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Stability and distribution of the block temperature
During the development of this protocol, we tested the linearity and temporal stability of the temperature inside the block. After switching the cooling system and the heater ON, the initialization time of the block is approximately one hour, during which time most of the eight evenly distributed temperature sensors reach the target temperature and then remain constant after an overshoot (Figure 13A). After this period, the temperatures recorded by the eight sensors confirm a perfect linear distribution of the temperature along the aluminum block (Figure 13B).

Figure 13: Linearity and temporal stability inside the temperature gradient block. (A) Temporal stability of the temperatures inside the block over the incubation period, and (B) temperature recorded by the sensors at the starting time of the incubation. Please click here to view a larger version of this figure.
Block temperature and soil temperature
We tested the time required for the soil sample inside the block to reach the temperature recorded by the eight sensors (Figure 14). In this study, we measured the temperature of soil samples at eight different positions within the block, located near the sensors. The sensors, positioned inside the block were pre-stabilized at their target temperature. Following the above-described protocol, once the block temperatures were stable, soil samples were placed inside the block. For this test, we used extra sensors that are separated from the block. We used 15 g of soil, ensuring that the sensor probe was in full contact with the soil. The soil samples were left uncapped, and the temperature was recorded every minute for a total of 30 min. During this test, the block was slightly closed to minimize temperature variation and reproduce as much as possible real utilization conditions (completely closed). We found that it takes approximately 12 min for the soil samples to stabilize at the target temperature. We deemed this stabilization time to be acceptable, given that the incubations last for a minimum of 3.5 h. Additionally, we assessed the linearity of soil temperature after 12 min of block incubation. The results indicate that the soil temperatures exhibit a linear relationship, closely aligning with the linearity observed in the eight sensors (Figure 15).

Figure 14: Recorded soil temperature incubated at different temperatures. Samples A, B, C, and D were incubated in vials positioned near the corresponding sensors (see Figure 10 for reference). The soil temperature was recorded by a thermocouple inserted directly into the soil samples. The specific temperatures monitored by each sensor are as follows: (A) Sensor 1 (S1) at 4.1 °C , (B) Sensor 2 (S2) at 12.5 °C, (C) Sensor 3 (S3) at 20.1 °C, (D) Sensor 4 (S4) at 28.1 °C, (E) Sensor 5 (S5) at 36.1 °C, (F) Sensor 6 (S6) at 43.8 °C, (G) Sensor 7 (S7) at 51.9 °C, and (H) Sensor 8 (S8) at 60 °C. After placing the soil samples into the block, it takes approximately 12 min to reach the target temperature. Please click here to view a larger version of this figure.

Figure 15: Strong linear correlation between soil temperature and sensor temperature. Four vials with soil were placed close to the eight sensors in block positions A, B, C, and D. The soil temperature was recorded by a thermocouple inserted directly into the soil samples. Please click here to view a larger version of this figure.
Temperature-moisture interaction
There is an inevitable interaction between temperature and moisture that needs to be assessed during the incubation period. For instance, high temperatures can accelerate evaporation, while low temperatures can cause water condensation. For this test, we used four randomly selected soil samples with different textures (Supplementary Table 2). According to the protocol, each soil sample was placed in the same block position across all 22 temperatures. The results show that after an average incubation time of 3.5 h, higher temperatures resulted in greater moisture loss compared to lower temperatures, regardless of soil texture (Figure 16). Soils incubated at 60 °C lost on average 12% of the total water added, whereas soils incubated at 4.1 °C lost on average only 1.88% of the total water added. This means that during the 3.5 h of block incubation, soils were maintained within optimal moisture conditions, between 50% and 60% water holding capacity, irrespective of incubation temperature44,45 (Supplementary Figure 6).

Figure 16: Relative loss of soil moisture during block incubation in four different samples. Moisture loss was calculated relative to the total amount of water added to adjust for WHC. Please click here to view a larger version of this figure.
CO2 concentration measurements
To test the accuracy and precision of the gas analyzer, we carried out four measurements of a certified reference gas (413 ± 5 ppm CO2), for which the analyzer recorded 413.71 ± 0.60 (ppm CO2, mean ± SD). This confirmed the high accuracy and precision of the CO2 measurements recorded by the gas analyzer. In addition, to adhere to the manufacturer's specifications, a yearly test using a certified reference gas should be done.
In view of the lag time caused by the injection line and the flow reduction rate kit to the gas analyzer, multiple tests were performed to determine the optimal measuring time. Results show that the injection line causes a delay of approximately five seconds. In this setup, the ideal measuring time is 20 s, allowing sufficient time to fill the CO2 detection unit and reach an equilibrium for 5 s (Figure 17). Given that the flow reduction rate kit measures at a rate of 1.17 mL/s, this measuring time corresponds to sampling 39% of the air content in the 60 mL vials. Additionally, we observed that when the gas analyzer is used as a closed system, a pressure drop occurs. This drop arises during the one-second interval when there is no air injection as the needle is extracted from the vial. To account for this drop in pressure during data processing, we excluded CO2 values that are slightly lower (between 3% and 5%) than the previous or next value.

