microBIOMETER® in University of Michigan Research Study

Joshua Mikesell utilized microBIOMETER® in a University of Michigan Intern Student Program last fall for his 501(c)3 compost business Happy Coast.  The goal of his compost business is to seek out organic waste products and develop ways to reduce and recycle these materials. In preparation for the study, Joshua created multiple controlled scenarios to test biomass in certain situations and in several types of compost.

For the project, they sorted through food waste obtained from local businesses and developed a process and ingredient list to produce their own organic fertilizer. microBIOMETER® was used to perform the initial tests. Then after their pellet applications was used again to determine effectiveness.

The University of Michigan was so impressed with Joshua’s study they now want to send him as many students as possible to continue this work.

Click here to read the entire report as well as view all the microBIOMETER® data collected.

Soil Carbon Q & A with Dr. Judy

soil carbon

We recently received the following questions from one of our customers and below are the responses from Dr. Fitzpatrick.

Part of my research is surrounding the soil organic carbon results we attained from microBIOMETER®, and I am wondering if someone from your team could provide more information on what this means relative to total organic carbon (TOC) in a sample and if they are comparable?

The literature shows a strong correlation between available organic carbon and microbial biomass carbon (MBC). Since your compost is not soil, the available organic carbon in your sample would be TOC and would correlate. MBC by microBIOMETER® is even better than that: a big number tells you that you have carbon and all the nutrients needed by microbes and plants.

Since MBC has correlations to TOC is there a formula or percentage to convert MBC to TOC? Or approximately how much MBC makes up a TOC number?

There is no formula to correlate TOC with MBC. TOC includes carbon that we consider stored as well as carbon that is easily available to microbes. Increasing easily available carbon for example by applying compost will increase microbes and eventually increase TOC, but as microbes rarely exceed 1% of TOC, it would have little effect on TOC short term. In long term stable systems we see a correlation but the correlation is not the same for example in forest as in agriculture as the capacity to store TOC is different soils under different conditions. In studying the effect of long term (40 years) different management systems at U. of TN on MBC and TOC, MBC by microBIOMETER® correlated with the TOC demonstrating the effectiveness of sustainable practice on increasing TOC and the positive correlation with MBC levels.

Does a high MBC usually mean a higher F:B ratio? And if so, could we draw any conclusions about carbon sequestration capabilities from that?

Generally as the MBC increases there is an increase in fungi. The soil food web is a balanced community. Some communities are more fungal dominated some less, but similar communities tend to have the same F:B ratio. It is generally believed that fungi, especially mycorrhizal fungi, contribute more to carbon sequestration than bacteria. This may be because glomalin is carbon rich and tends to sequester.

To further my understanding of soil/compost mixtures. I performed two microBIOMETER® tests. One test was on “active compost” which is compost in a medium stage of decomposition, and generates some CO2 and another one “finished compost” which is cured, ready for usage, and low CO2 production. However, I found that they had similar amounts of MBC and F:B ratio. Is this normal?

A study with microBIOMETER® at University showed a higher F:B in finished compost. The higher respiration/MBC indicates that your unfinished compost is still being digested — working microbes make more CO2. Holding MBC stable in your finished product is good.


Variance in soil samples explained

Often, we are asked about variance – different results when you test the same sample. Our answer is that nature produces most of this variance. To explain, when you measure out 0.5 cc of soil, you have on average about 0.6 grams of soil. If your microBIOMETER® results read 300ugMBC/gram of soil, that means you have 600ug of microbial biomass – we divide the number we get by ½ because the literature tells us that 50% of the dried MB is carbon. As dried bacteria is estimated to weigh 1pg, if this were all bacteria, it constitutes 600,000,000pg or 600 million bacteria.

Now imagine that I have 600 apartment buildings in NYC that each contain 1 million people, and I decide to check 10 apartments in 10 buildings at 4 p.m. to estimate the number of people actually in the building. Obviously, it would vary because people are not always in their apartment and different apartments have different numbers of inhabitants – the same is true for soil.

Soil contains microscopic aggregates of different sizes and the number and type of inhabitants in each varies on the physical and chemical composition of the space as well as the nutrient, pH and hydration level. Each sample you take is like looking at a number of different apartments in a number of apartment buildings.

