Biology subjects

Ushijima, B.

Publications and source records attributed to Ushijima, B..

10 recordsLinked to original sources

bioRxiv2026

Microcalorimetry reveals bacterial motility as an expensive trait during starvation

Quantifying the energetic costs of cellular traits is important to understand their evolutionary constraints and ecological function. However, direct measurements of energy expenditure of distinct traits are rare. Here, we present direct measurements of the power dissipation due to bacterial flagellar motility using microcalorimetry, based on measuring the power dissipation of a motile population and a non-motile mutant. For the single-flagellated marine bacterium \textit{Vibrio coralliilyticus}, we determined the power dissipated by motility in cultures to be 0.91 W/mL/OD. Per swimming cell this amounts to 2.0E-15 W, or a turnover of 2.5E4 ATP molecules per second. The power dissipated for motility equals 35 % of total metabolism during starvation, indicating this is likely the most expensive cellular trait during starvation. The dissipation for motility is in good agreement with that predicted using resistive force theory, indicating that any thermodynamic inefficiencies upstream of the flagellar motor, such as metabolic inefficiencies, are small. We further show that the multiflagellated bacterium Escherichia coli dissipates 0.70 W/mL/OD when in motility buffer, comparable to marine bacteria despite the much lower swimming speed, and hence indicating lower efficiency of swimming. Finally, we show that the energy spent by Vibrio coralliilyticus on motility can have major consequences on their survival under starvation, causing a 40 % reduction in survival after 3 weeks of starvation of a motile compared to non-motile mutant. These results reveal the large costs involved in an individual trait that shapes microbial life in heterogeneous environments.

biophysics↗

bioRxiv2026

Widespread attraction of marine bacteria to the macroalgae-derived polysaccharide fucoidan

Fucoidan is the second most abundant polysaccharide in brown macroalgae, contributing up to 50% of the dissolved organic matter released daily from these algae into the ocean, substantially influencing the marine carbon cycle. Due to its complex chemical structure, fucoidan is highly resistant to microbial degradation and accumulates on the surface of macroalgae, where it contributes to regulating their microbiome. Here, we used a range of microfluidic assays to quantify the chemotactic and physiological responses of marine bacteria to fucoidan. Our results reveal that all the strains tested (14 out of 14) are attracted to fucoidan produced by two different species of brown macroalgae. Attraction occurred only at high fucoidan concentrations (0.1 to 1 mg/mL), such as those expected in the immediate vicinity of algal surfaces, whereas low concentrations elicited no response or modest chemorepulsion. Although fucoidan did not support bacterial growth under our experimental conditions, it did not impair the utilization of other carbon sources. Together, these findings suggest that fucoidan gradients can act as chemical cues guiding marine bacteria toward the nutrient-rich microenvironment of macroalgal surfaces, pointing to a potential ecological role of fucoidan in shaping macroalgal microbiota, bacterial behavior, and ultimately carbon cycling in the ocean.

microbiology↗

bioRxiv2026

Temperate and filamentous bacteriophages as reservoirs of bacterial virulence in stony coral tissue loss disease

Lysogenic conversion, in which bacteriophages (viruses that infect bacteria) integrate into bacterial genomes and confer new phenotypic traits on their hosts, is a well-established mechanism for the emergence of pathogens. While this process underpins many bacterial diseases in humans and other animals, its role in coral disease remains largely unexplored. Here, we investigate the potential role of lysogenic conversion in stony coral tissue loss disease (SCTLD), which has caused unprecedented mortality of Caribbean corals since 2014 and for which the etiological agent remains unknown. Across 27 original coral samples and 178 publicly available metagenomes from the Florida Reef Tract spanning seven coral species, we detected a greater number of unique viral genomes capable of lysogeny in diseased corals or visually healthy portions of diseased corals (DD and HD, respectively) compared to visually healthy (VH) corals. SCTLD-associated bacteriophages were primarily predicted to infect bacterial taxa previously implicated in the disease, such as Vibrionales, Rhodobacterales, and Flavobacteriia, and carried abundant and widespread virulence genes with the potential to enhance bacterial colonization, competition, or direct host damage, including homologs of Tse2, Zot, RTX, pneumolysin, and cytolytic delta-endotoxin. Although causal relationships remain unresolved, our findings indicate that phages capable of lysogenic conversion have the genomic capacity to laterally transfer bacterial virulence genes in SCTLD-affected corals. The acquisition of genes via lysogenic conversion could contribute to bacterial virulence while maintaining community taxonomic profiles, helping to explain previous community profiling observations and providing a mechanistic framework for disease pathogenesis.

