Endolithic fungi in marine ecosystems

The microbiome dynamics and interaction of endosymbiotic Symbiodiniaceae and fungi are associated with thermal bleaching susceptibility of coral holobionts

The thermal bleaching percentage of coral holobionts shows interspecific 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 confirmed 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.IMPORTANCEGlobal 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 heat-tolerant 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 interspecific differences in coral thermal bleaching.

Tubule system of earliest shells as a defense against increasing microbial attacks

The evolutionary mechanism behind the early Cambrian animal skeletonization was a complex and multifaceted process involving environmental, ecological, and biological factors. Predation pressure, oxygenation, and seawater chemistry change have frequently been proposed as the main drivers of this biological innovation, yet the selection pressures from microorganisms have been largely overlooked. Here we present evidence that calcareous shells of the earliest mollusks from the basal Cambrian (Fortunian Age, ca. 539-529 million years ago) of Mongolia developed advanced tubule systems that evolved primarily as a defensive strategy against extensive microbial attacks within a microbe-dominated marine ecosystem. These high-density tubules, comprising approximately 35% of shell volume, enable nascent mineralized mollusks to cope with increasing microbial bioerosion caused by boring endolithic cyanobacteria, and hence represent an innovation in shell calcification. Our finding demonstrates that enhanced microboring pressures played a significant role in shaping the calcification of the earliest mineralized mollusks during the Cambrian Explosion.

Searching for microbial contribution to micritization of shallow marine sediments

Micritization is an early diagenetic process that gradually alters primary carbonate sediment grains through cycles of dissolution and reprecipitation of microcrystalline calcite (micrite). Typically observed in modern shallow marine environments, micritic textures have been recognized as a vital component of storage and flow in hydrocarbon reservoirs, attracting scientific and economic interests. Due to their endolithic activity and the ability to promote nucleation and reprecipitation of carbonate crystals, microorganisms have progressively been shown to be key players in micritization, placing this process at the boundary between the geological and biological realms. However, published research is mainly based on geological and geochemical perspectives, overlooking the biological and ecological complexity of microbial communities of micritized sediments. In this paper, we summarize the state-of-the-art and research gaps in micritization from a microbial ecology perspective. Since a growing body of literature successfully applies in vitro and in situ 'fishing' strategies to unveil elusive microorganisms and expand our knowledge of microbial diversity, we encourage their application to the study of micritization. By employing these strategies in micritization research, we advocate promoting an interdisciplinary approach/perspective to identify and understand the overlooked/neglected microbial players and key pathways governing this phenomenon and their ecology/dynamics, reshaping our comprehension of this process.

An investigation of the inter and intra post-mortem microstructural change seen in an experimental series of pigs exposed to a marine environment

The identification of marine post-mortem microstructural change in human bone tissue is valuable in forensic casework as evidence of an individual's burial history. This study examined micro-tunneling in pig-bone tissue microstructure that had been submerged in a marine environment. The objective of the experiment was to assess total distribution of post-mortem microstructural change and degree of preservation within and between individual submerged pig skeletons. 14 juvenile pig carcasses were submerged in British Columbia at 92-300 m depths, between four to eight months. Seven pigs were individually submerged within caged platforms, seven were tied to open platforms. Six bones were selected from each carcass: first rib, radius, ulna, middle-rib, tibia, and femur. Two transverse thin sections were sampled at each bone mid-shaft (n = 148) and examined using circularly polarized transmitted light. The distribution of tunnels was assessed by measuring tunnel maximum ingress and diameter at 40 locations of the peripheral cortex. All element types were impacted by peripheral tunneling from the periosteum to the central cortex. Tunnels were observed as radiating, bifurcating with no remineralization boundary, isolated and in clusters. Tunnel diameters ranged between 2.00 μm and 12.8 μm, with a 3.7 μm mean. Ingress measurements ranged between 7.5 μm and 435.8 μm with a 93.0 μm mean. Distribution of post-mortem microstructural change across skeletal elements showed the averaged maximum ingress was deeper in the uncaged (99.6 μm), when compared to caged material (78.5 μm). The averaged tunnel ingress had statistically significant differences between uncaged and caged carcasses overall (p-value=0.02). Results of the study indicate microboring is present in marine submersed mammalian bone microstructure in as little as 134 days. This informs forensic investigators of the rate of skeletal destruction and of the narrow window for forensic recoveries, particularly in an enclosed environment. Furthermore, the presence of marine microboring in bone can assist forensic practitioners to histologically interpret the environmental history of a corpse.

Adaptation of the Endolithic Biome in Antarctic Volcanic Rocks

Endolithic microorganisms, ranging from microeukaryotes to bacteria and archaea, live within the cracks and crevices of rocks. Deception Island in Antarctica constitutes an extreme environment in which endoliths face environmental threats such as intense cold, lack of light in winter, high solar radiation in summer, and heat emitted as the result of volcanic eruptions. In addition, the endolithic biome is considered the harshest one on Earth, since it suffers added threats such as dryness or lack of nutrients. Even so, samples from this hostile environment, collected at various points throughout the island, hosted diverse and numerous microorganisms such as bacteria, fungi, diatoms, ciliates, flagellates and unicellular algae. These endoliths were first identified by Scanning Electron Microscopy (SEM). To understand the molecular mechanisms of adaptation of these endoliths to their environment, genomics techniques were used, and prokaryotic and eukaryotic microorganisms were identified by metabarcoding, sequencing the V3-V4 and V4-V5 regions of the 16S and 18S rRNA genes, respectively. Subsequently, the sequences were analyzed by bioinformatic methods that allow their metabolism to be deduced from the taxonomy. The results obtained concluded that some of these microorganisms have activated the biosynthesis routes of pigments such as prodigiosin or flavonoids. These adaptation studies also revealed that microorganisms defend themselves against environmental toxins by activating metabolic pathways for the degradation of compounds such as ethylbenzene, xylene and dioxins and for the biosynthesis of antioxidant molecules such as glutathione. Finally, these Antarctic endolithic microorganisms are of great interest in astrobiology since endolithic settings are environmentally analogous to the primitive Earth or the surfaces of extraterrestrial bodies.