For this reason, when conducting research, soil and medical researchers run duplicates or triplicates. Because of cost, soil labs generally do not run duplicates and they see 10- 25% variation. We are recommending running duplicates when using microBIOMETER® unless you are doing academic research. Generally, we see <10% variation for a given sample, and for a field that looks homogeneous. Pastures can have much higher variation because the nutrients level across the area varies tremendously.

How do plants farm soil microbes?

Source: How Plants ‘Farm’ Soil Microbes and Endophytes in Roots

UPDATE: Dr. White sat down with Dr. Fitzpatrick and Jeff Lowenfels to discuss rhizophagy. Click here to view the webinar. (Jan. 15, 2021)

A summary of James F. White’s presentation at BioFarm, 2020 (Nov. 12, 2020). 

The rhizophagy cycle is an amazing process recently discovered by James White’s laboratory at the University of New Jersey, by which root tips “ingest” bacteria and absorb nitrogen and phosphorus and other nutrients from them.

The microbes pictured here in roots are called endophytes because they can live inside plants. The bacteria are attracted to the root tip by root exudates. They then enter the root where the cell walls are dissolved using superoxide, allowing nutrients to leak out to the plant. But the plant does not kill the microbes instead the microbes stimulate the formation of root hairs, which are escape routes for the microbes.

After ejection from root hair tips, bacterial cell walls re-form. The bacteria fatten up and are soon ready to acquire soil nutrients and become another meal for the plant.

Source: How Plants ‘Farm’ Soil Microbes and Endophytes in Roots

Not only does rhizophagy provide mineral nutrients, it is also the stimulus for formation of root hairs, which are critical to the establishment of a healthy root as can be seen in this photo of a plant root with and without endophytes.




How much carbon can be stored by increasing your soil microbes?

microBIOMETER® reports the microbial biomass as ug of microbial carbon/gram of soil. The chart pictured here shows how much carbon can be stored in an acre just by increasing microbial biomass alone. (Chemically fertilized farmland averages about 100 ug/microbial C/g of soil.)

Microbial biomass is the best single estimate of soil quality. It is the bodies of dead microbes that build humus/soil organic carbon, returning carbon to the soil and building soil structure which prevents erosion and pollutant run off. (Chemical nitrogen fertilizers have been shown to inhibit microbial biomass.)

The literature reports that lab measurements of soil organic carbon are not sufficiently accurate in monitoring an increase in carbon sequestration in less than 3 years but that a yearly increase in microbial biomass can indicate that the process of carbon accumulation is occurring.

microBIOMETER® has been used to demonstrate increases in soil carbon due to increases in microbial biomass on the Apple campus in Texas and for 3 years by the NYC Arts and Science Carbon Sponge Project.

Source: Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls.

Can you carbon farm in a city?

Excerpt from the Carbon Sponge guide

Carbon Sponge is an interdisciplinary collaboration exploring the potential for urban soils to sequester carbon as a means to mitigate anthropogenic greenhouse gases and build healthy soil.

At microBIOMETER® we were very excited to work with Brooke Singer and play a role in this important project. Brooke initiated Carbon Sponge during her residency at the New York Hall of Science in 2018. Being introduced to the early version of microBIOMETER® (pictured here) was one of the factors that paved the way for Carbon Sponge. An excerpt from the guide, “Getting access to a tool that quickly, easily and cheaply measures microbial biomass in a soil sample, without needing a lab test, holds a lot of potential.”

Click here to order the Carbon Sponge Guide. All proceeds go to support the project.

Currently, Brooke along with her colleague Sara Perl Egendorf  are working with five New York City farms and gardens that are participating in Carbon Sponge’s pilot testing program using a collection of tools, including the microBIOMETER®, to track urban soil health over time and consider the readiness of the soil to sequester carbon. The affiliates (a few pictured below) are: Bronx River Foodway, GrowNYC Teaching Garden on Governor’s Island, Pioneer Works, Prospect Farm and Red Hook Farms.

What is “priming” and how does it affect your soil?

