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  • OPEN ACCESS
    Characterization of “Brachyspira hampsonii” clades I and II isolated from commercial swine in Western Canada
    FACETS • Vol. 1 • pp. 163 - 172
    A novel Brachyspira emerged in 2009 and has since become a production-limiting pathogen of pigs in North America. The name “Brachyspira hampsonii” has been proposed for this novel taxon. “Brachyspira hampsonii” is divided into two phylogenetically distinct clades based on the sequence of the NADH-oxidase (nox) gene, although the clinical disease associated with clades I and II is indistinguishable and phenotypic characteristics that discriminate the clades have not been determined. The objectives of the current study were to enhance the description of the provisional species “B. hampsonii” with biochemical profiles and morphometric data from isolates affecting Canadian swine and to investigate potentially diagnostically informative characteristics for this emerging pathogen. Biochemical profiles of isolates from different commercial swine barns in Western Canada showed that biochemical profiles were insufficient to distinguish “B. hampsonii” clades I and II from each other or from other pathogenic Brachyspira. Hippurate hydrolysis, previously reported as uniformly negative in “B. hampsonii,” was variable among Canadian isolates. Spirochete dimensions and flagella numbers for “B. hampsonii” overlapped with other Brachyspira species. Taken together, these results indicate that nox gene sequencing remains a preferred method for identification and discrimination of “B. hampsonii” from other pig-associated Brachyspira spp.
  • OPEN ACCESS
    Identification of leaf-mining insects via DNA recovered from empty mines
    FACETS • Vol. 1 • pp. 217 - 224
    We report the development of an improved method for the extraction and amplification of leaf miner DNA recovered from empty mines. Our method is simple, easy to use, and foregoes the time-consuming task of scraping out mines required by previous methods. We collected leaves with 1- and 2-day-old vacated mines, cut out and then ground the mined portions, and amplified the mtDNA COI barcode sequence using universal insect primers. We obtained high-quality sequences for 31% of our empty mines: 20% yielded sequences associated with a leaf miner species; and an additional 11% yielded sequences associated with whiteflies, mites, or fungi. Our improved method will facilitate ecological studies determining herbivore community dynamics and agricultural studies for pest monitoring and identification.
  • OPEN ACCESS
    Substrate utilization by endophytic bacteria Paenibacillus polymyxa P2b-2R that may facilitate bacterial entrance and survival inside diverse plant hosts
    FACETS • Vol. 2 • pp. 120 - 130
    Bacterial endophytes are thought to enter plants either through pre-existing openings in plant tissues or by creating openings by hydrolyzing major plant cell wall components. A lodgepole endophyte, Paenibacillus polymyxa P2b-2R, consistently formed endophytic colonies when inoculated in diverse plant hosts, viz., lodgepole pine, western red cedar, corn, canola, and tomato. We were interested to know, whether or not this bacterial strain possesses enzymes that can hydrolyze three major plant cell wall components namely cellulose, xylan, and pectin to facilitate entrance into the host plants. Using a BIOLOG assay, we also tested this bacterial strain’s ability to utilize carbon sources that might facilitate its entrance and hence its survival inside host plants. Paenibacillus polymyxa P2b-2R hydrolyzed sodium carboxymethylcellulose, beechwood xylan, and sodium polypectate and utilized 39 of the 95 carbon sources (41%) tested. Of the 39 carbon substrates oxidized by P2b-2R, the “carbohydrates” group represents the largest source of utilizable carbon (23 out of 39). Thus, it can be concluded that P. polymyxa P2b-2R is able to degrade major cell wall components (cellulose, xylan, and pectin) and utilize some of the available carbon substrates, possibly to gain entry and survive inside the plant and form endophytic colonies thereafter.