An introduction to lesions and histology of scleractinian corals

Stony corals (Scleractinia) are in the Phylum Cnidaria (cnidae referring to various types of stinging cells). They may be solitary or colonial, but all secrete an external, supporting aragonite skeleton. Large, colonial members of this phylum are responsible for the accretion of coral reefs in tropical and subtropical waters that form the foundations of the most biodiverse marine ecosystems. Coral reefs worldwide, but particularly in the Caribbean, are experiencing unprecedented levels of disease, resulting in reef degradation. Most coral diseases remain poorly described and lack clear case definitions, while the etiologies and pathogenesis are even more elusive. This introductory guide is focused on reef-building corals and describes basic gross and microscopic lesions in these corals in order to serve as an invitation to other veterinary pathologists to play a critical role in defining and advancing the field of coral pathology.

A carbonate corrosion experiment at a marine methane seep: The role of aerobic methanotrophic bacteria

Methane seeps are typified by the formation of authigenic carbonates, many of which exhibit corrosion surfaces and secondary porosity believed to be caused by microbial carbonate dissolution. Aerobic methane oxidation and sulfur oxidation are two processes capable of inducing carbonate corrosion at methane seeps. Although the potential of aerobic methanotrophy to dissolve carbonate was confirmed in laboratory experiments, this process has not been studied in the environment to date. Here, we report on a carbonate corrosion experiment carried out in the REGAB Pockmark, Gabon-Congo-Angola passive margin, in which marble cubes were deployed for 2.5 years at two sites (CAB-B and CAB-C) with apparent active methane seepage and one site (CAB-D) without methane seepage. Marble cubes exposed to active seepage (experiment CAB-C) were found to be affected by a new type of microbioerosion. Based on 16S rRNA gene analysis, the biofilms adhering to the bioeroded marble mostly consisted of aerobic methanotrophic bacteria, predominantly belonging to the uncultured Hyd24-01 clade. The presence of abundant ¹³ C-depleted lipid biomarkers including fatty acids (n-C_16:1ω8c , n-C_18:1ω8c , n-C_16:1ω5t ), various 4-mono- and 4,4-dimethyl sterols, and diplopterol agrees with the dominance of aerobic methanotrophs in the CAB-C biofilms. Among the lipids of aerobic methanotrophs, the uncommon 4α-methylcholest-8(14)-en-3β,25-diol is interpreted to be a specific biomarker for the Hyd24-01 clade. The combination of textural, genetic, and organic geochemical evidence suggests that aerobic methanotrophs are the main drivers of carbonate dissolution observed in the CAB-C experiment at the REGAB pockmark.

Prokaryotic and eukaryotic microbial communities associated with coral species have high host specificity in the South China Sea

Reef-building corals are well known for their obligate association with Symbiodiniaceae, and an array of other microbes, including bacteria, fungi, and symbiotic algae (i.e., total microbiome), which together form the coral holobiont. The total microbiome plays an intricate part in maintaining the homeostasis of the coral holobiont and is closely associated with host health. However, the composition of the coral associated microbiome and interaction between its different members remains elusive because few analyses have bridged taxonomically disparate groups. This research gaps have prevented a holistic understanding of the total microbiome. Thus, to simultaneously characterize the bacterial, fungal and symbiotic algal communities associated with different coral species, and explore the relationship between these symbionts and coral health, healthy and bleached tissues from four coral species, Acropora muricata, Galaxea fascicularis, Platygyra daedalea, and Pavona explanulata, were collected from the Xisha Islands of the South China Sea. Using high throughput sequencing, a high degree of host-specificity was observed among bacterial, fungal, and algal groups across coral species. There were no obvious changes in the microbial community structure of apparently healthy and bleached corals, but host bleaching allowed colonization of the holobionts by diverse opportunistic microbes, resulting in a significant elevation in the α-diversity of microbial communities. In addition, co-occurrence analysis of the coral microbiota also identified more complex microbial interactions in bleached corals than in healthy ones. In summary, this study characterized the structure of coral-associated microbiomes across four coral species, and systematically studied microbiome differences between healthy and bleached corals. The findings improve our understanding of the heterogeneity of symbiotic microorganisms and the impact of coral's physiological status on its associated microbial communities composition.

The coral microbiome: towards an understanding of the molecular mechanisms of coral-microbiota interactions

Corals live in a complex, multipartite symbiosis with diverse microbes across kingdoms, some of which are implicated in vital functions, such as those related to resilience against climate change. However, knowledge gaps and technical challenges limit our understanding of the nature and functional significance of complex symbiotic relationships within corals. Here, we provide an overview of the complexity of the coral microbiome focusing on taxonomic diversity and functions of well-studied and cryptic microbes. Mining the coral literature indicate that while corals collectively harbour a third of all marine bacterial phyla, known bacterial symbionts and antagonists of corals represent a minute fraction of this diversity and that these taxa cluster into select genera, suggesting selective evolutionary mechanisms enabled these bacteria to gain a niche within the holobiont. Recent advances in coral microbiome research aimed at leveraging microbiome manipulation to increase coral's fitness to help mitigate heat stress-related mortality are discussed. Then, insights into the potential mechanisms through which microbiota can communicate with and modify host responses are examined by describing known recognition patterns, potential microbially derived coral epigenome effector proteins and coral gene regulation. Finally, the power of omics tools used to study corals are highlighted with emphasis on an integrated host-microbiota multiomics framework to understand the underlying mechanisms during symbiosis and climate change-driven dysbiosis.

Genomic view of the diversity and functional role of archaea and bacteria in the skeleton of the reef-building corals Porites lutea and Isopora palifera

At present, our knowledge on the compartmentalization of coral holobiont microbiomes is highly skewed toward the millimeter-thin coral tissue, leaving the diverse coral skeleton microbiome underexplored. Here, we present a genome-centric view of the skeleton of the reef-building corals Porites lutea and Isopora palifera, through a compendium of ∼400 high-quality bacterial and archaeal metagenome-assembled genomes (MAGs), spanning 34 phyla and 57 classes. Skeletal microbiomes harbored a diverse array of stress response genes, including dimethylsulfoniopropionate synthesis (dsyB) and metabolism (DMSP lyase). Furthermore, skeletal MAGs encoded an average of 22 ± 15 genes in P. lutea and 28 ± 23 in I. palifera with eukaryotic-like motifs thought to be involved in maintaining host association. We provide comprehensive insights into the putative functional role of the skeletal microbiome on key metabolic processes such as nitrogen fixation, dissimilatory and assimilatory nitrate, and sulfate reduction. Our study provides critical genomic resources for a better understanding of the coral skeletal microbiome and its role in holobiont functioning.

