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Synaptic connectivity between neocortical neurons is highly structured. The network structure of synaptic connectivity includes first-order properties that can be described by pairwise statistics, such as strengths of connections between different neuron types and distance-dependent connectivity, and higher order properties, such as an abundance of cliques of all-to-all connected neurons. The relative impact of first- and higher order structure on emergent cortical network activity is unknown. Here, we compare network structure and emergent activity in two neocortical microcircuit models with different synaptic connectivity. Both models have a similar first-order structure, but only one model includes higher order structure arising from morphological diversity within neuronal types. We find that such morphological diversity leads to more heterogeneous degree distributions, increases the number of cliques, and contributes to a small-world topology. The increase in higher order network structure is accompanied by more nuanced changes in neuronal firing patterns, such as an increased dependence of pairwise correlations on the positions of neurons in cliques. Our study shows that circuit models with very similar first-order structure of synaptic connectivity can have a drastically different higher order network structure, and suggests that the higher order structure imposed by morphological diversity within neuronal types has an impact on emergent cortical activity.

To compete effectively, living organisms must adjust the allocation of available energy resources for growth, survival, maintenance, and reproduction throughout their life histories. Energy demands and allocations change throughout the life history of an organism, and understanding their energy allocation strategies requires determination of the relative age of individuals. As most scleractinian corals are colonial, the relationship between age and mass/size is complicated by colony fragmentation, partial mortality, and asexual reproduction. To overcome these limitations, solitary mushroom corals, Herpolitha limax from Okinawa, Japan and Fungia fungites from Okinawa and the Great Barrier Reef (GBR), Australia, were used to investigate how energy allocation between these fundamental processes varies as a function of age. Measurements of the relative growth, biochemical profiles, fecundity of individuals of different sizes, and the settlement success of their progeny have revealed physiological trade-offs between growth and reproduction, with increasing body mass ultimately leading to senescence. The importance of energy allocation for reproduction led us to examine the reproductive strategies and sex allocation in the two studied species. In the present study, the smallest individuals of both species studied were found to invest most of their energy in relative growth, showing higher lipid and carbohydrate content than the later stages. In medium-sized corals, this pattern was overturned in favour of reproduction, manifesting in terms of both the highest fecundity and settlement success of the resulting brooded larvae. Finally, a phase of apparent senescence was observed in the largest individuals, characterized by a decrease in most of the parameters measured. In addition, complex reproductive plasticity has been revealed in F. fungites in the GBR, with individual females releasing eggs, embryos, planulae, or a combination of these. These data provide the most direct estimates currently available for physiological, age-related trade-offs during the life history of a coral. The unusual reproductive characteristics of the GBR F. fungites indicate previously unknown layers of complexity in the reproductive biology of corals and have implications for their adaptive potential across a wide geographical scale.

Plankton show preferential swimming towards fluorescent cues compared to non-fluorescent targets in both the laboratory and the sea. Further, green fluorescence enhances predation success, suggesting a prey-luring effect of fluorescence in corals.

High-latitude habitats have become increasingly recognized as a potential climate refuge for coral communities, supporting both tropical and sub-tropical corals. Despite the increasing interest in the ecology of high-latitude corals, our current knowledge of their temporal dynamics is limited, especially within urbanized settings. Here, we examined the entire history of a high-latitude coral reef ecosystem in an urbanized setting. We surveyed Holocene fossil and modern coral communities along a water quality gradient in Moreton Bay, southeast Queensland, Australia, representing near-river (Wellington Point), intermediate (Peel Island) and near-oceanic (Myora Reef) environmental conditions. Reef accretion occurred during three discrete episodes from 7,400 to 5,800, 4,900 to 3,000, and 2,100 to 300 years BP, each separated by roughly 1,000-year hiatuses, where conditions were probably not favorable enough for reef accretion to occur. Episodic reef initiation and termination suggests strong environmental controls over reef development. Eastern Australian Holocene reef growth and cessation has been linked previously to sea level fluctuations and climatic regimes (e.g., ENSO). Within each reef building episode, there were few changes in coral assemblages over time. The fast growing and branching Acropora had a relative abundance greater than 90% in ten of the 13 sediment cores and all the submerged terrace excavations. However, substantial modification of adjacent coastal catchments from European colonization in the mid 1800’s resulted in increased sediment and nutrient discharge into the bay. This perturbation coincided with a greater abundance of stress-tolerant coral species (e.g., Dipsastraea, Goniastrea, and Goniopora) and the near extirpation of Acropora in the modern coral communities of near-river and intermediate sites due to poor water quality. In contrast, the modern coral assemblage at the near-oceanic site (Myora Reef) continues to be dominated by Acropora, likely due to the consistent oceanic input, resulting in lower sediment loading and higher water quality. In order for conditions for reef growth to improve, especially within the near-river portions of the bay, further sediment and nutrient runoff from anthropogenic land-use changes need to be mitigated. Given the historical abundance of Acropora, we recommend this genus be used as an indicator of natural resource management success in the bay.

