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Microbes perform critical functions in corals, yet most knowledge is derived from the photic zone. Here, we discover two mollicutes that dominate the microbiome of the deep-sea octocoral, Callogorgia delta, and likely reside in the mesoglea. These symbionts are abundant across the host's range, absent in the water, and appear to be rare in sediments. Unlike other mollicutes, they lack all known fermentative capabilities, including glycolysis, and can only generate energy from arginine provided by the coral host. Their genomes feature several mechanisms to interact with foreign DNA, including extensive CRISPR arrays and restriction-modification systems, which may indicate their role in symbiosis. We propose the novel family Oceanoplasmataceae which includes these symbionts and others associated with five marine invertebrate phyla. Its exceptionally broad host range suggests that the diversity of this enigmatic family remains largely undiscovered. Oceanoplasmataceae genomes are the most highly reduced among mollicutes, providing new insight into their reductive evolution and the roles of coral symbionts. Corals and other marine invertebrates host diverse microbes that remain poorly characterized, especially in the deep sea. Here the authors discover a new clade of bacteria with uniquely streamlined genomes in the tissue of a deep-sea coral that provide insights into the genome reduction of symbionts. [ABSTRACT FROM AUTHOR]

Coral reefs are facing threats from a variety of global change stressors, including ocean warming, acidification, and deoxygenation. It has been hypothesized that growing corals near primary producers such as macroalgae or seagrass may help to ameliorate acidification and deoxygenation stress, however few studies have explored this effect in situ. Here, we investigated differences in coral growth rates across a natural gradient in seawater temperature, pH, and dissolved oxygen (DO) variability in a nearshore seagrass bed on Dongsha Atoll, Taiwan, South China Sea. We observed strong spatial gradients in temperature (5°C), pH (0.29 pH units), and DO (129 μmol O2 kg-1) across the 1-kilometer wide seagrass bed. Similarly, diel variability recorded by an autonomous sensor in the shallow seagrass measured diel ranges in temperature, pH, and DO of up to 2.6°C, 0.55, and 204 μmol O2 kg-1, respectively. Skeletal cores collected from 15 massive Porites corals growing in the seagrass bed at 4 sites revealed no significant differences in coral calcification rates between sites along the gradients. However, significant differences in skeletal extension rate and density suggest that the dynamic temperature, pH, and/or DO variability may have influenced these properties. The lack of differences in coral growth between sites may be because favorable calcification conditions during the day (high temperature, pH, and DO) were proportionally balanced by unfavorable conditions during the night (low temperature, pH, and DO). Alternatively, other factors were simply more important in controlling coral calcification and/or corals were acclimated to the prevailing conditions at each site. [ABSTRACT FROM AUTHOR]

Mutualistic relationships with photosynthetic organisms are common in cnidarians, which form an intracellular symbiosis with dinoflagellates in the family Symbiodiniaceae. The establishment and maintenance of these symbionts are associated with the suppression of key host immune factors. Because of this, there are potential trade-offs between the nutrition that cnidarian hosts gain from their symbionts and their ability to successfully defend themselves from pathogens. To investigate these potential trade-offs, we utilized the facultatively symbiotic polyps of the upside-down jellyfish Cassiopea xamachana and exposed aposymbiotic and symbiotic polyps to the pathogen Serratia marcescens. Symbiotic polyps had a lower probability of survival following S. marcescens exposure. Gene expression analyses 24 hours following pathogen exposure indicate that symbiotic animals mounted a more damaging immune response, with higher levels of inflammation and oxidative stress likely resulting in more severe disruptions to cellular homeostasis. Underlying this more damaging immune response may be differences in constitutive and pathogen-induced expression of immune transcription factors between aposymbiotic and symbiotic polyps rather than broadscale immune suppression during symbiosis. Our findings indicate that in facultatively symbiotic polyps, hosting symbionts limits C. xamachana's ability to survive pathogen exposure, indicating a trade-off between symbiosis and immunity that has potential implications for coral disease research. [ABSTRACT FROM AUTHOR]

ABSTRACT Ostreobium comprises endolithic algae commonly seen in conjunction with scleractinian corals. In the past, it was solely recognized as a coral skeleton bioeroder. Their relationship with corals is critical because they give photosynthetic byproducts and help the coral when it loses its primary symbionts due to stress. The variety of these algae in coral species of the genus Porites in the Tropical Eastern Pacific and western Atlantic was investigated. Ostreobium samples from seven Porites species including two from the Tropical Eastern Pacific (TEP) (P. panamensis and P. lobata) and five from the Caribbean (P. furcata, P. porites, P. colonensis, P. branneri, and P. astreoides) were extracted. Published rbcL sequences from algae found within various coral species from other parts of the world were also compared. A biogeographic analysis and two methodologies, PTP (Poisson tree process) and GMYC (general mixed Yule‐coalescent), were used to delineate the different species. The findings revealed a significant degree of genetic diversity within Ostreobium, with more than 15 groups of not more than three individuals and 40 individual lineages. Its origins date back to the Ordovician, 500 Ma, and it does not appear to preserve host specificity. The sampled locations still have a wide variety of Ostreobium. Biogeographically patterns were also confirmed, making it impossible to pinpoint the precise origins of most clades. The ancestry analyses revealed convergent events for not only the emergence of Ostreobium in a few genera of local corals, but also the phenomenon occurred in genera from far‐off places. [ABSTRACT FROM AUTHOR]

The partnership between corals and their intracellular algal symbionts has long been a textbook example of a mutually beneficial association. Here I argue that this view has been made obsolete by a steady accumulation of evidence over the past three decades. The coral–algal relationship is perhaps better viewed as one of domestication — think of it like a cattle farm, in which the coral is the farmer and the algae are the cows. I synthesize old and new evidence in support of this updated view and highlight remaining knowledge gaps, the largest of which continues to be the natural history of algal symbionts. The partnership between corals and their intracellular algal symbionts has long been a textbook example of mutually beneficial association. In this essay, Mikhail Matz argues for an updated view in which the coral acts more as a farmer of algal cells to support its own growth. [ABSTRACT FROM AUTHOR]

Some marine microalgae and cyanobacteria form mutualistic symbioses with diverse invertebrates, particularly cni-darians. Among microalgae, dinoflagellates in the family Symbiodiniaceae are the most well-known symbiotic partners of jellyfish and corals. However, the symbioses involving other dinoflagellate families, nano- and micro-flagellates, diatoms, and cyanobacteria with cnidarians are not well understood. As an initial step, it is essential to explore the survival of these microorganisms inside cnidarians. We monitored the survival of eight microalgal species (nine strains) and one cyanobacterium species every day for seven days after injecting each into the medusa of the moon jellyfish Aurelia au-rita. The dinoflagellates Effrenium voratum (free-living [FL] and living-in-coral strains), Cladocopium infistulum, Pro-rocentrum cordatum, Prorocentrum koreanum, Symbiodinium microadriaticum, the prasinophyte Tetraselmis suecica, the chlorophyte Dunaliella salina, and the raphidophyte Heterosigma akashiwo survived inside the medusa, while the cyanobacterium Synechococcus sp. was not detected. Additionally, E. voratum (FL) survived within the medusa for 60 days and gradually spread to adjacent areas, indicating potential for artificially established symbiosis. The results of this study provide a basis for artificial symbiosis between microalgae and invertebrates. [ABSTRACT FROM AUTHOR]

Guanosine Triphosphate (GTP)ases of Immunity Associated Proteins (GIMAP) are small G proteins that in vertebrates, regulate immunity, apoptosis, and autophagy. While previously thought to be limited to vertebrates and plants, this family of proteins was recently characterized in a diversity of dinoflagellates. However, information regarding the function of GIMAPs in dinoflagellates is lacking. Therefore, the goal of this study (conducted from March-November of 2022) was to assess the expression of GIMAPs in the cnidarian symbiont Breviolum minutum (formerly Symbiodinium minutum, referred to as Bm_GIMAPs) in response to low light (25 vs 8 μmol m−2 s−1 for 9 d), thermal stress (22 vs 28 °C for 48 h), and symbiotic state (cultured vs in hospite). These factors were selected due to their importance in the lifestyle of a photosynthetic symbiont and relevance to the ecologically important issue of coral bleaching. The results indicate Bm_GIMAP expression increased under both low light and elevated temperature, suggesting a role in the response to bleaching related stressors. Cultured B. minutum had lower baseline Bm_GIMAP expression than those in association with a cnidarian host, but a stronger response to thermal stress, suggesting their function is influenced by symbiosis. Lastly, further support for the responsiveness of GIMAPs to thermal stress was provided by a comparison with previously published RNA-seq data from cultured Symbiodiniaceae. Collectively, the results presented here represent the first functional investigation of GIMAPs in an ecologically important group of protists and provide a greater understanding of the molecular response of dinoflagellates to stressors related to bleaching. [ABSTRACT FROM AUTHOR]