  • OPEN ACCESS
    Survey of mercury in boreal chorus frog (Pseudacris maculata) and wood frog (Rana sylvatica) tadpoles from wetland ponds in the Prairie Pothole Region of Canada
    FACETS • Vol. 2 • pp. 315 - 329
    Tadpoles are important prey items for many aquatic organisms and often represent the largest vertebrate biomass in many fishless wetland ecosystems. Neurotoxic mercury (Hg) can, at elevated levels, decrease growth, lower survival, and cause developmental instability in amphibians. We compared total Hg (THg) body burden and concentration in boreal chorus frog (Pseudacris maculata) and wood frog (Rana sylvatica) tadpoles. Overall, body burden and concentration were lower in boreal chorus frog tadpoles than wood frog tadpoles, as expected, because boreal chorus frog tadpoles consume at lower trophic levels. The variables species, stage, and mass explained 21% of total variation for body burden in our models but had negligible predictive ability for THg concentration. The vast majority of the remaining variation in both body burden and THg concentration was attributable to differences among ponds; tadpoles from ponds in three areas had considerably higher THg body burden and concentration. The pond-to-pond differences were not related to any water chemistry or physical parameter measured, and we assumed that differences in wetland geomorphology likely played an important role in determining Hg levels in tadpoles. This is the first report of Hg in frog tadpoles in the Prairie Pothole Region of North America.
  • OPEN ACCESS
    How to build a low-cost underwater camera housing for aquatic research
    FACETS • Vol. 2 • pp. 150 - 159
    Remote cameras are an increasingly important tool in field-based biological research. Terrestrial researchers can purchase inexpensive off-the-shelf cameras, but aquatic researchers face challenges in adopting similar systems for underwater science. Although technology allows researchers to deploy cameras in any aquatic environment, high procurement costs are often a barrier, particularly for studies that require the collection of lengthy videos. In this note, we provide a detailed guide explaining how to assemble an underwater camera system for less than $425 USD. We focus especially on the construction of the underwater housing, which is typically the most expensive component of an underwater camera system. As described, this system can record 13 h full high-definition videos in depths up to 100 m. It can be constructed and assembled with limited technical background using tools available in most workshops. The guide includes a general overview of the system, a full list of components, detailed instructions on constructing the camera housing, and suggestions on how to mount and use the camera in fieldwork. Our goal for this note is to promote the wider use of remote underwater cameras in aquatic research by making them accessible to those with limited financial means.
  • OPEN ACCESS
    Physiological responses to a short-term, environmentally realistic, acute heat stress in Atlantic salmon, Salmo salar
    FACETS • Vol. 2 • pp. 330 - 341
    Atlantic salmon populations are declining, and warming river temperatures in the summer months are thought to be a significant contributing factor. We describe the time course of cellular and metabolic responses to an ecologically relevant short-term thermal cycle in juvenile Atlantic salmon. We then examined whether this heat event would affect tolerance to a subsequent heat shock in terms of critical thermal maximum (CTmax). Fish induced heat shock protein 70 in red blood cells, heart, liver, and red and white muscle; whole blood glucose and lactate transiently increased during the heat cycle. In contrast, we observed no significant effect of a prior heat shock on CTmax. The CTmax was positively correlated with Fulton’s condition factor suggesting that fish with greater energy reserves are more thermally tolerant. Atlantic salmon activate cellular protection pathways in response to a single thermal cycle and appear to cope with this short-term, ∼1 d heat shock, but this challenge may compromise the ability to cope with subsequent heat events.
  • OPEN ACCESS
    Microplastics in the gastrointestinal tracts of fish and the water from an urban prairie creek
    FACETS • Vol. 2 • pp. 395 - 409
    Microplastics are defined as any plastic with a diameter ≤5 mm. Problems associated with these plastics such as contamination of both marine and freshwater environments and ingestion by aquatic organisms are of increasing concern. Our study quantifies the number of microplastics in a prairie creek immediately downstream of Regina, Saskatchewan, Canada. Water samples and five species of fish were collected from sample sites upstream and downstream of a wastewater treatment plant (WWTP) in the summers of 2015 and 2016. Samples were digested in either a Fe(II)/H2O2 or NaClO solution and observed under a microscope where plastics present were enumerated by colour and type. At least one microplastic was detected in 73.5% of fish and 95.6% of water samples, showing that the creek does, in fact, contain microplastics. Concentrations were higher in water from upstream sites, likely due to dilution of creek water by the release of treated effluent. The results of this study provide baseline conditions for the presence of plastics in the creek prior to a major upgrade of the WWTP scheduled for completion in 2016.
