Search bioRxiv⌕ Search

Biology subjects

Boehm, A. B.

Publications and source records attributed to Boehm, A. B..

8 recordsLinked to original sources

Sunflower sea star (Pycnopodia helianthoides) environmental DNA (eDNA) shedding and decay: Influence of sunlight and comparison to other marine organisms

Conservation practitioners increasingly turn to environmental DNA (eDNA) for biomonitoring, yet interpreting DNA-based data requires attention to organismal shedding and decay dynamics. Here, we characterize shedding rates and decay rate constants of eDNA from Pycnopodia helianthoides, a critically endangered and ecologically important sea star in the Northeast Pacific Ocean. Shedding rates were quantified via a mesocosm experiment utilizing twelve stars of varying sizes, and decay rate constants were calculated for naturally shed P. helianthoides eDNA under natural sunlit and dark conditions for 96 hours. We additionally completed a systematic search and review of marine organism shedding rates and decay rate constants. P. helianthoides decay rate constants (k) were not different under sunlit and dark conditions (average k=0.0257 hr-1) and among the lowest third reported for marine organisms. Similarly, biomass-normalized shedding rates (between 896 and 19,800 copies/hr/g) and shedding rates per individual (between 22,000 and 548,000 copies/hr/individual) were among the lowest recorded across marine organisms. Shedding rates were influenced, in part, by organism stress levels. This work aids interpretation of measured eDNA concentrations in marine environments and serves as a roadmap for integrating shedding and decay studies into eDNA assay design.

ecology↗

Molecular Star Gazing: Development and Validation of an Environmental DNA Assay for the Imperiled Sunflower Sea Star (Pycnopodia helianthoides)

The sunflower sea star (Pycnopodia helianthoides) suffered a catastrophic population decline across its range from 2013 to 2017 due to the devastating Vibrio pectenicida FHCF-3 driven sea star wasting disease (SSWD) pandemic with minimal signs of population recovery. The functional extinction of this apex predator across substantial parts of its range has created a need to identify and track the remaining intact populations. Environmental DNA (eDNA) approaches provide a simple, cost-effective, and non-destructive method for monitoring occurrences, and in some cases abundances, of marine species, consistently outperforming visual occurrence monitoring efforts in sensitivity, speed, and cost. Here, we designed, developed, and validated a P. helianthoides-specific eDNA assay to identify refugia, using both quantitative and digital droplet PCR approaches. We first generated the most comprehensive sea star mitochondrial genome reference database to date (n=93 taxa, n= 15 novel). We then used unikseq and Geneious bioinformatics software to identify the unique nad5 gene region and design a highly specific hydrolysis probe-based PCR assay. We validated the performance of this assay through laboratory, mesocosm, and field testing, demonstrating a highly specific and sensitive assay. In a field application of the new assay across regions in British Columbia, Canada, we found a positive correlation between P. helianthoides eDNA concentrations and biomass density, especially when appropriately accounting for spatiotemporal integration scales (R2=0.67). The eDNA assay provides a rapid and scalable tool for monitoring the sunflower sea star which has been proposed for listing as threatened under the U.S. Endangered Species Act of 1973. Molecular tools like the one presented here enhance management and recovery efforts not only by identification and monitoring of remnant wild populations, but also by helping to assess population level response and recovery following reintroduction efforts.

molecular biology↗

Investigating Cement-Based Surfaces as a Sustainable Flooring Solution to Improve Ascaris Egg Removal and Inactivation in Low-Resource Settings

Soil-transmitted helminths, like Ascaris, are significant contributors to disease burden in low- and middle-income countries (LMICs). Infections are associated with growth faltering and mortality in children and are often transmitted through contact with eggs in fecally contaminated soil. Interventions, like replacing household soil floors with cement-based alternatives, may reduce exposure to Ascaris eggs, but there are currently no estimates on the removal or survival of Ascaris eggs on cement-based surfaces. This study addresses that knowledge gap by evaluating the removal of Ascaris eggs from mopping and the survival of Ascaris eggs on two cement-based mixes: an Ordinary Portland Cement (OPC) mortar and an OPC mortar with fly ash, which provides a more sustainable alternative to the OPC mortar mix. We assessed egg survival at two temperatures representing the dry (15{degrees}C) and wet (34{degrees}C) seasons in Bangladesh using two different egg enumeration methods. After mopping, over 92% of viable eggs were removed from surfaces, with no significant differences between cement-based mixes (p = 0.51). The first-order decay rate constants (k) of Ascaris eggs were similar between mix designs (p = 0.62) but varied significantly between temperatures (p = 4.2 x 10-25) and egg enumeration methods (p = 2.4 x 10-8). The k values were of greater magnitude at 34{degrees}C compared to at 15{degrees}C. At 15{degrees}C, k values were not significantly different from zero, indicating no inactivation. The k values we obtained were comparable to those reported in previous studies for different matrices, indicating comparable inactivation of Ascaris eggs on cement-based surfaces compared to liquid and semi-solid matrices. These results provide some of the first estimates of removal efficiencies and inactivation times in realistic environmental conditions for Ascaris on surfaces while supporting the use of OPC mortar mix designs with fly ash in interventions to reduce Ascaris transmission in rural LMIC households. Author SummarySoil-transmitted helminths, like Ascaris, are parasites that are major contributors to disease in children and women of childbearing age in low- and middle-income countries. Interventions, like replacing soil floors in households with cement-based flooring, may reduce exposure to Ascaris eggs which cause infections, but there is little information on how or why these interventions may be effective. This study investigates the effectiveness of simple cleaning methods, like mopping, in removing Ascaris eggs from cement-based surfaces and explores how long these eggs can survive on these surfaces under different environmental conditions. We tested two types of cement-based surfaces, a traditional cement-based mortar mix, and a more sustainable cement-based mortar mix, and found that mopping removed over 92% of Ascaris eggs, with no differences between cement mixes. Experiments simulating wet and dry seasonal conditions showed that Ascaris eggs survive longer in cooler environments, again with no differences between cement mixes. These findings provide important insights into the role of cement-based flooring in interrupting disease transmission and suggest sustainable cement-based mortar mixes are a feasible alternative to traditional cement-based mortar mixes.

