Monitoring For Soil Health

Cover photo

October 11 & 13, 2023 – Menang & Bibulman-Wadandi Noongar Boodja

Across two days, first in Albany hosted by Murray Gomm at Oranje Tractor Wines¹ and then hosted by Murray and Raquel Johnson at Galloway Springs² farm near Bridgetown, over 50 people attended workshops on Soil and Plant Health Monitoring co-sponsored by COBWA and Agrifutures. The identical workshops provided farmers vital background information on soil and plant health to support them to make more informed decisions about the tools they use to monitor their farm.

There is no shortage of ways for farmers to spend their precious capital on tools to monitor their land and the food they produce. There is a lot of information available on the internet and on social media and unfortunately, a lot of misinformation too. This creates problems for farmers who don’t have the necessary time or expertise to sift out the relevant from the irrelevant information to make decisions that suit their specific context.

This article aims to simplify the information that was presented at both workshops and importantly, guide some of the thinking needed before you invest time or money in a new technology to monitor your farm. Full disclosure here: we aren’t farmers, and we don’t have any vested interest in any technology mentioned, or not mentioned, in this report. Rather, we are certified Holistic Management educators committed to farmers making appropriate choices to benefit their land and their financial viability.

A major theme across the workshops was that plants, animals, microbes and soil all co-exist and are interconnected. The soils that we now walk on have been transformed over millennia by the co-evolution of plants, animals and the soil microbiome.

Soil has three main components: chemical, physical and biological.

For many years following the green revolution agronomists tried to separate soil chemistry and physics from soil biology. However, we now know this is impossible due to their interconnection. Both workshops were fortunate to have experts to discuss and share information on all three aspects:

  1. Paul Galloway, DPIRD
  2. Prof. Lyn Abbott, University of Western Australia
  3. Mark Tupman, Productive Ecology

Although Professor Abbott spoke second it is pertinent to start with a summary of her top takeaways as these are very salient points to keep in mind:

1. Monitoring is more important than measuring.

Measuring something only once isn’t useful. Monitoring is valuable when measurements are made regularly e.g., annually, to track progress or the lack thereof. An important question to consider is, why measure something if you can’t use the data or don’t know how to use the data?

2. What do the assessments or measurements indicate?

They’re only indicators if they point to something specific to your place or they can be used to predict something. Otherwise they’re just measurements which alone aren’t that useful.

3. Many soil assessments are for research purposes only.

The big question is, are the tests for scientific research OR farm management? For instance, we can measure many things in soil that scientists want to know. An example is the breakdown of bacterial species or specific enzyme activities present in soil using fancy DNA sequence analyses. While this may hold significant academic interest, the results may not be that useful to farmers.

The important takeaway here is that you need to be very clear why you want to know what you’re measuring and, what you’re going to do with the information (data) once you have it. Without a clear reason you might end up spending a lot of time and money to measure something that you don’t know what to do with.

Paul Galloway began with a discussion on soil health. The United States Department of Agriculture (USDA) lists four major principles:

  1. Minimise soil disturbance – i.e., minimise physical disturbance, this includes chemical use
  2. Maximise soil cover – ideally 100% soil cover 100% of the time
  3. Maximise biodiversity – diversity creates stability
  4. Maximise living roots – enhance soil biology, increase carbon, improve water infiltration,

Principles 1 and 2 aim to protect the soil habitat.

Principles 3 and 4 aim to feed soil organisms.

Consider the practices you use on your farm and how they impact these principles. Adhering to these 4 principles wherever possible takes us a long way to where we want to get to restore soil health.

Paul then introduced several aspects on the physical and chemical health of soil and some of the tools used to measure them with.

1) Sodicity is at the interface of soil chemistry and physical properties and measures the level of sodium ions relative to other cations bound to clay particles in soil.

2) pH measures the acidity or basicity of soil. Soil pH affects nutrient availability to plants. A pH range of 6.0-7.5 provides optimal availability of most nutrients for many plants. However, the microenvironment around plant roots can affect nutrient availability and allow some plants to grow well outside this pH range. Many pH kits are available, inexpensive and easy to use. To reduce variability in monitoring pH, use the same kit over time to track progress.

3) Eh measures the redox (reduction/oxidation) potential in soil. Redox reactions involve electron transfer and are the reactions of life. Biological enzymes make redox reactions happen. Enzymes can increase the speed of a redox reaction as much as 10^17 (10 to the power of 17) times faster than it would occur on its own. Thus, enzymes make life possible. Eh is therefore a surrogate measure of soil ‘life’.

