Biology subjects

Bentlage, B.

Publications and source records attributed to Bentlage, B..

11 recordsLinked to original sources

bioRxiv2026

Skin microbiome mirrors habitat divergence in amphibious combtooth blenny fish (Teleostei, Blenniidae)

Host-associated microbiomes play vital roles in organismal health, ecological interactions, and evolution, yet little is known about how microbial communities shift during the transition from aquatic to increasingly terrestrial habitats. Here, we characterize the skin microbiomes of three combtooth blenny species (Blenniella paula, Praealticus labrovittatus, and Alticus arnoldorum) that occupy distinct positions along the intertidal gradient in Guam--from fully subtidal (and exclusively aquatic) to intertidal (amphibious) and supratidal environments (exclusively terrestrial). Using 16S rRNA amplicon sequencing, we compared skin-associated bacterial communities with those in surrounding seawater and substrate biofilms to assess habitat influences on microbiome structure. Skin microbiomes were distinct from environmental microbial communities, indicating strong ecological filtering by the host. The divergence between skin and substrate microbiomes in the three species parallels their distribution along progressively higher zones of the intertidal gradient. The most divergent skin microbiome was that of the supratidal fish A. arnoldorum, characterized by higher Gammaproteobacteria abundance and enrichment of epiphytic and mucus-associated taxa. Across all species, we identified 32 microbial orders significantly enriched on the skin relative to environmental samples, including taxa commonly associated with fish mucosa (e.g., Vibrio, Alteromonas, Cetobacterium) and others rarely reported in aquatic marine fish (e.g., Rubritalea, Granulosicoccus). Several rare taxa with potential pathogenicity were also detected at low abundances. Together, these findings suggest that habitat-specific selective pressures strongly shape fish skin microbiomes along subtidal (aquatic) to supratidal (terrestrial) habitats and suggest that microbial symbionts may contribute to the ecological and physiological adaptations enabling amphibious lifestyles. This study provides the first comparative assessment of skin microbiome divergence across amphibious fish species along an intertidal gradient and offers a framework for predicting microbiome responses to environmental change.

evolutionary biology↗

bioRxiv2026

Seasonal microbiome community dynamics in the massive coral Porites lobata impacted by sedimentation

Near-shore coral reefs in southern Guam (Mariana Islands) experience severe sedimentation, in particular during the wet season when rainfall and erosion are high. We sampled fragments of the reef-forming coral Porites lobata from opposite ends of a sedimentation gradient in Fouha Bay, southern Guam, during dry and wet seasons. Using DNA metabarcoding, we characterized the diversity and composition of P. lobata-associated Symbiodiniaceae and bacterial microbiome communities. As in many species of Porites, Symbiodiniaceae communities of P. lobata were dominated by variants of Cladocopium C15 with sites showing differences in Symbiodiniaceae communities attributable to variation in these Cladocopium C15 variants. Bacterial microbiomes of P. lobata were dominated by Endozoicomonadaceae, a family of putative coral bacterial endosymbionts involved in nutrient cycling. Site and seasonal differences in bacterial diversity and community composition were apparent. In close proximity to the mouth of the river draining into Fouha Bay, bacterial diversity was highest during the wet season when sedimentation is generally severe. Microbiome reorganization in response to sedimentation may explain this result, but we also found overrepresentation of bacteria associated with terrestrial origin close to the river mouth and/or during the wet season. Together these patterns highlight that coral Symbiodiniaceae and bacterial communities are both spatially and temporally structured in this disturbed system. IMPORTANCEThis study provides a time series dataset of coral-associated microorganisms, including dinoflagellate algae and bacteria, from a tropical bay impacted by sedimentation that results from upstream erosion of disturbed soils. Characterizing temporal patterns of coral-associated microbes provides insights into the dynamic nature of these communities. While microbiome variability across sites and seasons may be a result of acclimatization to different environmental conditions, we identified bacterial groups of putative terrestrial origin in sampled coral microbiomes that may have been exported from eroded soils to the near-shore reef. Considering that disturbed soils act as hotspots for the proliferation of potentially harmful substances, such as antimicrobial resistance genes, understanding microbial community connections at the marine-freshwater-terrestrial interface is an important step toward evaluating environmental impacts across connected ecosystems from ridge to reef.

