Biology subjects

Wright, R. M.

Publications and source records attributed to Wright, R. M..

14 recordsLinked to original sources

bioRxiv2026

Pumping stations negatively affect the distribution of critically endangered European eel (Anguilla anguilla); a landscape-scale study using environmental DNA metabarcoding

Context Pumping stations pose a threat to fish globally through land use change, habitat fragmentation and entrainment risk, with the catadromous and critically endangered European eel particularly impacted. Objectives/methods Establish, model, assess and understand the present-day distribution of European eel and resident fishes in 152 pumping station catchments in a once extensive wetland (The Fens) using eDNA metabarcoding (855 samples over two and half years), with specific focus on anthropogenic influences on hydrological connectivity and habitat quality. A removal survey design maximised confidence in negative results while minimising time and consumable costs. Results Eel occurrence upstream of pumping stations was low (occupancy = 28.3%) and positively associated with catchment area, fish species richness and natural hydrological connectivity (gravity drainage or flooding) and negatively associated with distance from the tidal limit. Fish species richness replaced catchment area and improved model performance, potentially acting as a biotic indicator of habitat quality and connectivity. Pumped catchments with manually operated upstream water transfers had reduced eel presence, potentially linked to the direction of water flow or the timing of operation. By contrast, fish species richness increased in these catchments during summer, suggesting displacement into unsuitable long-term habitats. Physical habitat maintenance had no detectable effect on eel occurrence or fish species richness. Conclusions This study provides the first landscape-scale assessment of European eel distribution and drivers of occurrence in pumped river catchments. The highly novel and comprehensive insights have implications for European eel conservation as well as infrastructure and catchment management, including compliance with legislation (EC Regulation No. 1100/2007).

ecology↗

bioRxiv2026

Species-specific versus community-wide assays in eDNA monitoring of European eel Anguilla anguilla: Trade-offs between detection sensitivity and the value of additional community data

Effective monitoring of the critically endangered European eel (Anguilla anguilla) is essential for conservation planning and regulatory decision-making, particularly in heavily fragmented rivers. Environmental DNA (eDNA) methods offer sensitive alternatives to traditional surveys, but there is uncertainty around whether targeted assays or community-wide approaches are better suited to achieve monitoring objectives. We compared eDNA metabarcoding and species-specific quantitative PCR (qPCR) for detecting A. anguilla across 145 pumped catchments in the Fens, East Anglia, England. All sites were sampled once initially, and sites negative for A. anguilla were re-sampled based on metabarcoding results. This allowed comparison of detection rates from a single water sample and site-level retrospective identification of sites where qPCR could have identified A. anguilla in earlier samples. The findings were also set in the context of the wider biodiversity information generated by metabarcoding. From the initial (single) water sample, qPCR detected A. anguilla at seven more sites than metabarcoding (17 versus 10). With repeated sampling, metabarcoding detected A. anguilla at 43 sites, including all but one of the sites where qPCR detected A. anguilla, and ten sites where qPCR did not detect A. anguilla within the same number of samples. Indeed, the additional sampling effort required to detect A. anguilla with metabarcoding at sites also positive with qPCR was small relative to the overall sampling effort. Furthermore, metabarcoding additionally detected 28 non-target fish species alongside fish, amphibian and mammal species of conservation concern. Our results highlight trade-offs between target-species sensitivity and the broader ecological information provided by each method, and support metabarcoding as an effective tool for a holistic conservation approach, with the additional community data outweighing the marginally increased sensitivity of qPCR.

ecology↗

bioRxiv2024

Seasonal changes in fish eDNA signal vary between contrasting river types

Due to the societal reliance on goods and services provided by river systems, and their close proximity to settlements, few modern-day rivers are without significant anthropogenic modifications. The natural river hydrology is often altered as a consequence of pumping water for flood alleviation, retaining water for irrigation and modifying channels for navigation. In recent years, water pumping stations have been found to have several adverse impacts, including fish mortality (direct and indirect) and habitat fragmentation. More broadly, modern-day river systems face a myriad of anthropogenic flow and channel modifications, with varying impacts on different fish life stages. To manage such risks in line with policy, knowledge of the overall fish community and priority species present is required. It is therefore important to understand the robustness of developing survey strategies across differently managed river systems. This study investigates the seasonal patterns of environmental DNA (eDNA) metabarcoding detections from water samples, taken across three differently managed river types over a one-year period. We observed some significant seasonal variation in detection rates and fish communities; however, this variation was not consistent among river types. Despite this, we found comparatively poor fish communities upstream of pumping stations all year-round, with pumped catchments containing significantly fewer species than the adjacent main river channel and our regional control site. Finally, we highlight that seasonal variation in detectability for the overall fish community may not always reflect that of priority species. In our case, we found favourable European eel (Anguilla anguilla) detection in the summer months across all river types. It is therefore recommended that rather than focusing on overall detectability, policy driven targeted surveys should be designed with priority species ecology in mind.

