Scholarly Works, Biological Sciences

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Queer- and trans-inclusive faculty hiring—A call for change
Weissman, J. L.; Chappell, C. R.; de Oliveira, B. F. R.; Evans, N.; Fagre, A. C.; Forsythe, D.; Frese, S. A.; Gregor, R.; Ishaq, S. L.; Johnston, J.; Bittu, K. R.; Matsuda, S. B.; McCarren, S.; de la Campa, M. O. A.; Roepke, T. A.; Sinnott-Armstrong, N.; Stobie, C. S.; Talluto, L.; Vargas-Muñiz, José M.; Ray, A.; Rodríguez-Gijón, A.; Weiss, A. C. B.; Soares, B. E.; Lima, B. P.; Qin, C.; Grijseels, D. M.; Taylor, E. J.; Krichilsky, E.; Vyas, H. K. N.; Palevsky, H. I.; Ramírez-Sánchez, I.; Benoit, J. M.; Parks, J. M.; Gordon, J.; Goodheart, J. A.; McMonigal, K.; van Schijndel, L. L. M.; Dietz, L.; Hamilton, M.; Cattau, M.; Yang, M.; Henson, M. W.; Santiago-Martínez, M. G.; Penrice-Randal, R.; Sridhar, S.; James, V.; Agnew, W.; Wan, Y. (Public Library of Science, 2024-11-22)
As queer and trans scientists, we face varied and systemic barriers to our professional success, resulting in our relative absence from faculty ranks at many institutions. In this Perspective, we call for a change in faculty hiring practices and present concrete guidance to make it a more inclusive process.
Winter cover cropping increases albedo and latent heat flux in a Texas High Plains agroecosystem
McNellis, Risa; van Gestel, Natasja; Thomas, R. Quinn; Smith, Nicholas G. (2024-02-22)
Winter cover crops represent a land cover change that may sequester carbon in the soil and improve agricultural sustainability. Their adoption may also change the Earth’s radiative balance and result in biophysical feedbacks to climate through alterations in albedo and latent heat fluxes. Understanding the mechanisms underlying these alterations to the radiative balance is important for making reliable future climate projections. However, data on cover crop biophysics are limited, requiring models to rely on data from summer plants for parameterization, likely biasing predictions. To address this gap, we measured the albedo and stomatal conductance of two summer crops and three winter crops on farms in the High Plains region of Texas. We also established a winter cover crop field experiment with two cover crops and fallow fields to estimate the change in albedo and latent heat flux that results from a switch to winter cover cropping. We found that albedo was significantly higher in winter-like conditions than in summer-like conditions due to an increase in plant albedo and a reduction in leaf area index. The albedo of winter cover crops was higher than the soil albedo, resulting in an increase in top-of-atmosphere reflected radiation of 7%–14% when converting from fallow fields to winter cover cropped fields. There was an additional cooling effect through doubling of the estimated latent heat flux caused by the presence of cover crops. The combined changes in albedo and latent heat resulted in a change in the surface energy balance that is associated with an overall cooling effect of winter cover crops on surface atmospheric temperatures. While this effect is likely to be region-specific, these results strongly indicate that winter cover crops alter the surface albedo and latent heat flux of agricultural fields and provide a direct cooling effect in the High Plains region of Texas.