ecology↗

bioRxiv2026

Comparative genomics reveals modular virulence repertoires and extensive horizontal gene transfer in Vibrio species associated with white syndrome of Porites cylindrica

Coral white syndrome (WS) is a widespread condition characterized by tissue loss and skeletal exposure, with multiple bacterial pathogens--particularly Vibrio species--implicated in its etiology. To investigate the genomic basis of potential virulence in Vibrio associated with WS of Porites cylindrica, we isolated 57 Vibrio strains from healthy and diseased coral tissues collected from reefs in Guam. Thirteen representative strains from five dominant species--V. coralliilyticus, V. owensii, V. tubiashii, V. harveyi, and V. tetraodonis--were selected for whole-genome sequencing using Oxford Nanopore Technology. Comparative genomic analyses revealed a conserved repertoire of extracellular enzymes, including hemolysins, cytolysins, metalloproteases, and subtilisin-like peptidases, alongside lineage-specific toxin and regulatory modules. Variation in secretion systems (T1SS-T6SS), particularly in T3SS, T4SS, and T6SS subtypes, reflected diversification of host-interaction and competitive capacities across species. Mobile genetic elements, including plasmids and prophages, contributed additional virulence-associated genes and secretion clusters, underscoring the role of horizontal gene transfer in shaping the accessory genome content. Notably, V. coralliilyticus harbored cholera toxin-related genes (ace and zot), while conjugative plasmid systems indicated potential for gene dissemination across lineages. Together, these findings demonstrate that virulence potential in coral-associated Vibrio is broadly distributed and structured by a conserved ecological core overlaid with flexible, horizontally acquired modules. This study provides the first comparative genomic framework for Vibrio associated with P. cylindrica, advancing our understanding of how genomic plasticity and modular virulence repertoires may contribute to opportunistic disease dynamics in coral reef ecosystems.

microbiology↗

bioRxiv2024

Evolutionary genomics of two co-occurring congeneric fore reef coral species on Guam (Mariana Islands).

Population structure provides essential information for developing meaningful conservation plans. This is especially important in remote places, such as oceanic islands, where limited population sizes and genetic isolation can make populations more susceptible and self-dependent. In this study, we assess and compare the relatedness, population genetics and molecular ecology of two sympatric Acropora species, A. surculosa sensu Randall & Myers (1983) and A. cf. verweyi Veron & Wallace, 1984 around Guam, using genome-wide sequence data (ddRAD). We further contrast our findings with the results of a recent study on back reef A. cf. pulchra (Brook, 1891) to assess the impact of habitat, colony morphology and phylogenetic relatedness on these basic population genetic characteristics and generate testable hypotheses for future studies. Both target species were found to have small effective population sizes, low levels of genetic diversity, and minimal population structure around Guam. Nonetheless, A. cf. verweyi had significantly higher levels of genetic diversity, some population structure as well as more clones, close relatives and putative loci under selection. Comparisons with A. cf. pulchra indicate a potentially significant impact by habitat on population structure and genetic diversity while colony morphology seems to significantly impact clonality. This study revealed significant differences in the basic population genetic makeup of two sympatric Acropora species on Guam. Our results suggest that colony morphology and habitat/ecology may have a significant impact on the population genetic make-up in reef corals, which could offer valuable insights for future management decisions in the absence of genetic data.

evolutionary biology↗

bioRxiv2024

Light exposure induces phenotypic plasticity of the upside-down jellyfish Cassiopea and its endosymbiotic dinoflagellates

