Using a Microscope to improve your soil

In a few of my Soil threads I've mentioned the importance of a Microscope.
I gave a few links to decent models and I thought it might be good to do a thread that was all about the Microscope.
In this thread I'll give links to several different models that go from decent to not quite awesome and I'll end the links with one awesome model just so we all can drool a little.
I'm also going to be describing what extras you need, and some goodie varieties of extras that while not necessary would be great to add as you can or find that you really want them.
We will finish up with how to use the microscope, this will be the majority of this thread.
I'll also go over some of the other uses such as plant disease indentification at the cellular level.

Let's get started.
For our purposes (identifying microorganisms that are in our soil) we need 2500X magnification, we want at least an Abbe condenser (focuses the light through the slide) and an adjustable iris (quantity of light adjustment) we also want a good slide table (stage) with coarse and fine adjustments and smooth movement.
Even if you don't have lots of funds to spend, you can get a good microscope. Our list starts with;

bottom of the line up  This is adequate for soil work and only cost a little over 200 dollars US.

A step up and only 252.00 dollars US

Add a camera for taking photos and we are still under 300.00 dollars US

From these three we step up to Kohler illumination, infinity focusing, a slew of better controls along with a dedicated camera port so you can be looking at the same time you take your photos.
There is a large price jump due to the much better lighting and controls, a filter holder for changing the light type or color and some other niceties for microbiologists.

Infinity focus with kohler illumination and triocular head with camera  This step up is 1056.00 dollars US
Worth the money mostly to professionals and gadget lovers. If you want crystal clear images or are trying to identify specific bacteria species, this is the scope you have to have.

From there we can simply say the sky is the limit. Illumination types are many; Polarized, Phase Contrast, Brightfield, Darkfield and EPI fluoresence are the ones we might be interested in if money is no object.
I've used microscopes that the university paid 50,000 dollars for, I would not ever own one myself simply because I don't need to have two or three people looking at the same slide at the same time nor do I need to put that image online while I am looking at it.
I have found that for our uses (microbiologists) that 1056.00 dollar unit is very nice and even though I could justify spending up to 4 thousand, I really don't get much extra that I would use most of the time for that large expenditure.
My first six years of university I used that second in the list microscope and it did everything I needed it to do.
It wasn't until I got into my Phd that I had to have phase contrast illumination and even then it was for less than half my research work.
What I'm trying to get across is that while you can go "whole Hog" if you do you are probably spending far more for features you might never use or need, better to have lots of slides, coverslips, tweezers, pipettes, dyes and cement (which you will use a lot of if you get into looking at your soil, compost and compost teas).

So with all that in mind, this link is that drool inducing "OMG" microscope.
The Woo Hoo Microscope

and I'll be back with the second installment soon.

Redhawk

Link to List of Bryant RedHawk's Epic Soil Series Threads

Now that we have picked out the microscope that will best fit our needs (you did do that didn't you?) we need a few items so that we can actually use it.

Slides, these are glass and you can get flat ones or you can get dished ones (the dished ones are used mostly for water samples, they work great for compost tea inspections), I like to have more flat slides than dished mostly because you end up using more flats and I sometimes make a slide permanent by gluing the cover slip in place. box of flat slides  single depression slides

Cover slips, these help to keep the objective lens of the microscope clean and they flatten the sample you place on the slide, never look at anything without a cover slip. standard size cover slips  Cover slips also crack if you press on them with the objective lens, that means stop, you need to do something different to get into focus.

Or you can buy a slide kit like this which gives you both types of slides and the cover slips in a package deal slide package
But best of all, you can get a whole kit, that gives you slides, cover slips, stains and all the goodies to apply those stains like this  living cells kit

This link is to a page that shows most of the items you will need and many options you might find you would like to have around later on.  accessories and slides
And this link is to the page of microscope accessories like illumination options, polarizers optic options and other goodies accessories for the microscope proper

If you can use dry objective lenses you are far better off than having to use a drop of oil between the coverslip and objective lens, that has to be cleaned every time you change slides and especially at the end of your session.

Perhaps one of the most important "accessories" you will need is this book  Ultimate guide to your microscope Unless you have used microscopes for a long time, this is priceless.

next time it will be the Big Finish, how to use the scope and I'm trying to put together a list of good books with microphotos of what you will be looking at in your soil.