Coral growth anomalies, neoplasms, and tumors in the Anthropocene

One of the most widespread coral diseases linked to anthropogenic activities and recorded on reefs worldwide is characterized by anomalous growth formations in stony corals, referred to as coral growth anomalies (GAs). The biological functions of GA tissue include limited reproduction, reduced access to resources, and weakened ability to defend against predators. Transcriptomic analyses have revealed that, in some cases, disease progression can involve host genes related to oncogenesis, suggesting that the GA tissues may be malignant neoplasms such as those developed by vertebrates. The number of studies reporting the presence of GAs in common reef-forming species highlights the urgency of a thorough understanding of the pathology and causative factors of this disease and its parallels to higher organism malignant tissue growth. Here, we review the current state of knowledge on the etiology and holobiont features of GAs in reef-building corals.

Phosphorus biogeochemistry regulated by carbonates in soil

Phosphates are the dominant phosphorus (P) source on Earth. The phosphates govern available P in soil, or even the complete ecosystem. The common deficiency of available P in carbonate-enriched soils suggests the tight correlation between P and C biogeochemistry, although the two elements have diverse abundance in soil. The influences of carbonates on P cycle were reviewed in this study, via both abiotic and biotic pathways. The abiotic processes at geochemical scale include element release, transport, sorption, desorption, weathering, precipitation, etc. The sorption of P on carbonate and buffering ability of carbonates were particularly addressed. Biotic factors are ascribed to various microorganisms in soil. As the most active P pool in soil, microorganisms prefer to consume abundant P, and then accumulate it in their biomass. Carbonates, however, are usually utilized by microorganisms after conversion to organic C. Meanwhile, extracellular precipitation of Ca-P phases significantly regulates the transportation of P in/out the cells. Moreover, they boost and complexify both carbonates and P turnover in soil via bioweathering and biomineralization, i.e., the intense interactions between biosphere and lithosphere. Based on this review, we proposed that carbonates may negatively affect P supply in soil system. This comprehensive review regarding the regulation by carbonates on P biogeochemistry would shed a light on predicting long-term P availability influenced by C biogeochemistry.

A roadmap to understanding diversity and function of coral reef-associated fungi

Tropical coral reefs are hotspots of marine productivity, owing to the association of reef-building corals with endosymbiotic algae and metabolically diverse bacterial communities. However, the functional importance of fungi, well-known for their contribution to shaping terrestrial ecosystems and global nutrient cycles, remains underexplored on coral reefs. We here conceptualize how fungal functional traits may have facilitated the spread, diversification, and ecological adaptation of marine fungi on coral reefs. We propose that functions of reef-associated fungi may be diverse and go beyond their hitherto described roles of pathogens and bioeroders, including but not limited to reef-scale biogeochemical cycles and the structuring of coral-associated and environmental microbiomes via chemical mediation. Recent technological and conceptual advances will allow the elucidation of the physiological, ecological, and chemical contributions of understudied marine fungi to coral holobiont and reef ecosystem functioning and health and may help provide an outlook for reef management actions.

Exploring confocal laser scanning microscopy (CLSM) and fluorescence staining as a tool for imaging and quantifying traces of marine microbioerosion and their trace-making microendoliths

Microscopic organisms that penetrate calcareous structures by actively dissolving the carbonate matrix, namely microendoliths, have an important influence on the breakdown of marine carbonates. The study of these microorganisms and the bioerosion traces they produce is crucial for understanding the impact of their bioeroding activity on the carbonate recycling in environments under global climate change. Traditionally, either the extracted microendoliths were studied by conventional microscopy or their traces were investigated using scanning electron microscopy (SEM) of epoxy resin casts. A visualisation of the microendoliths in situ, that is within their complex microbioerosion structures, was previously limited to the laborious and time-consuming double-inclusion cast-embedding technique. Here, we assess the applicability of various fluorescence staining methods in combination with confocal laser scanning microscopy (CLSM) for the study of fungal microendoliths in situ in partly translucent mollusc shells. Among the tested methods, specific staining with dyes against the DNA (nuclei) of the trace making organisms turned out to be a useful and reproducible approach. Bright and clearly delineated fluorescence signals of microendolithic nuclei allow, for instance, a differentiation between abandoned and still populated microborings. Furthermore, infiltrating the microborings with fluorescently stained resin seems to be of great capability for the visualisation and quantification of microbioerosion structures in their original spatial orientation. Potential fields of application are rapid assessments of endolithic bio- and ichnodiversity and the quantification of the impact of microendoliths on the overall calcium carbonate turnover. The method can be applied after CLSM of the stained microendoliths and retains the opportunity for a subsequent investigation of epoxy casts with SEM. This allows a three-fold approach in studying microendoliths in the context of their microborings, thereby fostering the integration of biological and ichnological aspects of microbial bioerosion.

Foul-weather friends: Modelling thermal stress mitigation by symbiotic endolithic microbes in a changing environment

Temperature extremes are predicted to intensify with climate change. These extremes are rapidly emerging as a powerful driver of species distributional changes with the capacity to disrupt the functioning and provision of services of entire ecosystems, particularly when they challenge ecosystem engineers. The subsequent search for a robust framework to forecast the consequences of these changes mostly ignores within-species variation in thermal sensitivity. Such variation can be intrinsic, but can also reflect species interactions. Intertidal mussels are important ecosystem engineers that host symbiotic endoliths in their shells. These endoliths unexpectedly act as conditionally beneficial parasites that enhance the host's resistance to intense heat stress. To understand how this relationship may be altered under environmental change, we examined the conditions under which it becomes advantageous by reducing body temperature. We deployed biomimetic sensors (robomussels), built using shells of mussels (Mytilus galloprovincialis) that were or were not infested by endoliths, at nine European locations spanning a temperature gradient across 22°of latitude (Orkney, Scotland to the Algarve, Portugal). Daily wind speed and solar radiation explained the maximum variation in the difference in temperature between infested and non-infested robomussels; the largest difference occurred under low wind speed and high solar radiation. From the robomussel data, we inferred body temperature differences between infested and non-infested mussels during known heatwaves that induced mass mortality of the mussel Mytilus edulis along the coast of the English Channel in summer 2018 to quantify the thermal advantage of endolith infestation during temperature extremes. Under these conditions, endoliths provided thermal buffering of between 1.7°C and 4.8°C. Our results strongly suggest that sustainability of intertidal mussel beds will increasingly depend on the thermal buffering provided by endoliths. More generally, this work shows that biomimetic models indicate that within-species thermal sensitivity to global warming can be modulated by species interactions, using an intertidal host-symbiont relationship as an example.