genomics↗

bioRxiv2026

Phylogenetically distinct Vibrio mediterranei lineages confer robust protection under thermal stress against oyster pathogens

Marine bivalve mortality events cause substantial economic losses in aquaculture and threaten global food security. While pathogenic Vibrio species are frequently implicated, growing evidence suggests that loss of beneficial microbes can increase host susceptibility to disease. We previously observed that Vibrio mediterranei was consistently isolated from healthy oysters but systematically disappeared prior to mortality events, coinciding with proliferation of pathogenic Vibrio species. Here, we test whether this pattern reflects a protective functional role. Pre-colonization with V. mediterranei strain Vm02 increased Crassostrea virginica oyster larval survival from 10-19% (pathogen-only controls) to 94-97% when challenged with V. harveyi or V. coralliilyticus, representing near-complete protection from pathogen-induced mortality. Protection was maintained at both ambient (28{degrees}C) and thermal stress (32{degrees}C) temperatures where pathogen virulence is enhanced, rapid (effective from co-inoculation), and durable (maintained for >96 hours). Fluorescence microscopy confirmed stable colonization of larval digestive tissues by fluorescently-tagged Vm02. Larval colonization by eleven V. mediterranei strains revealed three distinct phenotypes - protective, pathogenic, and intermediate - corresponding to monophyletic clades with 97.1-97.8% average nucleotide identity between protective and pathogenic lineages. Pangenome analysis identified 230 protective-specific versus 80 pathogenic-specific orthogroups. Protective strains encode unique regulatory systems, stress tolerance mechanisms, and metabolic versatility while lacking Type I and Type VI secretion system variants associated with pathogenicity. Together, these findings demonstrate that beneficial versus pathogenic phenotypes are phylogenetically constrained within distinct V. mediterranei lineages. This supports reports that V. mediterranei acts as both a pathogen and potential symbiont in marine hosts and reveals a clade that provides robust protection against oyster pathogens. ImportanceAquaculture disease management has traditionally emphasized either prophylactic treatment using antibiotics to avoid disease and dysbiosis or has focused entirely on pathogen detection. Both of these approaches have overlooked the potential contributions of beneficial microbes to host defense and grow-out performance. Developing beneficial probiotic tools for disease prevention represents an emerging opportunity for sustainable aquaculture management. This study demonstrates that specific lineages of Vibrio mediterranei function as protective symbionts capable of rescuing oyster larvae from near-complete pathogen-induced mortality. By integrating field observations of microbial succession during mortality events with experimental validation and comparative genomics, we show that protective versus pathogenic phenotypes are phylogenetically constrained within V. mediterranei clades separated by 97.1-97.8% average nucleotide identity. This resolution of strain-level functional variation provides fundamental insights into how host-microbe mutualisms evolve within species complexes that also harbor pathogens. The unique genomic markers identified here enable reliable screening for protective symbionts, while the temperature-stable and durable protection demonstrated in this study highlights the potential for biological control strategies in shellfish hatcheries increasingly affected by warming oceans and Vibrio-driven mortality events.

microbiology↗

bioRxiv2026

Building the Marine Probiotic Platform: Developing a High-Throughput Process to Discover Coral Probiotics for Stony Coral Tissue Loss Disease

Stony coral tissue loss disease (SCTLD) is a deadly, waterborne coral disease. Since 2014, SCTLD has spread throughout Floridas Coral Reef and is now confirmed in 28 Caribbean countries and territories. The causative agent(s) remain unknown; however, pathogenic bacteria are implicated in disease progression. In contrast, a beneficial microbe (a probiotic) with antibacterial activity isolated from a disease-resistant coral has arrested SCTLD transmission and progression during laboratory and field trials. Due to host and environmental specificity, more probiotics sourced from vulnerable coral species and different SCTLD-impacted regions are needed. Conventional methods used for probiotic discovery include plating samples for single colonies, streaking for purification, and then testing strains for antibacterial activity with drop culture assays. However, these manually intensive methods are low-throughput and the measurements for antibacterial activity can be subjective. Given these constraints, this study developed a platform to greatly increase the isolation and screening of coral probiotics. Using the new platform, microbial cells were isolated from a coral mucus sample using a microfluidic cell sorter, and isolates were then screened for inhibitory activity against target pathogenic bacteria modified to express yellow fluorescent protein (YFP) that allows growth quantification using a microplate reader. In a single run using the platform, 433 isolates were sorted then individually screened against two target pathogens within six days. The workflow described herein represents a proof of concept for high-throughput environmental probiotic discovery with potential to push forward treatment development for SCTLD and future disease outbreaks.

