Biology subjects

Baker, D. M.

Publications and source records attributed to Baker, D. M..

9 recordsLinked to original sources

bioRxiv2026

Energy quality shapes biodiversity across coastal oceans

Earth's biodiversity is distributed unevenly, typically peaking in warm, vegetated, and stable environments. This has frequently been linked to energy availability, which boosts productivity, bolsters populations, and facilitates coexistence. Here, we examine the relationship between energy and biodiversity across coastal oceans using particulate organic matter biogeochemistry and environmental DNA. We reveal that energy quantity (concentrations of carbon, nitrogen, and hydrolyzable amino acids) and salinity, two variables that co-vary with freshwater inflow, jointly predict species richness at regional and global scales. Biodiversity was lowest at sites and locations with high energy inflow and low salinity, suggesting that environmental filtering associated with the osmotic stress induced by freshwater inflow outweighs raw resource availability in governing species richness. Independent of this gradient, however, energy quality (defined via C:N ratios, {delta}C values, and amino acid profiles) was associated with higher biodiversity. Labile, protein-rich, marine-derived resources supported higher biodiversity across all taxa at the regional scale, and a larger number of planktonic consumer taxa at both regional and global scales. High energy quality sites were also enriched in key planktonic groups such as calanoid and cyclopoid copepods, suggesting that these sites act as hotspots of planktonic biodiversity across coastal seascapes. Our findings suggest that few species can directly harness the plentiful resources provided by terrestrial subsidies in coastal oceans because they arrive in low salinity waters. In turn, high-quality food attracts a diverse range of consumers, which may seed the patchy foraging hotspots that characterize open-water food webs. Altered coastal hydrodynamics and biogeochemistry may therefore affect nearshore biodiversity, food webs, and fisheries.

ecology↗

bioRxiv2025

Autonomous Reef Monitoring Structures (ARMS) Reveal Human-Induced Biodiversity Shifts in Urban Coastal Ecosystems

Biodiversity thrives in coastal marine habitats which host foundational species such as corals, mangroves, and seagrasses. However, coastal development and the growth of megacities along shorelines impose an array of stressors on the marine environment. These stressors inevitably impact biodiversity which dictates ecosystem functions and services. Despite extensive research on biodiversity responses to anthropogenic stressors, phylum-specific resistance and resilience dynamics - particularly in coastal marine ecosystems - remain poorly understood. Considering the global scale of coastal development, it is imperative to develop a more comprehensive understanding of how biodiversity, in terms of richness and community composition, is influenced by various anthropogenic stressors. Here, we present the first application of standardized Autonomous Reef Monitoring Structures (ARMS) as an experimental unit - using a common garden experimental design - to examine community responses to stress within an urbanized seascape. ARMS were seeded within two marine reserves for one year and then transplanted to sites of stress, including domestic sewage, and mariculture. We hypothesized that 1) human impacts reduce richness and alter composition of established communities; and 2) increasing intensity of these impacts reduces community resistance and resilience to stress. Using metabarcoding, we quantified richness and taxonomic composition and assessed their changes along an impact gradient. Our results showed that nutrient pollution, particularly inorganic nitrogen, significantly reduced species richness and restructured communities. Communities exhibited low resistance, yet high resilience - suggesting that urbanized seascapes have high recovery potential when stress is mitigated.

ecology↗

bioRxiv2025

Assessing the Effectiveness of 3D-Printed Ceramic Structures for Coral Restoration: Growth, Survivorship, and Biodiversity Using Visual Surveys and eDNA

Coral reef degradation has spurred the development of artificial structures to mitigate losses in coral cover. These structures serve as substrates for coral transplantation, with the expectation that growing corals will attract reef-associated taxa -- while the substrates ability to directly support biodiversity is often neglected. We evaluated a novel 3D-printed modular tile made of porous terra cotta, designed with complex surface structures to enhance micro- and cryptic biodiversity, through a restoration project in Hong Kong. Over four years, we monitored 378 outplanted coral fragments using diver assessments and photography, while biodiversity changes were assessed through visual surveys and eDNA metabarcoding. Coral survivorship was high, with 88% of transplants surviving by the studys end. The restoration site exhibited greater fish and macroinvertebrate abundance compared to a nearby unrestored area. eDNA analyses revealed 23.5% higher eukaryote ASV richness at the restoration site than the unrestored site and a 13.3% increase relative to a natural reference coral community. This study highlights the tiles dual functionality: (1) supporting coral growth and (2) enhancing cryptic biodiversity, an aspect often neglected in traditional reef restoration efforts. Our findings underscore the potential of 3D-printed ceramic structures to improve both coral restoration outcomes and broader reef ecosystem recovery.