Climate-driven species range expansions are underway with more tropically affiliated species, including Scleractinian corals, becoming increasingly abundant at higher latitudes. However, uncertainty remains on how these range shifts will affect reef-scale ecosystem processes, which will ultimately depend on the traits of the taxa that dominate these assemblages. Here, we quantified spatiotemporal patterns in the taxonomic and trait structure of coral assemblages along the subtropical-temperate coast of Western Australia (27°–34°S). Coral abundance was generally low and coral cover < 5% across our study sites. Coral assemblages shared similarities in morphological trait structures across the latitudinal gradient, mostly characterised by taxa with simple morphologies; yet subtle differences were also observed across latitudes, with high-latitude corals characterised by slower growth rates and reduced maximum colony sizes. We found a 3.4-fold increase (from 1 to 3.4 individuals m−2) in coral abundance at one heavily disturbed location, where canopy-forming seaweeds were replaced by turfing algae, a pattern that was partly driven by an increase in the relative contribution of warm affinity taxa, such as Acropora spp. We predicted these changes would be reflected in different components of functional diversity; yet, despite a localised signal of tropicalisation, we only observed subtle changes in the functional identity, richness, evenness, and divergence. The spatially invariant trait structure of coral assemblages suggests that the nature of ecosystem functions will likely remain unchanged during early stages of tropicalisation, and hence their contribution to temperate reef-scale ecological processes will depend on dominance over other benthic foundational species. [ABSTRACT FROM AUTHOR]

Sexual propagation of corals is a promising strategy for coral restoration, but one of the main challenges is the high mortality of coral spat due to competitive interactions with macroalgae during the early life history stages. Optimising the properties of settlement substrates such as material types and surface roughness has the potential to improve the survival of spat by limiting the recruitment and growth of macroalgae. In this study, we assessed the effects of modifying surface roughness across three different tile materials (alumina-based ceramic, calcium carbonate (CaCO3), and concrete) on the settlement success and post-settlement survivorship of Acropora kenti coral larvae in six mesocosm tanks, each with different established macroalgal communities. The macroalgal community compositions on the tiles were significantly different among material types, but not surface roughness, although the type and abundance of macroalgal species were heavily influenced by the established tank communities. Increasing surface roughness did not affect larval settlement success or spat survivorship. Substantially higher larval settlement density was found on concrete tiles (1.92 ± 0.10 larvae cm−2), but spat survival was the highest on CaCO3 tiles (73.4 ± 4.2% survived). Very strong competitive interactions were observed between spat and macroalgae, with overgrowth by the crustose coralline alga Crustaphytum sp. and the brown alga Lobophora sp. being the primary cause of spat mortality. Overall, when taking into account both settlement and survival rates, concrete was the best performing among the tile types tested here. [ABSTRACT FROM AUTHOR]

Symbiotic microorganisms in reef-building corals, including algae, bacteria, archaea, fungi, and viruses, play critical roles in the adaptation of coral hosts to adverse environmental conditions. However, their adaptation and functional relationships in nutrient-rich environments have yet to be fully explored. This study investigated Duncanopsammia peltata and the surrounding seawater and sediments from protected and non-protected areas in the summer and winter in Dongshan Bay. High-throughput sequencing was used to characterize community changes, co-occurrence patterns, and factors influencing symbiotic coral microorganisms (zooxanthellae, bacteria, and archaea) in different environments. The results showed that nutrient enrichment in the protected and non-protected areas was the greatest in December, followed by the non-protected area in August. In contrast, the August protected area had the lowest nutrient enrichment. Significant differences were found in the composition of the bacterial and archaeal communities in seawater and sediments from different regions. Among the coral symbiotic microorganisms, the main dominant species of zooxanthellae is the C1 subspecies (42.22–56.35%). The dominant phyla of bacteria were Proteobacteria, Cyanobacteria, Firmicutes, and Bacteroidota. Only in the August protected area did a large number (41.98%) of SAR324_cladeMarine_group_B exist. The August protected and non-protected areas and December protected and non-protected areas contained beneficial bacteria as biomarkers. They were Nisaea, Spiroplasma, Endozoicomonas, and Bacillus. No pathogenic bacteria appeared in the protected area in August. The dominant phylum in Archaea was Crenarchaeota. These symbiotic coral microorganisms' relative abundances and compositions vary with environmental changes. The enrichment of dissolved inorganic nitrogen in environmental media is a key factor affecting the composition of coral microbial communities. Co-occurrence analysis showed that nutrient enrichment under anthropogenic disturbances enhanced the interactions between coral symbiotic microorganisms. These findings improve our understanding of the adaptations of coral holobionts to various nutritional environments. [ABSTRACT FROM AUTHOR]

Hundreds of studies now document positive relationships between biodiversity and critical ecosystem processes, but as ecological communities worldwide shift toward new species configurations, less is known regarding how the biodiversity of undesirable species will shape the functioning of ecosystems or foundation species. We manipulated macroalgal species richness in experimental field plots to test whether and how the identity and diversity of competing macroalgae affected the growth, survival, and microbiome of a common coral in Mo'orea, French Polynesia. Compared to controls without algal competitors, coral growth was significantly suppressed across three macroalgal monocultures, a polyculture of the same three macroalgae, and plots containing inert seaweed mimics; coral mortality was limited and did not differ significantly among treatments. One macroalga suppressed coral growth significantly less than the other two, but none differed from the inert mimic in terms of coral suppression. The composition, dispersion, and diversity of coral microbiomes in treatments with live macroalgae or inert plastic mimics did not differ from controls experiencing no competition. Microbiome composition differed between two macroalgal monocultures and a monoculture versus plastic mimics, but no other microbiome differences were observed among macroalgal or mimic treatments. Together, these findings suggest that algal diversity does not alter harmful impacts of macroalgae on coral performance, which could be accounted for by physical structure alone in these field experiments. While enhancing biodiversity is a recognized strategy for promoting desirable species, it would be worrisome if biodiversity also enhanced the negative impacts of undesirable species. We documented no such effects in this investigation. [ABSTRACT FROM AUTHOR]

Edible seaweed - Caulerpa lentillifera is being cultivated along the coast of Khanh Hoa province, Vietnam, and makes a relatively large contribution to the economic development of this region. Bacterial strains originating from marine sources such as those associated with seaweed and hard coral were screened for properties of promote plant growth with the capacity of indole-3-acetic acid (IAA) - a phytohormone belonging to auxin group, the phosphate solubilization ability and antibacterial activity of IAA-producing strains were also performed in this study. Robust strains were identified by morphological methods with biochemical tests and analysis of 16s RNA sequences. Isolate RN06 produced high amounts of IAA, utilized inorganic phosphate, and inhibited Bacillus subtilis ATCC6633, Escherichia coli 0157, and Serratia marcescens PDL100. The IAA producer HRA5 isolated from hard coral demonstrated the ability to solubilize phosphate and exhibited antibacterial activity against B. subtilis. Morphological analysis and 16sRNA sequencing showed that isolate RN06 was the closest strain to Bacillus amyloliquefaciens and HRA5 was linked to Pseudomonas sp. This is the first report of isolated bacteria from seaweed and corals from the Vietnamese sea served as potential strains for further research of the application of biological inoculants specifically for seaweed farming. [ABSTRACT FROM AUTHOR]

Ferroptosis is an iron-dependent cell death that was discovered recently. For beneficial microbes to establish mutualistic relationships with hosts, precisely controlled cell death in plant cells is necessary. However, whether ferroptosis is involved in the endophyte‒plant system is poorly understood. Here, we reported that endophytic Streptomyces hygroscopicus OsiSh-2, which established a sophisticated and beneficial interaction with host rice plants, caused ferroptotic cell death in rice characterized by ferroptosis- and immune-related markers. Treatments with ferroptosis inhibitors and inducers, different doses of OsiSh-2, and the siderophore synthesis-deficient mutant ΔcchH revealed that only moderate ferroptosis induced by endophytes is essential for the establishment of an optimal symbiont to enhance plant growth. Additionally, ferroptosis involved in a defence-primed state in rice, which contributed to improved resistance against rice blast disease. Overall, our study provides new insights into the mechanisms of endophyte‒plant interactions mediated by ferroptosis and suggests new directions for crop yield promotion. Ferroptosis is of great importance in plant immunity including microbe-plant interactions. Here, the authors unveil that a regulated ferroptosis process is involved in the mutualistic symbiosis and disease resistance of endophyte OsiSh-2 and host rice. [ABSTRACT FROM AUTHOR]