Eh is widely used as an indirect measure of oxygen status i.e., is the soil normoxic (normal oxygen) or anoxic (low oxygen). Plants can’t live in anoxic soils which form when soil gets compacted or waterlogged as the space between particles (pores) is lost. Soil compaction can be measured easily with a penetrometer or by physical inspection of the ground. Salinity also affects waterlogging and creates a more reduced (anoxic) environment due to less oxygen in the soil as water fills the pores leaving less space available for gas exchange.

Soil physical health is influenced by many things: soil organic matter (SOM); soil organic carbon (SOC); soil life (roots, fungal hyphae, protists, bacteria, archaea, animals, biopores); soil (bio)chemistry; texture; structure and porosity and connectedness. For example, due to capillary action smaller soil pores suck water in better and hold on to water more tightly. Conversely, larger pores suck water in more slowly and hold onto it less tightly.

Texture (how it feels) is an intrinsic property of soil that changes with depth and reflects the proportion of sand, clay and silt particles. Sand takes in water quickly and releases stored water and nutrients readily to plants. Conversely, clay lets water in slowly and holds onto nutrients and stored water. A mixture of both sand and clay with various pore sizes is therefore ideal e.g., in a loam (a higher proportion of sand = sandy loam; whereas more clay = clay loam). A simple field test involves wetting a handful of soil: i) if it can be worked into a ball in the hand it’s a loam ii) if it doesn’t form a ball it’s sand and iii) if it can be rolled into a pencil and the ends can be joined in a circle it’s clay.

Physical tests for soil include: texture (see earlier) – this affects pore size; structure and stability – field tests assess slaking and dispersion; density – porosity is a good measure of density and particle size – a lab test. Paul emphasised that these tests, if done, are only done once for each soil type. Other tests like measuring pH or sodicity can be done regularly e.g., annually. Soil compaction can be assessed using a penetrometer (see earlier). Water storage can be measured using a moisture meter. Higher SOC and better structure improves water storage. On average 1% more SOC holds 16 L more of water for every square metre of land per year or 160,000 L per hectare annually.

Water infiltration can be measured using an infiltrometer, however, this might require uploading raw data to a company website to determine infiltration rates. However, low-tech alternative tests can be done. 10 cm PVC pipe pushed or hammered into the soil and recording how long 200 mL of water takes to absorb. A reduced time indicates an improved infiltration rate. Also, visual sighting of persistent puddles after rain suggests poor infiltration whereas their absence in the same place after rain indicates improved infiltration. As these examples show the test you choose doesn’t have to be expensive to be informative. More important however, is that you monitor and repeat the same test, the same way, at the same time, in the same place every year to track improvement over time.

A huge range of chemical tests can be performed to assess a wide range of chemicals and properties. Examples include the aforementioned pH; Eh and SOC but also; electrical conductance (EC); cation exchange capacity (CEC); P; K; Ca; Mg; S and micronutrients Cu; Zn; Mn; Fe plus many others. Paul mentioned that many WA soils in higher rainfall areas are boron (B) deficient and drier areas tend to be B toxic. However, as mentioned earlier you need to be clear on the reason why you want to measure these chemicals or properties.

Prof Lyn Abbott is a pioneer in soil research and was one of the first scientists to ever teach about soil fertility at the intersection of soil, plants and biology namely, microbes and animals.

Lyn began with a review of the Tier 1 soil tests from the US Soil Health Institute and noted that none of them involved biology and only Tier 2 tests measured for any type of soil biology. Lyn suggested the Soil Quality Website is a reliable resource to find local data for ‘good’ and ‘bad’ soil conditions based on locations around Australia that address climate and soil for crop production. Lyn emphasised some assays test for the presence (they are present) of things like microbial biomass (C, N, P); organisms e.g. rhizobia and earthworms or fungal/bacterial ratios. Other tests measure the activity or potential activity in soil. Examples include measuring CO2 evolved to assess soil respiration (more organisms produce more CO2); catalase which breaks down lignin and arbuscular mycorrhizal fungi that assesses hyphal activity in roots. Lyn stressed that measuring things like soil respiration (CO2 evolved) doesn’t tell you if your soil is healthy or not. For instance, soil organic matter breakdown also releases CO2 into the air. It is important to understand the limitations of the test, what it does and doesn’t do.