Process-based forecasts of lake water temperature and dissolved oxygen outperform null models, with variability over time and depth
Woelmer, Whitney M.; Thomas, R. Quinn; Olsson, Freya; Steele, Bethel G.; Weathers, Kathleen C.; Carey, Cayelan C. (Elsevier, 2024-09-17)
Near-term iterative ecological forecasting has great potential for providing new insights into our ability to predict multiple ecological variables. However, true, out-of-sample probabilistic forecasts remain rare, and variability in forecast performance has largely been unexamined in process-based forecasts which predict multiple ecosystem variables. To explore how forecast performance varies for water temperature and dissolved oxygen, two freshwater variables important for lake ecosystem functioning, we produced probabilistic forecasts at multiple depths over two open-water seasons in Lake Sunapee, NH, USA. Our forecasting system, FLARE (Forecasting Lake And Reservoir Ecosystems), uses a 1-D coupled hydrodynamic-biogeochemical process model, which we assessed relative to both climatology and persistence null models to quantify how much information process-based FLARE forecasts provide over null models across varying environmental conditions. We found that FLARE water temperature forecasts were always more skillful than FLARE oxygen forecasts. Specifically, temperature forecasts outperformed both null models up to 11 days into the future, as compared to only two days for oxygen. Across different years, we observed variable forecast skill, with performance generally decreasing with depth for both variables. Overall, all temperature forecasts and surface oxygen, but not deep oxygen, forecasts were more skillful than at least one null model >80 % of the forecasted period, indicating that our process-based model was able to reproduce the dynamics of these two variables with greater reliability than the null models. However, process-based oxygen forecasts from deeper waters were less skillful than both null models during a majority of the forecasted period, which suggests that deep-water oxygen dynamics are dominated by autocorrelation and seasonal change, which are inherently captured by the null forecasts. Our results highlight that forecast performance varies among lake water quality metrics and that process-based forecasts can provide important information in conjunction with null models in varying environmental conditions. Altogether, these process-based forecasts can be used to develop quantitative tools which inform our understanding of future ecosystem change.
Climate Change Could Negate U.S. Forest Ecosystem Services Benefits Gained Through Reductions in Nitrogen and Sulfur Deposition
Phelan, Jennifer N.; Van Houtven, George; Clark, Christopher M.; Buckley, John; Cajka, James; Hargrave, Ashton; Horn, Kevin; Thomas, R. Quinn; Sabo, Robert D. (Nature Portfolio, 2024-05-10)
Climate change and atmospheric deposition of nitrogen (N) and sulfur (S) impact the health and productivity of forests. Here, we explored the potential impacts of these environmental stressors on ecosystem services provided by future forests in the contiguous U.S. We found that all stand-level services benefitted (+ 2.6 to 8.1%) from reductions in N+S deposition, largely attributable to positive responses to reduced S that offset the net negative effects of lower N levels. Sawtimber responded positively (+ 0.5 to 0.6%) to some climate change, but negatively (− 2.4 to − 3.8%) to the most extreme scenarios. Aboveground carbon (C) sequestration and forest diversity were negatively impacted by all modelled changes in climate. Notably, the most extreme climate scenario eliminated gains in all three services achieved through reduced deposition. As individual tree species responded differently to climate change and atmospheric deposition, associated services unique to each species increased or decreased under future scenarios. Our results suggest that climate change should be considered when evaluating the benefits of N and S air pollution policies on the services provided by U.S. forests.
FaaSr: R Package for Function-as-a-Service Cloud Computing
Park, Sungjae; Ku, Yun-Jung; Mu, Nan; Daneshmand, Vahid; Thomas, R. Quinn; Carey, Cayelan C.; Figueiredo, Renato J. (The Open Journal, 2024-11)
The FaaSr software makes it easy for scientists to execute computational workflows developed natively using the R programming language in Function-as-a-Service (FaaS) serverless cloud infrastructures and using S3 cloud object storage (Amazon, 2024b; MinIO, 2024). A key objective of the software is to reduce barriers to entry to cloud computing for scientists in domains such as environmental sciences, where R is widely used (Lai et al., 2019). To this end, FaaSr is designed to hide complexities associated with using cloud Application Programming Interfaces (APIs) for different FaaS and S3 providers, and exposes to the end user a set of simple function interfaces to: 1) register and invoke FaaS functions, 2) compose functions to create workflow execution graphs, and 3) access cloud storage at run time. The software supports encapsulation of execution environments in Docker images that can be deployed reproducibly across multiple providers: AWS Lambda (Amazon, 2024a), GitHub Actions (Github, 2024), and OpenWhisk (Apache, 2024), where users are able to leverage a baseline image with the widely-used Rocker/Tidyverse runtime (Nüst et al., 2020), as well as customize their execution environment if needed. FaaSr is available as a CRAN package to facilitate its installation in R environments.