The diversity of marine cyanobacteria has been extensively studied due to their vital roles in ocean primary production. However, little is understood about the diversity of cyanobacterial species involved in symbiotic relationships. In this study, we successfully sequenced the complete genome of a cyanobacterium in symbiosis with Citharistes regius, a dinoflagellate species thriving in the open ocean. A phylogenomic analysis revealed that the cyanobacterium (CregCyn) belongs to the marine picocyanobacterial lineage, akin to another cyanobacterial symbiont (OmCyn) of a different dinoflagellate closely related to Citharistes. Nevertheless, these two symbionts are representing distinct lineages, suggesting independent origins of their symbiotic lifestyles. Despite the distinct origins, the genome analyses of CregCyn revealed shared characteristics with OmCyn, including an obligate symbiotic relationship with the host dinoflagellates and a degree of genome reduction. In contrast, a detailed analysis of genome subregions unveiled that the CregCyn genome carries genomic islands that are not found in the OmCyn genome. The presence of the genomic islands implies that exogenous genes have been integrated into the CregCyn genome at some point in its evolution. This study contributes to our understanding of the complex history of the symbiosis between dinoflagellates and cyanobacteria, as well as the genomic diversity of marine picocyanobacteria. [ABSTRACT FROM AUTHOR]

Hundreds of species of true bugs (Hemiptera) within the seed bugs, leaf-footed bugs, and allies (superfamilies Lygaeoidea and Coreoidea) depend on symbiotic Caballeronia bacteria which they must acquire from the environment every generation. There has been much recent interest in studying this symbiosis, in part because several of the insects that participate are agricultural pests, and in part because it is an interesting model system for understanding the environmental mode of symbiont acquisition. Researchers who want to rear and study these insects in captivity must ensure that the insects are successfully colonized by Caballeronia, but there is no standard method for doing so. We set out to assess five different methods of exposing insects to these bacteria. We tested the introduction of the bacteria via inoculated water, broth, plant sprig, potting soil, and uninoculated agricultural soil. No significant difference was seen between treatments in average adult weight or development time. However, the method of inoculation did affect the number of insects that reached adulthood. Insects exposed to agricultural soil and symbiont cells in water and were significantly less likely to reach adulthood than insects inoculated via cells in broth, on plant sprigs, or in potting soil. We therefore recommend use of inoculated broth as a simple and effective method to provide true bugs with their symbiotic Caballeronia in laboratory experiments. [ABSTRACT FROM AUTHOR]

In facultative symbioses, only a fraction of hosts are associated with symbionts. Specific host and symbiont pairings may be the result of host–symbiont coevolution driven by reciprocal selection or priority effects pertaining to which potential symbiont is associated with a host first. Distinguishing between these possibilities is important for understanding the evolutionary forces that affect facultative symbioses. We used the social amoeba, Dictyostelium discoideum , and its symbiont, Paraburkholderia bonniea , to determine whether ongoing coevolution affects which host–symbiont strain pairs naturally cooccur within a facultative symbiosis. Relative to other Paraburkholderia , including another symbiont of D. discoideum , P. bonniea features a reduced genome size that indicates a significant history of coevolution with its host. We hypothesized that ongoing host–symbiont coevolution would lead to higher fitness for naturally cooccurring (native) host and symbiont pairings compared to novel pairings. We show for the first time that P. bonniea symbionts can horizontally transmit to new amoeba hosts when hosts aggregate together during the social stage of their life cycle. Here we find evidence for a virulence–transmission trade-off without host specificity. Although symbiont strains were significantly variable in virulence and horizontal transmission rate, hosts and symbionts responded similarly to associations in native and novel pairings. We go on to identify candidate virulence factors in the genomes of P. bonniea strains that may contribute to variation in virulence. We conclude that ongoing coevolution is unlikely for D. discoideum and P. bonniea. The system instead appears to represent a stable facultative symbiosis in which naturally cooccurring P. bonniea host and symbiont pairings are the result of priority effects. [ABSTRACT FROM AUTHOR]

A habitat's structural complexity is a key determinant of the recruitment and composition of associated communities. While the influence of the physical structure of corals on coral reef fish recruitment is well studied, the significance of other benthic components, like macroalgae, remains unclear. We used experimental patches of the canopy-forming macroalga Sargassum to assess the influence of macroalgal complexity, which was manipulated by altering thallus density and biomass, on coral reef fish recruitment. We established twenty-five 75 × 75 cm patches on the reef flat of Orpheus Island, (inshore, central Great Barrier Reef) during austral summer. Patches were randomly divided into five treatments of varying Sargassum thallus density (3–9 thalli) and/or biomass (177–779 g per patch) and surveyed daily for recruiting fishes for 18 d. We recorded 35 fish species recruiting to our patches, with Sargassum biomass having the greatest influence on fish recruits' abundance and species richness. Comparisons between treatments with equal thallus density but varying biomass revealed a positive association between Sargassum biomass and fish species richness and abundance (up to ~ 2.5-fold differences). Additionally, treatments with similar total Sargassum biomass but different density revealed a negative relationship between density and fish species richness and abundance (20–30% reduction). These positive associations with Sargassum thallus biomass suggest that recruiting fishes favour the fine-scale complexity of intra-thallus spaces, rather than the larger, inter-thallus gaps. This study highlights that fine-scales of complexity within tropical macroalgal beds may influence the reef fish recruitment value of these often-underappreciated areas. [ABSTRACT FROM AUTHOR]

The speciose scarinine clade of coral reef parrotfishes display significant variation in trophic cranial morphology, yet are often described as generalist herbivores. The hypothesis that many parrotfishes target micro-photoautotrophs is a new framework within which to clarify parrotfish diets. Here, we investigate the dietary targets of Scarus rubroviolaceus using the feeding substrata extraction method and then compare the results to fourteen other syntopic parrotfish species. Scarus rubroviolaceus were followed on snorkel until repeated biting was observed. A 22 mm × 20 mm core was extracted around the bite. We identified and quantified the bite core biota by scraping the top 1 mm from bite cores for microscopy and 16S/18S small subunit rRNA metabarcoding. Filamentous cyanobacteria density on S. rubroviolaceus bite cores did not differ from the other fourteen parrotfish species, Calothrix (Nostocales) being the most frequently observed filamentous cyanobacteria for all fifteen parrotfish species. The 18S metabarcoding analysis detected the encrusting, endolithic sponge taxon Clionaida in the S. rubroviolaceus bite cores. We investigated the possibility of spongivory across all fifteen parrotfish species including an analysis of sponge-associated microbiota detected on the bite cores. This revealed a new axis of trophic partitioning with varying levels of spongivory amongst the fifteen Indo-Pacific parrotfish species. The bite cores of Cetoscarus ocellatus, Chlorurus spilurus, Chlorurus microrhinos, Scarus frenatus and S. rubroviolaceus particularly indicated spongivory. Our findings develop our understanding of parrotfish diet and provide further evidence that parrotfishes are specialized feeders and partition benthic trophic resources. [ABSTRACT FROM AUTHOR]

The symbiotic relationship between corals and their associated microorganisms is crucial for the health of coral reef eco-environmental systems. Recently, there has been a growing interest in unraveling how the manipulation of symbiont nutrient cycling affects the stress tolerance in the holobiont of coral reefs. However, most studies have primarily focused on coral–Symbiodiniaceae–bacterial interactions as a whole, neglecting the interactions between Symbiodiniaceae and bacteria, which remain largely unexplored. In this study, we proposed a hypothesis that there exists an inner symbiotic loop of Symbiodiniaceae and bacteria within the coral symbiotic loop. We conducted experiments to demonstrate how metabolic exchanges between Symbiodiniaceae and bacteria facilitate the nutritional supply necessary for cellular growth. It was seen that the beneficial bacterium, Ruegeria sp., supplied a nitrogen source to the Symbiodiniaceae strain Durusdinium sp., allowing this dinoflagellate to thrive in a nitrogen-free medium. The Ruegeria sp.–Durusdinium sp. interaction was confirmed through 15N-stable isotope probing–single cell Raman spectroscopy, in which 15N infiltrated into the bacterial cells for intracellular metabolism, and eventually the labeled nitrogen source was traced within the macromolecules of Symbiodiniaceae cells. The investigation into Symbiodiniaceae loop interactions validates our hypothesis and contributes to a comprehensive understanding of the intricate coral holobiont. These findings have the potential to enhance the health of coral reefs in the face of global climate change. [ABSTRACT FROM AUTHOR]