Redhawk

When we are ready to check our compost or soil for which microorganisms are there we might want to own a few test tubes.
What we want are the microoganisms, not the minerals (although with polarized or darkfield illumination we can look to see which minerals are present) so we need to be able to offer a liquid (water) environment for those microbes to suspend in.
Test tubes make this a lot easier since we can use small amounts (5 gm) of our growing medium (soil or compost) add around 10 ml or more of water, mix it up and use a pipette to draw off the liquid to apply to a slide.
Placing a cover slip thins out the liquid on the slide, which  makes for easier viewing, staining and these make counting a lot easier, a grid plate placed under the slide gives us the ability to count organisms per mm or per cm which is nice for mathematical extrapolation to larger areas.

If we want to observe how the organisms move about, a depression slide is the ticket again we want to add a cover slip to protect our objective lens.
If we want to identify specific bacteria, we will use a gram stain which will instantly identify gram positive and gram negative bacteria.
Most of the bacteria we want in our soil are gram positive and will show up nicely tinted from our stain. This makes them easier to count, it also makes it easier to see their shapes.
At the same time, other organisms, larger than bacteria will be stained (amoeba, ciliates, nematodes, etc.) which also makes their identification easier for us.

If you are looking at your highest magnification and there are many blurry objects it is time to reduce the amount of magnification by switching objective lenses until those objects come into focus enough to be able to see sharp outlines, then we can use our table adjusters to bring these into sharp focus.

The deeper you delve into building your soil, you might want to add some of the goodies from those links of lists I put in the first installment, these will allow you to check for other parts of good soil that don't show up so well with our "normal" illumination.
There are special filters that can help, without having to use stains, to identify many organisms in your soil samples.
This site is an alternate to amscope, they offer quite a lot of options and equipment selection Microscope world

When I am checking organism counts and types in our garden soil or compost I like to have a polarizing filter close to hand or already in place, this limits the light wave frequencies and makes organisms show up sharper.
When you first place a slide on the table and slip it under the slide holders you want to decide if you are going to work from low magnification to high or the other way around, because you will raise or lower the table accordingly.
The coarse adjustment knob (outer knobs on left and right, at the back of the table) is used to get things close to focused, then you use the inner knob(s) to fine tune the focus.
These days, with the camera options you can then look at a bigger screen or take a photo of what you are looking at.
When I started my Masters degree, we still had to hand draw or use a standard camera with film, the new age of digital photos is quite awesome to me since I can show a class the object we are talking about and use a pointer to distinguish the parts of the organism.
My personal microscope doesn't have this feature, yet, but I can see a time coming up soon when I will be retrofitting it with a fairly high resolution rig to connect it to a computer and monitor.
Currently if I need to make micrographs I use one of the Universities microscopes, but mostly I still make drawings because I just prefer to do that.

If you want to really get into using a microscope to improve your soil or compost tea microorganism counts, you might want to look into a small vortex mixer. inexpensive vortex mixer
To make slide prep easier you can check this link out for different stains and other items that you might find handy as you get further into microscopy Slide prep kits

For those who find they have sunken into the scientific abyss, where you just have to know more and more answers, a list of Laboratory supply companies can be the wish list of all wish lists.
Carolina scientific
Fisher scientific
Thomas scientific
USA scientific
Path supply

If you do find yourselves going to the dark side, welcome to my world, they know me here.

Redhawk

For many of the same reasons that Redhawk outlines for integrating a microscope into your operations, I recommend a refractometer. This is especially if you are wanting to optimize peak flavor in the fruits and vegetables you harvest.  I wrote an article about use of the tool and it seems like a good place here to drop it in. Redhawk, if this is too out of line with your thread, you can delete this post.

IS A REFRACTOMETER IN YOUR FUTURE?

Have you considered use of an optical refractometer on your farm or homestead? As more holistic growers better understand the biochemistry of growing plants and soil, they are adopting use of this simple-to-use tool to help determine the health or nutritional value of their crops.

A hand-held refractometer is a relatively inexpensive optical instrument that measures the particulate level in an aqueous solution compared to mass. What that means in everyday language is that the tool gives an indication of the amount of sugar (and a few other things) in plant juice.

We can use these small devices to tell us the Brix value or the sugar content in the juice we extract from plant material. Along with other indications of plant health, we can use Brix values to help us make management decisions about our soils and crops. Brix is a unit of measure (technically degrees Brix) indicating the sucrose content of an aqueous solution. The scale in many basic hand-held refractometers ranges from 0-32. This scale is seen when looking through the viewpiece. If it is properly calibrated, the instrument should be set to zero when pure distilled water is placed on the prism of the refractometer.

Gathered plant material is put into a garlic press and squeezed to produce a drop or two of juice to place on the prism. Then, the user holds the refractometer up to a light source as if looking through a telescope and obtains a reading. This reading is useful if you know what a previous baseline reading was for that paddock or plant and you have a good idea what Brix reading those plants should have.