ecology↗

bioRxiv2024

Proving a negative; estimating species 'Confidence in Absence for Decision-Making' (CIADM) using environmental DNA monitoring

O_LIPolicy-driven decision-making is an important aspect of environmental management globally, often focused on protecting priority species. However, declining trends in freshwater biodiversity have resulted in a lack of up-to-date knowledge regarding the distribution of rare and elusive species. Furthermore, when dealing with priority species, it is sometimes more important to provide a confident assessment of absence, than merely confirm their presence. Without such confident assessments, resource intensive management plans may be misplaced, and not adequately targeted to conserve important remaining populations. C_LIO_LIHere, we present a framework to estimate confidence in absence, referred to as "Confidence in Absence for Decision-Making" (CIADM), based on single-visit environmental DNA metabarcoding data obtained from water samples. It uses a case study of European eel presence / absence upstream of 44 water pumping stations, given their critically endangered status and the legislative drivers for remediation (EC Eel Regulation 1100/2007, Eels (England and Wales) Regulation 2009). Through a high degree of biological (sample) and technical (PCR) replication, we retrospectively assigned confidence in absence values and proposed various strategies to achieve the required confidence levels in future surveys. C_LIO_LIOur findings indicate that 17 out of 44 pumping stations tested positive for eel, and we were able to assign a >99% confidence level that the remaining 27 sites were negative for eel DNA at the time of sampling. Increasing both biological and technical replication increased confidence in absence values. For example, using three PCR replicates per sample, required four replicate biological samples to achieve >95% and six to achieve >99% confidence in eel absence given non-detection. However, we estimate that by using seven PCR replicates per sample a >99% confidence in eel absence following non-detection could be achieved with only three replicate biological samples. Furthermore, we found that eel positive sites had significantly higher species richness, and fish communities differed between eel positive and eel negative sites. C_LIO_LIThis study highlights the importance of optimising workflow specific replication, and provides an adaptable framework to produce confidence estimations of priority species absence given non-detection. C_LI

ecology↗

bioRxiv2023

Symbiosis modulates gene expression of symbionts, but not hosts, under thermal challenge

Increasing ocean temperatures are causing dysbiosis between coral hosts and their symbionts. Previous work suggests that coral host gene expression responds more strongly to environmental stress compared to their intracellular symbionts; however, the causes and consequences of this phenomenon remain untested. We hypothesized that symbionts are less responsive because hosts modulate symbiont environments to buffer stress. To test this hypothesis, we leveraged the facultative symbiosis between the scleractinian coral Oculina arbuscula and its symbiont Breviolum psygmophilum to characterize gene expression responses of both symbiotic partners in and ex hospite under thermal challenges. To characterize host and in hospite symbiont responses, symbiotic and aposymbiotic O. arbuscula were exposed to three treatments: 1) control (18{degrees}C), 2) heat (32{degrees}C), and 3) cold (6{degrees}C). This experiment was replicated with B. psygmophilum cultured from O. arbuscula to characterize ex hospite symbiont responses. Both thermal challenges elicited classic environmental stress responses (ESRs) in O. arbuscula regardless of symbiotic state, with hosts responding more strongly to cold challenge. Hosts also exhibited stronger responses than in hospite symbionts. In and ex hospite B. psygmophilum both downregulated genes associated with photosynthesis under thermal challenge; however, ex hospite symbionts exhibited greater gene expression plasticity and differential expression of genes associated with ESRs. Taken together, these findings suggest that O. arbuscula hosts may buffer environments of B. psygmophilum symbionts; however, we outline the future work needed to confirm this hypothesis.

molecular biology↗

bioRxiv2023

Macrophage Xanthine Oxidoreductase Links LPS Induced Lung Inflammatory Injury to NLRP3 Inflammasome Expression and Mitochondrial Respiration