  • OPEN ACCESS
    Using a linked table-based structure to encode self-describing multiparameter spatiotemporal data
    FACETS • Vol. 3 • No. 1 • pp. 326 - 337
    Multiparameter data with both spatial and temporal components are critical to advancing the state of environmental science. These data and data collected in the future are most useful when compared with each other and analyzed together, which is often inhibited by inconsistent data formats and a lack of structured documentation provided by researchers and (or) data repositories. In this paper we describe a linked table-based structure that encodes multiparameter spatiotemporal data and their documentation that is both flexible (able to store a wide variety of data sets) and usable (can easily be viewed, edited, and converted to plottable formats). The format is a collection of five tables (Data, Locations, Params, Data Sets, and Columns), on which restrictions are placed to ensure data are represented consistently from multiple sources. These tables can be stored in a variety of ways including spreadsheet files, comma-separated value (CSV) files, JavaScript object notation (JSON) files, databases, or objects in a software environment such as R or Python. A toolkit for users of R statistical software was also developed to facilitate converting data to and from the data format. We have used this format to combine data from multiple sources with minimal metadata loss and to effectively archive and communicate the results of spatiotemporal studies. We believe that this format and associated discussion of data and data storage will facilitate increased synergies between past, present, and future data sets in the environmental science community.
  • OPEN ACCESS
    Parental overweight is associated with less encouragement of child dietary balance and variety and involvement in meal planning and preparation
    FACETS • Vol. 3 • No. 1 • pp. 155 - 163
    Little is known about how the body composition of parents of preschool-aged children is associated with their food parenting practices. In this study, we examined associations between parental body composition and food parenting practices in a sample of Canadian families with preschool-aged children. We conducted a cross-sectional analysis of 68 parents and 52 preschool-aged children. Measures included height, weight, waist circumference (WC), and percentage of fat mass (%FM) measured by BOD POD™. Parents completed an adapted version of the Comprehensive Feeding Practices Questionnaire. To account for correlated observations within families, we used generalized estimating equations with linear regression modelling to examine associations between parent body composition and food parenting practices, with child body mass index (BMI) z-score, child sex, parental sex, and family household income entered as covariates in all models. Parent BMI, WC, and %FM were each significantly and inversely associated with the encouragement of a balanced diet (
    cover
     = −0.021, p = 0.006;
    cover
     = −0.007, p = 0.038;
    cover
     = −0.010, p = 0.034, respectively) and child involvement in meal planning and preparation (
    cover
     = −0.082, p = 0.002;
    cover
     = −0.025, p = 0.032;
    cover
     = −0.038, p = 0.049, respectively). We provide preliminary evidence that overweight/obesity may be associated with select food parenting practices in Canadian families with preschool-age children. Parental body composition may be an important consideration in intervention strategies that target food parenting practices.
  • OPEN ACCESS
    Determining the effects of biochar and an arbuscular mycorrhizal inoculant on the growth of fowl mannagrass (Glyceria striata) (Poaceae)
    FACETS • Vol. 3 • No. 1 • pp. 441 - 454
    Biochar is gaining attention as an organic soil amendment that can increase plant yields and improve soil fertility. We studied the effect of biochar on the growth of fowl mannagrass (Glyceria striata (Lam.) Hitchc.) (Poaceae), propagated in a greenhouse for future re-introduction into restored wetlands. Three different application rates (10%, 50%, and 75% biochar volume/substrate volume (v/v)) of nutrient-charged (i.e., nutrients added) and uncharged biochar were tested with and without a commercial arbuscular mycorrhizal fungal (AMF) inoculant. Aboveground biomass (shoot mass), belowground biomass (root mass), and shoot height of 166 G. striata samples were recorded after 92 d of growth. Using generalized linear models our data indicated a 50% (v/v) application rate of nutrient-charged biochar without AMF produces a significantly greater growth response (4.4× greater shoot height and 85× greater shoot mass compared with 0% biochar (AMF negative) control). We propose that the increased G. striata growth may be due to changes in pH, and (or) increased nutrient availability due to the addition of biochar. We recommend an application rate of 50% biochar (v/v) charged with nutrients as an advantageous amendment for propagating G. striata.