A multi-model ensemble of baseline and process-based models improves the predictive skill of near-term lake forecasts
Olsson, Freya; Moore, Tadhg N.; Carey, Cayelan C.; Breef-Pilz, Adrienne; Thomas, R. Quinn (2024-03)
Water temperature forecasting in lakes and reservoirs is a valuable tool to manage crucial freshwater resources in a changing and more variable climate, but previous efforts have yet to identify an optimal modeling approach. Here, we demonstrate the first multi‐model ensemble (MME) reservoir water temperature forecast, a forecasting method that combines individual model strengths in a single forecasting framework. We developed two MMEs: a three‐model process‐based MMEand a five‐modelMMEthat includes process‐based and empirical models to forecast water temperature profiles at a temperate drinking water reservoir. We found that the five‐model MME improved forecast performance by 8%–30% relative to individual models and the process‐based MME, as quantified using an aggregated probabilistic skill score. This increase in performance was due to large improvements in forecast bias in the five‐model MME, despite increases in forecast uncertainty. High correlation among the process‐based models resulted in little improvement in forecast performance in the process‐based MME relative to the individual process‐based models. The utility of MMEs is highlighted by two results: (a) no individual model performed best at every depth and horizon (days in the future), and (b) MMEs avoided poor performances by rarely producing the worst forecast for any single forecasted period (<6% of the worst ranked forecasts over time). This work presents an example of how existing models can be combined to improve water temperature forecasting in lakes and reservoirs and discusses the value of utilizing MMEs, rather than individual models, in operational forecasts.
Stochastic Boolean model of normal and aberrant cell cycles in budding yeast
Taoma, Kittisak; Tyson, John J.; Laomettachit, Teeraphan; Kraikivski, Pavel (Nature Portfolio, 2024-10-18)
The cell cycle of budding yeast is governed by an intricate protein regulatory network whose dysregulation can lead to lethal mistakes or aberrant cell division cycles. In this work, we model this network in a Boolean framework for stochastic simulations. Our model is sufficiently detailed to account for the phenotypes of 40 mutant yeast strains (83% of the experimentally characterized strains that we simulated) and also to simulate an endoreplicating strain (multiple rounds of DNA synthesis without mitosis) and a strain that exhibits ‘Cdc14 endocycles’ (periodic transitions between metaphase and anaphase). Because our model successfully replicates the observed properties of both wild-type yeast cells and many mutant strains, it provides a reasonable, validated starting point for more comprehensive stochastic-Boolean models of cell cycle controls. Such models may provide a better understanding of cell cycle anomalies in budding yeast and ultimately in mammalian cells.
FaaSr: Cross-Platform Function-as-a-Service Serverless Scientific Workflows in R
Park, Sungjae; Thomas, R. Quinn; Carey, Cayelan C.; Delany, Austin D.; Ku, Yun-Jung; Lofton, Mary E.; Figueiredo, Renato J. (IEEE, 2024-09)
Modern Function-as-a-Service (FaaS) cloud platforms offer great potential for supporting event-driven scientific workflows. Nonetheless, there remain barriers to adoption by the scientific community in domains such as environmental sciences, where R is the focal language used for the development of applications and where users are typically not well-versed with FaaS APIs. This paper describes the design and implementation of FaaSr, a novel middleware system that supports event-driven scientific workflows in R. A key novelty in FaaSr is the ability to deploy workflows across FaaS providers without the need for any managed servers for coordination. With FaaSr: 1) functions are written in R; 2) the runtime environments for their execution are customizable containers; 3) functions access data in cloud storage (S3) with a familiar file-based abstraction supporting both full file put/get primitives and subsetting using the Parquet format; and 4) function invocation and workflow coordination only requires S3 cloud object storage, without relying on any dedicated, active workflow engine server or cloud-specific queues/databases. The paper reports on the functionality and performance of FaaSr for micro-benchmarks and two case studies: event-driven forecast and batch job workflows. These demonstrate the ability to deploy workflows across multiple platforms (GitHub Actions, Amazon Web Services Lambda, and the open-source OpenWhisk), without the need for dedicated coordination servers, across both cloud and edge resources. FaaSr is open-source and available as a CRAN package.