Acute lung injury (ALI) and the acute respiratory distress syndrome (ARDS) remain poorly treated inflammatory lung disorders. Both reactive oxygen species (ROS) and macrophages are involved in the pathogenesis of ALI/ARDS. Xanthine oxidoreductase (XOR) is an ROS generator that plays a central role in the inflammation that contributes to ALI. To elucidate the role of macrophage-specific XOR in endotoxin induced ALI, we developed a conditional myeloid specific XOR knockout in mice. Myeloid specific ablation of XOR in LPS insufflated mice markedly attenuated lung injury demonstrating the essential role of XOR in this response. Macrophages from myeloid specific XOR knockout exhibited loss of inflammatory activation and increased expression of anti-inflammatory genes/proteins. Transcriptional profiling of whole lung tissue of LPS insufflated XORfl/fl//LysM-Cre mice demonstrated an important role for XOR in expression and activation of the NLRP3 inflammasome and acquisition of a glycolytic phenotype by inflammatory macrophages. These results identify XOR as an unexpected link between macrophage redox status, mitochondrial respiration and inflammatory activation.

immunology↗

bioRxiv2022

Integrating environmental DNA monitoring to inform eel (Anguilla anguilla) status in freshwaters at their easternmost range - A case study in Cyprus

AimDespite significant population declines and targeted EU regulations aimed at A. anguilla conservation, little attention has been given to their status at their easternmost range. This study applies wide scale integrated monitoring to uncover the present-day eel distribution in Cyprus inland freshwaters. These are subject to increasing pressures from water supply requirements and dam construction, as seen throughout the Mediterranean. LocationCyprus. MethodsWe applied environmental DNA metabarcoding of water samples to determine A. anguilla distribution in key freshwater catchments. In addition, we present this alongside ten years of electrofishing/netting data. Refuge traps were also deployed to establish the timing of glass eel recruitment. These outputs are used together, alongside knowledge of the overall fish community and barriers to connectivity, to provide eel conservation and policy insights. ResultsWe confirm the presence of A. anguilla in Cyprus inland freshwaters, with recruitment occurring in March. Eel distribution is restricted to lower elevation areas, and is negatively associated with distance from coast and barriers to connectivity. Many barriers to connectivity are identified, though eels were detected in 2 reservoirs upstream of dams. The overall fish community varies between freshwater habitat types. Main ConclusionsEels are much more widespread in Cyprus than previously thought, yet mostly restricted to lowland intermittent systems. This makes for a case to reconsider the requirement for eel management plans. Environmental DNA based data collected in 2020 indicate that present-day eel distribution is representative of 10-year survey trends. Suggesting that inland freshwaters may act as an unrealised refuge at A. anguillas easternmost range. Conservation efforts in Mediterranean freshwaters should focus on improving connectivity, therefore enabling eels to access inland perennial refugia. Thus, mitigating the impact of climate change and the growing number of fragmented artificially intermittent river systems.

ecology↗

bioRxiv2021

MicroRNA-like snoRNA-derived RNAs (sdRNAs) promote castration resistant prostate cancer

We have identified 38 specifically excised, differentially expressed snoRNA fragments (sdRNAs) in TCGA prostate cancer (PCa) patient samples as compared to normal prostate controls. SnoRNA-derived fragments sdRNA-D19b and -A24 emerged among the most differentially expressed and were selected for further experimentation. We found that overexpression of either sdRNA significantly increased PC3 (a well-established model of castration-resistant prostate cancer (CRPC)) cell proliferation, and that sdRNA-D19b overexpression also markedly increased the rate of PC3 cell migration. In addition, both sdRNAs provided drug-specific resistances with sdRNA-D19b levels correlating with paclitaxel resistance and sdRNA-24A conferring dasatinib resistance. In silico and in vitro analyses revealed that two established PCa tumor suppressor genes, CD44 and CDK12, represent targets for sdRNA-D19b and sdRNA-A24 respectively. This outlines a biologically coherent mechanism by which sdRNAs downregulate tumor suppressors in AR-PCa to enhance proliferative and metastatic capabilities and to encourage chemotherapeutic resistance. Aggressive proliferation, rampant metastasis, and recalcitrance to chemotherapy are core characteristics of CRPC that synergize to produce a pathology that ranks 2nd in cancer-related deaths for men. This study defines sdRNA-D19b and -A24 as contributors to AR-PCa potentially providing novel biomarkers and therapeutic targets of use in PCa clinical intervention.

cancer biology↗

bioRxiv2020

Gene expression associated with disease resistance and long-term growth in a reef-building coral

