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1. A low‐cost modular control system for multistressor experiments

   https://doi.org/10.1002/lom3.10389  

   Low, Natalie H. N.; Ng, Crystal A.; Micheli, Fiorenza (September 2020, Limnology and Oceanography: Methods)

   Abstract Marine organisms and ecosystems face multiple, temporally variable stressors in a rapidly changing world. Realistic experiments that incorporate these aspects of physiological stress are important for advancing our ability to understand, predict, and manage their ecological impacts. However, the experimental systems needed to conduct such experiments can be costly. Here, we describe a low‐cost, modular control system that can be used with seawater sensors and actuators to dynamically manipulate multiple seawater variables. It enables researchers to run a variety of realistic multiple‐stressor, variable exposure experiments with a range of marine organisms. This tank controller system is based on the open‐source Arduino prototyping platform and features a custom‐made circuit board with a 16‐bit analog‐to‐digital converter, a real‐time clock, a MicroSD memory card reader, a high‐voltage transistor array, and solderless screw terminal connectors for easy connection of sensors, actuators, and power supplies. The assembly and use of this controller system does not require extensive electronics engineering or programming experience, and each module can be assembled for under 80 USD in parts. To demonstrate the system's capabilities, we present seawater manipulations from experiments involving (1) simultaneous manipulations of dissolved oxygen and pH; (2) fluctuating dissolved oxygen levels; and (3) a controlled stepwise decrease in dissolved oxygen at different temperatures. The low cost and high customizability of this Arduino‐based control system can contribute to expanding capacities for running global change experiments for researchers and students worldwide. 

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2. Arduino allows development of a low-cost, high-resolution metabolic and behavioral phenotyping system for birds

   https://doi.org/10.1242/jeb.249921  

   Rogers, Elizabeth J; Elowe, Cory; Stager, Maria; Gerson, Alexander R (April 2025, Journal of Experimental Biology)

   Technological advancements now enable the use of flow-through respirometry for rapid, high-throughput metabolic phenotyping, though live-in systems currently do not exist for birds. We designed live-in respirometry chambers for small birds with an Arduino-based electronic system to continuously monitor bird body weight, food intake, and water intake in sync with metabolic data collection. To demonstrate how this system can be implemented, we kept birds in the metabolic phenotypic chambers for 10 days while we progressively lowered the temperature from 25 °C to 5 °C. We used the data to calculate hourly energy expenditure and food/water intake during acute cold acclimation. We provide all plans and code for the live-in chambers, Arduino biomonitoring system, and additional RFID module as a low-cost, DIY alternative to commercially available systems and to enable the use of standard respirometry equipment for metabolic phenotyping in birds. 

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3. A Software Debugger for E-textiles and Arduino Microcontrollers

   Schneider, M.; Hill, C.; Eisenberg, A.; Gross, M.; Blum, A. (October 2020, FabLearn 2020 - 9th Annual Conference on Maker Education (FabLearn ’20))

   Today’s STEM classrooms have expanded the domain of computer science education from a basic two-toned terminal screen to now include helpful Integrated Development Environments(IDE) (BlueJ, Eclipse), block-based programming (MIT Scratch, Greenfoot), and even physical computing with embedded systems (Arduino, LEGO Mindstorm). But no matter which environment a student starts programming in, all students will eventually need help in finding and fixing bugs in their code. While the helpful IDE’s have debugger tools built in (breakpoints for pausing your program, ways to view/modify variable values, and "stepping" through code execution), in many of the other programming environments, students are limited to using print statements to try and "see" what is happening inside their program. Most students who learn to write code for Arduino microcontrollers will start within the Arduino IDE, but the official Arduino IDE does not currently provide any debugging tools. Instead, a student would have to move on to a professional IDE such as Atmel Studio or acquire a hardware debugger in order to add breakpoints or view their program’s variables. But each of these options has a steep learning curve, additional costs, and can require complex configurations. Based on research of student debugging practices[3, 7] and our own classroom observations, we have developed an Arduino software library, called Arduino Debugger, which provides some of these debugging tools (ex. breakpoints) while staying within the official Arduino IDE. This work continues a previous library, (redacted), which focused on features specific to e-textiles development boards. The Arduino Debugger library has been modified to support not only e-textile boards (Lilypad, Adafruit Circuit Playground) but most AVR and ARM based Arduino boards.We are also in the process of testing a set of Debugging Code Templates to see how they might increase student adoption of debugging tools. 

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4. Evaluating Methods of Preserving Aquatic Invertebrates for Microbiome Analysis

   https://doi.org/10.3390/microorganisms10040811  

   Vaughn, Stephanie N.; Jackson, Colin R. (April 2022, Microorganisms)

   Research on the microbiomes of animals has increased substantially within the past decades. More recently, microbial analyses of aquatic invertebrates have become of increased interest. The storage method used while collecting aquatic invertebrates has not been standardized throughout the scientific community, and the effects of common storage methods on the microbial composition of the organism is unknown. Using crayfish and dragonfly nymphs collected from a natural pond and crayfish maintained in an aquarium, the effects of two common storage methods, preserving in 95% ethanol and freezing at −20 °C, on the invertebrate bacterial microbiome was evaluated. We found that the bacterial community was conserved for two sample types (gut and exoskeleton) of field-collected crayfish stored either in ethanol or frozen, as was the gut microbiome of aquarium crayfish. However, there were significant differences between the bacterial communities found on the exoskeleton of aquarium crayfish stored in ethanol compared to those that were frozen. Dragonfly nymphs showed significant differences in gut microbial composition between species, but the microbiome was conserved between storage methods. These results demonstrate that preserving field-collected specimens of aquatic invertebrates in 95% ethanol is likely to be a simple and effective sample preservation method for subsequent gut microbiome analysis but is less reliable for the external microbiome. 

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5. Cryptic Constituents: The Paradox of High Flux–Low Concentration Components of Aquatic Ecosystems

   https://doi.org/10.3390/w13162301  

   Olofsson, Malin; Power, Mary E.; Stahl, David A.; Vadeboncoeur, Yvonne; Brett, Michael T. (August 2021, Water)

   The interface between terrestrial ecosystems and inland waters is an important link in the global carbon cycle. However, the extent to which allochthonous organic matter entering freshwater systems plays a major role in microbial and higher-trophic-level processes is under debate. Human perturbations can alter fluxes of terrestrial carbon to aquatic environments in complex ways. The biomass and production of aquatic microbes are traditionally thought to be resource limited via stoichiometric constraints such as nutrient ratios or the carbon standing stock at a given timepoint. Low concentrations of a particular constituent, however, can be strong evidence of its importance in food webs. High fluxes of a constituent are often associated with low concentrations due to high uptake rates, particularly in aquatic food webs. A focus on biomass rather than turnover can lead investigators to misconstrue dissolved organic carbon use by bacteria. By combining tracer methods with mass balance calculations, we reveal hidden patterns in aquatic ecosystems that emphasize fluxes, turnover rates, and molecular interactions. We suggest that this approach will improve forecasts of aquatic ecosystem responses to warming or altered nitrogen usage. 

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