Measurement(s) Point in Time Date and Time Data Type • Spawning Technology Type(s) Observation • digital curation Sample Characteristic - Organism Scleractinia Sample Characteristic - Environment ocean Sample Characteristic - Location Pacific Ocean • Indian Ocean region Machine-accessible metadata file describing the reported data: https://doi.org/10.6084/m9.figshare.13100552

The distinction between shallow coral reefs and mesophotic coral ecosystems (MCEs) has not been fully clarified yet. The original definition of MCEs, by depths of 30–150 m, fixes their bathymetrical limits and fails to accommodate environmental and biological variation. Recent studies have indicated that water transparency and light availability may explain why MCEs do not occur at fixed depths but vary among localities. This study aimed to evaluate the presence and distribution of MCEs, along the central coast of Oaxaca, through optical depths and the associated benthic community. Using MODIS-Aqua satellite data (Kd490), we estimated the mesophotic optical depths monthly (z10%, z1%, z0.1%), over the last four years. In addition, to characterize benthic community structure, we conducted underwater photo quadrat surveys at two locations on the southern Mexican Pacific coast from 10 to 55 m depth. Significant differences between depths and locations were found in benthic communities. Furthermore, the lower distribution of photosynthetic taxa was different between the two locations but indicative to the z10% and z1% in both cases. Those differences were associated with the upwelling season, which reduces, drastically and differentially, the light availability for benthic communities between the two locations and limits the development of MCEs on the central coast of Oaxaca.

Population size structure provides information on demographic characteristics, such as growth and decline, enabling post-hoc assessment of spatial differences in susceptibility to disturbance. Nevertheless, very few studies have quantified size data of scleractinian corals along a shallow-mesophotic gradient, partly because of previously inaccessible depths. Here, we report the coral size-frequency distributions at the morphology level (six growth forms) and at the species level for ten representative locally abundant species along a broad depth gradient (5–100 m) in the Gulf of Eilat/Aqaba (GoE/A). A total of 18,865 colonies belonging to 14 families and 45 genera were recorded and measured over four reef sites. Colonies were found to be 11.2% more abundant at mesophotic (40–100 m; 55.6%) depths compared with shallow (5–30 m; 44.4%). The coral taxa exhibited heterogeneity in their size-structure, with marked differences among depths, morphological growth forms, and species. Branching and corymbose corals were more prevalent in shallow waters, while encrusting and laminar forms comprised the majority of mesophotic corals. Nevertheless, massive morphology was the most abundant growth form across all sites and depths (39%), followed by laminar (26%) and encrusting (20%). Corymbose corals (primarily Acroporidae) revealed constrained size at all depths; with the lack of small-size groups indicating populations at risk of decline. Depth-generalist species belonging to massive and laminar morphologies generally exhibited a larger colony size at the mesophotic depths, but were typified by a higher number of small colonies. Furthermore, we refute the widely and long-accepted assertion that Stylophora pistillata is the most abundant coral in the northern GoE/A, and assert that Leptoseris glabra is the one. Here, we provide a baseline for future monitoring of coral population structures, insights to recent ecological dynamics, retrospective assessment of coral community recovery following disturbances and grounds for conservation assessments and management actions.

Abstract Light quality is a crucial physical factor driving coral distribution along depth gradients. Currently, a 30 m depth limit, based on SCUBA regulations, separates shallow and deep mesophotic coral ecosystems (MCEs). This definition, however, fails to explicitly accommodate environmental variation. Here, we posit a novel definition for a regional or reef‐to‐reef outlook of MCEs based on the light vs. coral community–structure relationship. A combination of physical and ecological methods enabled us to clarify the ambiguity in relation to the mesophotic definition. To characterize coral community structure with respect to the light environment, we conducted wide‐scale spatial studies at five sites along shallow and MCEs of the Gulf of Eilat/Aqaba (0–100 m depth). Surveys were conducted by technical‐diving and drop‐cameras, in addition to one year of light spectral measurements. We quantify two distinct coral assemblages: shallow (