Priming is currently a hot topic as it affects whether the fertilizer you are using is effective. For instance, when you prime a pump, the water you add allows the pump to start pumping water. If there is not enough water, you just wasted the priming water.

This is exactly what happens in your soil. When the microbes in the soil are fed nutrients “primed”, by the plant or amendment, it wakes them up and they start growing. But, whether they can continue to grow depends on the continual supply of nutrients. If there is enough balanced organic matter in the soil, they are fine. If not, the microbes will work hard to harvest some of the stored carbon, nitrogen and phosphorus in the soil. And instead of storing carbon in the soil, their labors will produce CO2.

A key point is “balanced” nutrition available in the fresh organic matter which is most available to microbes. Like us, if microbes do not have access to one of the key nutrients, e.g. N, P, S, K, Mg, Mn, B, etc. they cannot thrive. Clive Kirby’s group in Australia has demonstrated that by balancing the ratio of key nutrients in fertilizer regimens to bring the ratio of fresh organic matter to a C:N:P:S ratio of 10,000:261:32:48 they increased yield and substantially increased the stored soil carbon.

Source: Coonan, E.C., Kirkby, C.A., Kirkegaard, J.A., Richardson, A., Amidy, M. and Strong, C., 2020. Microorganisms and nutrient stoichiometry as mediators of soil organic matter dynamics. NUTRIENT CYCLING IN AGROECOSYSTEMS, 117(3), pp.273-298.

Simple ways to increase the microbial biomass in your soil

Healthy soil is brimming with beneficial microbes, and those microbes are one of the important keys to ensuring the health of your plants. Along with breaking down key nutrients for your plants, they’ll aerate the soil so nutrients are evenly distributed, and fend off parasitic microbes so your garden can grow in peace.

Considering the wealth of benefits, it’s no surprise that it is recommended that you do everything you can to maximize the microbial biomass in your soil. While there’s complicated science behind it, nourishing and increasing the amount of microbes in your soil is simple, and can be accomplished with a few tried and true methods. And  thanks to the microBIOMETER®  soil test, even amateur gardeners can track their microbial biomass levels. 

First, let’s detail how you can take care of those important microbes and enhance their numbers. It’ll involve shedding some old gardening habits, along with taking on some new ones, but we promise the end results will be worth it. 

What To Avoid

Before you start taking extra steps to care for and increase your microbial biomass, you should ensure you’re avoiding certain tactics that are known to hinder their growth.

  • Pesticides

While you might think avoiding pesticides wouldn’t enhance plant health, a close look at the ingredients of most pesticides will show you they do far more harm than good. Amongst a variety of issues, one of the most harmful is the fact they decimate microbial populations in the soil. If you want to ensure pests will stay away in the absence of pesticides, try utilizing companion plants instead.

  • Fungicides

While pesticides are bad, fungicides are even more of a threat. Some of the most vital microbes in your soil, being fungi, would be directly targeted by these treatments. The harshness of these chemicals would also wreak havoc on the non-fungi microbes, all but eliminating any trace of a microbial biomass. Even if you can’t do everything on this list, ensure you at least abide by this particular rule. 

  • Tilling

Lastly, while many gardeners and farmers consider tilling a standard gardening process, you’ll want to abstain from it if you’re focusing on your soil’s microbes. That, of course, is due to the level of soil disturbance that occurs during the process. The process leads to lost microbes (especially fungi), and any benefits gained from additions made to the soil end up being cancelled out. By avoiding tilling, you’ll allow the delicate environment in your soil to function undisturbed and, in turn, at full capacity. 

What To Do

Now that you’ve cut those bad habits out of your gardening routine, you have room for a few that’ll greatly benefit your soil in the long run.

  • Composting

Nothing gets microbes into the soil like a nice big pile of compost! All that food breaking down in one big pile is basically a feast for all the helpful microbes you want around your plants. Once you add it onto your soil, then turn it to make sure air hits every part of it, you’ll be ensuring the microbes have plenty of energy to break down nutrients. To ensure the best compost possible, make sure you add in natural components like grass clippings, fruits, vegetables, wood chips, and straw. There’s no need to exclude other foods, even processed ones, but a healthy blend of green and brown material is a must. 