Bioerosion ichnodiversity in barnacles from the Ross Sea, Antarctica

Breakdown of skeletal and lithic hard substrates by organisms, a process referred to as bioerosion, is part of the global carbon cycle and receives increased attention, but little is known about bioerosion in polar environments. Here, we study bioerosion traces (addressed by their respective ichnotaxa) recorded in the barnacle Bathylasma corolliforme from the Ross Sea, Antarctica. Traces were visualized via scanning electron microscopy of epoxy casts prepared with the vacuum cast-embedding technique. In 50 samples from shallow 37 m to bathyal 1680 m water depths, 16 different bioerosion traces were found, classified into microborings presumably produced by cyanobacteria (1), chlorophytes (1), fungi (9), foraminifera (1), unknown organotrophs (5), and macroborings produced by cirripeds (1). Statistical ichnodiversity analysis resulted in a significant (p = 0.001) ANOSIM with moderate differences (R = 0.5) between microbioerosion trace assemblages at different water depths and revealed two main clusters (NMDS, SIMPROF) corresponding to the photic and aphotic stations. A comparison between this study and a corresponding study from the Svalbard archipelago, Arctic Ocean, shows that the ichnodiversity in calcareous barnacle skeletons is similar in polar waters of both hemispheres. This includes several ichnotaxa that are indicative for cool- to cold-water environments, such as Flagrichnus baiulus and Saccomorpha guttulata. Nine of the investigated ichnotaxa occur in both polar regions and seven ichnotaxa show an extensive bathymetrical range down to the deep sea at bathyal 1680 m water depth.

Ectoparasites reduce scope for growth in a rocky-shore mussel (Perna perna) by raising maintenance costs

Endolithic cyanobacteria are ubiquitous colonisers of organic and inorganic carbonate substrata that frequently attack the shells of mussels, eroding the shell to extract carbon, often with population infestation rates of >80%. This reduces host physiological condition and ultimately leads to shell collapse and mortality, compromising the services provided by these important ecosystem engineers. While the ecological implications of this and similar interactions have been examined, our understanding of the underlying mechanisms driving the physiological responses of infested hosts remains limited. Using field and laboratory experiments, we assessed the energetic costs of cyanobacterial infestation to the intertidal brown mussel (Perna perna). In the field we found that growth (measured as both increase in shell length and rate of biomineralization) and reproductive potential of clean mussels are greater than those of infested individuals. To explore the mechanisms behind these effects, we compared the energy allocation of parasite-free and infested mussels using the scope for growth (SFG) framework. This revealed a lower SFG in parasitized mussels attributed to an energetic imbalance caused by increased standard metabolic rates, without compensation through increased feeding or reduced excretion of ammonia. Separate laboratory assays showed no differences in calcium uptake rates, indicating that infested mussels do not compensate for shell erosion through increased mineralization. This suggests that the increased maintenance costs detected reflect repair of the organic component of the inner nacreous layer of the shell, an energetically more demanding process than mineralization. Thus, parasite-inflicted damage reduces SFG directly through the need for increased basal metabolic rate to drive shell repair without compensatory increases in energy intake. This study provides a first perspective of the physiological mechanisms underlying this parasite-host interaction, a critical step towards a comprehensive understanding of the ecological processes driving dynamics of this intertidal ecosystem engineer.

Defining Coral Bleaching as a Microbial Dysbiosis within the Coral Holobiont

Coral microbiomes are critical to holobiont health and functioning, but the stability of host–microbial interactions is fragile, easily shifting from eubiosis to dysbiosis. The heat-induced breakdown of the symbiosis between the host and its dinoflagellate algae (that is, “bleaching”), is one of the most devastating outcomes for reef ecosystems. Yet, bleaching tolerance has been observed in some coral species. This review provides an overview of the holobiont’s diversity, explores coral thermal tolerance in relation to their associated microorganisms, discusses the hypothesis of adaptive dysbiosis as a mechanism of environmental adaptation, mentions potential solutions to mitigate bleaching, and suggests new research avenues. More specifically, we define coral bleaching as the succession of three holobiont stages, where the microbiota can (i) maintain essential functions for holobiont homeostasis during stress and/or (ii) act as a buffer to mitigate bleaching by favoring the recruitment of thermally tolerant Symbiodiniaceae species (adaptive dysbiosis), and where (iii) environmental stressors exceed the buffering capacity of both microbial and dinoflagellate partners leading to coral death.

Functional diversity of microboring Ostreobium algae isolated from corals

The filamentous chlorophyte Ostreobium sp. dominates shallow marine carbonate microboring communities, and is one of the major agents of reef bioerosion. While its large genetic diversity has emerged, its physiology remains little known, with unexplored relationship between genotypes and phenotypes (endolithic versus free-living growth forms). Here, we isolated nine strains affiliated to two lineages of Ostreobium (>8% sequence divergence of the plastid gene rbcL), one of which was assigned to the family Odoaceae, from the fast-growing coral host Pocillopora acuta Lamarck 1816. Free-living isolates maintained their bioerosive potential, colonizing pre-bleached coral carbonate skeletons. We compared phenotypes, highlighting shifts in pigment and fatty acid compositions, carbon to nitrogen ratios and stable isotope compositions (δ¹³ C and δ¹⁵ N). Our data show a pattern of higher chlorophyll b and lower arachidonic acid (20:4ω6) content in endolithic versus free-living Ostreobium. Photosynthetic carbon fixation and nitrate uptake, quantified via 8 h pulse-labeling with ¹³ C-bicarbonate and ¹⁵ N-nitrate, showed lower isotopic enrichment in endolithic compared to free-living filaments. Our results highlight the functional plasticity of Ostreobium phenotypes. The isotope tracer approach opens the way to further study the biogeochemical cycling and trophic ecology of these cryptic algae at coral holobiont and reef scales.