microbiology↗

bioRxiv2025

Multidisciplinary assessments of a potentially novel acute tissue loss disease on Florida Orbicella corals

Coral disease outbreaks are an increasingly common threat to reefs. While coral disease research is expanding rapidly, there are still monumental challenges in diagnosing and differentiating among the different diseases on a reef. We used a collaborative multidisciplinary approach to characterize a potentially novel disease affecting Orbicella faveolata colonies in the Florida Keys. We tagged and fate-tracked individual lesions for progression and cessation rates, reanalyzed in situ photographs of previously monitored corals to determine prevalence and seasonality, and assessed the efficacy of amoxicillin treatments. Samples collected from lesions as well as unaffected and healthy controls were used to examine microbiomes, assess nine coral pathological parameters via histology, and measure 19 symbiont-specific physiological metrics using transmission electron microscopy (TEM). Across all analyses, we concluded that the observed disease is unlikely to be SCTLD. Many, but not all, metrics had similarities to previous descriptions of white plague, and so we additionally conducted preliminary histology on presumed white plague samples of O. franksi for comparison. However, the dearth of quantifiable histology and TEM studies on white plague did not allow us to conclusively confirm or refute comparisons to white plague. Using the recommended coral disease nomenclature, we define this specific outbreak as "Orbicella acute tissue loss disease" (OATLD). We provide unprecedented, quantified descriptions across numerous metrics of both diseased and control colonies. We suggest that these data lay the groundwork for future efforts on this disease as well as a comprehensive set of parameters against which other diseases can be compared.

physiology↗

bioRxiv2024

A T6SS in the coral pathogen Vibrio coralliilyticus secretes an arsenal of anti-eukaryotic effectors and contributes to virulence

Vibrio coralliilyticus (Vcor) is a pathogen of coral and shellfish, leading to devastating economic and ecological consequences worldwide. Although rising ocean temperatures correlate with increased Vcor pathogenicity, the specific molecular mechanisms and determinants contributing to virulence remain poorly understood. Here, we systematically analyzed the type VI secretion system (T6SS), a contact-dependent toxin delivery apparatus, in Vcor. We identified two omnipresent T6SSs that are activated at temperatures in which Vcor becomes virulent; T6SS1 is an antibacterial system mediating interbacterial competition, whereas T6SS2 mediates anti-eukaryotic toxicity and contributes to mortality during infection of an aquatic model organism, Artemia salina. Using comparative proteomics, we identified the T6SS1 and T6SS2 toxin arsenals of three Vcor strains with distinct disease etiologies. Remarkably, T6SS2 secretes at least nine novel anti-eukaryotic toxins comprising core and accessory repertoires. We propose that T6SSs differently contribute to Vcors virulence: T6SS2 plays a direct role by targeting the host, while T6SS1 plays an indirect role by eliminating competitors. Author SummaryCoral reefs are diverse ecosystems providing habitats for various fish, invertebrates, and microorganisms. Climate change, leading to rising ocean water temperatures, correlates with coral bleaching and mass mortality events. An implicated causal agent of coral disease outbreaks is the marine bacterium Vibrio coralliilyticus. Here, we found that two toxin injection systems present in all Vibrio coralliilyticus strains are regulated by temperature; we revealed the toxins that they secrete and their function in competition against rival bacteria and in the intoxication of an animal host. Our findings implicate these systems as previously unappreciated contributors to Vibrio coralliilyticus virulence, illuminating possible targets to treat or prevent coral infection.