Rampant coral disease, exacerbated by climate change and other anthropogenic stressors, threatens reefs worldwide, especially in the Caribbean. Physically isolated yet genetically connected reefs such as Flower Garden Banks National Marine Sanctuary (FGBNMS) may serve as potential refugia for degraded Caribbean reefs. However, little is known about the mechanisms and trade-offs of pathogen resistance in reef-building corals. Here we measure pathogen resistance in Montastraea cavernosa from FGBNMS. We identified individual colonies that demonstrated resistance or susceptibility to Vibrio spp. in a controlled laboratory environment. Long-term growth patterns suggest no trade-off between disease resistance and calcification. Predictive (pre-exposure) gene expression highlights subtle differences between resistant and susceptible genets, encouraging future coral disease studies to investigate associations between resistance and replicative age and immune cell populations. Predictive gene expression associated with long-term growth underscores the role of cation transporters and extracellular matrix remodelers, contributing to the growing body of knowledge surrounding genes that influence calcification in reef-building corals. Together these results demonstrate that coral genets from isolated sanctuaries such as FGBNMS can withstand pathogen challenges and potentially aid restoration efforts in degraded reefs. Furthermore, gene expression signatures associated with resistance and long-term growth help inform strategic assessment of coral health parameters.

genomics↗

bioRxiv2019

Eukaryotic plankton community stability across reef environments in Bocas del Toro Archipelago (Panama)

Variation in light and temperature can influence the genetic diversity and structure of marine plankton communities. While open ocean plankton communities receive much scientific attention, little is known about how environmental variation affects tropical coral reef plankton communities. Here, we characterize eukaryotic plankton communities on coral reefs across the Bocas del Toro Archipelago in Panama. Temperature loggers were deployed for one year and mid-day light levels were measured to quantify environmental differences across reef zones at four inner and four outer reef sites: Inner: Punta Donato, Smithsonian Tropical Research Institute (STRI) Point, Cristobal, Punta Laurel and Outer: Drago Mar, Bastimentos North, Bastimentos South, and Popa Island. Triplicate vertical plankton tows were collected mid-day and high-throughput 18S ribosomal DNA metabarcoding was leveraged to investigate the relationship between eukaryotic plankton community structure and reef zones. Plankton communities from STRI Point were additionally characterized in the morning ([~]08:00), mid-day ([~]12:00), and evening ([~]16:00) to quantify diel variation within a single site. We found that inshore reefs experienced higher average seawater temperatures, while offshore sites offered higher light levels, presumably associated with reduced water turbidity on reefs further from shore. However, these significant reef zone-specific environmental differences did not correlate with overall plankton community differences or changes in plankton genetic diversity. Instead, we found that time of day within a site and diel vertical migration played structuring roles within these plankton communities, and therefore conclude that the time of community sampling is an important consideration for future studies. Overall, plankton communities in the Bocas del Toro Archipelago appear relatively well mixed across space; however, follow-up studies focusing on more intensive sampling efforts across space and time coupled with techniques that can detect more subtle genetic differences between and within communities will more fully capture plankton dynamics in this region.

ecology↗

bioRxiv2019

Gene expression of endangered coral (Orbicella spp.) in the Flower Garden Banks National Marine Sanctuary after Hurricane Harvey

About 160 km south of the Texas-Louisiana border, the East and West Flower Garden Banks (FGB) have maintained >50% coral cover with infrequent and minor incidents of disease or bleaching since monitoring began in the 1970s. However, a storm that generated coastal flooding, which ultimately interacted with the reef system, triggered a mortality event in 2016 that killed 2.6% of the East FGB. To capture the immediate effects of storm-driven freshwater runoff on coral and symbiont physiology, we leveraged the heavy rainfall associated with Hurricane Harvey in late August 2017 by sampling FGB corals at two times: September 2017, when salinity was reduced; and one month later when salinity had returned to typical levels (~36 ppt in October 2017). Tissue samples (N = 47) collected midday were immediately preserved for gene expression profiling from two congeneric coral species (Orbicella faveolata and Orbicella franksi) from the East and West FGB to determine the physiological consequences of storm-derived runoff. In the coral, differences between host species and sampling time points accounted for the majority of differentially expressed genes. Gene ontology enrichment for genes differentially expressed immediately after Hurricane Harvey indicated increases in cellular oxidative stress responses. Although tissue loss was not observed on FGB reefs following Hurricane Harvey, our results suggest that poor water quality following this storm caused FGB corals to experience sub-lethal stress. We also found dramatic expression differences across sampling time points in the corals algal symbiont, Breviolum minutum. Some of these differentially expressed genes may be involved in the symbionts response to changing environments, whereas a group of differentially expressed post-transcriptional RNA modification genes also suggest a critical role of post-transcriptional processing in symbiont acclimatization. In this study, we cannot disentangle the effects of reduced salinity from the collection time point, so these expression patterns may also be related to seasonality. These findings highlight the urgent need for continued monitoring of these reef systems to establish a baseline for gene expression of healthy corals in the FGB system across seasons, as well as the need for integrated solutions to manage stormwater runoff in the Gulf of Mexico.