Beneath the surface: community assembly and functions of the coral skeleton microbiome

Coral microbial ecology is a burgeoning field, driven by the urgency of understanding coral health and slowing reef loss due to climate change. Coral resilience depends on its microbiota, and both the tissue and the underlying skeleton are home to a rich biodiversity of eukaryotic, bacterial and archaeal species that form an integral part of the coral holobiont. New techniques now enable detailed studies of the endolithic habitat, and our knowledge of the skeletal microbial community and its eco-physiology is increasing rapidly, with multiple lines of evidence for the importance of the skeletal microbiota in coral health and functioning. Here, we review the roles these organisms play in the holobiont, including nutritional exchanges with the coral host and decalcification of the host skeleton. Microbial metabolism causes steep physico-chemical gradients in the skeleton, creating micro-niches that, along with dispersal limitation and priority effects, define the fine-scale microbial community assembly. Coral bleaching causes drastic changes in the skeletal microbiome, which can mitigate bleaching effects and promote coral survival during stress periods, but may also have detrimental effects. Finally, we discuss the idea that the skeleton may function as a microbial reservoir that can promote recolonization of the tissue microbiome following dysbiosis and help the coral holobiont return to homeostasis.

Diversity of filamentous fungi associated with coral and sponges in coastal reefs of northeast Brazil

Fungi are known to form associations with various marine organisms and substrata such as sponges and corals, both as potential symbionts or pathogens. These microorganisms occupy an ecological niche that has recently attracted great attention due to their potential in either ecological or pharmaceutical advances. However, the interaction between marine invertebrates and fungi is still poorly understood, including how they are affected by anthropogenic actions. Here, we identified 89 fungal isolates through sequencing of the ITS rDNA region obtained from the various sponge and coral species collected at two northeast Brazilian reefs. We found 43 species of fungi from 16 genera, all belonging to phylum Ascomycota. The sponges and coral shared four genera: Aspergillus, Penicillium, Trichoderma, and Cladosporium, all commonly found in terrestrial habitats and associated with marine invertebrates. We observed some unusual species in relation to the marine environment, such as Clonostachys rosea and Neopestalotiopsis clavispora, most of them related to plants, either as saprophytic or pathogenic, suggesting that these species were transported from the surrounding terrestrial environment to the reefs. In addition, some isolates represent possible undescribed species, reinforcing the importance of studying the marine environment in relation to its ecological and biotechnological importance.

Down to the bone: the role of overlooked endolithic microbiomes in reef coral health

Reef-building corals harbour an astonishing diversity of microorganisms, including endosymbiotic microalgae, bacteria, archaea, and fungi. The metabolic interactions within this symbiotic consortium are fundamental to the ecological success of corals and the unique productivity of coral reef ecosystems. Over the last two decades, scientific efforts have been primarily channelled into dissecting the symbioses occurring in coral tissues. Although easily accessible, this compartment is only 2–3 mm thick, whereas the underlying calcium carbonate skeleton occupies the vast internal volume of corals. Far from being devoid of life, the skeleton harbours a wide array of algae, endolithic fungi, heterotrophic bacteria, and other boring eukaryotes, often forming distinct bands visible to the bare eye. Some of the critical functions of these endolithic microorganisms in coral health, such as nutrient cycling and metabolite transfer, which could enable the survival of corals during thermal stress, have long been demonstrated. In addition, some of these microorganisms can dissolve calcium carbonate, weakening the coral skeleton and therefore may play a major role in reef erosion. Yet, experimental data are wanting due to methodological limitations. Recent technological and conceptual advances now allow us to tease apart the complex physical, ecological, and chemical interactions at the heart of coral endolithic microbial communities. These new capabilities have resulted in an excellent body of research and provide an exciting outlook to further address the functional microbial ecology of the “overlooked” coral skeleton.

Biogeographical Patterns of Endolithic Infestation in an Invasive and an Indigenous Intertidal Marine Ecosystem Engineer

By altering the phenotypic properties of their hosts, endolithic parasites can modulate the engineering processes of marine ecosystem engineers. Here, we assessed the biogeographical patterns of species assemblages, prevalence and impact of endolithic parasitism in two mussel species that act as important ecosystem engineers in the southern African intertidal habitat, Perna perna and Mytilus galloprovincialis. We conducted large-scale surveys across three biogeographic regions along the South African coast: the subtropical east coast, dominated by the indigenous mussel, P. perna, the warm temperate south coast, where this species coexists with the invasive Mediterranean mussel, M. galloprovincialis, and the cool temperate west coast dominated by M. galloprovincialis. Infestation increased with mussel size, and in the case of M. galloprovincialis we found a significantly higher infestation in the cool temperate bioregion than the warm temperate region. For P. perna, the prevalence of infestation was higher on the warm temperate than the subtropical region, though the difference was marginally non-significant. On the south coast, there was no significant difference in infestation prevalence between species. Endolith-induced mortality rates through shell collapse mirrored the patterns for prevalence. For P. perna, endolith species assemblages revealed clear grouping by bioregions. Our findings indicate that biogeography affects cyanobacteria species composition, but differences between biogeographic regions in their effects are driven by environmental conditions.

Fungi in the Marine Environment: Open Questions and Unsolved Problems

Terrestrial fungi play critical roles in nutrient cycling and food webs and can shape macroorganism communities as parasites and mutualists. Although estimates for the number of fungal species on the planet range from 1.5 to over 5 million, likely fewer than 10% of fungi have been identified so far. To date, a relatively small percentage of described species are associated with marine environments, with ∼1,100 species retrieved exclusively from the marine environment. Nevertheless, fungi have been found in nearly every marine habitat explored, from the surface of the ocean to kilometers below ocean sediments. Fungi are hypothesized to contribute to phytoplankton population cycles and the biological carbon pump and are active in the chemistry of marine sediments. Many fungi have been identified as commensals or pathogens of marine animals (e.g., corals and sponges), plants, and algae. Despite their varied roles, remarkably little is known about the diversity of this major branch of eukaryotic life in marine ecosystems or their ecological functions. This perspective emerges from a Marine Fungi Workshop held in May 2018 at the Marine Biological Laboratory in Woods Hole, MA. We present the state of knowledge as well as the multitude of open questions regarding the diversity and function of fungi in the marine biosphere and geochemical cycles.