Despite over a century of observations, the obligate insect parasites within the order Entomophthorales remain poorly characterized at the genetic level. In this manuscript, we present a genome for a laboratory-tractable Entomophthora muscae isolate that infects fruit flies. Our E. muscae assembly is 1.03 Gb, consists of 7810 contigs and contains 81.3% complete fungal BUSCOs. Using a comparative approach with recent datasets from entomophthoralean fungi, we show that giant genomes are the norm within Entomophthoraceae owing to extensive, but not recent, Ty3 retrotransposon activity. In addition, we find that E. muscae and its closest allies possess genes that are likely homologs to the blue-light sensor white-collar 1, a Neurospora crassa gene that has a well-established role in maintaining circadian rhythms. We uncover evidence that E. muscae diverged from other entomophthoralean fungi by expansion of existing families, rather than loss of particular domains, and possesses a potentially unique suite of secreted catabolic enzymes, consistent with E. muscae's species-specific, biotrophic lifestyle. Finally, we offer a head-to-head comparison of morphological and molecular data for species within the E. muscae species complex that support the need for taxonomic revision within this group. Altogether, we provide a genetic and molecular foundation that we hope will provide a platform for the continued study of the unique biology of entomophthoralean fungi. [ABSTRACT FROM AUTHOR]

The composition of species and the physiological status of microalgal cells serve as significant indicators for monitoring marine environments. Symbiotic with corals, Symbiodiniaceae are more sensitive to the environmental response. However, current methods for evaluating microalgae tend to be population-based indicators that cannot be focused on single-cell level, ignoring potentially heterogeneous cells as well as cell state transitions. In this study, we proposed a microalgal cell detection method based on computer vision and microfluidics, which combined microscopic image processing, microfluidic chip and convolutional neural network to achieve label-free, sheathless, automated and high-throughput microalgae identification and cell state assessment. By optimizing the data import, training process and model architecture, we solved the problem of identifying tiny objects at the micron scale, and the optimized model was able to perform the tasks of cell multi-classification and physiological state assessment with more than 95% mean average precision. We discovered a novel transition state and explored the thermal sensitivity of three clades of Symbiodiniaceae, and discovered the phenomenon of cellular heat shock at high temperatures. The evolution of the physiological state of Symbiodiniaceae cells is very important for directional cell evolution and early warning of coral ecosystem health. [ABSTRACT FROM AUTHOR]

Species' persistence in increasingly variable climates will depend on resilience against the fitness costs of environmental stochasticity. Most organisms host microbiota that shield against stressors. Here, we test the hypothesis that, by limiting exposure to temporally variable stressors, microbial symbionts reduce hosts' demographic variance. We parameterized stochastic population models using data from a 14‐year symbiont‐removal experiment including seven grass species that host Epichloë fungal endophytes. Results provide novel evidence that symbiotic benefits arise not only through improved mean fitness, but also through dampened inter‐annual variance. Hosts with "fast" life‐history traits benefited most from symbiont‐mediated demographic buffering. Under current climate conditions, contributions of demographic buffering were modest compared to benefits to mean fitness. However, simulations of increased stochasticity amplified benefits of demographic buffering and made it the more important pathway of host–symbiont mutualism. Microbial‐mediated variance buffering is likely an important, yet cryptic, mechanism of resilience in an increasingly variable world. [ABSTRACT FROM AUTHOR]

Endozoicomonas is globally the most prevalent and consistently found bacterial genus associated with Cnidaria; strains of Endozoicomonas are known to codiversify with their coral hosts, and they are widely presumed to be key mutualists. A high abundance of Endozoicomonas in corals is associated with a decreased capacity to adjust to environmental change as well as with life history trade-offs. In other marine host–microbe systems, such as clams and fish, Endozoicomonas is a known parasite and pathogen. Genomic characteristics – such as genome size and structure, and the presence of eukaryote-like proteins and effectors – do not support the view that Endozoicomonas is an obligate and exclusive coral mutualist but may suggest a diverse and potentially intracellular lifestyle, including commensalism, parasitism, or pathogenicity. Stony corals are poster child holobionts due to their intimate association with diverse microorganisms from all domains of life. We are only beginning to understand the diverse functions of most of these microbial associates, including potential main contributors to holobiont health and resilience. Among these, bacteria of the elusive genus Endozoicomonas are widely perceived as beneficial symbionts based on their genomic potential and their high prevalence and ubiquitous presence in coral tissues. Simultaneously, evidence of pathogenic and parasitic Endozoicomonas lineages in other marine animals is emerging. Synthesizing the current knowledge on the association of Endozoicomonas with marine holobionts, we challenge the perception of a purely mutualistic coral– Endozoicomonas relationship and propose directions to elucidate its role along the symbiotic spectrum. [ABSTRACT FROM AUTHOR]

Monitoring coral cover can describe the ecology of reef degradation, but rarely can it reveal the proximal mechanisms of change, or achieve its full potential in informing conservation actions. Describing temporal variation in Symbiodiniaceae within corals can help address these limitations, but this is rarely a research priority. Here, we augmented an ecological time series of the coral reefs of St. John, US Virgin Islands, by describing the genetic complement of symbiotic algae in common corals. Seventy-five corals from nine species were marked and sampled in 2017. Of these colonies, 41% were sampled in 2018, and 72% in 2019; 28% could not be found and were assumed to have died. Symbiodiniaceae ITS2 sequencing identified 525 distinct sequences (comprising 42 ITS2 type profiles), and symbiont diversity differed among host species and individuals, but was in most cases preserved within hosts over 3 yrs that were marked by physical disturbances from major hurricanes (2017) and the regional onset of stony coral tissue loss disease (2019). While changes in symbiont communities were slight and stochastic over time within colonies, variation in the dominant symbionts among colonies was observed for all host species. Together, these results indicate that declining host abundances could lead to the loss of rare algal lineages that are found in a low proportion of few coral colonies left on many reefs, especially if coral declines are symbiont-specific. These findings highlight the importance of identifying Symbiodiniaceae as part of a time series of coral communities to support holistic conservation planning. Repeated sampling of tagged corals is unlikely to be viable for this purpose, because many Caribbean corals are dying before they can be sampled multiple times. Instead, random sampling of large numbers of corals may be more effective in capturing the diversity and temporal dynamics of Symbiodiniaceae metacommunities in reef corals. [ABSTRACT FROM AUTHOR]

Hereditary, or vertically-transmitted, symbioses affect a large number of animal species and some plants. The precise mechanisms underlying transmission of functions of these associations are often difficult to describe, due to the difficulty in separating the symbiotic partners. This is especially the case for plant-bacteria hereditary symbioses, which lack experimentally tractable model systems. Here, we demonstrate the potential of the leaf symbiosis between the wild yam Dioscorea sansibarensis and the bacterium Orrella dioscoreae (O. dioscoreae) as a model system for hereditary symbiosis. O. dioscoreae is easy to grow and genetically manipulate, which is unusual for hereditary symbionts. These properties allowed us to design an effective antimicrobial treatment to rid plants of bacteria and generate whole aposymbiotic plants, which can later be re-inoculated with bacterial cultures. Aposymbiotic plants did not differ morphologically from symbiotic plants and the leaf forerunner tip containing the symbiotic glands formed normally even in the absence of bacteria, but microscopic differences between symbiotic and aposymbiotic glands highlight the influence of bacteria on the development of trichomes and secretion of mucilage. This is to our knowledge the first leaf symbiosis where both host and symbiont can be grown separately and where the symbiont can be genetically altered and reintroduced to the host. [ABSTRACT FROM AUTHOR]

Background: Trombiculid mites are globally distributed, highly diverse arachnids that largely lack molecular resources such as whole mitogenomes for the elucidation of taxonomic relationships. Trombiculid larvae (chiggers) parasitise vertebrates and can transmit bacteria (Orientia spp.) responsible for scrub typhus, a zoonotic febrile illness. Orientia tsutsugamushi causes most cases of scrub typhus and is endemic to the Asia-Pacific Region, where it is transmitted by Leptotrombidium spp. chiggers. However, in Dubai, Candidatus Orientia chuto was isolated from a case of scrub typhus and is also known to circulate among rodents in Saudi Arabia and Kenya, although its vectors remain poorly defined. In addition to Orientia, chiggers are often infected with other potential pathogens or arthropod-specific endosymbionts, but their significance for trombiculid biology and public health is unclear. Results: Ten chigger species were collected from rodents in southwestern Saudi Arabia. Chiggers were pooled according to species and screened for Orientia DNA by PCR. Two species (Microtrombicula muhaylensis and Pentidionis agamae) produced positive results for the htrA gene, although Ca. Orientia chuto DNA was confirmed by Sanger sequencing only in P. agamae. Metagenomic sequencing of three pools of P. agamae provided evidence for two other bacterial associates: a spirochaete and a Wolbachia symbiont. Phylogenetic analysis of 16S rRNA and multi-locus sequence typing genes placed the spirochaete in a clade of micromammal-associated Borrelia spp. that are widely-distributed globally with no known vector. For the Wolbachia symbiont, a genome assembly was obtained that allowed phylogenetic localisation in a novel, divergent clade. Cytochrome c oxidase I (COI) barcodes for Saudi Arabian chiggers enabled comparisons with global chigger diversity, revealing several cases of discordance with classical taxonomy. Complete mitogenome assemblies were obtained for the three P. agamae pools and almost 50 SNPs were identified, despite a common geographic origin. Conclusions: P. agamae was identified as a potential vector of Ca. Orientia chuto on the Arabian Peninsula. The detection of an unusual Borrelia sp. and a divergent Wolbachia symbiont in P. agamae indicated links with chigger microbiomes in other parts of the world, while COI barcoding and mitogenomic analyses greatly extended our understanding of inter- and intraspecific relationships in trombiculid mites. [ABSTRACT FROM AUTHOR]