microbiology↗

Evaluating the Survival and Removal of Escherichia coli from Surfaces Made with Traditional and Sustainable Cement-Based Materials in Field-Relevant Conditions

Soil household floors are common in low- and middle-income countries (LMICs) and can serve as reservoirs of enteric pathogens. Cement-based floors may interrupt pathogen transmission, but little is known about pathogen survival or removal from cement-based surfaces. This study investigated the survival of Escherichia coli (E. coli), an indicator of fecal contamination, on cement-based surfaces and evaluated its reduction through common household activities (mopping, sweeping, and walking). We compared E. coli fate on three mixes: 1) Ordinary Portland Cement (OPC) concrete (used in the United States), 2) OPC mortar (used in Bangladesh), and 3) OPC mortar with fly ash (a sustainable alternative to the Bangladesh mix). Additionally, we compared outcomes on cement-based surfaces with and without soil and at two temperatures representing the dry and wet seasons in Bangladesh. After 4 hours on the cement-based surfaces, E. coli decayed more than 1.1 log10(C/Co) under all conditions tested, which is significantly faster than in bulk soils. The higher temperature increased the decay rate constant (p = 5.56*10-8) while soil presence decreased it (p = 2.80*10-6). Sweeping and mopping resulted in high levels of removal for all mixes, with a mean removal of 71% and 78%, respectively, versus 22% for walking. The concrete and mortar mix designs did not impact E. coli survival or removal (p > 0.20). Cement-based floors made with a fly ash mix performed similarly to traditional cement-based floors, supporting its potential use as a more sustainable intervention to reduce fecal contamination in rural LMIC household settings. ImportanceCement-based surfaces may serve as a health intervention to reduce the fecal-oral transmission of pathogens in household settings, but there is a critical lack of evidence about the fate of indicator organisms on these surfaces, especially in field-relevant conditions. This study provides some of the first insights into E. coli survival on cement-based surfaces and the effectiveness of daily activities for removing E. coli. Additionally, this study explores the fate of E. coli on cement-based surfaces made with fly ash (which contributes fewer CO2 emissions) versus traditional cement mixes. We found that E. coli had similar survival and removal across all mix designs, demonstrating that fly ash mixes are feasible for use in household settings (e.g., in floors). The findings enhance understanding of fecal-oral transmission pathways and support the use of fly ash mixes in cement-based flooring in future epidemiologic studies assessing effects on enteric disease burdens.

microbiology↗

Persistence and Free Chlorine Disinfection of Human Coronaviruses and Their Surrogates in Water

The COVID-19 pandemic illustrates the importance of understanding the behavior and control of human pathogenic viruses in the environment. Exposure via water (drinking, bathing, and recreation) is a known route of transmission of viruses to humans, but the literature is relatively void of studies on the persistence of many viruses, especially coronaviruses, in water and their susceptibility to chlorine disinfection. To fill that knowledge gap, we evaluated the persistence and free chlorine disinfection of human coronavirus OC43 (HCoV-OC43) and its surrogates, murine hepatitis virus (MHV) and porcine transmissible gastroenteritis virus (TGEV), in drinking water and laboratory buffer using cell culture methods. The decay rate constants of human coronavirus and its surrogates in water varied depending on virus and water matrix. In drinking water prior to disinfectant addition, MHV showed the largest decay rate constant (2.25 day-1) followed by HCoV-OC43 (0.99 day-1) and TGEV (0.65 day-1); while in phosphate buffer, HCoV-OC43 (0.51 day-1) had a larger decay rate constant than MHV (0.28 day-1) and TGEV (0.24 day-1). Upon free chlorine disinfection, the inactivation rates of coronaviruses were independent of free chlorine concentration and not affected by water matrix, though they still varied between viruses. TGEV showed the highest susceptibility to free chlorine disinfection with the inactivation rate constant of 113.50 mg-1 min-1 L, followed by MHV (81.33 mg-1 min-1 L) and HCoV-OC43 (59.42 mg-1 min-1 L). ImportanceThis study addresses an important knowledge gap on enveloped virus persistence and disinfection in water. Results have immediate practical applications for shaping evidence-based water policies, particularly in the development of disinfection strategies for pathogenic virus control.

