I've selected the basic components for the first prototypes. They include the basic necessary parts for running everything as well as a few sensors that I believe are useful in ecological analysis. Here are the parts and their purposes:

Raspberry pi 3 - The computer that runs everything on this system. I'd like to test with a pi zero, which should be compatible with evertything here as well.

2.8" touchscreen TFT - This is an RPi compatible screen available on adafruit that seems perfect for this application.

GP-20U7 (56 Channel) GPS - This is for geologging collected data.

Pi NoIR camera module - Infrared cameras can be used to view plant health and a wealth of other information about the environment.

SparkFun Soil Moisture Sensor - Sparkfun's soil moisture sensor data could yield some interesting data about water retention.

Si7021 Humidity and Temperature Sensor - Humidity and temperature data can help calibrate sensors and give further insights into the environment.

Methane CNG Gas Sensor MQ-4 - Methane

I'll test with these components to see what makes sense for this application. In the meantime I'm going to mock up an interface to make it easier to test. I'm thinking about using python's Kivy framework which I have heard good things about.