The microbiota of moon snail egg collars is shaped by host-specific factors
Piedl, Karla; Aylward, Frank O.; Mevers, Emily (American Society for Microbiology, 2024-10-04)
Moon snails (Family: Naticidae) lay eggs using a mixture of mucus and sediment to form an egg mass commonly referred to as an egg collar. These egg collars do not appear to experience micro-biofouling or predation, and this observation led us to hypothesize that the egg collars possess a chemically rich microbiota that protect the egg collars from pathogens. Herein, we sought to gain an understanding of the bacterial composition of egg collars laid by a single species of moon snails, Neverita delessertiana, by amplifying and sequencing the 16S rRNA gene from the egg collar and sediment samples collected at four distinct geographical regions in southwest Florida. Relative abundance and non-metric multidimensional scaling plots revealed distinct differences in the bacterial composition between the egg collar and sediment samples. In addition, the egg collars had a lower α-diversity than the sediment, with specific genera being significantly enriched in the egg collars. Analysis of microorganisms consistent across two seasons suggests that Flavobacteriaceae make up a large portion of the core microbiota (36%-58% of 16S sequences). We also investigated the natural product potential of the egg collar microbiota by sequencing a core biosynthetic gene, the adenylation domains (ADs), within the gene clusters of non-ribosomal peptide synthetase (NRPS). AD sequences matched multiple modules within known NRPS gene clusters, suggesting that these compounds might be produced within the egg collar system. This study lays the foundation for future studies into the ecological role of the moon snail egg collar microbiota. IMPORTANCE Animals commonly partner with microorganisms to accomplish essential tasks, including chemically defending the animal host from predation and/or infections. Understanding animal-microbe partnerships and the molecules used by the microbe to defend the animals from pathogens or predation has the potential to lead to new pharmaceutical agents. However, very few of these systems have been investigated. A particularly interesting system is nutrient-rich marine egg collars, which often lack visible protections, and are hypothesized to harbor beneficial microbes that protect the eggs. In this study, we gained an understanding of the bacterial strains that form the core microbiota of moon snail egg collars and gained a preliminary understanding of their natural product potential. This work lays the foundation for future work to understand the ecological role of the core microbiota and to study the molecules involved in chemically defending the moon snail eggs.
Temporal and Spatial Variations in Microplastic Concentrations in Small Headwater Basins in the Southern Blue Ridge Mountains, North Carolina, USA
Miller, Jerry; Barrett, Nathaniel; Love, Jason; Gray, Austin; Youker, Robert; Hall, Chloe; Meiri, Noa; Gaesser, Megan; Randall, Georgeanna; Jarrett, Reagan; Spafford, Juliet (MDPI, 2024-10-30)
Microplastics (MPs) are ubiquitous contaminants of emerging concern that require additional study in freshwater streams. We examined the spatial-temporal variations in MP concentrations and characteristics within two headwater basins in the Southern Appalachian Mountains of western North Carolina over ~1 year. Atmospheric samples were also collected to determine the significance of atmospheric MP deposition to these relatively small streams. MP concentrations in both basins were within the upper quartile of those reported globally, reaching maximum values of 65.1 MPs/L. Approximately 90% of MPs were fibers. MP composition was dominated by polystyrene, polyamides, and polyethylene terephthalate. Spatially, concentrations were highly variable and increased with development, indicating anthropogenic inputs from urbanized areas. MP concentrations were also elevated in forested tributary subbasins with limited anthropogenic activity, suggesting atmospheric deposition was an important MPs source. Significant atmospheric inputs are supported by high atmospheric depositional rates (ranging between 7.6 and 449.8 MPs/m²/day across our study sites) and similarities in morphology, color, and composition between atmospheric and water samples. Temporally, MP concentrations during storm events increased, decreased, or remained the same in comparison to base flows, depending on the site. The observed spatial and temporal variations in concentrations appear to be related to the complex interplay between precipitation and runoff intensities, channel transport characteristics, and MP source locations and contributions.