Figure 17: Optimal measuring time for an individual soil sample incubated at three different temperatures. This graph shows the injection and extraction time of the needle, the equilibrium of CO2 for 5 s, and the pressure drop associated with the selected time frame. Incubation_ID shows block position (C) and vial positions (5, 10, and 15). Please click here to view a larger version of this figure.
Testing the full protocol
To evaluate the functionality and reproducibility of the protocol, we incubated two different samples, each with four technical replicates, across the 22 discrete temperatures ranging from 4 °C to 60 °C. These soil samples were chosen to demonstrate the type of data generated with this setup and its performance. Specific sample characteristics can be found in Supplementary Table 2. The temperature gradient block reliably captured the soil respiration rates of the different soil samples at each temperature point, allowing us to visualize the temperature response curve. Additionally, the resulting temperature response curves for all replicates were nearly identical, as reflected by the small standard deviation around the mean respiration rates across all temperatures (Figure 18). These results demonstrate high reproducibility and confirm the precision of the protocol.

Figure 18: Representative SOM decomposition rates (Rs) for two soils, each measured with four technical replicates incubated across the full temperature gradient. Points represent the mean of respiration rates at each temperature, and error bars indicate the standard deviation among technical replicates. Please click here to view a larger version of this figure.
A second test was performed to demonstrate the scientific applicability of the protocol. We measured soil respiration rates across the full temperature gradient and fitted the data using the Arrhenius or MMRT model (Figure 19). These soil samples were chosen to demonstrate the system performance for contrasting temperature response curves (sample characteristics are provided in Supplementary Table 2). Results show that the data collected with the temperature gradient block can be further analyzed by testing different theories about the temperature sensitivity of SOM decomposition rates. However, challenges arise when working with fresh soil in any experiment. During the 10 days pre-incubation period, we observed fungal communities growing inside some of the vials in soil samples beyond the set of representative samples. Despite our efforts to carefully remove the fungal communities without disturbing the soil, this growth impacted the results of some samples (Figure 20). Consequently, we decided to discard the affected samples by removing the entire sample, not just the individual vials impacted by fungal growth.

Figure 19: Representative results and respiration rates (Rs) of four different soil samples incubated in the temperature gradient block. The red line represents the (A,B) Arrhenius fit, and the blue line represents the (C,D) MMRT fit. Please click here to view a larger version of this figure.

Figure 20: Respiration rate patterns for some samples affected by fungal growth. These results are examples of (A,B) two contaminated samples that were excluded from further analysis. Please click here to view a larger version of this figure.
Supplementary Figure 1: Basic NO/NC circuit. "C" may also be labeled as "COM" for Common. Please click here to download this File.
Supplementary Figure 2: Cooling system control panel. Please click here to download this File.
Supplementary Figure 3: System switch and light indicator. (A) Temperature gradient block control system switch; and (B) green light indicating the sensors and heating system are ON. Please click here to download this File.
Supplementary Figure 4: Temperature gradient block heater control in the online interface. Please click here to download this File.
Supplementary Figure 5: Diagnostic section of the gas analyzer. Everything is green means that the instrument is ready for measurements. Please click here to download this File.
Supplementary Figure 6: Water holding capacity of soils incubated at different temperatures, measurements recorded after 3.5 h of block incubation. Please click here to download this File.
Supplementary File 1: Detailed wiring instructions. Please click here to download this File.
Supplementary Table 1: List of materials with the required quantity. Please click here to download this File.
Supplementary Table 2: Characteristics of soil samples used for the moisture loss test and full protocol. These samples were chosen to demonstrate the functionality of the protocol. Texture classification follows the USDA system, with coarse, clay, silt, and sand expressed as percentages. OC refers to organic carbon content (g C·kg-1 soil), pH was measured in water, and CaCO3 represents calcium carbonate content (g·kg-1 soil). Please click here to download this File.