Dinoflagellates are ecologically important and essential to corals and other cnidarians as phytosymbionts, but their photosystems had been underexplored. Recently, photosystem I (PSI) of dinoflagellate Symbiodinium sp. was structurally characterized using cryo-Electron Microscopy (cryo-EM). These analyses revealed a distinct organization of the PSI supercomplex, including two previously unidentified subunits, PsaT and PsaU, and shed light on interactions between light harvesting antenna proteins and the PSI core. These results have implications with respect to the evolution of dinoflagellates and their association with cnidarians. [ABSTRACT FROM AUTHOR]

Ocean alkalinity enhancement (OAE), one of the marine carbon dioxide removal strategies, is gaining importance in its role towards alleviating the consequences of climate change as well as mitigating against ocean acidification (OA). OAE is based on adding alkalinity to open-ocean and coastal marine systems through a variety of different approaches, which raises carbonate chemistry parameters (such as pH, total alkalinity, aragonite saturation state), and enhances the uptake of carbon dioxide (CO2) from the atmosphere. There are large uncertainties in both short- and long-term outcomes related to potential environmental impacts, which would ultimately decide on the success of OAE as a climate strategy. This paper represents a meta-analyses effort, leveraging on the OA studies, data, observed patterns and generalizable responses. We propose a conceptual framework of categorized responses that are predicted under OAE implementation. The synthesis was done using raw experimental OA data based on 96 collected studies, capturing the responses of eleven biological groups (coralline algae, corals, dinoflagellates, mollusks, gastropods, pteropods, coccolithophores, annelids, crustacean, echinoderms, and foraminifera), using regression analyses to predict biological responses and thresholds to NaOH or Na2CO3 concentrations. Predicted responses were categorized into six different categories (linear positive and negative, threshold positive and negative, parabolic and neutral) to delineate species- and group-specific responders: 40 % of species are predicted to respond positively (N=38), 20 % of species negatively (N=20), and 40 % (N=38) were found to demonstrate a neutral response upon alkalinity addition. For negatively impacted species, biological thresholds corresponding to 10 to 500 µmol/kg NaOH addition were found, occurring at much lower values than previously expected. Such lower threshold values represent realistic conditions related to OAE field deployments but contrast with the conditions where current OAE lab experiments are conducted. We thus explicitly emphasize the importance of including much lower additions of alkalinity in experimental trials to realistically evaluate in situ biological responses. Due to practicality and high correlation with Ωar, we propose using the TA:DIC ratio as a helpful proxy to explore regional applications and biological response to OAE. The ultimate goal of the study is to provide a framework that can serve as a tool for predicting biological responses and thresholds to delineate OAE risks, guide and prioritize future OAE biological research and regional OAE monitoring efforts. With 60 % of species showing non-neutral response, a precautionary approach for OAE implementation is warranted, identifying the conditions where potential negative ecological outcomes could happen, which is key for scaling up while also avoiding potential risks. [ABSTRACT FROM AUTHOR]

Rhizopus microsporus is an example of a fungal holobiont. Strains of this species can harbor bacterial and viral endosymbionts inherited by the next generation. These microbial allies increase pathogenicity and defense and control asexual and sexual reproduction. Rhizopus microsporus is an example of a fungal holobiont, harboring bacterial and viral endosymbionts. This Perspective article discusses how these microbial allies increase pathogenicity and defense and control asexual and sexual reproduction in the fungus. [ABSTRACT FROM AUTHOR]

Coral reef ecosystems are now commonly affected by major climate and disease disturbances. Disturbance impacts are typically recorded using reef benthic cover, but this may be less reflective of other ecosystem processes. To explore the potential for reef water‐based disturbance indicators, we conducted a 7‐year time series on US Virgin Island reefs where we examined benthic cover and reef water nutrients and microorganisms from 2016 to 2022, which included two major disturbances: hurricanes Irma and Maria in 2017 and the stony coral tissue loss disease outbreak starting in 2020. The disease outbreak coincided with the largest changes in the benthic habitat, with increases in the percent cover of turf algae and Ramicrusta, an invasive alga. While sampling timepoint contributed most to changes in reef water nutrient composition and microbial community beta diversity, both disturbances led to increases in ammonium concentration, a mechanism likely contributing to observed microbial community shifts. We identified 10 microbial taxa that were sensitive and predictive of increasing ammonium concentration. This included the decline of the oligotrophic and photoautotrophic Prochlorococcus and the enrichment of heterotrophic taxa. As disturbances impact reefs, the changing nutrient and microbial regimes may foster a type of microbialization, a process that hastens reef degradation. [ABSTRACT FROM AUTHOR]

Corals engage in symbioses with micro‐organisms that provide nutrients and protect the host. Where the prokaryotic microbes perform their symbiotic functions within a coral is, however, poorly understood. Here, we studied the tissue‐specific microbiota of the coral Corallium rubrum by dissecting its tissues from the skeleton and separating the white polyps from the red‐coloured coenenchyme, followed by 16S rRNA gene metabarcoding of the three fractions. Dissection was facilitated by incubating coral fragments in RNAlater, which caused tissues to detach from the skeleton. Our results show compartmentalisation of the microbiota. Specifically, Endozoicomonas, Parcubacteria and a Gammaproteobacteria were primarily located in polyps, whereas Nitrincolaceae and one Spirochaeta phylotype were found mainly in the coenenchyme. The skeleton‐associated microbiota was distinct from the microbiota in the tissues. Given the difference in tissue colour and microbiota of the polyps and coenenchyme, we analysed the microbiota of three colormorphs of C. rubrum (red, pink, white), finding that the main difference was a very low abundance of Spirochaeta in white colormorphs. While the functions of C. rubrum's symbionts are unknown, their localisation within the colony suggests that microhabitats exist, and the presence of Spirochaeta appears to be linked to the colour of C. rubrum. [ABSTRACT FROM AUTHOR]

Vibrio species are prevalent in ocean ecosystems, particularly Vibrio coralliilyticus, and pose a threat to corals and other marine organisms under global warming conditions. While microbiota manipulation is considered for coral disease management, understanding the role of commensal bacteria in stress resilience remains limited. Here, a single bacterial species (Ruegeria profundi) rather than a consortium of native was used to combat pathogenic V. coralliilyticus and protect corals from bleaching. R. profundi showed therapeutic activity in vivo, preventing a significant reduction in bacterial diversity in bleached corals. Notably, the structure of the bacterial community differed significantly among all the groups. In addition, compared with the bleached corals caused by V. coralliilyticus, the network analysis revealed that complex interactions and positive correlations in the bacterial community of the R. profundi protected non-bleached corals, indicating R. profundi's role in fostering synergistic associations. Many genera of bacteria significantly increased in abundance during V. coralliilyticus infection, including Vibrio, Alteromonas, Amphritea, and Nautella, contributing to the pathogenicity of the bacterial community. However, R. profundi effectively countered the proliferation of these genera, promoting potential probiotic Endozoicomonas and other taxa, while reducing the abundance of betaine lipids and the type VI section system of the bacterial community. These changes ultimately influenced the interactive relationships among symbionts and demonstrated that probiotic R. profundi intervention can modulate coral-associated bacterial community, alleviate pathogenic-induced dysbiosis, and preserve coral health. These findings elucidated the relationship between the behavior of the coral-associated bacterial community and the occurrence of pathological coral bleaching. IMPORTANCE Changes in the global climate and marine environment can influence coral host and pathogen repartition which refers to an increased likelihood of pathogen infection in hosts. The risk of Vibrio coralliilyticus-induced coral disease is significantly heightened, primarily due to its thermos-dependent expression of virulent and populations. This study investigates how coral-associated bacterial communities respond to bleaching induced by V. coralliilyticus. Our findings demonstrate that Ruegeria profundi exhibits clear evidence of defense against pathogenic bacterial infection, contributing to the maintenance of host health and symbiont homeostasis. This observation suggests that bacterial pathogens could cause dysbiosis in coral holobionts. Probiotic bacteria display an essential capability in restructuring and manipulating coral-associated bacterial communities. This restructuring effectively reduces bacterial community virulence and enhances the pathogenic resistance of holobionts. The study provides valuable insights into the correlation between the health status of corals and how coral-associated bacterial communities may respond to both pathogens and probiotics. [ABSTRACT FROM AUTHOR]