It is worth recalling that many tests are both valuable and inexpensive to carry out. For instance, to assess rhizobia, which are the organisms that form nodules on legume roots, their presence can be determined visually by inspecting plant roots and noting the location, size and number of the nodules. Leghemoglobin, that occurs in rhizobial nodules, binds oxygen and turns a pink colour the same way haemoglobin in our blood turns red. Leghaemoglobin keeps oxygen away from the enzyme nitrogenase which converts nitrogen gas (N2) into ammonia (NH3) and puts it into soil. Thus, pink nodules are active and put NH3 into soil. Conversely, white nodules are inactive and don’t put NH3 into soil.

Another simple way to monitor soil biology is to visually inspect soil for insects. The presence of earthworms and slaters, and smaller insects like mites visible under a microscope indicates the soil is biologically active. Larger insects feed on smaller insects that in turn feed on even smaller insects and so forth down the food soil web until ultimately, the tiny insects feed on bacteria and other microorganisms. The presence of large insects doesn’t tell you which microbes you do or don’t have, however, their presence suggests microbes are present. Thus, the more earthworms (a late marker) you can see indicates the soil is richer in microbial content. Conversely, their absence indicates the soil is microbially deficient.

Soil biology tests come with some conceptual challenges. First, we need to define soil health (quality) as biological fertility. Second, we need to establish baselines (where are we now?) and local knowledge is essential. Third, individual biological components can change daily, however, trends can be seen over time. If something doesn’t change within 5 years it may not be worth measuring. Last, we need to monitor and see how things change in response to management. There are also practical challenges to keep in mind. Be consistent as we are often dealing with complex methodologies. Choose appropriate sites wisely as samples will vary depending on time and location and usually more than one sample per site is needed. Local knowledge, understanding your soil type and climate zone will support your choices.

Lyn summarised the sampling process this way: 1) WHAT to sample depends on your question; 2) WHEN to sample depends on the seasonal effects; 3) WHERE to sample depends on the variability of the site; 4) HOW MANY samples depends on the test and 5) HOW OFTEN to sample depends on the reason. It is important to remember that independent experts like Lyn, can only offer advice based on what it is you want to know. Researchers might ask you to measure things based on their own interests but these measurements may not necessarily help you manage your farm.

Some biological tests are really informative. For example, we can determine if your soil has mycorrhizal fungi. If it’s low, the question is, why is it low? It is probably a management issue. Lyn cautioned that mycorrhizal fungi are difficult to culture and very difficult to establish in soil. While people will happily sell you expensive inoculants, if your management practices are poor you will likely waste your money. It might be wiser to invest your resources into developing better management practices.

Lyn summarised her key points. It is the diversity that makes the system work, the more diverse the better. Biological tests let you know the direction you’re heading in (forwards or backwards). It is important to know what is going at in your place. Your data is only relevant to you. Indicators can predict something while measurements only give you context of where you are at present.

Mark Tupman, our final speaker, began with a discussion on plant health. He emphasised the place to start is to understand what each test shows and know what their limitations are. Parameters to consider when assessing plant health include:

  1. physiological health – form e.g., a plant that is leaning or stunted might indicate poor health.
  2. nutrient status – in leaves or sap levels.
  3. sugar levels – e.g., Brix levels, tell you how well the plant is photosynthesising.
  4. pH – in sap which measures levels of alkaline minerals in plants.
  5. electrical conductivity (EC) – in sap measures total nutrient levels but not which ones. High sodium will give a high EC reading but the plant may be in poor condition due to the high sodium.

Field assessments can be done visually – a visual inspection may reveal a mineral deficiency or excess, or using refractometers e.g. a Brix meter. Spectrometers are rapidly gaining popularity because they produce a range of data in real time, however, they are still quite expensive. It is important to remember that by the time you see a visual symptom you are already a long way down the path. In other words, visual symptoms are a late indicator of a plant health problem.

A range of comprehensive laboratory tests can be done on leaf tissue or sap samples. When sampling you need to consider which part of the plant e.g., petiole, leaves (young or old) or fruit to test. As discussed below, plants can petition mobile nutrients depending on their needs. Old leaves might reveal a deficiency that young leaves won’t. You need to ensure the sample volume is adequate for the tests. Also, be aware of the weather conditions and the time of the day samples are collected. For instance it might be difficult to extract a lot of sap out of leaves from plants that haven’t received much rain in the preceding period. Mark stressed that you need to be careful how you handle, store and transport your samples as these can affect the results. It is important to remember that 1) all tests have limitations 2) you need to be aware of these limits and how you interpret the data and 3) what are you going do with the information?