  • OPEN ACCESS
    Gender and language use in scientific grant writing
    FACETS • Vol. 4 • No. 1 • pp. 442 - 458
    Women in science, technology, engineering, and math are not equally represented across tenure-track career stages, and this extends to grant funding, where women applicants often have lower success rates compared with men. While gender bias in reviewers has been documented, it is currently unknown whether written language in grant applications varies predictably with gender to elicit bias against women. Here we analyse the text of ∼2000 public research summaries from the 2016 Natural Sciences and Engineering Research Council (NSERC) individual Discovery Grant (DG) program. We explore the relationship between language variables, inferred gender and career stage, and funding levels. We also analyse aggregated data from the 2012–2018 NSERC DG competitions to determine whether gender impacted the probability of receiving a grant for early-career researchers. We document a marginally significant gender difference in funding levels for successful grants, with women receiving $1756 less than men, and a large and significant difference in rejection rates among early-career applicants (women: 40.4% rejection; men: 33.0% rejection rate). Language variables had little ability to predict gender or funding level using predictive modelling. Our results indicate that NSERC funding levels and success rates differ between men and women, but we find no evidence that gendered language use affected funding outcomes.
  • OPEN ACCESS
    Global patterns of ranavirus detections
    FACETS • Vol. 6 • pp. 912 - 924
    Ranaviruses are emerging pathogens of poikilothermic vertebrates. In 2015 the Global Ranavirus Reporting System (GRRS) was established as a centralized, open access, online database for reports of the presence (and absence) of ranavirus around the globe. The GRRS has multiple data layers (e.g., location, date, host(s) species, and methods of detection) of use to those studying the epidemiology, ecology, and evolution of this group of viruses. Here we summarize the temporal, spatial, diagnostic, and host-taxonomic patterns of ranavirus reports in the GRRS. The number, distribution, and host diversity of ranavirus reports have increased dramatically since the mid 1990s, presumably in response to increased interest in ranaviruses and the conservation of their hosts, and also the availability of molecular diagnostics. Yet there are clear geographic and taxonomic biases among the reports. We encourage ranavirus researchers to add their studies to the portal because such collation can provide collaborative opportunities and unique insights to our developing knowledge of this pathogen and the emerging infectious disease that it causes.
  • OPEN ACCESS
    Relaxin peptides reduce cellular damage in cultured brain slices exposed to transient oxygen–glucose deprivation: an effect mediated by nitric oxide
    FACETS • Vol. 6 • pp. 118 - 130
    The effect of treatment with human relaxins on cell death was studied in oxygen- and glucose-deprived brain slices. In addition, involvement of nitric oxide and the relaxin receptor, RXFP3, was studied. Brain slices (n = 12–18/group) were cultured under standard conditions for two weeks and then exposed to: (i) an oxygenated balanced salt solution, (ii) a deoxygenated, glucose-free balanced salt solution (OGD media), or (iii) OGD media containing 10−7 mol/L H2 relaxin, 10−7 mol/L H2 relaxin with 50 μmol/L L-NIL, 10−7 mol/L H3 relaxin, or 10−7 mol/L H3 relaxin with 50 μmol/L L-NIL. Cell death was assessed using propidium iodide fluorescence. In a separate experiment, 10−5 mol/L R3 B1-22R (an antagonist of RXFP3) was added to both H2 and H3 relaxin treatments. H2 and H3 relaxin treatment reduced cell damage or death in OGD slices and L-NIL partially attenuated the effect of H3 relaxin. Antagonism of RXFP3 blocked the effect of H3 but not H2 relaxin. These data increase our understanding of the role of relaxin ligands and their receptors in protecting tissues throughout the body from ischemia and reperfusion injury.
