Rolling out ! (August 2023)
by David J. Castillo (ASU Biodesign Institute, Center for Mechanisms of Evolution / Glyxon Biolabs)
A few weeks ago (August 16, 2023). I had the pleasure to meet with Alexandra (Ali) Schuessler (Desert Botanical Garden), Ross Satchell (Microchip Technology), and Toby Sinkinson (ASU/Microchip Technology), at the Schiling library of the Desert Botanical Garden (DBG). The place is a great enclosure, holding a respectable and incredible collection of books, publications and artifacts related to the desert biomes and literature about the botanical and cultural diversity of the Sonoran desert. The DBG withholds one of the most outstanding collection of biomes in America and perhaps the world, housing a collection of many representatives of current and endangered species of the region, extending its conservation efforts with great tenacity. The Sonoran desert covers multiple states and also an international border line extending from the northern areas of Mexico, Arizona, New Mexico and Utah, containing also a massive cluster of cultural diversity.
We had the opportunity to discuss the following steps in the design and implementation of our new environmental sensor based on the AgrIoT-LoRa initially development by Ross and his team at Microchip Technology (Chandler, Arizona) with further enhanced capabilities, e.g. soil respiration.
Ali will offer us access to areas of the DBG where we can test out the new version of the sensor in different individuals of Creosote bush or grease bush. There are many individuals of Creosote already growing at the DBG in different stages of maturity.
Creosote or its scientific name Larrea tridentata was chosen my one of our colleague at Glyxon Biolabs (Whaleeha Gudiño), given the readily available body or work regarding its ecological and physiological adaptations to arid environment. Its is not only a bush that can resist temperature fluctuations of 20°C along a day, but also its a fierce competitor for water and soil resources. We believe it can be a great starting point for understanding the process in which many plants adapt to arid biomes at the microbial level, including its potential interactions of its mycorrhizal populations. Creosote has particular chronogeological adaptations and multiple cross species interaction along is evolutionary history, for example its has developed multiple secondary metabolites as deterrents for predatory behavior and in parallel, it has evolved specific pollination strategies. Despite its nearly endemic distribution, Creosote can be found also in arid regions of South American deserts including Chile and Argentina, meaning it could have had a more wide distribution when the desertification process of these regions were triggered by large scale climate events, since the evolutionary history of Creosote is more recent. If you want to know more about Creosote and its impactful influence on the Sonoran desert ecological make up, visit this video.
The new sensor will incorporate multiple new capabilities that are intended for measuring the soil respiration performance of the selected species. Traditionally, those variables are measured with expensive pieces of equipment and AgrIoT-LoRa represent no just a turn key solution that trims-off costs, but also could reduce the training time, its modularity offers optional interchangeable capabilities, and real time remote communication, given its Lo-Ra capabilities. It's basically a USB like sized environmental sensor on steroids at an unparalleled cost! The multiple benefits of AgrIoT-LoRa are not merely economic, but its modularity and programable features represent a greater flexibility for further researchers than could help them planning their experimental measurements on the field with greater resolution.
An environmental sensor designed to measure soil respiration using this configuration typically incorporates an EEPROM (Electrically Erasable Programmable Read-Only Memory) protocol to facilitate communication and data storage. This technical explanation will break down how this works:
Purpose of the Environmental Sensor: The environmental sensor is designed to monitor and record soil respiration, which is the release of carbon dioxide (CO2) from the soil as a result of microbial activity. This data is crucial for understanding soil health and its impact on ecosystems, agriculture, and climate change.
Microcontroller and EEPROM: Inside the sensor, there is a microcontroller responsible for collecting and processing data. The EEPROM is a crucial component connected to the microcontroller. It serves as non-volatile memory for storing critical configuration settings, calibration data, and measured values.
EEPROM Protocol for Communication: The EEPROM protocol is a set of rules and commands that define how the microcontroller communicates with and accesses data stored in the EEPROM. This protocol is necessary for reading and writing data to the EEPROM, allowing the sensor to store and retrieve information efficiently.
Data Collection and Storage: Here's how environmental sensor works with the EEPROM protocol to measure soil respiration:
Data Acquisition: The sensor collects data related to soil respiration through various sensors and transducers, such as CO2 sensors or soil moisture sensors.
Data Processing: The microcontroller processes the collected data, performing calculations or calibration based on its configuration settings.
EEPROM Interaction: The microcontroller uses the EEPROM protocol to write the processed data to the EEPROM. This involves sending specific commands and data addressing the EEPROM's memory locations.
Data Logging: Over time, as more data is collected, it is continuously written to the EEPROM, creating a historical record of soil respiration measurements.
Data Retrieval and Communication: To retrieve data from the sensor, typically, a user connects the "USB-sized sensor" to a computer or another device. The sensor's EEPROM protocol enables the following:
Read Operations: The microcontroller communicates with the EEPROM to read stored data, such as historical soil respiration measurements or calibration settings.
USB Interface: The sensor likely has a USB interface, allowing it to connect to a computer. The microcontroller can communicate with the computer through USB using appropriate drivers and software.
Data Transfer: The data read from the EEPROM is transferred to the connected device (e.g., a computer) via the USB connection, typically in a structured format like CSV or JSON.
User Interface and Analysis: The data transferred to the computer can be analyzed using specialized software, which may come with the sensor or be developed by the user. Users can visualize and interpret the soil respiration data to make informed decisions about soil management and environmental monitoring.
Using a plastic dome to measure soil respiration with a CO2 sensor is a common technique in environmental science and agriculture. The plastic dome, often referred to as a "chamber," serves several essential functions in this process:
1. Gas Isolation and Collection: The plastic dome is placed over a specific area of soil, effectively isolating that section from the surrounding environment. This isolation is crucial for accurately measuring the CO2 released by microbial activity in the soil. The dome creates a closed system where the gas produced by soil respiration accumulates.
2. Controlled Environment: The plastic dome creates a controlled microenvironment within its confines. This control allows scientists to regulate various environmental factors, such as temperature, humidity, and light, which can influence soil respiration rates. By maintaining consistent conditions, researchers can make more accurate measurements and compare data across different time periods or locations.
3. Gas Sampling Port: A gas sampling port or valve is typically integrated into the plastic dome. This port allows for the collection of gas samples from within the dome without disturbing the soil or the enclosed microenvironment. It's through this port that a CO2 sensor is connected to measure the concentration of carbon dioxide.
4. CO2 Sensor Integration: A CO2 sensor is connected to the gas sampling port. This sensor is highly sensitive and capable of accurately measuring the concentration of CO2 in the air within the dome. As microbial activity in the soil produces CO2, the sensor detects changes in CO2 levels over time. These measurements provide valuable data on the rate of soil respiration.
5. Data Logging and Recording: The CO2 sensor is often connected to a data logger or a computer system, allowing for continuous monitoring and recording of CO2 concentration data over time. This data provides insights into the soil's respiratory activity, including diurnal and seasonal variations.
6. Calculation of Soil Respiration Rate: From the data collected by the CO2 sensor, researchers can calculate the rate of soil respiration. This involves determining how much CO2 is released by the soil per unit of time, typically expressed in units like grams of carbon per square meter per day.
7. Non-Destructive Measurement: One of the advantages of using a plastic dome is that it allows for non-destructive measurements of soil respiration. Researchers can repeatedly monitor the same soil area without disturbing the ecosystem, making it suitable for long-term studies and assessments of soil health.
In addition to soil respiration, the sensor will be able to measure rain, temperature, soil pH, and indecent light. All of those variable would be integrated into the data logs and condo be reprogrammed according to the temporal resolution desired.
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