Mark highlighted some assessments that are worth noting here.

Brix measures dissolved sugars and ionic nutrients and are an indicator of plant health. Higher sugar levels result in higher Brix readings. A fuzzy line indicates the presence of other nutrients especially calcium and higher levels tend to be fuzzier. Brix varies with the weather and time of day and plant store sugars in their roots during the night. Higher nitrate levels can reduce Brix readings and if the reading doesn’t go up and down it may indicate a boron deficiency.

Mark introduced LaquaTwin meters for leaf sap analyses. These relatively inexpensive handheld devices retail for about $490 each can be used to measure things like pH (very reliable), EC, potassium, calcium and nitrate (may be less reliable) levels. It is important to note, that a separate meter is required for each assay. These meters need to be calibrated every time they’re used and they can be tricky to use. For reliability they need to be washed and dried thoroughly between samples. Extracting sap from leaves is also tricky. In extracting sap, watery fluid comes first followed by the more ‘solid’ extract which is what we want to test. During the practical phase of the workshop we used several of these meters and were able to see firsthand how useful they could be to identify potential issues like mineral deficiencies or excesses.

Sap nitrate levels should ideally be zero (0) because in healthy plants all the nitrate is converted into amino acids and protein. If sap readings are high it suggests the plant is not converting nitrate into amino acids and indicates there is a problem.

Some minerals like potassium (K) are mobile in plants. Young leaves are more important than old leaves and when deficient, a plant will mobilise a nutrient out of old leaves into young leaves to preserve their health. Similarly, if a mineral is in excess a plant will store the excess in older leaves in favour of young leaves. Comparisons like this can help identify deficiencies and excesses and potentially avoid problems. For instance, K is important for fruit setting. If K is deficient, plants will literally suck K out of old leaves. If there is too much K, the plants will store the excess in old leaves. Comparing K levels in young versus old leaves can identify these issues and potentially correct with a foliar spray.

Sap analysis of leaves and petioles is a good indicator of nutrient supply and what is readily available to the plant. However, it is important to remember that nutrient levels can vary 30-40% in petioles every day. Nutrients are removed from leaves via their petiole and may give a high reading despite the leaf itself being deficient. Therefore, petiole sampling alone might miss deficiencies.

Mark shared a couple of final interesting points:

  • Most oxidised soils have very few plants and the best way to reduce oxidised soils is via photosynthesis in plants.
  • If you use foliar sprays, bicarbonate (HCO3‾) in water can dramatically inhibit mineral absorption via leaves. Less than 70 ppm HCO3‾ won’t affect foliar uptake into plants therefore to maximise your investment it is worth checking your water before applying.

The major takeaway from Mark’s presentation is that measuring nutrient levels in plants is likely more informative than soil analyses. Clearly, soil analysis will indicate mineral deficiencies or excesses and might suggest plants suited to these conditions and which species to avoid trying to grow. For example, cauliflowers have a high molybdenum (Mo) requirement. Therefore cauliflowers might be well suited to grow in soils high in Mo but not in Mo-deficient soil. However, once plants are established consider leaf sap or tissue analysis might be more valuable. For instance, if a plant is deficient in calcium (Ca) despite being grown in Ca-replete soil, this suggests that Ca is not available to the plant and indicates the problem is with the soil biology and not the soil per se. Improving the soil biology through better management might be more productive and cheaper in the long-term rather than applying costly soil amendments.


1. Pam and Murray Gomm bought the 20-acre property in 1996 that is now Oranje Tractor Wines. They started with a bare paddock, a shed and planted a dozen fruit trees. They established a vineyard on 8-acres in 1998 and farm regeneratively and have been organic certified since 2005. In addition to the vines, their picturesque property is lush and green and has several attractive buildings and has many fruit trees, especially citrus trees, and a fully netted market garden and orchard.

2. Murray and Raquel Johnson purchased the 200-acre Galloway Springs farm in 2016 and having been farming without chemicals since they took over the property. They run a mixed farm with stacked enterprises. Their centrepiece enterprise for the past few years has been organic garlic. Additionally, they run a small herd of cattle and sheep, and their daughter, Emily, raises pasture chickens. They also have a fully irrigated apple and plum orchard and two market gardens and lastly, an ‘Into The Wild’ tiny home for agritourists.