Inter-domain microbial diversity within the coral holobiont Siderastrea siderea from two depth habitats

Corals host diverse microbial communities that are involved in acclimatization, pathogen defense, and nutrient cycling. Surveys of coral-associated microbes have been particularly directed toward Symbiodinium and bacteria. However, a holistic understanding of the total microbiome has been hindered by a lack of analyses bridging taxonomically disparate groups. Using high-throughput amplicon sequencing, we simultaneously characterized the Symbiodinium, bacterial, and fungal communities associated with the Caribbean coral Siderastrea siderea collected from two depths (17 and 27 m) on Conch reef in the Florida Keys. S. siderea hosted an exceptionally diverse Symbiodinium community, structured differently between sampled depth habitats. While dominated at 27 m by a Symbiodinium belonging to clade C, at 17 m S. siderea primarily hosted a mixture of clade B types. Most fungal operational taxonomic units were distantly related to available reference sequences, indicating the presence of a high degree of fungal novelty within the S. siderea holobiont and a lack of knowledge on the diversity of fungi on coral reefs. Network analysis showed that co-occurrence patterns in the S. siderea holobiont were prevalent among bacteria, however, also detected between fungi and bacteria. Overall, our data show a drastic shift in the associated Symbiodinium community between depths on Conch Reef, which might indicate that alteration in this community is an important mechanism facilitating local physiological adaptation of the S. siderea holobiont. In contrast, bacterial and fungal communities were not structured differently between depth habitats.

13C and 15N assimilation and organic matter translocation by the endolithic community in the massive coral Porites lutea

Corals evolved by establishing symbiotic relationships with various microorganisms (the zooxanthellae, filamentous algae, cyanobacteria, bacteria, archaea, fungi and viruses), forming the 'coral holobiont'. Among them, the endolithic community is the least studied. Its main function was considered to be translocation of photo-assimilates to the coral host, particularly during bleaching. Here, we hypothesize that (i) endolithic algae may show similar primary production rates in healthy or bleached corals by changing their pigment ratios, and therefore that similar production and translocation of organic matter may occur at both conditions and (ii) diazotrophs are components of the endolithic community; therefore, N₂ fixation and translocation of organic nitrogen may occur. We tested these hypotheses in incubation of Porites lutea with ¹³C and ¹⁵N tracers to measure primary production and N₂ fixation in coral tissues and endoliths. Assimilation of the ¹³C atom (%) was observed in healthy and bleached corals when the tracer was injected in the endolithic band, showing translocation in both conditions. N₂ fixation was found in coral tissues and endolithic communities with translocation of organic nitrogen. Thus, the endolithic community plays an important role in supporting the C and N metabolism of the holobiont, which may be crucial under changing environmental conditions.

The roles of endolithic fungi in bioerosion and disease in marine ecosystems. II. Potential facultatively parasitic anamorphic ascomycetes can cause disease in corals and molluscs

Anamorphic ascomycetes have been implicated as causative agents of diseases in tissues and skeletons of hard corals, in tissues of soft corals (sea fans) and in tissues and shells of molluscs. Opportunist marine fungal pathogens, such as Aspergillus sydowii, are important components of marine mycoplankton and are ubiquitous in the open oceans, intertidal zones and marine sediments. These fungi can cause infection in or at least can be associated with animals which live in these ecosystems. A. sydowii can produce toxins which inhibit photosynthesis in and the growth of coral zooxanthellae. The prevalence of many documented infections has increased in frequency and severity in recent decades with the changing impacts of physical and chemical factors, such as temperature, acidity and eutrophication. Changes in these factors are thought to cause significant loss of biodiversity in marine ecosystems on a global scale in general, and especially in coral reefs and shallow bays.

The roles of endolithic fungi in bioerosion and disease in marine ecosystems. I. General concepts

Endolithic true fungi and fungus-like microorganisms penetrate calcareous substrates formed by living organisms, cause significant bioerosion and are involved in diseases of many host animals in marine ecosystems. A theoretical interactive model for the ecology of reef-building corals is proposed in this review. This model includes five principle partners that exist in a dynamic equilibrium: polyps of a colonial coelenterate, endosymbiotic zooxanthellae, endolithic algae (that penetrate coral skeletons), endolithic fungi (that attack the endolithic algae, the zooxanthellae and the polyps) and prokaryotic and eukaryotic microorganisms (which live in the coral mucus). Endolithic fungi and fungus-like boring microorganisms are important components of the marine calcium carbonate cycle because they actively contribute to the biodegradation of shells of animals composed of calcium carbonate and calcareous geological substrates.

Biodiversity of Pigmented Fungi Isolated from Marine Environment in La Réunion Island, Indian Ocean: New Resources for Colored Metabolites

Marine ecosystems cover about 70% of the planet surface and are still an underexploited source of useful metabolites. Among microbes, filamentous fungi are captivating organisms used for the production of many chemical classes of secondary metabolites bound to be used in various fields of industrial application. The present study was focused on the collection, isolation, screening and genotyping of pigmented filamentous fungi isolated from tropical marine environments around La Réunion Island, Indian Ocean. About 150 micromycetes were revived and isolated from 14 marine samples (sediments, living corals, coral rubble, sea water and hard substrates) collected in four different locations. Forty-two colored fungal isolates belonging to 16 families, 25 genera and 31 species were further studied depending on their ability to produce pigments and thus subjected to molecular identification. From gene sequence analysis, the most frequently identified colored fungi belong to the widespread Penicillium, Talaromyces and Aspergillus genera in the family Trichocomaceae (11 species), then followed by the family Hypocreaceae (three species). This study demonstrates that marine biotopes in La Réunion Island, Indian Ocean, from coral reefs to underwater slopes of this volcanic island, shelter numerous species of micromycetes, from common or uncommon genera. This unstudied biodiversity comes along with the ability for some fungal marine inhabitants, to produce a range of pigments and hues.