In an endeavor to study natural systems at multiple spatial and taxonomic resolutions, there is an urgent need for automated, high-throughput frameworks that can handle plethora of information. The coalescence of remote-sensing, computer-vision, and deep-learning elicits a new era in ecological research. However, in complex systems, such as marine-benthic habitats, key ecological processes still remain enigmatic due to the lack of cross-scale automated approaches (mms to kms) for community structure analysis. We address this gap by working towards scalable and comprehensive photogrammetric surveys, tackling the profound challenges of full semantic segmentation and 3D grid definition. Full semantic segmentation (where every pixel is classified) is extremely labour-intensive and difficult to achieve using manual labeling. We propose using label-augmentation, i.e., propagation of sparse manual labels, to accelerate the task of full segmentation of photomosaics. Photomosaics are synthetic images generated from a projected point-of-view of a 3D model. In the lack of navigation sensors (e.g., a diver-held camera), it is difficult to repeatably determine the slope-angle of a 3D map. We show this is especially important in complex topographical settings, prevalent in coral-reefs. Specifically, we evaluate our approach on benthic habitats, in three different environments in the challenging underwater domain. Our approach for label-augmentation shows human-level accuracy in full segmentation of photomosaics using labeling as sparse as 0.1%, evaluated on several ecological measures. Moreover, we found that grid definition using a leveler improves the consistency in community-metrics obtained due to occlusions and topology (angle and distance between objects), and that we were able to standardise the 3D transformation with two percent error in size measurements. By significantly easing the annotation process for full segmentation and standardizing the 3D grid definition we present a semantic mapping methodology enabling change-detection, which is practical, swift, and cost-effective. Our workflow enables repeatable surveys without permanent markers and specialized mapping gear, useful for research and monitoring, and our code is available online. Additionally, we release the Benthos data-set, fully manually labeled photomosaics from three oceanic environments with over 4500 segmented objects useful for research in computer-vision and marine ecology.

Mesophotic ecosystems (MEs) are characterized by the presence of light-dependent organisms, found at depths ranging from ~30 to 150 m in temperate, subtropical and tropical regions. These communities occasionally create massive reef structures with diverse but characteristic morphologies, which serve as the framework builders of those ecosystems. In many localities, MEs are physically linked with shallow and deep-sea habitats, and while taxa from both environments share this space, a unique and endemic biodiversity is also found. The main MEs studied to date are the mesophotic coral ecosystems (MCEs) and the temperate mesophotic ecosystems (TMEs), which have received increased attention during the last decade. As shallow coral reef ecosystems are among the most threatened habitats on Earth, the potential of MEs to act as refugia and contribute to the resilience of the whole ecosystem has been a subject of scrutiny. New technologies and methods have become more available to study these deeper parts of the reef ecosystems, yielding many new discoveries. However, basic gaps in knowledge remain in our scientific understanding of the global diversity of MEs, limiting our ability to recognize biogeographic patterns and to make educated decisions for the management and conservation of these ecosystems.

Corals and their photosymbionts experience inherent changes in light along depth gradients, leading them to have evolved several well-investigated photoacclimation strategies. As coral calcification is influenced by light (a process described as LEC—‘light-enhanced calcification’), studies have sought to determine the link between photosynthesis and calcification, but many puzzling aspects still persist. Here, we examine the physiology of Euphyllia paradivisa, a coral species found at a wide range of depths but that is strictly mesophotic in the Red Sea; and also examines the coupling between photosynthesis and LEC by investigating the response of the coral under several controlled light regimes during a long-term experiment. E. paradivisa specimens were collected from 40 to 50 m depth and incubated under three light conditions for a period of 1 year: full-spectrum shallow-water light (approx. 3 m, e.g. shallow-light treatment); blue deep-water light (approx. 40 m, e.g. mesophotic-light treatment) or total darkness (e.g. dark treatment). Net photosynthesis remained similar in the shallow-light-treated corals compared to the mesophotic-light-treated corals, under both low and high light. However, calcification increased dramatically with increasing light intensity in the shallow-light-treated corals, suggesting a decoupling between these processes. Photoacclimation to shallow-water conditions was indicated by enhanced respiration, a higher density of zooxanthellae per polyp and lower chlorophyll a content per cell. The dark-treated corals became completely bleached but did not lower their metabolism below that of the mesophotic-light-treated corals. No Symbiodinium clade shift was found following the year-long light treatments. We conclude that E. paradivisa, and its original symbiont clade, can adapt to various light conditions by controlling its metabolic rate and growth energy investment, and consequently induce LEC.