microbiology↗

bioRxiv2023

MscS is a critical component for osmotic survival of Vibrio cholerae

Like other intestinal bacteria, the facultative pathogen Vibrio cholerae adapts to a wide range of osmotic environments. Under drastic osmotic down-shifts, Vibrio avoids mechanical rupture by rapidly releasing excessive metabolites through mechanosensitive (MS) channels that belong to two major types, low-threshold MscS and high-threshold MscL. To investigate each channels individual contribution to V. choleraes osmotic permeability response, we generated individual{Delta} mscS, {Delta}mscL, and double{Delta} mscL {Delta}mscS mutants in V. cholerae O395 and characterized their tension-dependent activation in patch-clamp experiments, as well as their millisecond-scale osmolyte release kinetics using a stopped-flow light scattering technique. We additionally generated numerical models reflecting the kinetic competition of osmolyte release with water influx. Both mutants lacking MscS exhibited delayed osmolyte release kinetics and decreased osmotic survival rates compared to WT. The{Delta} mscL mutant showed comparable release kinetics to WT, but a higher osmotic survival, while {Delta}mscS had low survival, comparable to the double{Delta} mscL {Delta}mscS mutant. By analyzing release kinetics following rapid medium dilution, we illustrate the sequence of events and define the set of parameters that characterize discrete phases of the osmotic response. Osmotic survival rates are directly correlated to the extent and duration of cell swelling, the rate of osmolyte release and the onset time, and the completeness of the post-shock membrane resealing. Not only do the two channels interact functionally during the resealing phase, but there is also a compensatory up-regulation of MscS in the{Delta} mscL strain suggesting some transcriptional crosstalk. The data reveal the advantage of the low-threshold MscS channel in curbing tension surges, without which MscL becomes toxic, and the role of MscS in the proper termination of the osmotic permeability response in Vibrio.

biophysics↗

bioRxiv2021

Metabolomics of healthy and stony coral tissue loss disease affected Montastraea cavernosa corals

Stony coral tissue loss disease, first observed in Florida in 2014, has now spread along the entire Florida Reef Tract and on reefs in many Caribbean countries. The disease affects a variety of coral species with differential outcomes, and in many instances results in whole-colony mortality. We employed untargeted metabolomic profiling of Montastraea cavernosa corals affected by stony coral tissue loss disease to identify metabolic markers of disease. Herein, extracts from apparently healthy, diseased, and recovered corals, Montastraea cavernosa, collected at a reef site near Ft. Lauderdale, Florida were subjected to liquid-chromatography mass spectrometry-based metabolomics. Unsupervised principal component analysis reveals wide variation in metabolomic profiles of healthy corals of the same species, which differ from diseased corals. Using a combination of supervised and unsupervised data analyses tools, we describe metabolite features that explain variation between the apparently healthy corals, between diseased corals, and between the healthy and the diseased corals. By employing a culture-based approach, we assign sources of a subset of these molecules to the endosymbiotic dinoflagellates, Symbiodiniaceae. Specifically, we identify various endosymbiont-specific lipid classes, such as betaine lipids, glycolipids, and tocopherols, which differentiate samples taken from apparently healthy corals and diseased corals. Given the variation observed in metabolite fingerprints of corals, our data suggests that metabolomics is a viable approach to link metabolite profiles of different coral species with their susceptibility and resilience to numerous coral diseases spreading through reefs worldwide.

systems biology↗

bioRxiv2019

Microbial community shifts associated with the ongoing stony coral tissue loss disease outbreak on the Florida Reef Tract

As many as 22 of the 45 coral species on the Florida Reef Tract are currently affected by stony coral tissue loss disease (SCTLD). The ongoing disease outbreak was first observed in 2014 in Southeast Florida near Miami and as of early 2019 has been documented from the northernmost reaches of the reef tract in Martin County down to Key West. We examined the microbiota associated with disease lesions and apparently healthy tissue on diseased colonies of Montastraea cavernosa, Orbicella faveolata, Diploria labyrinthiformis, and Dichocoenia stokesii. Analysis of differentially abundant taxa between disease lesions and apparently healthy tissue identified five unique amplicon sequence variants enriched in the diseased tissue in three of the coral species, namely an unclassified genus of Flavobacteriales and sequences identified as Fusibacter (Clostridiales), Planktotalea (Rhodobacterales), Algicola (Alteromonadales), and Vibrio (Vibrionales). In addition, several groups of likely opportunistic or saprophytic colonizers such as Epsilonbacteraeota, Patescibacteria, Clostridiales, Bacteroidetes, and Rhodobacterales were also enriched in SCTLD disease lesions. This work represents the first microbiological characterization of SCTLD, as an initial step toward identifying the potential pathogen(s) responsible for SCTLD.

microbiology↗