A mycological baseline study based on a multidisciplinary approach in a coastal area affected by contaminated torrent input

Fungi include a vast group of eukaryotic organisms able to colonise different natural, anthropised and extreme environments, including marine areas contaminated by metals. The present study aims to give a first multidisciplinary characterisation of marine bottom sediments contaminated by metals (Cd, Co, Cr, Cu, Ni, and Zn), originating in the water leakage from an abandoned Fe-Cu sulphide mine (Libiola, north-western Italy), and evaluate how the chemical and physical parameters of water and sediments may affect the benthic fungal communities. Our preliminary results showed the high mycodiversity of the marine sediments studied (13 genera and 23 species of marine fungi isolated), and the great physiological adaptability that this mycobiota evolved in reaction to the effects of the ecotoxic bottom sediment contamination, and associated changes in the seawater parameters.

The Geomycology of Elemental Cycling and Transformations in the Environment

Geomicrobiology addresses the roles of microorganisms in geological and geochemical processes, and geomycology is a part of this topic focusing on the fungi. Geoactive roles of fungi include organic and inorganic transformations important in nutrient and element cycling, rock and mineral bioweathering, mycogenic biomineral formation, and metal-fungal interactions. Lichens and mycorrhizas are significant geoactive agents. Organic matter decomposition is important for cycling of major biomass-associated elements, e.g., C, H, N, O, P, and S, as well as all other elements found in lower concentrations. Transformations of metals and minerals are central to geomicrobiology, and fungi affect changes in metal speciation, as well as mediate mineral formation or dissolution. Such mechanisms are components of biogeochemical cycles for metals as well as associated elements in biomass, soil, rocks, and minerals, e.g., S, P, and metalloids. Fungi may have the greatest geochemical influence within the terrestrial environment. However, they are also important in the aquatic environment and are significant components of the deep subsurface, extreme environments, and habitats polluted by xenobiotics, metals, and radionuclides. Applications of geomycology include metal and radionuclide bioleaching, biorecovery, detoxification, bioremediation, and the production of biominerals or metal(loid) elements with catalytic or other properties. Adverse effects include biodeterioration of natural and synthetic materials, rock and mineral-based building materials (e.g., concrete), cultural heritage, metals, alloys, and related substances and adverse effects on radionuclide mobility and containment. The ubiquity and importance of fungi in the biosphere underline the importance of geomycology as a conceptual framework encompassing the environmental activities of fungi.

Antiproliferative effect of extract from endophytic fungus Curvularia trifolii isolated from the "Veracruz Reef System" in Mexico

CONTEXT

It is well known that marine fungi are an excellent source of biologically active secondary metabolites, and by 2011, it was reported that over 400 bioactive metabolites were derived from marine fungi.

OBJECTIVE

This study establishes the basis for future research on antiproliferative compounds of marine endophytes inhabited in the Veracruz Reef System.

MATERIALS AND METHODS

Isolation of the 34 fungal strains was carried out by microbiological method from samples of sponges, corals, and other biological material from the Veracruz Reef System. The fungal biomass and broth were separated and extracted with a mixture of solvents MeOH:CHCl3. Characterization and molecular identification of the fungal strains were performed through microbiological methods and the analysis of the ITS-rDNA regions. Antiproliferative activity was tested at a dose of 250 μg/mL on human solid tumor cell lines HBL-100, HeLa, SW1573, T-47D, and WiDr by the SRB assay after 48 h-exposure to the fungal extracts.

RESULTS

The extracts from five isolates showed an antiproliferative effect against one or more of the tested cell lines (percentage growth < 50%). The mycelial extract from the isolate LAEE 03 manifested the highest activity against the five cell lines (% PG of 17 HBL-100, 19 HeLa, 23 SW1573, -6 T-47D, and 10 WiDr) and the strain was identified as Curvularia trifolii (Kauffman) Boedijn (Pleosporaceae).

DISCUSSION AND CONCLUSION

The results obtained indicate that the extract from a marine derived C. trifolii has the antiproliferative effect, thus suggesting that this organism is a good candidate for further analysis of its metabolites.

Insights into the Coral Microbiome: Underpinning the Health and Resilience of Reef Ecosystems

Corals are fundamental ecosystem engineers, creating large, intricate reefs that support diverse and abundant marine life. At the core of a healthy coral animal is a dynamic relationship with microorganisms, including a mutually beneficial symbiosis with photosynthetic dinoflagellates (Symbiodinium spp.) and enduring partnerships with an array of bacterial, archaeal, fungal, protistan, and viral associates, collectively termed the coral holobiont. The combined genomes of this coral holobiont form a coral hologenome, and genomic interactions within the hologenome ultimately define the coral phenotype. Here we integrate contemporary scientific knowledge regarding the ecological, host-specific, and environmental forces shaping the diversity, specificity, and distribution of microbial symbionts within the coral holobiont, explore physiological pathways that contribute to holobiont fitness, and describe potential mechanisms for holobiont homeostasis. Understanding the role of the microbiome in coral resilience, acclimation, and environmental adaptation is a new frontier in reef science that will require large-scale collaborative research efforts.

Successive shifts in the microbial community of the surface mucus layer and tissues of the coral Acropora muricata under thermal stress

The coral mucus may harbor commensal bacteria that inhibit growth of pathogens. Therefore, there is a need to understand the dynamics of bacterial communities between the coral mucus and tissues. Nubbins of Acropora muricata were subjected to increasing water temperatures of 26°C-33°C, to simultaneously explore the bacterial diversity in coral mucus and tissues by 16S rRNA gene amplicon sequencing. Photochemical efficiency of symbiotic dinoflagellates within the corals declined above 31°C. Both the mucus and tissues of healthy A. muricata were dominated by γ-Proteobacteria, but under thermal stress there was a shift towards bacteria from the Verrucomicrobiaceae and α-Proteobacteria. Members of Cyanobacteria, Flavobacteria and Sphingobacteria also become more prominent at higher temperatures. The relative abundance of Vibrio spp. in the coral mucus increased at 29°C, but at 31°C, there was a drop in the relative abundance of Vibrio spp. in the mucus, with a reciprocal increase in the tissues. On the other hand, during bleaching, the relative abundance of Endozoicomonas spp. decreased in the tissues with a reciprocal increase in the mucus. This is the first systematic experiment that shows the potential for a bacterial community shift between the coral surface mucus and tissues in a thermally stressed coral.