  • Compost Teas

Following the same logic, compost teas can do wonders for the microbes in your soil. All you have to do is take some compost and put it in a water permeable pouch,  add some microbe feeding nutrients (perhaps like molasses), and let it brew (bubbling air into it) until the microbes in the compost have multiplied and the tea is full of microbes. Once done, pour it all around the base of your plants. One round will do your plants good, but repeating this process a few times during your growing process will really make a difference.

  • Optimize soil moisture, pH, and temperature

This last step is actually three steps and if these conditions aren’t met, virtually nothing else on this list will have a noticeable effect. To start, making sure you have adequate moisture is as simple as regularly watering your plants. You may also want to consider purchasing a moisture meter to assure your levels are ideal. Next, the ideal pH range for soil is between 6.0 and 7.0, so you’ll have to test your soil to see where you’re at. If your soil pH is too low try adding limestone and if your pH is too high you can add aluminum sulfate and sulfur to get things balanced. Lastly, mulching is a great way to help your soil maintain an even temperature. 

Incorporating these simple tactics into your crop management is an important first step to building the microbial biomass in your soil. Another critical step is testing and quantifying the results of these inputs since decision making without data is like driving blindfolded. microBIOMETER® is a rapid, on-site soil test for microbial biomass. Microbes respond very quickly to any changes in the soil, therefore, you can set a baseline then retest within a week to see if you are heading in the right direction.


Soil Health Improvement Tracking

Microbial biomass (MB) is the best single indicator of soil health (Doran, 2000). Microbes feed and protect plants, build soil structure which prevents erosion, increase water holding capacity, and build soil organic matter (SOM). MB is low in any situation that is harmful to plant growth (and vice versa) and protects against pathogens, thereby reducing the need for pesticides. MB can predict success before plant outcome. The Fungal:Bacterial ratio (F:B) of the MB provides crucial information regarding colonization by Arbuscular Mycorrhizal Fungi (AMF), and the recycling metabolic processes of saprophytic fungi (SpF).

Soil stewards all over the world are seeking to understand the microbial levels in their soil and the ratio of fungal to bacterial life. The higher the microbial biomass, the more nutrients will be available to plants naturally, decreasing or eliminating the need for chemical fertilizers. Higher fungal to bacterial ratios are critical for building soil structure that prevents erosion and runoff off of pollutant chemicals while building moisture holding capacity of the soil and sequestering carbon.

Soil health is fast becoming one of the most important factors in agriculture and in the growing efforts to improve the earth’s stock of agricultural land. Farmers, industry, and environmentalists are looking for cost-effective and reliable ways to measure soil health and to assess impacts of progressive changes to soil and harvest management.

Testing soil in homogeneous sections at similar stages of the growth cycle can set a baseline for microbial biomass and fungal to bacterial ratio. That baseline can be used to assess how different stewardship practices are impacting the soil and allow for refinement to soil management plans and show soil health improvement over time. While every soil steward’s situation is unique, microBIOMETER® can help measure, follow, and assess efficacy of improvement to soil health.

Why should you grow your cannabis in microbe-rich soil?

grow cannabisMany first-time cannabis growers don’t think too hard about the soil their plants will be growing in. If the soil looks healthy enough, it should be good to go, right? Well, it might be, but that isn’t enough information to tell for sure. If you really want to know whether your cannabis will thrive, you’ll have to see whether or not your soil contains a solid amount of microbes.

Microbes have a mutually beneficial relationship with the plants in their soil, and supporting microbes is one of the best ways you can support your cannabis. As we go along, we’ll be discussing the details of microbial presence in soil, the relationship between microbes and plants, and the specific organisms that make optimal growth possible.

Why Microbes Play a Vital Role in your Cannabis Plant Health

Microbes are key if you want your cannabis plants to grow as well as they can. If the idea of beneficial bacteria is strange to you, remember that we, ideally, have loads of bacteria in our bodies that keep us healthy. We’re not made of soil, of course, so things don’t work exactly the same, but the microbes in soil and those in our guts share key functions in common. Namely, as we’re about to explore, microbes provide vital nutrients to the plants in their soil, along with protecting them from harmful forces.

