolerance in their coral hosts. While much of the world's coral succumb to the stresses associated with increasingly severe and frequent thermal bleaching events, live coral cover in Papua New Guinea (PNG) remains some of the highest reported globally despite the historically warm waters surrounding the country. Yet, in spite of the high coral cover in PNG and the acknowledged roles Symbiodiniaceae play within their hosts, these communities have not been characterized in this global biodiversity hotspot. Using high-throughput sequencing of the ITS2 rDNA gene, we profiled the endosymbionts of four coral species, Diploastrea heliopora, Pachyseris speciosa, Pocillopora acuta, and Porites lutea, across six sites in PNG. Our findings reveal patterns of Cladocopium and Durusdinium dominance similar to other reefs in the Coral Triangle, albeit with much greater intra- and intergenomic variation. Host- and site-specific variations in Symbiodiniaceae type profiles were observed across collection sites, appearing to be driven by environmental conditions. Notably, the extensive intra- and intergenomic variation, coupled with many previously unreported sequences, highlight PNG as a potential hotspot of symbiont diversity. This work represents the first characterization of the coral-symbiont community structure in the PNG marine biodiversity hotspot, serving as a baseline for future studies.

Wallace's line structures seagrass microbiota and is a potential barrier to the dispersal of marine bacteria

BACKGROUND

The processes that shape microbial biogeography are not well understood, and concepts that apply to macroorganisms, like dispersal barriers, may not affect microorganisms in the same predictable ways. To better understand how known macro-scale biogeographic processes can be applied at micro-scales, we examined seagrass associated microbiota on either side of Wallace's line to determine the influence of this cryptic dispersal boundary on the community structure of microorganisms. Communities were examined from twelve locations throughout Indonesia on either side of this theoretical line.

RESULTS

We found significant differences in microbial community structure on either side of this boundary (R2 = 0.09; P = 0.001), and identified seven microbial genera as differentially abundant on either side of the line, six of these were more abundant in the West, with the other more strongly associated with the East. Genera found to be differentially abundant had significantly smaller minimum cell dimensions (GLM: t923 = 59.50, P < 0.001) than the overall community.

CONCLUSION

Despite the assumed excellent dispersal ability of microbes, we were able to detect significant differences in community structure on either side of this cryptic biogeographic boundary. Samples from the two closest islands on opposite sides of the line, Bali and Komodo, were more different from each other than either was to its most distant island on the same side. We suggest that limited dispersal across this barrier coupled with habitat differences are primarily responsible for the patterns observed. The cryptic processes that drive macroorganism community divergence across this region may also play a role in the bigeographic patterns of microbiota.

Temporal and spatial dynamics of coral symbiont assemblages are affected by local and global impacts

The influence of abiotic variables and anthropogenic pressure on symbiodiniaceans associated with the scleractinian corals Mussismilia hispida and Siderastrea stellata were assessed quarterly at Armação dos Búzios, Brazil, for over 18 months. Thirty-eight Symbiodiniaceae ITS2 rDNA phylotypes were found by metabarcoding, with eight comprising new phylotypes. Both hosts maintained their generalist pattern, with 1-3 dominant lineages. An environmental pressure index and changes in seawater temperature explained the variations in the structure and diversity of Symbiodiniaceae assemblages over time and space. A mild bleaching event affected the photosymbiotic assemblage structure, even in non-bleached colonies. The highly dynamic and diverse photosymbiont assemblages were constantly driven by the influence of environmental variables and human-induced impacts. Furthermore, new strains of Symbiodiniaceae might be associated with lower temperatures caused by upwelling, which is characteristic of this subtropical coral community, highlighting the region's idiosyncrasy and the need for further studies of this coral system.

Marine heatwaves threaten cryptic coral diversity and erode associations among coevolving partners

Climate change-amplified marine heatwaves can drive extensive mortality in foundation species. However, a paucity of longitudinal genomic datasets has impeded understanding of how these rapid selection events alter cryptic genetic structure. Heatwave impacts may be exacerbated in species that engage in obligate symbioses, where the genetics of multiple coevolving taxa may be affected. Here, we tracked the symbiotic associations of reef-building corals for 6 years through a prolonged heatwave, including known survivorship for 79 of 315 colonies. Coral genetics strongly predicted survival of the ubiquitous coral, Porites (massive growth form), with variable survival (15 to 61%) across three morphologically indistinguishable-but genetically distinct-lineages. The heatwave also disrupted strong associations between these coral lineages and their algal symbionts (family Symbiodiniaceae), with symbiotic turnover in some colonies, resulting in reduced specificity across lineages. These results highlight how heatwaves can threaten cryptic genotypes and decouple otherwise tightly coevolved relationships between hosts and symbionts.

Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes

Endogenous viral elements (EVEs) offer insight into the evolutionary histories and hosts of contemporary viruses. This study leveraged DNA metagenomics and genomics to detect and infer the host of a non-retroviral dinoflagellate-infecting +ssRNA virus (dinoRNAV) common in coral reefs. As part of the Tara Pacific Expedition, this study surveyed 269 newly sequenced cnidarians and their resident symbiotic dinoflagellates (Symbiodiniaceae), associated metabarcodes, and publicly available metagenomes, revealing 178 dinoRNAV EVEs, predominantly among hydrocoral-dinoflagellate metagenomes. Putative associations between Symbiodiniaceae and dinoRNAV EVEs were corroborated by the characterization of dinoRNAV-like sequences in 17 of 18 scaffold-scale and one chromosome-scale dinoflagellate genome assembly, flanked by characteristically cellular sequences and in proximity to retroelements, suggesting potential mechanisms of integration. EVEs were not detected in dinoflagellate-free (aposymbiotic) cnidarian genome assemblies, including stony corals, hydrocorals, jellyfish, or seawater. The pervasive nature of dinoRNAV EVEs within dinoflagellate genomes (especially Symbiodinium), as well as their inconsistent within-genome distribution and fragmented nature, suggest ancestral or recurrent integration of this virus with variable conservation. Broadly, these findings illustrate how +ssRNA viruses may obscure their genomes as members of nested symbioses, with implications for host evolution, exaptation, and immunity in the context of reef health and disease.

Diversity and distribution of Symbiodiniaceae detected on coral reefs of Lombok, Indonesia using environmental DNA metabarcoding

Background

Dinoflagellates of family Symbiodiniaceae are important to coral reef ecosystems because of their contribution to coral health and growth; however, only a few studies have investigated the function and distribution of Symbiodiniaceae in Indonesia. Understanding the distribution of different kinds of Symbiodiniaceae can improve forecasting of future responses of various coral reef systems to climate change. This study aimed to determine the diversity of Symbiodiniaceae around Lombok using environmental DNA (eDNA).

Methods

Seawater and sediment samples were collected from 18 locations and filtered to obtain fractions of 0.4-12 and >12 µm. After extraction, molecular barcoding polymerase chain reaction was conducted to amplify the primary V9-SSU 18S rRNA gene, followed by sequencing (Illumina MiSeq). BLAST, Naïve-fit-Bayes, and maximum likelihood routines were used for classification and phylogenetic reconstruction. We compared results across sampling sites, sample types (seawater/sediment), and filter pore sizes (fraction).

Results

Phylogenetic analyses resolved the amplicon sequence variants into 16 subclades comprising six Symbiodiniaceae genera (or genera-equivalent clades) as follows: Symbiodinium, Breviolum, Cladocopium, Durusdinium, Foraminifera Clade G, and Halluxium. Comparative analyses showed that the three distinct lineages within Cladocopium, Durusdinium, and Foraminifera Clade G were the most common. Most of the recovered sequences appeared to be distinctive of different sampling locations, supporting the possibility that eDNA may resolve regional and local differences among Symbiodiniaceae genera and species.

Conclusions

eDNA surveys offer a rapid proxy for evaluating Symbiodiniaceae species on coral reefs and are a potentially useful approach to revealing diversity and relative ecological dominance of certain Symbiodiniaceae organisms. Moreover, Symbiodiniaceae eDNA analysis shows potential in monitoring the local and regional stability of coral-algal mutualisms.

Molecular diversity and assemblages of coral symbionts (Symbiodiniaceae) in diverse scleractinian coral species

The scleractinian coral-associated symbiotic algae Symbiodiniaceae plays an important role in bleaching tolerance and coral resilience. In this study, coral-associated Symbiodiniaceae communities of 14 reef sites of Perhentian and Redang Islands Marine Parks (Malaysia, South China Sea) were characterized using the high-throughput next-generation amplicon sequencing on the ITS2 rDNA marker to inventory the Symbiodiniaceae diversity from a healthy tropical reef system and to generate a baseline for future studies. A total of 64 coral-Symbiodiniaceae associations were characterized in 18 genera (10 families) of scleractinian corals using the SymPortal analytical framework. The results revealed the predominance of Symbiodiniaceae genera Cladocopium (average 82%) and Durusdinium (18%), while Symbiodinium, Breviolum, Fugacium, and Gerakladium were found as minor groups (<0.01%). Of the 39 Cladocopium and Durusdinium major ITS2 sequences, 14 were considered dominant/sub-dominant, with C3u as the predominant type (63.3%), followed by D1 (15%), C27 (10.1%), and C15 (6.9%). A total of 19 and 13 Cladocopium and Durusdinium ITS2-type profiles were detected across the coral species, respectively. Symbiodiniaceae diversity and richness recorded in this study were higher when compared to other reefs in the proximity. With the increasing coral-Symbiodiniaceae associations archived, the database would provide a baseline to assess the changes of Symbiodiniaceae communities in the coral hosts and to explore the potential adaptive roles of this coral-algal association.