Near-term ecological forecasting for climate change action
Dietze, Michael; White, Ethan P.; Abeyta, Antoinette; Boettiger, Carl; Bueno Watts, Nievita; Carey, Cayelan C.; Chaplin-Kramer, Rebecca; Emanuel, Ryan E.; Ernest, S. K. Morgan; Figueiredo, Renato J.; Gerst, Michael D.; Johnson, Leah R.; Kenney, Melissa A.; McLachlan, Jason S.; Paschalidis, Ioannis Ch.; Peters, Jody A.; Rollinson, Christine R.; Simonis, Juniper; Sullivan-Wiley, Kira; Thomas, R. Quinn; Wardle, Glenda M.; Willson, Alyssa M.; Zwart, Jacob (Springer Nature, 2024-11-08)
A substantial increase in predictive capacity is needed to anticipate and mitigate the widespread change in ecosystems and their services in the face of climate and biodiversity crises. In this era of accelerating change, we cannot rely on historical patterns or focus primarily on long-term projections that extend decades into the future. In this Perspective, we discuss the potential of near-term (daily to decadal) iterative ecological forecasting to improve decision-making on actionable time frames. We summarize the current status of ecological forecasting and focus on how to scale up, build on lessons from weather forecasting, and take advantage of recent technological advances. We also highlight the need to focus on equity, workforce development, and broad cross-disciplinary and non-academic partnerships.
First evidence of microplastic inhalation among free-ranging small cetaceans
Dziobak, Miranda K.; Fahlman, Andreas; Wells, Randall S.; Takeshita, Ryan; Smith, Cynthia; Gray, Austin D.; Weinstein, John; Hart, Leslie B. (Public Library of Science, 2024-10-16)
Plastic is a ubiquitous environmental contaminant, resulting in widespread exposure across terrestrial and marine spaces. In the environment, plastics can degrade into microparticles where exposure has been documented in a variety of fauna at all trophic levels. Human epidemiological studies have found relationships between inhaled microplastics and oxidative stress and inflammation. Previous studies of bottlenose dolphins (Tursiops truncatus) have reported prevalent exposure to plasticizing chemicals (e.g., phthalates) as well as particle loads in gastrointestinal tracts, but exposure from inhalation has not yet been studied. The objective of this study was to determine if inhalation is a viable route of microplastic exposure for free-ranging dolphins. Exhalation samples were opportunistically collected from dolphins residing in Sarasota Bay, Florida (n = 5) and Barataria Bay, Louisiana (n = 6) during catch-and-release health assessments to screen for microplastic particles. All dolphin samples contained at least one suspected microplastic particle, and polymer composition was determined for 100% of a subset (n = 17) of samples. Additional studies are warranted to better understand the extent of inhaled microplastics, as well as to explore impacts, given potential risks to lung function and health.
The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation
Kosch, Tiffany A.; Torres-Sánchez, María; Liedtke, H. C.; Summers, Kyle; Yun, Maximina H.; Crawford, Andrew J.; Maddock, Simon T.; Ahammed, Md. S.; Araújo, Victor L. N.; Bertola, Lorenzo V.; Bucciarelli, Gary M.; Carné, Albert; Carneiro, Céline M.; Chan, Kin O.; Chen, Ying; Crottini, Angelica; da Silva, Jessica M.; Denton, Robert D.; Dittrich, Carolin; Espregueira Themudo, Gonçalo; Farquharson, Katherine A.; Forsdick, Natalie J.; Gilbert, Edward; Che, Jing; Katzenback, Barbara A.; Kotharambath, Ramachandran; Levis, Nicholas A.; Márquez, Roberto; Mazepa, Glib; Mulder, Kevin P.; Müller, Hendrik; O’Connell, Mary J.; Orozco-terWengel, Pablo; Palomar, Gemma; Petzold, Alice; Pfennig, David W.; Pfennig, Karin S.; Reichert, Michael S.; Robert, Jacques; Scherz, Mark D.; Siu-Ting, Karen; Snead, Anthony A.; Stöck, Matthias; Stuckert, Adam M. M.; Stynoski, Jennifer L.; Tarvin, Rebecca D.; Wollenberg Valero, Katharina C. (2024-11-01)
Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomic resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomic resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, anti-predator strategies, and resilience and adaptive responses. They also serve as essential models for studying broad genomic traits, such as evolutionary genome expansions and contractions, as they exhibit the widest range of genome sizes among all animal taxa and possess multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The emergence of long-read sequencing technologies, combined with advanced molecular and computational techniques that improve scaffolding and reduce computational workloads, is now making it possible to address some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC, https://mvs.unimelb.edu.au/amphibian-genomics-consortium ) in early 2023. This burgeoning community already has more than 282 members from 41 countries. The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and call on the research and conservation communities to unite as part of the AGC to enable amphibian genomics research to “leap” to the next level.