The upside-down jellyfish, Cassiopea, is an increasingly popular model organism gaining prominence for both its endosymbiotic dinoflagellates from the family Symbiodiniaceae and its behavioral changes of bell pulsations associated with environmental cues. Pulsation provides a unique window into the hosts response to environmental conditions, a typically difficult to access component of other symbiotic cnidarians. Pulsation has also been hypothesized to play a regulatory role on the endosymbiotic assemblage, but the magnitude of this regulatory effect is not well understood. Here, we used two light-acclimation experiments to help disentangle the complex phenotypic responses of the cnidarian host and its endosymbiotic dinoflagellates. The first experiment examined the phenotypic plasticity (size, behavior, color) of Cassiopea sp. in response to repeated ambient light acclimation trials to determine the rate and magnitude of phenotypic plasticity. The second experiment compared the acclimation response of jellyfish across three experimental groups to test whether a variable environment and resulting short acclimation times destabilized the host-endosymbiont relationship. Our goal was to identify covarying host-endosymbiont phenotypes to gain new insights into the dynamics of this relationship. We employed flow cytometric phenotypic profiling for high-throughput phenotypic characterization of endosymbiotic dinoflagellates in addition to pulse-amplitude modulated (PAM) fluorometry to characterize photosynthetic efficiency (Fv/Fm). Host phenotypes responded predictably to light-dark cycles, and stabilized after nine to twelve days of exposure to consistent light conditions. However, disruption of this acclimation period affected both the hosts circadian rhythm and the endosymbionts phenotypic profile. We also found evidence that phenotypic responses of the host and endosymbionts were generally decoupled, indicating a stronger regulatory response of light conditions on phenotypes than possible host-regulatory strategies on the endosymbiotic assemblage. This study provides unique insights into the acclimation strategies of upside-down jellyfish, an emerging model for the study of cnidarian-dinoflagellate symbiosis. HighlightsO_LICassiopea behavior and color respond predictably to changing light conditions C_LIO_LIInadequate acclimation time destabilizes the hosts circadian rhythm and causes unique phenotypic characteristics of the endosymbionts C_LIO_LILight may be a stronger influence on host and endosymbiont phenotypes than host-endosymbiont relationships C_LI

ecology↗

bioRxiv2023

Transcriptomic signatures across a critical sedimentation threshold in a major reef-building coral

Sedimentation is a major cause of global near-shore coral reef decline. While negative impacts of sedimentation on coral reef community composition have been well documented, the effects of sedimentation on coral metabolism in situ have received comparatively little attention. Using transcriptomics, we identified gene expression patterns changing across a previously defined sedimentation threshold that was deemed critical due to changes in coral cover and community composition. We identified genes, pathways, and molecular processes associated with this transition that may allow corals, such as Porites lobata, to tolerate chronic, severe sedimentation and persist in turbid environments. Alternative energy generation pathways may help Porites lobata maintain a persistent stress response to survive while light and oxygen availability are diminished. We found evidence for the expression of genes linked to increased environmental sensing and cellular communication that likely allow Porites lobata to efficiently respond to sedimentation stress and associated pathogen challenges. Cell damage increases under stress; consequently, we found apoptosis pathways over-represented under severe sedimentation, a likely consequence of damaged cell removal to maintain colony integrity. The results presented here provide a framework for the response of Porites lobata to sedimentation stress under field conditions. Testing this framework and its related hypotheses using multi-omics approaches can further our understanding of metabolic plasticity and acclimation potential of corals to sedimentation and their resilience in turbid reef systems.

molecular biology↗

bioRxiv2023

Seasonal dynamics and environmental drivers of tissue and mucus microbiomes in the staghorn coral Acropora pulchra