The thermal bleaching percentage of coral holobionts shows inte rspecific differences under heat-stress conditions, which are closely related to the coral-associated microbiome. However, the ecological effects of community dynamics and interactions between Symbiodiniaceae and fungi on coral thermal bleaching susceptibility remain unclear. In this study, we analyzed the diversity, community structure, functions, and potential interaction of Symbiodiniaceae and fungi among 18 coral species from a high thermal bleaching risk atoll using next-generation sequencing. The results showed that heat-tolerant C3u sub-clade and Durusdinium dominated the Symbiodiniaceae community of corals and that there were no core amplicon sequence variants in the coral-associated fungal community. Fungal richness and the abundance of confirm ed functional animal-plant pathogens were significantly positively correlated with the coral thermal bleaching percentage. Fungal indicators, including Didymellaceae, Chaetomiaceae, Schizophyllum, and Colletotrichum, were identified in corals. Each coral species had a complex Symbiodiniaceae-fungi interaction network (SFIN), which was driven by the dominant Symbiodiniaceae sub-clades. The SFINs of coral holobionts with low thermal bleaching susceptibility exhibited low complexity and high betweenness centrality. These results indicate that the extra heat tolerance of coral in Huangyan Island may be linked to the high abundance of heat-tolerant Symbiodiniaceae. Fungal communities have high interspecific flexibility, and the increase of fungal diversity and pathogen abundance was correlated with higher thermal bleaching susceptibility of corals. Moreover, fungal indicators were associated with the degrees of coral thermal bleaching susceptibility, including both high and intermediate levels. The topological properties of SFINs suggest that heat-tolerant coral have limited fungal parasitism and strong microbial network resilience. IMPORTANCE Global warming and enhanced marine heatwaves have led to a rapid decline in coral reef ecosystems worldwide. Several studies have focused on the impact of coral-associated microbiomes on thermal bleaching susceptibility in corals; however, the ecological functions and interactions between Symbiodiniaceae and fungi remain unclear. We investigated the microbiome dynamics and potential interactions of Symbiodiniaceae and fungi among 18 coral species in Huangyan Island. Our study found that the Symbiodiniaceae community of corals was mainly composed of heattolerant C3u sub-clade and Durusdinium. The increase in fungal diversity and pathogen abundance has close associations with higher coral thermal bleaching susceptibility. We first constructed an interaction network between Symbiodiniaceae and fungi in corals, which indicated that restricting fungal parasitism and strong interaction network resilience would promote heat acclimatization of corals. Accordingly, this study provides insights into the role of microorganisms and their interaction as drivers of inte rspecific differences in coral thermal bleaching. [ABSTRACT FROM AUTHOR]

Photosymbiosis evolved recurrently within the tree of life. Oxygen could have provided the primary selection pressure for photosymbiont acquisition. Host recognition and immunity are involved in photosymbiont maintenance. Intracellular pathogens can trigger photosymbiont maintenance. Genetics will open up the analysis of the cellular mechanisms of photosymbiont maintenance. Oxygenic photosynthesis evolved in cyanobacteria around 3.2 giga-annum (Ga) ago and was acquired by eukaryotes starting around 1.8 Ga ago by endosymbiosis. Photosymbiosis results either from integration of a photosynthetic bacteria by heterotrophic eukaryotes (primary photosymbiosis) or by successive integration of photosymbiotic eukaryotes by heterotrophic eukaryotes (secondary photosymbiosis). Primary endosymbiosis is thought to have been a rare event, whereas secondary and higher-order photosymbiosis evolved multiple times independently in different taxa. Despite its recurrent evolution, the molecular and cellular mechanisms underlying photosymbiosis are unknown. In this opinion, we discuss the primary events leading to the establishment of photosymbiosis, and we present recent research suggesting that, in some cases, domestication occurred instead of symbiosis, and how oxygen and host immunity can be involved in symbiont maintenance. [ABSTRACT FROM AUTHOR]

Establishment of the coral–algal symbiosis begins during early ontogeny when juveniles acquire a mix of algae from their environment that often differs from the adults' algal assemblages. Despite the importance of the type of Symbiodiniaceae to this symbiosis, it is largely unknown how coral host identity and environment affect symbiosis establishment and is affected by the genetic composition of the symbionts. Here, we reciprocally transplanted planulae of the octocoral Rhytisma fulvum (Forskål, 1775) across depths and monitored the algal assemblages in the developing juveniles for 11 months. We then compared these to adult assemblages using ITS2 metabarcoding. Juveniles were consistently dominated by Symbiodinium, in addition to multiple Cladocopium species, which shifted in dominance with the juvenile age but maintained high similarity across depths. The type of Symbiodiniaceae environmentally available thus likely contributes to the algal symbionts that are initially acquired, while host identity may play a significant role in selecting for symbionts that are maintained during juvenile development. [ABSTRACT FROM AUTHOR]

Introduction: In the upside-down jellyfish, Cassiopea xamachana (Cnidaria: Scyphozoa), the establishment of photosymbiosis with dinoflagellates (family Symbiodiniaceae) is necessary for the sessile polyp to undergo metamorphosis (strobilation) into a free-swimming adult. C. xamachana has the capacity to associate with a wide variety of dinoflagellate species and representatives of divergent genera. While some studies have looked at the successful induction of symbiosis, none to date have examined the lasting effect of diverse symbiont taxa on host survivorship and development, which is needed to assess the fitness costs of such symbioses. Methods: Our study exposes C. xamachana polyps to 22 different cultured Symbiodinaceae strains representing 13 species from 5 genera. We analyzed the time to strobilation, the number of ephyra (juvenile medusa) produced, and the proportion of ephyra that died prematurely. Results: Here we show that C. xamachana strobilation can be induced by nearly each symbiodinacean strain we tested, with the exception of free-living species (i.e., unknown to establish symbiosis with any other marine host). Additionally, ephyrae did not display morphological variation or survivorship differences with varying symbionts. However, we observed intraspecific variation in time to induce strobilation with different cultured dinoflagellate strains. Discussion: This work expands the known symbiont species that can form stable mutualisms with C. xamachana, primarily in the genera Symbiodinium and Breviolum. Additionally, we provide evidence of differences in ability of cultured symbiodiniaceans to establish symbiosis with a host, which suggests population-level differences in dinoflagellate cultures impact their symbiosis success. By utilizing an animal like C. xamachana with flexible symbiont uptake, we are able to explore how symbiont diversity can influence the timing and success of symbiosis-driven development. [ABSTRACT FROM AUTHOR]

The genus Dendroctonus is a Holarctic taxon composed of 21 nominal species; some of these species are well known in the world as disturbance agents of forest ecosystems. Under the bark of the host tree, these insects are involved in complex and dynamic associations with phoretic ectosymbiotic and endosymbiotic communities. Unlike filamentous fungi and bacteria, the ecological role of yeasts in the bark beetle holobiont is poorly understood, though yeasts were the first group to be recorded as microbial symbionts of these beetles. Our aim was characterize and compare the gut fungal assemblages associated to 14 species of Dendroctonus using the internal transcribed spacer 2 (ITS2) region. A total of 615,542 sequences were recovered yielding 248 fungal amplicon sequence variants (ASVs). The fungal diversity was represented by 4 phyla, 16 classes, 34 orders, 54 families, and 71 genera with different relative abundances among Dendroctonus species. The α-diversity consisted of 32 genera of yeasts and 39 genera of filamentous fungi. An analysis of β-diversity indicated differences in the composition of the gut fungal assemblages among bark beetle species, with differences in species and phylogenetic diversity. A common core mycobiome was recognized at the genus level, integrated mainly by Candida present in all bark beetles, Nakazawaea, Cladosporium, Ogataea, and Yamadazyma. The bipartite networks confirmed that these fungal genera showed a strong association between beetle species and dominant fungi, which are key to maintaining the structure and stability of the fungal community. The functional variation in the trophic structure was identified among libraries and species, with pathotroph-saprotroph-symbiotroph represented at the highest frequency, followed by saprotroph-symbiotroph, and saprotroph only. The overall network suggested that yeast and fungal ASVs in the gut of these beetles showed positive and negative associations among them. This study outlines a mycobiome associated with Dendroctonus nutrition and provides a starting point for future in vitro and omics approaches addressing potential ecological functions and interactions among fungal assemblages and beetle hosts. [ABSTRACT FROM AUTHOR]