Detection, Isolation and Quantification of Myocardial Infarct with Four Different Histological Staining Techniques
Wu, Xiaobo; Meier, Linnea; Liu, Tom X.; Toldo, Stefano; Poelzing, Steven; Gourdie, Robert G. (MDPI, 2024-10-18)
Background/Objectives: The precise quantification of myocardial infarction is crucial for evaluating therapeutic strategies. We developed a robust, color-based semi-automatic algorithm capable of infarct region detection, isolation and quantification with four different histological staining techniques, and of the isolation and quantification of diffuse fibrosis in the heart. Methods: Our method is developed based on the color difference in the infarct and non-infarct regions after histological staining. Mouse cardiac tissues stained with Masson’s trichrome (MTS), hematoxylin and eosin (H&E), 2,3,5-Triphenyltetrazolium chloride and picrosirius red were included to demonstrate the performance of our method. Results: We demonstrate that our algorithm can effectively identify and produce a clear visualization of infarct tissue in the four staining techniques. Notably, the infarct region on an H&E-stained tissue section can be clearly visualized after processing. The MATLAB-based program we developed holds promise for infarct quantification. Additionally, our program can isolate and quantify diffuse fibrotic elements from an MTS-stained cardiac section, which suggests the algorithm’s potential for evaluating pathological cardiac fibrosis in diseased cardiac tissues. Conclusions: We demonstrate that this color-based algorithm is capable of accurately identifying, isolating and quantifying cardiac infarct regions with different staining techniques, as well as diffuse and patchy fibrosis in MTS-stained cardiac tissues.
Limitations of trait‐based approaches for stressor assessment: The case of freshwater invertebrates and climate drivers
Hamilton, Anna T.; Schäfer, Ralf B.; Pyne, Matthew I.; Chessman, Bruce; Kakouei, Karan; Boersma, Kate S.; Verdonschot, Piet F. M.; Verdonschot, Ralf C. M.; Mims, Meryl C.; Khamis, Kieran; Bierwagen, Britta; Stamp, Jen (Wiley, 2019-09)
The appeal of trait-based approaches for assessing environmental vulnerabilities arises from the potential insight they provide into the mechanisms underlying the changes in populations and community structure. Traits can provide ecologically based explanations for observed responses to environmental changes, along with predictive power gained by developing relationships between traits and environmental variables. Despite these potential benefits, questions remain regarding the utility and limitations of these approaches, which we explore focusing on the following questions: (a) How reliable are predictions of biotic responses to changing conditions based on single trait–environment relationships? (b) What factors constrain detection of single trait–environment relationships, and how can they be addressed? (c) Can we use information on meta-community processes to reveal conditions when assumptions underlying trait-based studies are not met? We address these questions by reviewing published literature on aquatic invertebrate communities from stream ecosystems. Our findings help to define factors that influence the successful application of trait-based approaches in addressing the complex, multifaceted effects of changing climate conditions on hydrologic and thermal regimes in stream ecosystems. Key conclusions are that observed relationships between traits and environmental stressors are often inconsistent with predefined hypotheses derived from current trait-based thinking, particularly related to single trait–environment relationships. Factors that can influence findings of trait-based assessments include intercorrelations of among traits and among environmental variables, spatial scale, strength of biotic interactions, intensity of habitat disturbance, degree of abiotic stress, and methods of trait characterization. Several recommendations are made for practice and further study to address these concerns, including using phylogenetic relatedness to address intercorrelation. With proper consideration of these issues, trait-based assessment of organismal vulnerability to environmental changes can become a useful tool to conserve threatened populations into the future.