BackgroundRainfall-induced coastal runoff represents an important environmental impact in near-shore coral reefs that may affect coral-associated bacterial microbiomes. Shifts in microbiome community composition and function can stress corals and ultimately cause mortality and reef declines. Impacts of environmental stress may be site specific and differ between coral microbiome compartments (e.g., tissue versus mucus). Coastal runoff and associated water pollution represent a major stressor for near-shore reef-ecosystems in Guam, Micronesia. MethodsAcropora pulchra colonies growing on the West Hag[a]tna reef flat in Guam were sampled over a period of eight months spanning the 2021 wet and dry seasons. To examine bacterial microbiome diversity and composition, samples of A. pulchra tissue and mucus were collected during late April, early July, late September, and at the end of December. Samples were collected from populations in two different habitat zones, near the reef crest (farshore) and close to shore (nearshore). Seawater samples were collected during the same time period to evaluate microbiome dynamics of the waters surrounding coral colonies. Tissue, mucus, and seawater microbiomes were determined using 16S DNA metabarcoding using Illumina sequencing. In addition, water samples were collected to determine fecal indicator bacteria (FIB) concentrations, as an indicator of water pollution. Water temperatures were recorded using data loggers and precipitation data obtained from a nearby rain gauge. The correlation structure of environmental parameters (temperature and rainfall), FIB concentrations, and A. pulchra microbiome diversity was evaluated using a struictural equation model. Beta diversity analyses were used to investigate spatio-temporal trends of microbiome composition. ResultsA. pulchra microbiome diversity differed between tissues and mucus, with mucus microbiome diversity being similar to the surrounding seawater. Rainfall and associated fluctuations of FIB concentrations were correlated with changes in tissue and mucus microbiomes, indicating their role as drivers of A. pulchra microbiome diversity. A. pulchra tiussue microbiome composition remained relatively stable throughout dry and wet seasons and were dominated by Endozoicomonadaceae, coral endosymbionts and putative indicators of coral health. In nearshore A. pulchra tissue microbiomes, Simkaniaceae, putative obligate coral endosymbionts, were more abundant than in A. pulchra colonies growing near the reef crest (farshore). A. pulchra mucus microbiomes were more diverse during the wet season than the dry season, a distinction that was also associated with drastic shifts in microbiome composition. This study highlights the seasonal dynamics of coral microbiomes and demonstrates that microbiome diversity and composition may differ between coral tissues and the surface mucus layer.

ecology↗

bioRxiv2022

Photosystem regulation in coral-associated dinoflagellates (Symbiodiniaceae) is the primary mode for seasonal acclimation

Coral-associated dinoflagellates (Symbiodiniaceae) are photosynthetic endosymbionts that influence coral acclimation and adaptation, as indicated by photo-physiological plasticity (phenotypic variance) in response to environmental change. Symbiont shuffling (shifts in endosymbiont community composition), changes in endosymbiont cell density, and phenotypic plasticity have all been proposed as mechanisms to adjust to environmental change. However, few studies have been able to partition which of the three strategies were responsible for observed phenotypic variance. Therefore, we quantified the biodiversity, cell density, and phenotypic variance of single cells for Acropora pulchra-associated Symbiodiniaceae assemblages. Using a combination of metabarcoding and flow cytometry, we simultaneously characterized Symbiodiniaceae assemblages at the community (biodiversity), population (cell density), and individual level (phenotype) under natural environmental conditions to determine whether phenotypic variation of Symbiodiniaceae communities is concomitant with either symbiont shuffling, changes in cell density, or phenotypic plasticity. Symbiodiniaceae assemblages displayed season-specific phenotypic variance, while biodiversity was geographically structured and cell density showed limited data structure. Based on these patterns, we reveal that phenotypic plasticity of individual Symbiodiniaceae cells is the source of a phenotypic variation, thus indicating that phenotypic plasticity is a mechanism for rapid acclimation to mild environmental change.

ecology↗

bioRxiv2022

High-throughput physiological profiling of endosymbiotic dinoflagellates (Symbiodiniaceae) using flow cytometry