ecology↗

bioRxiv2024

Trophic niche partitioning in symbiotic marine invertebrates

Fierce competition for food and space underpins coral reefs biodiversity - supported by photosymbiotic foundational species. In contrast to other ecosystems, there is scant evidence that competition is mitigated by niche partitioning. Indeed, the dynamic evolutionary lineages of symbiotic partners and their syntrophy create layers of nutritional complexity that obfuscate patterns that structurn reef communities. As conspicuous members of Indo-Pacific reefs - giant clams co-occur with reef-building corals and similarly associate with algal symbionts. Using a common garden experiment, we analyzed stable isotope values from six giant clam species in the Philippines. These data, along with published data from ten sympatric corals, were used to calculate a novel metric - the Host Evaluation: Reliance on Symbionts (HERS) index - to assess variations in relative trophic strategies. Consistent with trophic niche partitioning - all species fell along an autotrophy-heterotrophy gradient with little overlap. We found a significant phylogenetic signal in clam HERS score, highlighting the role of selection in their nutritional ecology. We conclude that niche partitioning comes with tradeoffs, where predominantly autotrophic species showed higher growth rates but higher susceptibility to stress and consequently - greater conservation concern. TeaserTrophic niche partitioning plays a role in symbiotic marine invertebrate evolution with benefits and costs.

ecology↗

bioRxiv2023

The bacterial microbiome of symbiotic and menthol-bleached polyps of Galaxea fascicularis

AO_SCPLOWBSTRACTC_SCPLOWCoral reefs support the livelihood of half a billion people but are at high risk of collapse due to the vulnerability of corals to climate change and local anthropogenic stressors. While understanding coral functioning is essential to guide conservation efforts, research is challenged by the complex nature of corals. They exist as metaorganisms (holobionts), constituted by the association between the (coral) animal host, its obligate endosymbiotic algae (Symbiodiniaceae), and other microorganisms comprising bacteria, viruses, archaea, fungi and other protists. Researchers therefore increasingly turn to model organisms to unravel holobiont complexity, dynamics, and how these determine the health and fitness of corals. The coral Galaxea fascicularis is an emerging model organism for coral symbiosis research with demonstrated suitability to aquarium rearing and reproduction, and to manipulation of the host-Symbiodiniaceae symbiosis. However, little is known about the response of the G. fascicularis microbiome to menthol bleaching--the experimental removal of the Symbiodiniaceae which represents the first step in coral-algal symbiosis manipulation. For this, we characterized the bacterial microbiome of symbiotic and menthol-bleached G. fascicularis originating from the Red Sea and South China Sea (Hong Kong) that were long-term aquarium-reared in separate facilities. We found that the coral-associated microbiomes were composed of relatively few bacterial taxa (10-78 ASVs). Symbiotic polyps (clonal replicates) from the same colony had similar microbiomes, which were distinct from those of other colonies despite co-culturing in shared aquaria. A pattern of seemingly differential response of the bacterial microbiome to menthol bleaching between the two facilities emerged, warranting further investigation into the role of rearing conditions. Nevertheless, the changes in community composition overall appeared to be stochastic suggesting a dysbiotic state. Considering the importance of bleaching treatment of captive corals for symbiosis research, our results--although preliminary--contribute fundamental knowledge for the development of the Galaxea model for coral symbiosis research.

microbiology↗

bioRxiv2023

Impact of light pollution at night on male reproductive success in Japanese medaka (Oryzias latipes)

Environmental light is perceived and anticipated by organisms to synchronize their biological cycles. Therefore, exposure to artificial light at night could disrupt diurnal and seasonal rhythmicity. Reproduction is a complex physiological process involving integration of environmental signals by the brain, and release of endocrine signals by the pituitary that regulate gametogenesis and spawning. In addition, males from many species form a dominance hierarchy that, through a combination of aggressive and protective behavior, influences their reproductive success. In this study, we investigated the effect of different light regimes, including light pollution at night and continuous light, on the fitness of male fish within a dominance hierarchy using a model fish, the Japanese medaka. In normal light/dark rhythm conditions, we observed that dominant males are more aggressive, remain closer to the female, and spend ten-fold more time spawning than subordinates. By using males with different genotypes, we determined the paternity of the progeny and found that even though subordinate males spend less time with the females, they are equally successful at fertilizing eggs in normal light conditions due to an efficient sneaking behavior. However, when exposed to light at night, dominant males fertilize more eggs. We indeed found that when exposed to nocturnal light pollution, dominant males produce higher quality sperm than subordinate males. Surprisingly, we did not find differences in circulating sex steroid levels, pituitary gonadotropin levels, or gonadosomatic index between dominant and subordinate males, neither in control nor night light condition. Continuous light was found to completely inhibit establishment of male hierarchy. This study is the first to report an effect of light pollution on sperm quality with an impact on male fertilization success in any vertebrate. It has broad implications for fish ecology in urban areas with potential impacts on the genetic diversity of these fish populations. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=95 SRC="FIGDIR/small/536935v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@149072dorg.highwire.dtl.DTLVardef@1763cd7org.highwire.dtl.DTLVardef@194586aorg.highwire.dtl.DTLVardef@38c518_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIIn a triadic relationship, subordinate medaka show sneaking behavior during female spawning, allowing them to produce about 50% of the offspring. C_LIO_LIContinuous light inhibits establishment of male hierarchy. C_LIO_LILight pollution at night shifts the balance of reproductive efficiency between dominant and subordinate males, benefiting dominant males. C_LIO_LIExposure to light pollution at night improves sperm quality in dominant fish relative to subordinates, but does not clearly affect reproductive hormone levels. C_LI