The recognition of the microbiota complexity and their role in the evolution of their host is leading to the popularization of the holobiont concept. However, the coral holobiont (host and its microbiota) is still enigmatic and unclear. Here, we explore the complex relations between different holobiont members of a mesophotic coral Euphyllia paradivisa. We subjected two lines of the coral—with photosymbionts, and without photosymbionts (apo-symbiotic)—to increasing temperatures and to antibiotics. The different symbiotic states were characterized using transcriptomics, microbiology and physiology techniques. The bacterial community’s composition is dominated by bacteroidetes, alphaproteobacteria, and gammaproteobacteria, but is dependent upon the symbiont state, colony, temperature treatment, and antibiotic exposure. Overall, the most important parameter determining the response was whether the coral was a symbiont/apo-symbiotic, while the colony and bacterial composition were secondary factors. Enrichment Gene Ontology analysis of coral host’s differentially expressed genes demonstrated the cellular differences between symbiotic and apo-symbiotic samples. Our results demonstrate the significance of each component of the holobiont consortium and imply a coherent link between them, which dramatically impacts the molecular and cellular processes of the coral host, which possibly affect its fitness, particularly under environmental stress.

The growth in human population along coastal areas is exposing marine environments to increasing anthropogenic light sources. Despite the potential effects of this modern phenomenon, very few studies have examined its implications for corals. Here, we present a long-term study of coral early life stages under light pollution conditions at night. Coral larvae were collected from Stylophora pistillata colonies, and then settled and grown under experimental conditions of two different common city lighting methods (fluorescent or LED). Effects of the artificial lighting on the coral settlement success, survivorship, growth rate, photosynthetic efficiency, and calcification rate were examined over a period of one year. The control exhibited ~30% higher settlement success compared to the two light treatments, while under the light treatments corals showed higher survivorship, growth, and calcification rates. In addition, an indication of damage to the photosynthetic system was found in the light-polluted corals, which was reflected in their photosynthesis efficiency parameters: i.e., lower maximum light utilization coefficient (α), lower maximum potential photosynthetic rate (Pmax), and lower photosynthetic maximal quantum yield (Fv/Fm). Our findings provide evidence of the potential adverse effects of artificial lighting methods on the natural environment of coral reefs. We conclude that the use of the LED lighting method has high interference potential for the early life stages of corals.

The profound mutualistic symbiosis between corals and their endosymbiotic counterparts, Symbiodiniaceae algae, has been threatened by the increase in seawater temperatures, leading to breakdown of the symbiotic relationship—coral bleaching. To characterize the heat-stress response of the holobiont, we generated vital apo-symbiotic Euphyllia paradivisa corals that lacked the endosymbiotic algae. Using RNA sequencing, we analyzed the gene expression of these apo-symbionts vs. symbiotic ones, to test the effect of the algal presence on the tolerance of the coral. We utilized literature-derived lists of “symbiosis differentially expressed genes” and “coral heat-stress genes” in order to compare between the treatments. The symbiotic and apo-symbiotic samples were segregated into two separate groups with several different enriched gene ontologies. Our findings suggest that the presence of endosymbionts has a greater negative impact on the host than the environmental temperature conditions experienced by the holobiont. The peak of the stress reaction was identified as 28 °C, with the highest number of differentially expressed genes. We suggest that the algal symbionts increase coral holobiont susceptibility to elevated temperatures. Currently, we can only speculate whether coral species, such as E. paradivisa, with the plasticity to also flourish as apo-symbionts, may have a greater chance to withstand the upcoming global climate change challenge.

Abstract Background Population outbreaks of the crown-of-thorns starfish (Acanthaster planci sensu lato; COTS), a primary predator of reef-building corals in the Indo-Pacific Ocean, are a major threat to coral reefs. While biological and ecological knowledge of COTS has been accumulating since the 1960s, little is known about its associated bacteria. The aim of this study was to provide fundamental information on the dominant COTS-associated bacteria through a multifaceted molecular approach. Methods A total of 205 COTS individuals from 17 locations throughout the Indo-Pacific Ocean were examined for the presence of COTS-associated bacteria. We conducted 16S rRNA metabarcoding of COTS to determine the bacterial profiles of different parts of the body and generated a full-length 16S rRNA gene sequence from a single dominant bacterium, which we designated COTS27. We performed phylogenetic analysis to determine the taxonomy, screening of COTS27 across the Indo-Pacific, FISH to visualize it within the COTS tissues, and reconstruction of the bacterial genome from the hologenome sequence data. Results We discovered that a single bacterium exists at high densities in the subcuticular space in COTS forming a biofilm-like structure between the cuticle and the epidermis. COTS27 belongs to a clade that presumably represents a distinct order (so-called marine spirochetes) in the phylum Spirochaetes and is universally present in COTS throughout the Indo-Pacific Ocean. The reconstructed genome of COTS27 includes some genetic traits that are probably linked to adaptation to marine environments and evolution as an extracellular endosymbiont in subcuticular spaces. Conclusions COTS27 can be found in three allopatric COTS species, ranging from the northern Red Sea to the Pacific, implying that the symbiotic relationship arose before the speciation events (approximately 2 million years ago). The universal association of COTS27 with COTS and nearly mono-specific association at least with the Indo-Pacific COTS provides a useful model system for studying symbiont-host interactions in marine invertebrates and may have applications for coral reef conservation. Video Abstract