Endoliths in Lithophaga lithophaga shells--Variation in intensity of infestation and species occurrence

Pronounced differences with respect to the extent of infestation and the degree of Lithophaga lithophaga shell damage inflicted by euendolithic taxa at two sites in the Adriatic Sea representing different productivity conditions, are described. Shells collected from the eastern part of Kaštela Bay, which is characterized by higher primary productivity, have significantly more shell damage then the shell collected from a site on the outer coast of the island of Čiovo exposed to the oligotrophic Adriatic Sea. The presence of endoliths and their perforations were detected in different layers of the shell, including solidly mineralized parts of the skeleton and within the organic lamellae incorporated into the shell. Phototrophic endoliths were not observed in the specimens. The most serious damage to L. lithophaga shells was the boring clionaid sponge Pione vastifica, which was more common in shells collected from Kaštela.

Paleoarchean trace fossils in altered volcanic glass

Microbial corrosion textures in volcanic glass from Cenozoic seafloor basalts and the corresponding titanite replacement microtextures in metamorphosed Paleoarchean pillow lavas have been interpreted as evidence for a deep biosphere dating back in time through the earliest periods of preserved life on earth. This interpretation has been recently challenged for Paleoarchean titanite replacement textures based on textural and geochronological data from pillow lavas in the Hooggenoeg Complex of the Barberton Greenstone Belt in South Africa. We use this controversy to explore the strengths and weaknesses of arguments made in support or rejection of the biogenicity interpretation of bioalteration trace fossils in Cenozoic basalt glasses and their putative equivalents in Paleoarchean greenstones. Our analysis suggests that biogenicity cannot be taken for granted for all titanite-based textures in metamorphosed basalt glass, but a cautious and critical evaluation of evidence suggests that biogenicity remains the most likely interpretation for previously described titanite microtextures in Paleoarchean pillow lavas.

Syn-vivo bioerosion of Nautilus by endo- and epilithic foraminiferans (New Caledonia and Vanuatu)

A variety of syn-vivo bioerosion traces produced by foraminiferans is recorded in shells of Nautilus sampled near New Caledonia and Vanuatu. These are two types of attachment scars of epilithic foraminiferans and two forms of previously undescribed microborings, a spiral-shaped and a dendritic one, both most likely being the work of endolithic 'naked' foraminiferans. Scanning electron microscopy of epoxy-resin casts of the latter revealed that these traces occur in clusters of up to many dozen individuals and potentially are substrate-specific. The foraminiferan traces are the sole signs of bioerosion in the studied Nautilus conchs, and neither traces of phototrophic nor other chemotrophic microendoliths were found. While the complete absence of photoautotrophic endoliths would be in good accordance with the life habit of Nautilus, which resides in aphotic deep marine environments and seeks shallower waters in the photic zone for feeding only during night-time, the absence of any microbial bioerosion may also be explained by an effective defence provided by the nautilid periostracum. Following this line of reasoning, the recorded foraminiferan bioerosion traces in turn would identify their trace makers as being specialized in their ability to penetrate the periostracum barrier and to bioerode the shell of modern Nautilus.

Effects of water depth, seasonal exposure, and substrate orientation on microbial bioerosion in the Ionian Sea (Eastern Mediterranean)

The effects of water depth, seasonal exposure, and substrate orientation on microbioerosion were studied by means of a settlement experiment deployed in 15, 50, 100, and 250 m water depth south-west of the Peloponnese Peninsula (Greece). At each depth, an experimental platform was exposed for a summer period, a winter period, and about an entire year. On the up- and down-facing side of each platform, substrates were fixed to document the succession of bioerosion traces, and to measure variations in bioerosion and accretion rates. In total, 29 different bioerosion traces were recorded revealing a dominance of microborings produced by phototrophic and organotrophic microendoliths, complemented by few macroborings, attachment scars, and grazing traces. The highest bioerosion activity was recorded in 15 m up-facing substrates in the shallow euphotic zone, largely driven by phototrophic cyanobacteria. Towards the chlorophyte-dominated deep euphotic to dysphotic zones and the organotroph-dominated aphotic zone the intensity of bioerosion and the diversity of bioerosion traces strongly decreased. During summer the activity of phototrophs was higher than during winter, which was likely stimulated by enhanced light availability due to more hours of daylight and increased irradiance angles. Stable water column stratification and a resulting nutrient depletion in shallow water led to lower turbidity levels and caused a shift in the photic zonation that was reflected by more phototrophs being active at greater depth. With respect to the subordinate bioerosion activity of organotrophs, fluctuations in temperature and the trophic regime were assumed to be the main seasonal controls. The observed patterns in overall bioeroder distribution and abundance were mirrored by the calculated carbonate budget with bioerosion rates exceeding carbonate accretion rates in shallow water and distinctly higher bioerosion rates at all depths during summer. These findings highlight the relevance of bioerosion and accretion for the carbonate budget of the Ionian Sea.

Gross and Microscopic Lesions in Corals from Micronesia

The authors documented gross and microscopic morphology of lesions in corals on 7 islands spanning western, southern, and eastern Micronesia, sampling 76 colonies comprising 30 species of corals among 18 genera, with Acropora, Porites, and Montipora dominating. Tissue loss comprised the majority of gross lesions sampled (41%), followed by discoloration (30%) and growth anomaly (29%). Of 31 cases of tissue loss, most lesions were subacute (48%), followed by acute and chronic (26% each). Of 23 samples with discoloration, most were dark discoloration (40%), with bleaching and other discoloration each constituting 30%. Of 22 growth anomalies, umbonate growth anomalies composed half, with exophytic, nodular, and rugose growth anomalies composing the remainder. On histopathology, for 9 cases of dark discoloration, fungal infections predominated (77%); for 7 bleached corals, depletion of zooxanthellae from the gastrodermis made up a majority of microscopic diagnoses (57%); and for growth anomalies other than umbonate, hyperplasia of the basal body wall was the most common microscopic finding (63%). For the remainder of the gross lesions, no single microscopic finding constituted >50% of the total. Host response varied with the agent present on histology. Fragmentation of tissues was most often associated with algae (60%), whereas necrosis dominated (53%) for fungi. Two newly documented potentially symbiotic tissue-associated metazoans were seen in Porites and Montipora. Findings of multiple potential etiologies for a given gross lesion highlight the importance of incorporating histopathology in coral disease surveys. This study also expands the range of corals infected with cell-associated microbial aggregates.