Endosymbiotic dinoflagellates (Family Symbiodiniaceae) are the primary producer of energy for many cnidarians, including corals. The intricate coral-dinoflagellate symbiotic relationship is becoming increasingly important under climate change, as its breakdown leads to mass coral bleaching and often mortality. Despite methodological progress, assessing the phenotypic traits of Symbiodiniaceae in-hospite remains a complex task. Bio-optics, biochemistry, or "-omics" techniques are expensive, often inaccessible to investigators, or lack the resolution required to understand single-cell phenotypic states within endosymbiotic dinoflagellate assemblages. To help address this issue, we developed a protocol that collects information on cell autofluorescence, shape, and size to simultaneously generate phenotypic profiles for thousands of Symbiodiniaceae cells, thus revealing phenotypic variance of the Symbiodiniaceae assemblage to the resolution of single cells. As flow cytometry is adopted as a robust and efficient method for cell counting, integration of our protocol into existing workflows allows researchers to acquire a new level of resolution for studies examining the acclimation and adaptation strategies of Symbiodiniaceae assemblages.

physiology↗

bioRxiv2022

Calcium homeostasis disruption initiates rapid growth after micro-fragmentation in the scleractinian coral Porites lobata

Coral reefs are ecosystems under increasing threat from global climate change. Coral restoration is a tool for preserving biological and ecological function of coral reefs by mitigating coral loss and maintaining the structural integrity and complexity of reefs. To generate the necessary stock for coral restoration, larger coral colonies are usually fragmented to generate smaller specimens for outplanting, taking advantage of the high regenerative ability of corals. In this study, we utilized RNA-seq technology to understand the physiological responses of Porites lobata colonies to physical fragmentation and outplanting, which have thus far not been characterized. Our results demonstrate that P. lobata fragments undergoing physical injury recover through two distinct phases: rapid wound regeneration of the cut margins, followed by a slower growth phase that cements the colony to the substrate. Our study found rapid physiological responses to acute physical injury and outplanting in the coral host that involved significantly increased energy production, calcium homeostasis disruption, and Endoplasmic Reticulum (ER) stress leading to increased antioxidant expression and rates of protein turnover. Our results suggest that phosphoinositide-mediated acute calcium homeostasis disruption stimulates wound recovery processes in response to physical injury. Symbiont gene expression revealed extremely low gene differences in response to fragmentation, growth, and outplanting. These results provide insight into the physiological mechanisms that allow for rapid wound healing and stabilization in response to physical injury in corals.

genetics↗

bioRxiv2020

Tackling the phylogenetic conundrum of Hydroidolina (Cnidaria: Medusozoa: Hydrozoa) by assessing competing tree topologies with targeted high-throughput sequencing.

Higher-level relationships of the Hydrozoan subclass Hydroidolina, which encompasses the vast majority of medusozoan cnidarian species diversity, have been elusive to confidently infer. The most widely adopted phylogenetic framework for Hydriodolina based on ribosomal RNA data received low support for several higher level relationships. To address this issue, we developed a set of RNA baits to target more than a hundred loci from the genomes of a broad taxonomic sample of Hydroidolina for high-throughput sequencing. Using these data, we inferred the relationships of Hydroidolina using maximum likelihood and Bayesian approaches. Both inference methods yielded well-supported phylogenetic hypotheses that largely agree with each other. Using maximum likelihood and Baysian hypothesis testing frameworks, we found that several alternate topological hypotheses proposed previously may be rejected in light of the genomic data generated for this study. Both the maximum likelihood and Bayesian topologies inferred herein consistently score well across testing frameworks, suggesting that their consensus represents the most likely phylogenetic hypothesis of Hydroidolina. This phylogenetic framework places Aplanulata as sister lineage to the remainder of Hydroidolina. This is a strong deviation from previous phylogenetic analyses that placed Capitata or Siphonophorae as sister group to the remainder of Hydroidolina. Considering that Aplanulata represents a lineage comprised of species that for the most part possess a life cycle involving a solitary polyp and free-swimming medusa stage, the phylogenetic hypotheses presented herein have potentially large implications for clarifying the evolution of life cycles, coloniality, and the division of labor in Hydrozoa as taxon sampling for phylogenetic analyses becomes more complete.

evolutionary biology↗