A modular curriculum to teach undergraduates ecological forecasting improves student and instructor confidence in their data science skills
Lofton, Mary E.; Moore, Tadhg N.; Woelmer, Whitney M.; Thomas, R. Quinn; Carey, Cayelan C. (Oxford University Press, 2024-10-10)
Data science skills (e.g., analyzing, modeling, and visualizing large data sets) are increasingly needed by undergraduates in the life sciences. However, a lack of both student and instructor confidence in data science skills presents a barrier to their inclusion in undergraduate curricula. To reduce this barrier, we developed four teaching modules in the Macrosystems EDDIE (for environmental data-driven inquiry and exploration) program to introduce undergraduate students and instructors to ecological forecasting, an emerging subdiscipline that integrates multiple data science skills. Ecological forecasting aims to improve natural resource management by providing future predictions of ecosystems with uncertainty. We assessed module efficacy with 596 students and 26 instructors over 3 years and found that module completion increased students’ confidence in their understanding of ecological forecasting and instructors’ likelihood to work with long-term, high-frequency sensor network data. Our modules constitute one of the first formalized data science curricula on ecological forecasting for undergraduates.
Surface hydrophilicity promotes bacterial twitching motility
O'Hara, Megan T.; Shimozono, Tori M.; Dye, Keane J.; Harris, David; Yang, Zhaomin (American Society for Microbiology, 2024-08-28)
Twitching motility is a form of bacterial surface translocation powered by the type IV pilus (T4P). It is frequently analyzed by interstitial colony expansion between agar and the polystyrene surfaces of petri dishes. In such assays, the twitching motility of Acinetobacter nosocomialis was observed with MacConkey but not Luria-Bertani (LB) agar media. One difference between these two media is the presence of bile salts as a selective agent in MacConkey but not in LB. Here, we demonstrate that the addition of bile salts to LB allowed A. nosocomialis to display twitching. Similarly, bile salts enhanced the twitching of Acinetobacter baumannii and Pseudomonas aeruginosa in LB. These observations suggest that there is a common mechanism, whereby bile salts enhance bacterial twitching and promote interstitial colony expansion. Bile salts disrupt lipid membranes and apply envelope stress as detergents. Surprisingly, their stimulatory effect on twitching appears not to be related to a bacterial physiological response to stressors. Rather, it is due to their ability to alter the physicochemical properties of a twitching surface. We observed that while other detergents promoted twitching like bile salts, stresses applied by antibiotics, including the outer membrane-targeting polymyxin B, did not enhance twitching motility. More importantly, bacteria displayed increased twitching on hydrophilic surfaces such as those of glass and tissue culture-treated polystyrene plastics, and bile salts no longer stimulated twitching on these surfaces. Together, our results show that altering the hydrophilicity of a twitching surface significantly impacts T4P functionality.
Geochemical drivers of manganese removal in drinking water reservoirs under hypolimnetic oxygenation
Ming, Cissy L.; Breef-Pilz, Adrienne; Howard, Dexter W.; Schreiber, Madeline E. (Elsevier, 2024-07)
Manganese (Mn) is a naturally occurring contaminant commonly found in drinking water supplies. In lakes and reservoirs, water authorities increasingly use in situ treatment by hypolimnetic oxygenation (HOx) systems to remove metals such as Mn from the water column. HOx systems introduce dissolved oxygen (DO) to the bottom waters (hypolimnion) to promote oxidation and subsequent removal of metals from the water column. Previous laboratory studies have shown the importance of individual geochemical drivers (pH, alkalinity, mineral surfaces) on Mn oxidation, but few studies have examined the influence of these drivers of Mn removal in concert. In this study, we conducted field monitoring and laboratory experiments to examine how pH, alkalinity and the presence of mineral particles influence Mn removal at two drinking water reservoirs in southwest Virginia, both with HOx systems: Falling Creek Reservoir (FCR) and Carvins Cove Reservoir (CCR). Both reservoirs have had historical issues with elevated (>0.05 mg/L) Mn concentrations during seasonal stratification (May–October). Watershed geology contributes to differences in pH and alkalinity between the reservoirs, with FCR having lower historical medians of hypolimnetic pH and alkalinity (6.6 and 18 mg/L CaCO₃, respectively) than CCR (7.2 and 62 mg/L CaCO₃, respectively). Results of laboratory experiments examining the influence of pH on Mn removal showed substantial Mn loss within 14 days only under high pH (10) conditions. Mn removal did not occur at pH 6 or 8 over the same 14-day period. In experiments with pH 10 and alkalinity >70 mg/L CaCO₃, near-total Mn removal occurred within 2 h. Mn removal occurred concurrently with precipitation of microscopic (<5 μm) particles, followed by formation of macroscopic (>100 μm) particles. Particles of both size classes were identified as Mn oxides (MnOx). These observations suggest that increasing pH and alkalinity promotes Mn oxidation and subsequent removal from solution. Results of experiments with pH 10 and alkalinity >70 mg/L CaCO₃ suggest that heterogeneous oxidation by MnOx partially drives rapid Mn removal. Thus, initial formation of MnOx creates a positive feedback loop that can enhance additional Mn loss. In experiments using water collected from FCR and CCR, we observed rapid Mn removal in unfiltered water (0.002–0.05 d⁻¹) but no significant removal of Mn in filtered water. These results, in combination with results of analysis of particles collected from reservoir water, suggest that minerals present in the water column likely catalyze MnOx formation. Together, our experimental results suggest that heterogenous oxidation is an important process of Mn removal, while pH and alkalinity variations of the range expected in natural freshwaters contribute less to differential Mn removal. The formation of MnOx particles during in situ oxygenation, as well as the presence of suspended minerals that occur naturally in water columns, play an important role in promoting Mn oxidation and should be accounted for in Mn removal treatment strategies.