It can also be a great tool for people with dairy or nursing animals. Ruminants produce more quality milk when the sugar content in their forage is high. Therefore, knowledge of the sugar content of that forage in any given paddock is important. There are some target Brix values for various forage plants. For example, a Brix reading of eight seems to be average for alfalfa for many traditionally managed pastures. But, those raising cattle should be working to grow alfalfa with a Brix reading of above 16. For grain crops, a Brix reading of 14 is good with 18 being excellent. But for a crop that has naturally higher levels of sugar, say sorghum, the base levels are higher. In sorghum, I would think a farmer is seeking middle to high 20s Brix readings.

You don’t have to be a cattle rancher to make use of a refractometer. The savvy gardener knows that if the leaf of a plant that measures 12 degrees Brix or higher it will usually not be molested by insect pests. Agriculture and food industry expert Dr. Allen Williams confirms this notion. “High Brix forages are more resistant to disease, pests, and drought.” He also reports that good livestock performance correlates to high Brix levels. “We have seen higher animal performance when Brix levels in forages are higher,” he said referring to a 200-acre study in Independence, Kansas, USA.

Glen Rabenberg, soil expert and president of Soil Works LLC, said “A a sugar content of 13 percent or more is very beneficial for your plant’s insect resistance. We also know that if sugar content is low, plants will never grow to the extent of their genetic potential. These plants will also be low in minerals, vitamins, amino acids, and have poor general nutrition. These same low sugar plants have also lost some of the ability to draw moisture from the air, which now increases the effects of a drought.”

Wineries use refractometers to track when they should pick their grapes for the precise sugar levels they are looking for to make a specific kind of wine. Though most of us are not making wine, the sugar levels of our crops are important for us to know what’s going on in the soils as indicated by the Brix value of the plants.

One practical application of the refractometer is using it to help know the general ripeness of a fruit or vegetable. Testing a sample can give some indication to know what the optimal harvest time should be. For example, most industrial-scale cantaloupe growers will pick their melons when Brix values reach nine degrees. However, an excellent cantaloupe has a Brix value of 15 or higher. This can be the difference between that amazingly sweet cantaloupe you tasted from your grandparent’s garden compared to that crappy melon on most restaurant salad bars.

Rabenberg teaches that increasing Brix levels help an operation become more productive. Harmful fungi thrive in an area where plants measure a Brix value below seven. When ensuring there is the proper balance of available minerals and nutrients, the Brix levels are often in the 10-11 range. At this value, Rabenberg reports seeing drought resistance in the crops and fewer weeds nearby. Finally, when plants are measured at Brix values of 13 or higher, Rabenberg reports resistance to harmful insects.

Conducting Brix valuations needs to be done with some care. The samples must be gathered at the same time of day and in the same general weather conditions. Plants are moving sugars and other nutrients up and down their systems at different times of the day and different time of the year. We can obtain false comparisons if we conduct Brix testing in the morning and then a few days later in the afternoon when it’s warmer. We should also take samples from the same kinds of locations on the plant.

Plant samples must also be taken when there is similar sunlight. I recommend testing after the same amount of sunlight has been available and around the same temperature. Because the refractometer is impacted by temperature, it’s a good idea to ensure the device and the sample are about the same temperature. I like to let the sample juice rest on the prism glass for at least 30 seconds before taking a reading.

Growers should not view the refractometer as a magic wand. A refractometer gives you only one primary measurement. As useful as knowing what Brix values are in your plants, we can gain a lot more if we take this one data set and use it with other information to make decisions on our homesteads, farms and ranches.

What does it all mean for you? Plant health and related sugar levels are often dependent on the quality of life in the soil and how the soil’s microbiology is working in harmony with the root system of the plant.

Often, an unfavorable Brix reading can be an indication of low nutrient uptake in the plant due to poor microbial interaction in the soil. A first remedy I’d tell people to do before expensive soil testing and inputs is to make sure they are feeding the soil microbes well. Adding finished compost or compost tea or even raw milk are excellent way to feed the soil and thus ensure a healthy system below the surface.

Even if I had a microscope (and space for it), how do I know who is who in the soil? I mean you have to learn to use it and it is not easy I guess.

The book I gave a link to Ultimate guide is an easy to use one which makes learning to use a microscope quite easy and faster than most people think they can learn.
For micrographs of the organisms we want (and the ones we don't want) you can go to the library and check out a microbiology book, go online to Tim Wilson's great site,
or if you have the funds and desire, purchase a microbiology book that has full descriptions and micrographs (these usually start at around 60 dollars US).

I recommend Tim Wilson's site and then the library, most folks don't want to have a thick book to hunt microbes in, time wise it can take a while to locate what you want.