genomics↗

bioRxiv2019

Positive genetic associations among fitness traits support evolvability of a reef-building coral under multiple stressors

Climate change threatens organisms in a variety of interactive ways that requires simultaneous adaptation of multiple traits. Predicting evolutionary responses requires an understanding of the potential for synergistic interactions among stressors and the genetic variance and covariance among fitness-related traits that may reinforce or constrain an adaptive response. Here we investigate the capacity of Acropora millepora, a reef-building coral, to adapt to multiple environmental stressors: rising sea surface temperature, ocean acidification, and increased prevalence of infectious diseases. We measured growth rates (weight gain), coral color (a proxy for Symbiodiniaceae density), and survival, in addition to nine physiological indicators of coral and algal health in 40 coral genets exposed to each of these three stressors singly and combined. Individual stressors resulted in predicted responses (e.g., corals developed lesions after bacterial challenge and bleached under thermal stress). However, corals did not suffer substantially more when all three stressors were combined. Nor were tradeoffs observed between tolerances to different stressors; instead, individuals performing well under one stressor also tended to perform well under every other stressor. An analysis of genetic correlations between traits revealed positive co-variances, suggesting that selection to multiple stressors will reinforce rather than constrain the simultaneous evolution of traits related to holobiont health (e.g., weight gain and algal density). These findings support the potential for rapid coral adaptation under climate change and emphasize the importance of accounting for corals adaptive capacity when predicting the future of coral reefs.

evolutionary biology↗

bioRxiv2019

Symbiont community diversity is more constrained in holobionts that tolerate diverse stressors

Coral reefs are experiencing global declines as climate change and other stressors cause environmental conditions to exceed the physiological tolerances of host organisms and their microbial symbionts (collectively termed the holobiont). To assess the role of symbiont community composition in holobiont stress tolerance, diversity metrics and abundances of obligate dinoflagellate endosymbionts (Family: Symbiodiniaceae) were quantified from eight Acropora millepora coral colonies (hereafter called genets) that thrived under or responded poorly to various stressors. Four best performer coral genets were selected for analysis because they survived 10 days of high temperature, high pCO2, bacterial addition, or combined stressors, whereas four worst performer coral genets were analyzed because they experienced significant mortality under these stressors. At the end of the experimental period, seven of eight coral genets mainly hosted Cladocopium symbionts, but also contained Brevolium, Durusdinium, and/or Gerakladinium symbionts at lower abundances (<0.1% of the total community). After 10 days of stress, symbiont communities varied significantly among host genets, but not stress treatments, based on alpha and beta diversity metrics. A generalized joint attribute model (GJAM) also predicted that symbiont communities were primarily sensitive to host genet at regional scales. Indicator species analysis and the regional GJAM model identified significant associations among particular symbionts and host genet performance. Specifically, Cladocopium 3k contributed to the success of best performer host genets under various stressful conditions, whereas Durusdinium glynnii and Durusdinium trenchii were significantly associated with one worst performer genet. Cladocopium 3k dominance should be more broadly investigated as a potential predictor of stress resistance in Acropora millepora populations across their geographic range. Symbiodiniaceae communities exhibited higher richness and variance (beta diversity) in the worst performing genets. These findings highlight that symbiont community diversity metrics may be important indicators of resilience in hosts central to diverse disciplines, from agriculture to medicine.

ecology↗

bioRxiv2018

Effects of thermal stress on amount, composition, and antibacterial properties of coral mucus

The surface mucus layer of reef-building corals supports several essential functions including feeding, sediment clearing, and protection from pathogenic invaders. For the reef ecosystem, coral mucus provides energy to support heterotrophic benthic communities. Mucus production represents a substantial metabolic investment on behalf of the coral: as much as half of the fixed carbon supplied by the corals algal symbionts is incorporated into expelled mucus. In this study, we examined if bleaching (disruption of the coral-algal symbiosis) has the potential to indirectly disturb reef ecosystem function by impacting the nutritional composition of coral mucus. In a controlled laboratory thermal stress challenge, visibly paled corals produced mucus with higher protein and lipid content and increased antibacterial activity relative to healthy corals. These results are likely explained by the expelled symbionts in the mucus of bleached individuals. This study illuminates how the immediate effects of coral bleaching could impact the reef-ecosystem indirectly through modulation of available nutrients within the ecosystem.

molecular biology↗