Symbiodinium are the photosynthetic endosymbionts for corals and play a vital role in supplying their coral hosts with photosynthetic products, forming the nutritional foundation for high-yield coral reef ecosystems. Here, we determine the cryo-electron microscopy structure of Symbiodinium photosystem I (PSI) supercomplex with a PSI core composed of 13 subunits including 2 previously unidentified subunits, PsaT and PsaU, as well as 13 peridinin-Chl a/c-binding light-harvesting antenna proteins (AcpPCIs). The PSI–AcpPCI supercomplex exhibits distinctive structural features compared to their red lineage counterparts, including extended termini of PsaD/E/I/J/L/M/R and AcpPCI-1/3/5/7/8/11 subunits, conformational changes in the surface loops of PsaA and PsaB subunits, facilitating the association between the PSI core and peripheral antennae. Structural analysis and computational calculation of excitation energy transfer rates unravel specific pigment networks in Symbiodinium PSI–AcpPCI for efficient excitation energy transfer. Overall, this study provides a structural basis for deciphering the mechanisms governing light harvesting and energy transfer in Symbiodinium PSI–AcpPCI supercomplexes adapted to their symbiotic ecosystem, as well as insights into the evolutionary diversity of PSI–LHCI among various photosynthetic organisms. Here the authors determine the cryoEM structure of Symbiodinium photosystem I, revealing a distinct architecture and pigment network of this light-harvesting supercomplex. [ABSTRACT FROM AUTHOR]

Moss-cyanobacteria symbioses were proposed to be based on nutrient exchange, with hosts providing C and S while bacteria provide N, but we still lack understanding of the underlying molecular mechanisms of their interactions. We investigated how contact between the ubiquitous moss Hylocomium splendens and its cyanobiont affects nutrient-related gene expression of both partners. We isolated a cyanobacterium from H. splendens and co-incubated it with washed H. splendens shoots. Cyanobacterium and moss were also incubated separately. After 1 week, we performed acetylene reduction assays to estimate N2 fixation and RNAseq to evaluate metatranscriptomes. Genes related to N2 fixation and the biosynthesis of several amino acids were up-regulated in the cyanobiont when hosted by the moss. However, S-uptake and the biosynthesis of the S-containing amino acids methionine and cysteine were down-regulated in the cyanobiont while the degradation of selenocysteine was up-regulated. In contrast, the number of differentially expressed genes in the moss was much lower, and almost no transcripts related to nutrient metabolism were affected. It is possible that, at least during the early stage of this symbiosis, the cyanobiont receives few if any nutrients from the host in return for N, suggesting that moss–cyanobacteria symbioses encompass relationships that are more plastic than a constant mutualist flow of nutrients. [ABSTRACT FROM AUTHOR]

Seagrasses, corals, marsh plants, kelps, and mangroves support valuable coastal ecosystems but are threatened by environmental stressors. The need to manage these foundation taxa has spurred more than a decade of study on the relationship between genetic diversity and function or stability. We synthesized this literature base (129 relevant publications) and found more reported instances of neutral to positive relationships between genetic diversity and function than negative. However, much of the scientific understanding is based on the response of three genera and from unreplicated observational studies that correlate genetic diversity to measured response variables. When a disturbance was present, the studies often lacked controls or baseline data. Only 5.5% of the studies robustly tested for stability. These shortcomings preclude a rigorous evaluation of whether more genetically diverse foundation populations increase stability and hinder the use of genetics-based conservation strategies. Future studies should be focused on diverse species and ecosystem-level impacts using manipulative designs. [ABSTRACT FROM AUTHOR]

In the marine environment, the symbiotic relationship between Symbiodinium and corals plays a pivotal role in coral growth and development. Against the backdrop of widespread coral bleaching due to the global climate change, the facile and efficient separation and enrichment of different strains of Symbiodinium hold significant importance for studying coral bleaching. This paper aims to report a platform that integrates dielectrophoretic and inertial forces for the separation and enrichment of Symbiodinium, comprising two modular components: a separation module and an enrichment module. Within the separation module, distinct strains of Symbiodinium undergo preliminary stratification in a contraction–expansion microchannel under the influence of inertial forces. Dielectrophoretic forces generated by the indium tin oxide electrodes divert them toward different outlets, achieving separation. In the enrichment module, the Symbiodinium collected from outlets is rapidly focused through a contraction–expansion microchannel and high-purity samples are concentrated through a single outlet. Evaluating separation efficiency is based on the purity of collected Symbiodinium at the outlet under three different flow rates: 13, 16, and 19 μl/min, while the concentration of enriched Symbiodinium at 100, 200, 300, and 400 μl/min flow rates evaluates the effectiveness of the enrichment process. The experimental results demonstrate a separation purity of approximately 90% and an enrichment factor of around 5.5. The platform holds promise for further applications in the selection and targeted enrichment of high-quality coral symbiotic algae, providing essential research foundations for the conservation of coral ecosystems. [ABSTRACT FROM AUTHOR]

Endosymbiosis is a widespread and important phenomenon requiring diverse model systems. Ciliates are a widespread group of protists that often form symbioses with diverse microorganisms. Endosymbioses between the ciliate Euplotes and heritable bacterial symbionts are common in nature, and four essential symbionts were described: Polynucleobacter necessarius, “Candidatus Protistobacter heckmanni,” “Ca. Devosia symbiotica,” and “Ca. Devosia euplotis.” Among them, only the genus Polynucleobacter comprises very close free-living and symbiotic representatives, which makes it an excellent model for investigating symbiont replacements and recent symbioses. In this article, we characterized a novel endosymbiont inhabiting the cytoplasm of Euplotes octocarinatus and found that it is a close relative of the free-living bacterium Fluviibacter phosphoraccumulans (Betaproteobacteria and Rhodocyclales). We present the complete genome sequence and annotation of the symbiotic Fluviibacter. Comparative analyses indicate that the genome of symbiotic Fluviibacter is small in size and rich in pseudogenes when compared with free-living strains, which seems to fit the prediction for recently established endosymbionts undergoing genome erosion. Further comparative analysis revealed reduced metabolic capacities in symbiotic Fluviibacter, which implies that the symbiont relies on the host Euplotes for carbon sources, organic nitrogen and sulfur, and some cofactors. We also estimated substitution rates between symbiotic and free-living Fluviibacter pairs for 233 genes; the results showed that symbiotic Fluviibacter displays higher dN/dS mean value than free-living relatives, which suggested that genetic drift is the main driving force behind molecular evolution in endosymbionts. IMPORTANCE In the long history of symbiosis research, most studies focused mainly on organelles or bacteria within multicellular hosts. The single-celled protists receive little attention despite harboring an immense diversity of symbiotic associations with bacteria and archaea. One subgroup of the ciliate Euplotes species is strictly dependent on essential symbionts for survival and has emerged as a valuable model for understanding symbiont replacements and recent symbioses. However, almost all of our knowledge about the evolution and functions of Euplotes symbioses comes from the Euplotes– Polynucleobacter system. In this article, we report a novel essential symbiont, which also has very close free-living relatives. Genome analysis indicated that it is a recently established endosymbiont undergoing genome erosion and relies on the Euplotes host for many essential molecules. Our results provide support for the notion that essential symbionts of the ciliate Euplotes evolve from free-living progenitors in the natural water environment. [ABSTRACT FROM AUTHOR]

Mountain pine beetles (MPBs) pose a substantial threat to North American pine forests, causing extensive tree mortality over large areas. Their tree‐killing ability is closely linked to mass aggregation on host trees triggered via pheromones and dependence on their symbiotic fungi. However, the influence of a changing climate on the biology of MPBs and their co‐evolved interactions with their fungal symbionts remains uncertain. To investigate this, male and female pairs of beetles were introduced into freshly cut logs from lodgepole pine trees and placed in controlled climate chambers with manipulated environmental conditions, including two levels of CO2 (ambient vs. 1000 ppm), O3 (ambient vs. 100 ppb) and humidity (33% vs. 65%). The beetle‐infested logs were left in these chambers for 1 month and then returned to ambient conditions until brood emergence. Emerging broods were collected for further analysis. Additionally, three species of fungal symbionts (Grosmannia clavigera, Ophiostoma montium and Leptographium longiclavatum) were subjected to the same CO2, O3 and humidity conditions for 5 days. Lower humidity promoted MPB reproduction and fungal growth. Elevated CO2 accelerated larval growth and emergence while improving brood pheromone production. Elevated O3 had a negative impact on MPB reproduction and brood fitness while improving its immune responses to an entomopathogenic fungus (Beauveria bassiana). It also inhibited fungal growth and reproduction, whereas elevated CO2 had varied (positive or negative) effects on fungal growth and ergosterol (proxy to fungal mass) production depending on the fungal species. Together, these findings suggest that climate change can potentially alter the interactions between MPBs and their fungal symbionts, highlighting the importance of understanding how climate change affects forest pests and their symbiotic relationships to develop effective management strategies in the future. [ABSTRACT FROM AUTHOR]

