Methods of Analysis

Coming from the world of chemistry I strongly believe that lab work is about fine tuning rather than about simply generating a result. To that end I am trying to publish reproducable methods with pro tips on this site. Comments, questions, and criticsm are all welcome!

Below I try to briefly introduce why one would go about measuring something, and then a link is provided to tell you everything I know about making the right decisions to get an accurate measurement with both anecdotal and literature based references were possible.

First, some notes on design

It is important to think about where variability lies in an experiment and sample accordingly. To help decide how many samples to take, consider using an a priori test of statistical power to estimate sample sizes that will be required. A short tutorial with R code is found here.

Then, comes design! I certainly can’t provide a comprehensive list, but a few common field designs are mentioned in brief here

Plant and Soil Sampling

As with any sampling there is no one way to sample soil and plants to observe interactive effects, but as soil is notoriously heterogenous, and you can only take a small number of plant samples to the lab, methods must be refined to a research question to avoid extraneous sampling. Some tips for how to start thinking about this are included here. Also you should pick up a free copy of the USDA NRCS Field Book for Describing and Sampling Soils.

Total Carbon and Nitrogen Analysis

Total carbon and nitrogen analysis are the ‘hammer’ of a soil scientist’s tool kit. This is most commonly measured using an elemental analyzer which quantitatively combusts a sample, generating CO2 and N2 which can then be measured. Investigations of carbon content are especially important for soils as organic carbon is important for agriculture (water holding capacity, infiltration, microbial activity) and in ecology as a tool quantifying those same things in the context of ecosystem services and the impacts of natural processes.

In addition, carbon and nitrogen together tell the most basic information about relative nitrogen limitation in a system. Whether in leaf, litter, or soil, C:N ratios are an important indicator of nitrogen status of a plant, or ecosystem. A rule of thumb is that if C:N>30 then the system is nitrogen depleted and microbial activity will tend to ‘immobilize’ nitrogen via increases in microbial biomass, less than 30 and nitrogen may be released by microbial mineralization of organic matter. Simply put, if microbes are limited, they stock up on N, if they have excess, they release it form the system.

The methods of analysis are going to be different for every lab, but I have summarized the preparation steps here

MODIS/TERRA bulk extraction of data in R

Modis provides a high frequency spatial data for many different parameters across the globe. My interest is most commonly in NDVI or EVI to look at productivity, but an amazing amount of data is available, see their list. Beware however, that some products are linked, e.g. evapotranspiration is calculated from a relationship NDVI, so they are not independent. See my code for an efficient way to download and aggregate large amounts of modis data in my tutorial here. You will also need to download the modis reprojection tool here. It can cause some grief with installation on a mac, if this happens to you, check out this help page which I found helpful.

Leaf Area Index

Leaf Area Index is an efficient way to measure the productivity of a site. It has been shown to relate to NDVI, evapotranspiration, and water use efficiency. An full hemispherical fisheye lens is required, but after that, you can get all the data you want! A description of how to take pictures in the field is here. I will not get into image processing, because there are liekly many options for that process. I have used free software that is available for processing images from the cary institute. This has worked well for me, and has excellent supporting documentation, and peer reviewed, published validation.

Soil Texture Analysis

There are many reasons people measure soil texture. Some basic interests include links to hydrologic properties within and between layers, i.e. drainage, storage, and their kinetics. Also, carbon and nutrient storage and cycling, and microbial activity are all interdependent and often relate to the ability of a soil to store available nutrients and water. There is a ‘goldilocks’ zone where there is enough surface area to store nutrients and water, while still allowing some active movement and cylcing, rather than immobilizing soil water and nutrient flows. There are many methods for measuring soil texture, most common are hydrometer and pipette methods described here. Additionally particle size analyzers are commercially available which use laser diffraction.

Soil Iron and Aluminum Mineralogy

Important for mineralogical analysis, and selective dissolution of different mineral forms of iron and aluminum. This method is growing in use and popularity for evaluating soil carbon storage potentia because of recently published work that suggests soil mineral characteristics may better predict carbon storage/potential than more classic concepts (i.e. texture). Methods here.

Soil and litter Bulk Density

Bulk density of soil and litter is very simple to measure and adds a significant component to stoichiometric analysis of a system. This measurement can convert total carbon and nitrogen data, to total carbon per unit area, increasing the scalability and improving the value of total carbon measurements.

For soil: you can buy brass or steel cylindrical rings, or make your own. It is important to disturb the soil as little as possible. One way to help, is to make one edge of your cylinder angled (but not quite sharp). This helps to push it into the soil. After pushing the cylinder into the soil, you extract it, now with a known volme of soil. Dry it in an oven at 105°C for 48 hours. With that weight you can calculate the g/cm3 of soil. Typical values are 1-1.6, or less for volcanic and organic rich soils, more for compacted or very ‘heavy’ clay soils.

For litter, I use a 3" diameter piece of pvc that can be purchased from any hardware store for about $1. It is nearly indescructable and is used as follows: it is placed on the ground, all the detritus around the frame is cleared away, and then that within the frame is collected and weighed after drying for 48 hours at 60°C. This gives units of g/cm2.

Soil pH

Similar to texture, pH is a soil property that is often used as a very general indicator of soil processes, as it corresponds to many things including microbial community, weathering, fertility. It is quite easy to measure, highly studied, and commonly varies across natural gradients (e.g. climate), so it can provide useful insight into how soils vary over space. pH is also critical to determining the solubility of organic matter, as well as base cations in solution impacting many soil processes. Some things to consider when measuring pH are drescribed here

Coming soon…

Cellulose Extraction from plant tissue
Specific Leaf Area Measurement
Soil/plant Phosphorous Analysis
Soil Avalable Water Capacity
Soil Nitrate and Ammonium Analysis
Basic use of Google Earth Engine for Time Series Analysis
Trace Gas sampling protocols