Mesophotic coral ecosystems (MCEs) are light-dependent coral-associated communities found at 30–150 m depth. Corals inhabiting these deeper reefs are often acclimatized to a limited and blue-shifted light environment, enabling them to maintain the relationship with their photosynthetic algal symbionts (family Symbiodiniaceae) despite the seemingly suboptimal light conditions. Among others, fluorescent proteins produced by the coral host may play a role in the modulation of the quality and spectral distribution of irradiance within the coral tissue through wavelength transformation. Here we examined the bio-optical properties and photosynthetic performances of different fluorescence morphs of two mesophotic coral species Goniopora minor and Alveopora ocellata, in order to test the photosynthesis enhancement hypothesis proposed for coral fluorescence. The green morph of G. minor and the low fluorescence morph of A. ocellata exhibit, in their natural habitats, higher abundance. The morphs also presented different spectral reflectance and light attenuation within the tissue. Nevertheless, chlorophyll a fluorescence-based, and O2 evolution measurements, revealed only minor differences between the photosynthetic abilities of three fluorescence morphs of the coral G. minor and two fluorescence morphs of A. ocellata. The fluorescence morphs did not differ in their algal densities or chlorophyll concentrations and all corals harbored Symbiodiniaceae from the genus Cladocopium. Thus, despite the change in the internal light quantity and quality that corals and their symbionts experience, we found no evidence for the facilitation or enhancement of photosynthesis by wavelength transformation.

Mesophotic coral ecosystems (MCEs) are characterized by the presence of photosynthetically active organisms such as corals and algae, and associated communities at depths ranging from 30 to 150 m in tropical and subtropical regions. Due to the increased awareness of the potential importance of these reefs as an integral part of coral reef ecosystems (i.e., deep reef refuge, specialized biodiversity, transition zone between shallow and deep-sea environments, and recreational and intrinsic values), interest from the scientific community has grown around the world over the last two decades. Several nations have already made management declarations and started to extend marine protected areas and fishery management to MCEs. The estimated area of Australian MCEs is likely equivalent to that of shallow reef ecosystems down to 30 m; however, Australian MCEs attract limited research effort compared to other major coral reef regions around the world. In this perspective, we briefly explore the reasons for this scarcity of research on mesophotic ecosystems of the Great Barrier Reef (GBR) of Australia (e.g., strict diving regulations, new researchers’ involvement, and logistics and cost). At present, research efforts on the mesophotic ecosystems of the GBR are in decline and if this trajectory is maintained, the global disparity in knowledge between MCEs near Australia and those from the other main coral reef regions worldwide will sharpen deeply. We call for action from the research community, grant agencies, and decision-makers toward a wider understanding of these important ecosystems in Australia.

The phenomenon of coral fluorescence in mesophotic reefs, although well described for shallow waters, remains largely unstudied. We found that representatives of many scleractinian species are brightly fluorescent at depths of 50-60 m at the Interuniversity Institute for Marine Sciences (IUI) reef in Eilat, Israel. Some of these fluorescent species have distribution maxima at mesophotic depths (40-100 m). Several individuals from these depths displayed yellow or orange-red fluorescence, the latter being essentially absent in corals from the shallowest parts of this reef. We demonstrate experimentally that in some cases the production of fluorescent pigments is independent of the exposure to light; while in others, the fluorescence signature is altered or lost when the animals are kept in darkness. Furthermore, we show that green-to-red photoconversion of fluorescent pigments mediated by short-wavelength light can occur also at depths where ultraviolet wavelengths are absent from the underwater light field. Intraspecific colour polymorphisms regarding the colour of the tissue fluorescence, common among shallow water corals, were also observed for mesophotic species. Our results suggest that fluorescent pigments in mesophotic reefs fulfil a distinct biological function and offer promising application potential for coral-reef monitoring and biomedical imaging.