Advances in our understanding of symbiotic stability have demonstrated that microorganisms are key to understanding the homeostasis of obligate symbioses. Fungus-gardening ants are excellent model systems for exploring how microorganisms may be involved in symbiotic homeostasis as the host and symbionts are macroscopic and can be easily experimentally manipulated. Their coevolutionary history has been well-studied; examinations of which have depicted broad clade-to-clade specificity between the ants and fungus. Few studies hitherto have addressed the roles of microbiomes in stabilizing these associations. Here, we quantified changes in microbiome structure as a result of experimentally induced horizontal exchange of symbionts. This was done by performing cross-fostering experiments forcing ants to grow novel fungi and comparing known temporally unstable (undergoing dysbiosis) and stable combinations. We found that fungus-gardening ants alter their unstable, novel garden microbiomes into configurations like those found in native gardens. Patterns of dysbiosis/symbiosis appear to be predictable in that two related species with similar specificity patterns also show similar patterns of microbial change, whereas a species with more relaxed specificity does not show such microbiome change or restructuring when growing different fungi. It appears that clade-to-clade specificity patterns are the outcomes of community-level interactions that promote stability or cause symbiotic collapse. [ABSTRACT FROM AUTHOR]

Increased stress on coastal ecosystems, such as coral reefs, seagrasses, kelp forests, and other habitats, can make them shift toward degraded, often algae-dominated or barren communities. This has already occurred in many places around the world, calling for new approaches to identify where such regime shifts may be triggered. Theoretical work predicts that the spatial structure of habitat-forming species should exhibit changes prior to regime shifts, such as an increase in spatial autocorrelation. However, extending this theory to marine systems requires theoretical models connecting field-supported ecological mechanisms to data and spatial patterns at relevant scales. To do so, we built a spatially explicit model of subtropical coral communities based on experiments and long-term datasets from Rapa Nui (Easter Island, Chile), to test whether spatial indicators could signal upcoming regime shifts in coral communities. Spatial indicators anticipated degradation of coral communities following increases in frequency of bleaching events or coral mortality. However, they were generally unable to signal shifts that followed herbivore loss, a widespread and well-researched source of degradation, likely because herbivory, despite being critical for the maintenance of corals, had comparatively little effect on their self-organization. Informative trends were found under both equilibrium and nonequilibrium conditions but were determined by the type of direct neighbor interactions between corals, which remain relatively poorly documented. These inconsistencies show that while this approach is promising, its application to marine systems will require detailed information about the type of stressor and filling current gaps in our knowledge of interactions at play in coral communities. [ABSTRACT FROM AUTHOR]

Tropical western Atlantic reefs have gradually shifted from being dominated by corals to being mainly covered by macroalgae. The mass-mortality of the sea urchin Diadema antillarum in the 80s and the slow to non-existent recovery exacerbated this shift. Chemical cues associated with these reefs are expected to have shifted too with potential negative effects on larval recruitment, possibly limiting recovery of important species like D. antillarum. In this study, we tested the effects of naturally derived biofilm and macroalgae species native to Caribbean coral reefs on the settlement rate of cultured D. antillarum larvae in two separate experiments. Crustose coralline algae (CCA) were included in both experiments, making it possible to compare settlement rates from both experiments. A biofilm of one week old yielded significantly lower settlement rates compared to two, four, and six weeks old biofilm and the highest settlement rate was found for CCA with over 62% of total larvae. All six tested macroalgae species resulted in settled larvae, with little significant difference between algal species, partly due to a high variation in settlement rates within treatments. Sargassum fluitans induced the highest settlement rate with 33%, which was not significantly different from CCA with 29%. We conclude that dominant macroalgae species likely to be encountered by D. antillarum on shifted reefs are no major constraint to settlement. Our findings increase the understanding of alternative stable state settlement dynamics for a keystone coral reef herbivore. [ABSTRACT FROM AUTHOR]

Context. Root symbionts affect forage production by influencing host plant growth, but their specific effects on canopy intercepted photosynthetically active radiation (IPAR) and its conversion to plant biomass have not been investigated. Aims. We evaluated the extent to which changes in plant biomass resulting from arbuscular mycorrhizal fungi (AMF) and rhizobia can be explained by alterations in IPAR and aboveground and total radiation-use efficiency (RUE: the ratio between shoot or total biomass and IPAR). Methods. Under controlled greenhouse conditions, we evaluated single and dual inoculation effects of AMF and rhizobia on the forage legume white clover (Trifolium repens L.). Experimental units comprised canopies created in trays (50 cm by 34 cm by 13 cm deep). Key results. On average, AMF inoculation increased IPAR by 43%, owing to greater leaf area and density, and decreased total RUE by 30%. Aboveground RUE was lower in AMF-inoculated plants without rhizobial inoculation, despite their higher leaf phosphorus status and greenness during the vegetative and reproductive stages, respectively. Rhizobial inoculation reduced the negative effect of AMF inoculation on aboveground RUE. Conclusions. Both AMF and rhizobia alter white clover structure and function at canopy level. These variations may not be detected if the analysis considers only the impact of root symbionts on plant biomass. Implications. These findings offer valuable insights into the intricate interactions between root symbionts and canopy-level processes, providing a basis for further research at agricultural scale. [ABSTRACT FROM AUTHOR]

Space can be limited in reef ecosystems leading to competitive interactions among sessile organisms. Some competitive mechanisms can require physical contact while others operate with proximity between organisms. We investigated how the scleractinian coral Siderastrea stellata and the hydrocoral Millepora alcicornis respond to physical contact and proximity to the macroalga Dictyopteris delicatula and the zoanthid Palythoa caribaeorum, common pairs of interactions in Southwestern Atlantic reefs in Northeast Brazil. We held two colonies of the same species within the same tank, one in physical contact and the other within 5 cm of the competitor for four days with macroalgae and three days with the zoanthid. We monitored the corals for 26 days taking photographs and measuring their photosynthetic efficiency (PE) at the point of contact and on the side where competitors were in proximity. Corals were only affected when physically contacted by the competitors, with the macroalga causing a slight damage on M. alcicornis and almost no effect on S. stellata. Contacts with P. caribaeorum reduced the PE and caused tissue discoloration in both corals. M. alcicornis recovered after 26 days but the contacted areas of S. stellata remained discolored and with low PE. Macroalgae and zoanthids required physical contact to damage corals, with the zoanthid causing more damage than the macroalgae. These results suggest that if local and global stressors make corals weaker competitors (e.g. warming) or favor macroalgae and zoanthid growth (e.g. nutrients), corals could be replaced by either of these organisms affecting ecosystem structure and functioning. [ABSTRACT FROM AUTHOR]

Background: Plant microbiomes play crucial roles in nutrient cycling and plant growth, and are shaped by a complex interplay between plants, microbes, and the environment. The role of bacteria as mediators of the 400-million-year-old partnership between the majority of land plants and, arbuscular mycorrhizal (AM) fungi is still poorly understood. Here, we test whether AM hyphae-associated bacteria influence the success of the AM symbiosis. Results: Using partitioned microcosms containing field soil, we discovered that AM hyphae and roots selectively assemble their own microbiome from the surrounding soil. In two independent experiments, we identified several bacterial genera, including Devosia, that are consistently enriched on AM hyphae. Subsequently, we isolated 144 pure bacterial isolates from a mycorrhiza-rich sample of extraradical hyphae and isolated Devosia sp. ZB163 as root and hyphal colonizer. We show that this AM-associated bacterium synergistically acts with mycorrhiza on the plant root to strongly promote plant growth, nitrogen uptake, and mycorrhization. Conclusions: Our results highlight that AM fungi do not function in isolation and that the plant-mycorrhiza symbiont can recruit beneficial bacteria that support the symbiosis. Aik4iJYbzAos1E2c5U4cFF Video Abstract [ABSTRACT FROM AUTHOR]