How Microbes and Cannabis Plants Work Together

With that in mind, let’s take a look at how the relationship between microbes and the cannabis plants you are growing play out in the soil. Plants need sufficient amounts of phosphorus, potassium, and nitrogen to survive and microbes have a direct hand in how much of those nutrients your plants receive.

While the nutrients may be in the soil already, they aren’t as accessible as they could be. Potassium, for example, is often shrouded in inorganic material. As microbes happen upon it, they’ll consume it, metabolize it, and excrete it in a form much more readily consumed by the plants. While the others aren’t as hard for the plant to get to, the microbes break them down nonetheless, and the plants benefit greatly from the enhanced access. This effort is further assisted by their ability to aerate the soil, ensuring there’s an even flow of water and nutrients.

The microbes aren’t only doing all this from the goodness of their heart, though. As the plants are fed, their roots excrete a collection of substances, called exudates, into the soil. These exudates, which include a variety of amino acids, organic acids, and sugars, happen to be a great source of nutrition for the microbes. With their microbe bellies full, the nutritional cycle is fully formed, and the plants are ready to thrive.

The Importance of Fungi for Growing Cannabis

While we think of fungi as separate from microbes, they’re part of the club too, and serve the same cause. To be clear, though, this is because they also partake in the exudates to stay fed.

Mycorrhiza fungi, in particular, can be found acting as the extension of plant roots, collecting nutrition from further down the soil than plants would be able to otherwise.

One type, ectomycorrhizae, acts as a sort of sheath for the root, extending out for nutrition. Endomycorrhizae, however, actually live inside the plant, helping to bring the nutrients straight into the root. To preserve them, ensure that you’re not being heavy-handed with fertilizers. Of course, you should also avoid fungicides entirely.

Microbial Dangers, and How Other Microbes Stop Them

As the fungi provide nutrients to the roots, they serve as a protective layer for them as well. But what, exactly, do they need protecting from? Well, among the beneficial microbes, there are thousands of microscopic worms, called parasitic nematodes, that feed on the roots of plants.

Looking from the outside, you’d notice roots facing attacks from ectoparasitic nematodes, which live in the soil right outside said roots (the rhizosphere). At the same time, endoparasitic nematodes are able to enter the roots themselves, breaking them down from the inside.

In anticipation of this threat, fungi will utilize their hyphae, which are the tiny strands that make up their mycelium. Using these strands, the fungi are able to locate and trap both types of nematodes, preventing them from further chewing at the root.

The fungi also receive help from, interestingly enough, other nematodes. They aren’t quite the same, though; while the others are parasitic, these are known as predatory nematodes. They, too, dwell in the rhizosphere, but only to eliminate plant-eating threats in the area.

How Earthworms Play a Part

Not every part of this underground battle is microscopic, though. In fact, the humble earthworm will be one of the main lines of defense for your cannabis plant. Parasitic nematodes happen to be a favorite prey of theirs, so they’ll munch up whatever your fungi and other microbes can’t catch. In turn, the waste they excrete contains nitrogen, phosphorus, and potassium (the three vital nutrients we mentioned earlier), along with calcium and magnesium. They also aerate the soil as they move around, ensuring the plant has easy access to the natural fertilizer.

How Benefits Show Themselves in Cannabis Plants

If you’re able to ensure optimal conditions for your soil microbes, you’ll notice it pretty quickly as your cannabis plants mature. Their leaves will be greener and fuller, they’ll end up on the taller side, and your buds will be notably larger and more resinous than average.

Your plant may be able to survive without a healthy amount of microbes, but it’ll look amateur in comparison. That’s not to mention the cost of those seeds adding up, leading you to lose money you could spend on expanding your growing operation. Armed with this new information, you won’t even have to worry yourself with the thought. Just keep those microbes and worms alive, and you’ll be on your way to hefty yields of potent buds!

microBIOMETER®, a rapid, on-site soil test, will help you determine the microbial levels in your cannabis soil as well as the fungal to bacterial ratio to ensure the healthiest environment for optimal growth of your plants.