  • OPEN ACCESS
    Inoculating rhizome-propagated Sporobolus pumilus with a native mycorrhizal fungus increases salt marsh plant growth and survival
    FACETS • Vol. 6 • pp. 1134 - 1145
    Salt marshes are ecosystems of significant ecological importance for coastal stability and fundamental roles in marine ecosystems. Salt marshes are declining due to anthropogenic and natural causes including sea level rise. Coastal restoration efforts have increased worldwide, but many fail in long-term coastal stability. We used a naturally occurring arbuscular mycorrhizal fungus (AMF) to test whether survival and early growth of the salt marsh grass Sporobolus pumilus (formerly Spartina patens) improved under simulated salt marsh conditions. Using a tidal mesocosm bench, we grew inoculated plants with varying AMF treatments under simulated tidal regimes to determine if AMF could aid in establishment of healthy Sporobolus communities. Rhizome-derived S. pumilus had greater survival and grew faster than seed-derived plants. Plants inoculated with propagated AMF consistently outperformed both sterile and native sediment controls in terms of plant survival and growth. Use of rhizome-derived Sporobolus inoculated with propagated Funneliformis geosporum showed the most promise in producing successful plant populations for salt marsh restoration. This may be due to plant life stage and improved plant nutrient status, allowing rhizome-derived plants to grow more quickly than seed-derived plants. Using these plants in future large-scale restoration may increase re-establishment of salt marsh ecosystems.
  • OPEN ACCESS
    Detection of SARS-CoV-2 in wastewater in Halifax, Nova Scotia, Canada, using four RT-qPCR assays
    FACETS • Vol. 6 • pp. 959 - 965
    Wastewater-based surveillance methods have been implemented in several countries as a tool for monitoring SARS-CoV-2 at a community scale. A variety of methods have been used for concentrating, extracting, and detecting the virus, with no clear consensus on the most effective approach. In this note, we report preliminary findings from a study that is tracking SARS-CoV-2 in wastewater in Halifax, Nova Scotia, with a specific focus on the use of four reverse transcriptase quantitative PCR (RT-qPCR) assays for detecting the virus in wastewater. We were able to detect the virus in wastewater samples during the initial rise of cases in the Halifax region in early November 2020. Levels of the targeted SARS-CoV-2 gene fragments increased and fell in response to reported cases of COVID-19. The CDC N1 and E RT-qPCR assays demonstrated greater relative sensitivity than the CDC N2 and N3 assays for detection of SARS-CoV-2 in raw sewage samples.
  • OPEN ACCESS
    Assessing gage: an online tool for improving gender visibility in STEMM
    FACETS • Vol. 6 • pp. 1601 - 1609
    Women continue to be underrepresented and less visible in the fields of science, technology, engineering, mathematics, and medicine (STEMM). 500 Women Scientists created and launched in January 2018 a global (>140 countries to date), online, open-access directory of women in STEMM fields. This directory—recently renamed gage—now also includes gender diverse persons (i.e., additional underrepresented genders) in STEMM fields. The purpose of the directory is to make these scientists’ expertise easier to locate and access for conference organizers, journalists, policy makers, educators, and others. Here, we undertake an assessment of the directory using surveys, Google Analytics, and focus groups to understand its efficacy and direction to date and identify future improvements we pledge to undertake. Through this assessment—conducted externally and in accordance with privacy protocols by Concolor Research—we identified who and how people are using our directory, why people signed up to be a resource, and areas for improvement. Through such assessment, we can learn how to enhance the directory’s efficacy and our broader efforts to boost the visibility of underrepresented people in STEMM.
  • OPEN ACCESS
    DNA metabarcoding of faecal pellets reveals high consumption of yew (Taxus spp.) by caribou (Rangifer tarandus) in a lichen-poor environment
    FACETS • Vol. 7 • pp. 701 - 717
    Woodland caribou (Rangifer tarandus caribou) are threatened in Canada because of the drastic decline in population size caused primarily by human-induced landscape changes that decrease habitat and increase predation risk. Conservation efforts have largely focused on reducing predators and protecting critical habitat, whereas research on dietary niches and the role of potential food constraints in lichen-poor environments is limited. To improve our understanding of dietary niche variability, we used a next-generation sequencing approach with metabarcoding of DNA extracted from faecal pellets of woodland caribou located on Lake Superior in lichen-rich (mainland) and lichen-poor (island) environments. Amplicon sequencing of fungal ITS2 region revealed lichen-associated fungi as predominant in samples from both populations, but amplification at the chloroplast trnL region, which was only successful on island samples, revealed primary consumption of yew (Taxus spp.) based on relative read abundance (83.68%) with dogwood (Cornus spp.; 9.67%) and maple (Acer spp.; 4.10%) also prevalent. These results suggest that conservation efforts for caribou need to consider the availability of food resources beyond lichen to ensure successful outcomes. More broadly, we provide a reliable methodology for assessing ungulate diet from archived faecal pellets that could reveal important dietary shifts over time in response to climate change.