zoology↗

bioRxiv2022

Symbiosis-driven development in an early branching metazoan

Microbes can initiate developmental gene regulatory cascades in animals. The molecular mechanisms underlying microbe-induced animal development and the evolutionary steps to integrate microbial signals into regulatory programs remain poorly understood. In the upside-down jellyfish Cassiopea xamachana, a dinoflagellate endosymbiont initiates the life stage transition from the sessile polyp to the sexual medusa. We found that metabolic products derived from symbiont carotenoids may be important to initiate C. xamachana development, in addition to expression of conserved genes involved in medusa development of non-symbiotic jellyfish. We also revealed the transcription factor COUP is expressed during metamorphosis, potentially as a co-regulator of nuclear receptor RXR. These data suggest relatively few steps may be necessary to integrate symbiont signals into gene regulatory networks and cements the role of the symbiont as a key trigger for life history transition in C. xamachana.

developmental biology↗

bioRxiv2022

The reef-building coral Galaxea fascicularis: a new model system for coral symbiosis

Reef-building corals owe their evolutionary success to their symbiosis with unicellular algae (Symbiodiniaceae). However, increasingly frequent heat waves lead to coral mass-bleaching events and pose a serious threat to the survival of reef ecosystems. Despite significant efforts, a mechanistic understanding of coral-algal symbiosis functioning, what leads to its breakdown and what can prevent it, remains incomplete. The main obstacles are low amenability of corals to experimental handling and, owing to its obligatory nature, the difficulties of manipulating the coral-algal association. Indeed, many studies on the symbiotic partnership are conducted on other cnidarian model organisms and their results may therefore not be fully transferable to tropical reef-building corals. Here, we identify the tropical stony coral species Galaxea fascicularis as a novel candidate coral model system. Individual polyps of this species can be separated, enabling highly replicated genotype studies, and are well suited to experimental investigation of the symbiosis as they can be easily and effectively rid of their algal symbionts (bleached). We show that bleached adult individuals can reestablish symbiosis with non-native symbionts, and we report the completion of the gametogenic cycle ex-situ, with the successful spawning in aquaria over multiple years. These achievements help overcome several of the major limitations to direct research on corals and highlight the potential of G. fascicularis as an important new model system for investigations of symbiosis functioning and manipulation.

systems biology↗

bioRxiv2021

The benefits of herbivory outweigh the costs of bioerosion in a eutrophic coral community

Herbivores play an integral part in maintaining the health of coral reefs by suppressing the growth of algae and accumulation of sediment and facilitating coral growth. However, in predator-depleted systems where densities of herbivores are unnaturally high, grazing can have detrimental effects on corals through excessive bioerosion. Yet, these benefits and costs are rarely investigated concurrently, especially in eutrophic systems where grazers may play a disproportionate role. We used a year-long exclusion experiment to elucidate the effect of natural densities of the dominant herbivore (the sea urchin Diadema setosum) on coral communities in a heavily fished and eutrophic system (Hong Kong, China). To assess benthic community response to grazing, we monitored the survival and growth of three locally abundant coral species (Pavona decussata, Platygyra carnosus and Porites sp.), algal and sediment accumulation, and bioerosion of coral skeletons across seasons. We found that urchins maintained our experimental coral assemblages, and when excluded, there was a 25 to 75-fold increase in algal-sediment matrix accumulation. Contrary to predictions, there was no general response of corals to urchin presence; Porites sp. survivorship increased while P. decussata was unaffected, and growth rates of both species was unchanged. Surprisingly, P. carnosus experienced higher mortality and bioerosion of up to 33% of their buoyant weight when urchins were present. Therefore, under natural densities, sea urchins clear substrate of algae and sediment, increase survival, maintain growth rates and health of coral assemblages, yet can accelerate the bioerosion of species with porous skeletons following mortality.

ecology↗