The seasonal investigation of Symbiodiniaceae in broadcast spawning, Acropora humilis and brooding, Pocillopora cf. damicornis corals

The density and diversity of Symbiodiniaceae associated with corals can be influenced by seasonal changes . This study provided the first annual investigation of Symbiodiniaceae density and diversity associated with Acropora humilis and Pocillopora cf. damicornis corals in the Gulf of Thailand using both zooxanthellae cell count and next-generation sequencing (ITS-1, ITS-2 regions) techniques, respectively. The results from this study indicated that zooxanthellae cell densities in both coral species differ significantly. The number of zooxanthellae was negatively correlated with the physical environment variable (light intensity). The diversity within A. humilis consisted of two genera, Cladocopium (Cspc_C3: 56.39%, C3w: 33.62%, C93type1: 4.42% and Cspf: 3.59%) and a small amount of Durusdinium (D1: 1.03%) whereas P. cf. damicornis was found to be 100% associated with Durusdinium (D1: 95.58%, D6: 1.01% and D10: 2.7%) suggesting that each coral species may select their appropriate genus/species of Symbiodiniaceae in response to local environmental stressors. The results of this study provided some information on the coral-Symbiodiniaceae relationship between seasons, which may be applied to predict the potential adaptation of corals in localized reef environments.

Atoll-dependent variation in depth zonation of benthic communities on remote reefs

The distribution and organisation of benthic organisms on tropical reefs are typically heterogenous yet display distinct zonation patterns across depth gradients. However, there are few datasets which inform our understanding of how depth zonation in benthic community composition varies spatially among and within different reef systems. Here, we assess the depth zonation in benthic forereef slope communities in the Central Indian Ocean, prior to the back-to-back bleaching events in 2014-2017. We compare benthic communities between shallow (5-10 m) and deep (20-25 m) sites, at two spatial scales: among and within 4 atolls. Our analyses showed the variation in both major functional groups and hard coral assemblages between depth varied among atolls, and within-atoll comparisons revealed distinct differences between shallow and deep forereef slope communities. Indicator taxa analyses characterising the hard coral community between depths revealed a higher number of coral genera characteristic of the deep forereef slopes (10) than the shallow forereef slopes (6). Only two coral genera consistently associated with both depths across all atolls, and these were Acropora and Porites. Our results reveal spatial variation in depth zonation of benthic communities, potentially driven by biophysical processes varying across depths and atolls, and provide a baseline to understand and measure the impacts of future global climate change on benthic communities across depths.

The Microbiome of the Reef Macroalga Sargassum ilicifolium in Singapore

The large canopy-forming macroalga, Sargassum ilicifolium, provides shelter and food for numerous coral reef species, but it can also be detrimental at high abundances where it outcompetes other benthic organisms for light and space. Here, we investigate the microbial communities associated with S. ilicifolium in Singapore, where it is an abundant and important member of coral reef communities. We collected eight complete S. ilicifolium thalli from eight island locations along an approximate 14 km east-to-west transect. Each thallus was dissected into three separate parts: holdfast, vesicles, and leaves. We then characterized the bacterial communities associated with each part via polymerase chain reaction (PCR) amplification of the 16S rRNA gene V4 region. We then inferred predicted metagenome functions using METAGENassist. Despite the comparatively short distances between sample sites, we show significant differences in microbial community composition, with communities further differentiated by part sampled. Holdfast, vesicles and leaves all harbor distinct microbial communities. Functional predictions reveal some separation between holdfast and leaf communities, with higher representation of sulphur cycling taxa in the holdfast and higher representation of nitrogen cycling taxa in the leaves. This study provides valuable baseline data that can be used to monitor microbial change, and helps lay the foundation upon which we can begin to understand the complexities of reef-associated microbial communities and the roles they play in the functioning and diversity of marine ecosystems.

Host-symbiont coevolution, cryptic structure, and bleaching susceptibility, in a coral species complex (Scleractinia; Poritidae)

The 'species' is a key concept for conservation and evolutionary biology, yet the lines between population and species-level variation are often blurred, especially for corals. The 'Porites lobata species complex' consists of branching and mounding corals that form reefs across the Pacific. We used reduced representation meta-genomic sequencing to examine genetic relationships within this species complex and to identify candidate loci associated with colony morphology, cryptic genetic structure, and apparent bleaching susceptibility. We compared existing Porites data with bleached and unbleached colonies of the branching coral P. compressa collected in Kāne'ohe Bay Hawai'i during the 2015 coral bleaching event. Loci that mapped to coral, symbiont, and microbial references revealed genetic structure consistent with recent host-symbiont co-evolution. Cryptic genetic clades were resolved that previous work has associated with distance from shore, but no genetic structure was associated with bleaching. We identified many candidate loci associated with morphospecies, including candidate host and symbiont loci with fixed differences between branching and mounding corals. We also found many loci associated with cryptic genetic structure, yet relatively few loci associated with bleaching. Recent host-symbiont co-evolution and rapid diversification suggests that variation and therefore the capacity of these corals to adapt may be underappreciated.