Response of a Terrestrial Polar Ecosystem to the March 2022 Antarctic Weather Anomaly
Barrett, John E.; Adams, Byron J.; Doran, Peter T.; Dugan, Hilary A.; Myers, Krista F.; Salvatore, Mark R.; Power, Sarah N.; Snyder, Meredith D.; Wright, Anna T.; Gooseff, Michael N. (American Geophysical Union, 2024-07-31)
Record high temperatures were documented in the McMurdo Dry Valleys, Antarctica, on 18 March 2022, exceeding average temperatures for that day by nearly 30°C. Satellite imagery and stream gage measurements indicate that surface wetting coincided with this warming more than 2 months after peak summer thaw and likely exceeded thresholds for rehydration and activation of resident organisms that typically survive the cold and dry conditions of the polar fall in a freeze‐dried state. This weather event is notable in both the timing and magnitude of the warming and wetting when temperatures exceeded 0°C at a time when biological communities and streams have typically entered a persistent frozen state. Such events may be a harbinger of future climate conditions characterized by warmer temperatures and greater thaw in this region of Antarctica, which could influence the distribution, activity, and abundance of sentinel taxa. Here we describe the ecosystem responses to this weather anomaly reporting on meteorological and hydrological measurements across the region and on later biological observations from Canada Stream, one of the most diverse and productive ecosystems within the McMurdo Dry Valleys.
Widespread exposure to SARS-CoV-2 in wildlife communities
Goldberg, Amanda R.; Langwig, Kate E.; Brown, Katherine L.; Marano, Jeffrey M.; Rai, Pallavi; King, Kelsie M.; Sharp, Amanda K.; Ceci, Alessandro; Kailing, Christopher D.; Kailing, Macy J.; Briggs, Russell; Urbano, Matthew G.; Roby, Clinton; Brown, Anne M.; Weger-Lucarelli, James; Finkielstein, Carla V.; Hoyt, Joseph R. (Springer, 2024-07-29)
Pervasive SARS-CoV-2 infections in humans have led to multiple transmission events to animals. While SARS-CoV-2 has a potential broad wildlife host range, most documented infections have been in captive animals and a single wildlife species, the white-tailed deer. The full extent of SARS-CoV-2 exposure among wildlife communities and the factors that influence wildlife transmission risk remain unknown. We sampled 23 species of wildlife for SARS-CoV-2 and examined the effects of urbanization and human use on seropositivity. Here, we document positive detections of SARS-CoV-2 RNA in six species, including the deer mouse, Virginia opossum, raccoon, groundhog, Eastern cottontail, and Eastern red bat between May 2022–September 2023 across Virginia and Washington, D.C., USA. In addition, we found that sites with high human activity had three times higher seroprevalence than low human-use areas. We obtained SARS-CoV-2 genomic sequences from nine individuals of six species which were assigned to seven Pango lineages of the Omicron variant. The close match to variants circulating in humans at the time suggests at least seven recent human-to-animal transmission events. Our data support that exposure to SARS-CoV-2 has been widespread in wildlife communities and suggests that areas with high human activity may serve as points of contact for cross-species transmission.

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