microbiology↗

Environmental DNA (eDNA) metabarcoding differentiates between micro-habitats within the rocky intertidal

While the utility of environmental DNA (eDNA) metabarcoding surveys for biodiversity monitoring continues to be demonstrated, the spatial and temporal variability of eDNA, and thus the limits of the differentiability of an eDNA signal, remains under-characterized. In this study, we collected eDNA samples from distinct micro-habitats ([~]40 m apart) in a rocky intertidal ecosystem over their exposure period in a tidal cycle. During this period, the micro-habitats transitioned from being interconnected, to physically isolated, to interconnected again. Using a well-established eukaryotic (cytochrome oxidase subunit I) metabarcoding assay, we detected 415 species across 28 phyla. Across a variety of univariate and multivariate analyses, using just taxonomically-assigned data as well as all detected amplicon sequence variants (ASVs), we identified unique eDNA signals from the different micro-habitats sampled. This differentiability paralleled ecological expectations and increased as the sites became more physically disconnected. Our results demonstrate that eDNA biomonitoring can differentiate micro-habitats in the rocky intertidal only 40 m apart, that these differences are ecologically meaningful, and that physical connectivity informs the degree of differentiation possible. These findings showcase the potential power of eDNA biomonitoring to increase the spatial and temporal resolution of marine biodiversity data, aiding research, conservation, and management efforts.

ecology↗

Tomato brown rugose fruit virus Mo gene is a novel microbial source tracking marker

Microbial source tracking (MST) identifies sources of fecal contamination in the environment using fecal host-associated markers. While there are numerous bacterial MST markers, there are few viral markers. Here we design and test novel viral MST markers based on tomato brown rugose fruit virus (ToBRFV) genomes. We assembled eight nearly complete genomes of ToBRFV from wastewater and stool samples from the San Francisco Bay Area in the United States of America. Next, we developed two novel probe-based RT-PCR assays based on conserved regions of the ToBRFV genome, and tested the markers sensitivities and specificities using human and non-human animal stool as well as wastewater. TheToBRFV markers are sensitive and specific; in human stool and wastewater, they are more prevalent and abundant than a currently used marker, the pepper mild mottle virus (PMMoV) coat protein (CP) gene. We applied the assays to detect fecal contamination in urban stormwater samples and found that the ToBRFV markers matched cross-assembly phage (crAssphage), an established viral MST marker, in prevalence across samples. Taken together, ToBRFV is a promising viral human-associated MST marker. ImportanceHuman exposure to fecal contamination in the environment can cause transmission of infectious diseases. Microbial source tracking (MST) can identify sources of fecal contamination so that contamination can be remediated and human exposures can be reduced. MST requires the use of fecal host-associated MST markers. Here we design and test novel MST markers from genomes of tomato brown rugose fruit virus (ToBRFV). The markers are sensitive and specific to human stool, and highly abundant in human stool and wastewater samples.

microbiology↗

Transfer rate of enveloped and non-enveloped viruses between fingerpads and surfaces

Fomites can represent a reservoir for pathogens, which may be subsequently transferred from surfaces to skin. In this study we aim to understand how different factors (including virus type, surface type, time since last handwash, and direction of transfer) affect virus transfer rates, defined as the fraction of virus transferred, between fingerpads and fomites. To determine this, 360 transfer events were performed with 20 volunteers using Phi6 (a surrogate for enveloped viruses) and MS2 (a surrogate for non-enveloped viruses), and three clean surfaces (stainless steel, painted wood, and plastic). Considering all transfer events (all surfaces and both transfer directions combined), the mean transfer rates of Phi6 and MS2 were 0.17 and 0.26, respectively. Transfer of MS2 was significantly higher than Phi6 (P<0.05). Surface type was a significant factor that affected the transfer rate of Phi6: Phi6 is more easily transferred to and from stainless steel and plastic than to and from painted wood. Direction of transfer was a significant factor affecting MS2 transfer rates: MS2 is more easily transferred from surfaces to fingerpads than from fingerpads to surfaces. Data from these virus transfer events, and subsequent transfer rate distributions, provide information which can be used to refine quantitative microbial risk assessments. This study is the first to provide a large-scale data set of transfer events with a surrogate for enveloped viruses, which extends the reach of the study to the role of fomites in the transmission of human enveloped viruses like influenza and SARS-CoV-2. ImportanceThis study created the first large-scale data set for the transfer of enveloped viruses between skin and surfaces. The data set produced by this study provides information on modelling the distribution of enveloped and non-enveloped virus transfer rates, which can aid in the implementation of risk assessment models in the future. Additionally, enveloped and non enveloped viruses were applied to experimental surfaces in an equivalent matrix to avoid matrix effects, so results between different viral species can be directly compared without confounding effects of different matrices. Our results indicating how virus type, surface type, time since last handwash, and direction of transfer affect virus transfer rates can be used in decision-making processes to lower the risk of viral infection from transmission through fomites.

microbiology↗