  • OPEN ACCESS
    Self-promotion and the need to be first in science
    FACETS • Vol. 6 • pp. 1881 - 1891
    Scientists, like all humans, are subject to self-deceptive valuations of their importance and profile. Vainglorious practice is annoying but mostly harmless when restricted to an individual’s perception of self-worth. Language that can be associated with self-promotion and aggrandizement is destructive when incorporated into scientific writing. So too is any practice that oversells the novelty of research or fails to provide sufficient scholarship on the uniqueness of results. We evaluated whether such tendencies have been increasing over time by assessing the frequencies of articles claiming to be “the first”, and those that placed the requirement for scholarship on readers by using phrases such as “to the best of our knowledge”. Our survey of titles and abstracts of 176 journals in ecology and environmental biology revealed that the frequencies of both practices increased linearly over the past half century. We thus warn readers, journal editors, and granting agencies to use caution when assessing the claimed novelty of research contributions. A system-wide reform toward more cooperative science that values humility, and abhors hubris, might help to rectify the problem.
  • OPEN ACCESS
    Using community science to advance grizzly bear conservation
    FACETS • Vol. 9 • pp. 1 - 11
    Alberta grizzly bears are classified as a threatened species in the province of Alberta as of 2010, with human-caused mortality and habitat loss a primary threat. The people who live, work, and recreate within bear habitat play a crucial role in their conservation. While the public is often enthusiastic about grizzly bears, and opportunistically report their observations to government staff, these reports are not systematic or rigorously collected and lack key information. As such, we developed GrizzTracker as a community science program. Following several years of successful deployment, we analyzed community scientist data and evaluated the efficacy of the program through an online user survey. We found that the GrizzTracker app was useful as a data collection and public engagement tool, yielding information for applied management, and that community scientists were generally satisfied. We provide considerations for future program development, including considerations for human, social, technological, and financial capital investment related to design, development, and implementation of data collection protocols, the importance of clearly communicating outcomes, and opportunities for educational outreach. While there is continued trepidation by traditionally trained scientists to develop or engage in community science programs, and some noted areas of improvement for our program specifically, we think that GrizzTracker offers a success story in community science.
  • OPEN ACCESS
    Heliocaminiform structures: plant organs that function as microgreenhouses
    FACETS • Vol. 9 • pp. 1 - 20
    Plant structures that enclose trapped air are morphologically and taxonomically diverse. They range from pubescence (trichomes) on various parts of plants to flowers, inflorescences, stems, culms (above-ground jointed stems of grasses), petioles, peduncles, scapes, fruits, bracts, leaves, galls, algal pneumatocysts, moss sporophytes, lichen podetia, and fungal fruiting bodies. Despite being familiar, such structures have not been studied systematically until recently when their complex thermodynamic functionality as microgreenhouses has been recognized. We propose the term “heliocaminiform” (Greco-Latin origin for “sun-room”) provides an umbrella term that describes form and function. Almost all the hollow structures we have examined have elevated internal temperatures of several degrees C above the surrounding air in sunshine, but those are abolished under cloud or at night. The potential importance for the additional heat is presumed to be in growth, maturation, reproduction, sexual function, and overall fitness of the plants. There seem to be no experimental studies on those effects even though they may help explain aspects of plants’ responses to climate change and to phenological mismatches with symbionts (mutualists and herbivores) as ecologically co-dependent partners. Our review and observations opens a remarkably new and hitherto surprisingly neglected avenue in botany which we hope others will explore.