Most people can learn to use a microscope in less than three hours, after just a couple of days they can be fairly expert at it.

Microscopes are more for those that really want to know how their soil building efforts are improving the soil, they are not absolutely necessary, but they can be very helpful (and they can be rather addictive).
You can still build superior soil without one.

My personal microscope, in the case takes up 16" x 16" x 26" storage space, the case holds the scope and all my "extras".

By the way, if you have any animals that become sick, your microscope can be a great tool for finding out exactly what "bug" they have caught, which means you can effect a cure faster.
There are lots of applications for a microscope on a farm, should you decide to go the science route, but people farmed for thousands of years without science so there is the question of "is it necessary? and is it better?" I would have to give the answer of "It depends on the farmer".

Redhawk

Nice post with a lot of good information Dan, Thanks for posting it.

Redhawk

Dr. Elaine Ingham gives advice on choosing a microscope for soil microbiology:



More videos (setting up the microscope, preparing samples, etc.) have been posted by SustainableStudies on YouTube:

https://www.youtube.com/user/SustainableStudies/videos

After being inspired first by Alan Booker's microscopy course in the 2021 PDC, then by reading this thread, I took the plunge and bought a microscope! I found a good deal on a mint condition Amscope B120C on Offerup, purchased from a local brewery that never wound up using it. Same entry level one that Redhawk mentioned.

Then I found this great resource, a well-designed Microscope Guide on the basics of soil sampling and microscopy. (I didn't take such diligent notes that night at the PDC because I was too busy watching Alan pilot through microbial space like a Jedi!)

Because I bought the 'scope used, it was a la carte-- no slides or camera. I am still awaiting the slide kit (which I bought from Home Science Tools) to be delivered.

Meantime, I've taken 5 samples from different garden beds and they're settling now in water (per the guide instructions on soil prep).

More to come once I get everything on slides and analyzed! I suppose I should also buy a digital camera attachment, too.

BTW, is there a PEP badge bit for soil microscopy? If not, there should beeeee! (Maybe I'll pitch it in the oddball category).

Bryant RedHawk wrote:Our list starts with;

bottom of the line up  This is adequate for soil work and only cost a little over 200 dollars US.

A step up and only 252.00 dollars US

Add a camera for taking photos and we are still under 300.00 dollars US

From these three we step up to Kohler illumination, infinity focusing, a slew of better controls along with a dedicated camera port so you can be looking at the same time you take your photos.
There is a large price jump due to the much better lighting and controls, a filter holder for changing the light type or color and some other niceties for microbiologists.

Infinity focus with kohler illumination and triocular head with camera  This step up is 1056.00 dollars US
Worth the money mostly to professionals and gadget lovers. If you want crystal clear images or are trying to identify specific bacteria species, this is the scope you have to have.

From there we can simply say the sky is the limit. Illumination types are many; Polarized, Phase Contrast, Brightfield, Darkfield and EPI fluoresence are the ones we might be interested in if money is no object.
I've used microscopes that the university paid 50,000 dollars for, I would not ever own one myself simply because I don't need to have two or three people looking at the same slide at the same time nor do I need to put that image online while I am looking at it.
I have found that for our uses (microbiologists) that 1056.00 dollar unit is very nice and even though I could justify spending up to 4 thousand, I really don't get much extra that I would use most of the time for that large expenditure.
My first six years of university I used that second in the list microscope and it did everything I needed it to do.
It wasn't until I got into my Phd that I had to have phase contrast illumination and even then it was for less than half my research work.
What I'm trying to get across is that while you can go "whole Hog" if you do you are probably spending far more for features you might never use or need, better to have lots of slides, coverslips, tweezers, pipettes, dyes and cement (which you will use a lot of if you get into looking at your soil, compost and compost teas).

So with all that in mind, this link is that drool inducing "OMG" microscope.
The Woo Hoo Microscope

and I'll be back with the second installment soon.

Redhawk

Link to List of Bryant RedHawk's Epic Soil Series Threads

Would you please update this, if possible referencing Labomed (Made in India, not China)?

1) The very first post and several after it indicate by context that there should be links to various websites, but they are missing....
2) If you happen to get a microscope that uses Kohler illumination, learn how to keep it aligned! Speaking as the proud owner of a "I learned Kohler from Keller" button alignment is not hard once you know what you are doing... But not so easy with out some training. I would try to explain with a long post but Nikon has done a brilliant job of building and maintaining https://www.microscopyu.com/ Even is a (former) professional microscopist, I find the site helpful.

I need to read this whole thread more carefully and go through the other linked threads so I am sure I will have other comments and I am looking forward to learning many things that I do not already know.