Inoculation with Bacteria / Fungus Frequency?

So I recently started inoculating the soil for my trees with beneficial bacteria and fungus.

I have not noticed, nor to I expect to notice until spring, any changes in my older trees. However, I will say that many of my seedlings have responded quite well to the treatment.

My question is:

Should I be treating my trees with a regular inoculation of bacteria and fungus?
If so with what frequency?

Hi @sparkytwobillion
I’m new to compost extracts and inoculates too. It is my limit understanding that the trees will lean on the microbes just before and during periods of growth.

@sparkytwobillion , just for the conversation, which source did you use for inoculation?
ANSWER: infrequently. They take time to grow and sort themselves out. A little goes a long way. Maybe once every other year…? Let the tree tell you. Balance.
I have, traditionally, included a hand full of old soil in a repot.
This works well for collected and older trees. Nursery trees might have sterile soil, over time they become naturally inoculated. Not always with the proper microbes.
I have been using Dr Earth; very satisfactorily. However this goes hand in hand with use of the ORGANIC fertilizer; Biogold, etc. Gives the microbes nutrients to grow. Also, the properly maintained top dressing helps shelter them. Balance of water and air…
I have gone out and grabbed a baggie of (to me…) a obvious fungal source from a wild Ponderosa. Worked great.
I have had a white truffle pop up in my Utah Oak forest a while back.
One thing that needs to be NOTED, you get the bad (and horrifyingly bad) microbes sneaking in too. Usually in a properly balanced system, the Good takes care of the Bad. Balance, keeps them in check. Slime molds and mushrooms are not always detrimental, usually just interesting.
The plant and animal biom is WAY deeper and more complex than even the Ian podcast leads into. The knowledge gets deaper every year. (Rabbit hole: The endosymbiotic theory of mitochondrial evolution… lead an informal undergraduate class for the Phds in college in 1981. Gotta love those microbes.)
Balance in all things; and patience…


@KurtP The source of inoculation! I meant to include that. My bad. After much research and many videos I landed on this product Microbe Life PH21227 717505 Photosynthesis Plus Fertilizer. As well as buying an inline filter to filter out the chlorine and chloramines used in our water system.

I am not endorsing it. Just saying that my research convinced me that at the very least it would not harm and probably might help.

For fertilizer I’ve been using Alaska Fish Emulsion Fertilizer 5-1-1 Concentrate and Alaska Morbloom Concentrate 0-10-10 Fertilizer. Depending on the tree, season, and reason.

As far as Balance in all things? I’m fine with that so long as it is balanced in my favor. :laughing:

As a side note though you bring up a good point. Patience. I started killing trees, I mean tending bonsai, ten years ago when I accidentally grew some plum trees from seed in my worm composter. If you ask anyone who knows me they will tell you that I am notoriously impatient. Which in my professional career as a software engineer serves me well.

In my personal life, it does not serve me so well. It’s not out of control because, well, I do have friends that can tell you how impatient I am. If it were completely out of control, I wouldn’t have friends that could inform you of that fact. :grinning:

So ten years ago I came to the choice of learning patience by growing, from seed, my own trees for bonsai. Countless tree seedlings have selflessly sacrificed themselves to help me learn patience. Hopefully, I will learn this lesson before I have to face them in the hereafter. If I fail learning it, I fear the Last March of the Ents will be a Sunday walk in the park compared to what they will do to me. :slight_smile:

But back to seriousness. Infrequently. OK. I will trust you on that point. I am currently saving up my pennies for a microscope so that I can actually look. Until then I just have to go with heuristics.

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Sounds safe. And sane. I like seaweed emulsion, too; micronutrients and enzymes…
I have MANY trees from seed. Plum, cherry, 5 kinds of oak, horse chestnut, mountain ash, linden, mulberry, Hawthorne, shore pine, etc… Someday my 5 tree 4yo Ponderosa forest will be awsome. From cones on my collected Colorado pondys Already have limbs. Need to wire for movement nexg spring. Remember to root prune early and often… the trees were 2"; the roots were 4" after first spring…

My 10 yo scots pines are great now. Two more years…

Bonsai on!

@KurtP Wow! those are impressive!

So as a follow up. I wrote the manufacturer. They suggested two different products that they produce specifically for trees. I’m not going to name them here because I am not trying to promote them.

The manufacturer disagreed with you. They recommended a more aggressive treatment of once or twice a month.

I don’t find this overly suspicious but maybe a little misguided. The manufacturer was originally focused on creating a product focused on cannabis growers. I’m not saying they are being dishonest I am simply saying that is where they were originally focused. The needs of annual plants are different than perennial plants.

On the other hand given that bonsai are not typically grown in what most people would identify as “soil”, mine certainly are definitely grown in a mostly inorganic mix of aggregates, I wonder if their advice is not correct.

This prompts the question, “What is the ideal mix to grow beneficial microbes and fungus?”. Lets face it, we can grow our trees in garden mud. After all, for millions of years trees have been growing in garden mud. :slight_smile:

Wow, I`m in the wrong buisness; AND, we need to regulate marihuana growing better. These would be considered an additive, and we consume this?..
May be a good product… I don’t SEE it. Sounds like the product is used more like a fertilizer. Benificial microbes for pines and decideous bonsai?
Re: I have a real problem with growing photosynthetic bacteria on my bonsai…algae gets scraped off… pouring sugars on a trees soil? Hmmm. The bacillous sounds ok? The fungi may be the ones pines need? A well composted ORGANIC soil amendment with a broad spectrum of healthy bacteria, fungus is what is called for.
However, just as a generality, once a media (soil…) is ‘innoculated’ with a microbe, they will grow until the ‘food’ runs out; or, until 'something ’ kills them. Some just don’t like the environment and are not capable of surviving. The symbiotic ones will be swapping nutrients and minerals with the tree to be happy.
Drying out doesn’t kill everybody… except the tree. Some microdes just curl up and wait…
Antibacterials dont kill everybody… SOME specific bacteria.
Antifungals dont kill everybody… SOME specific fungi.
Some fungi eat bacteria, some bacteria eat fungi.
They both eat bugs… and they ALL eat tree materials.
Don’t get me started on viruses… the will colonize everyone… and EVENTUALL take over the world…(they already have…)
In your pots, in inorganic soil, with daily leached organic feeding (biogold etc) and water… a microbes will find a nich (benificial biom of the tree and the micro environment involved), will set up shop and THRIVE. Infrequent re-innoculation will up the populations that are floundering.
EVERYTHING growing in a particular product is not ultimately compatible or good for the individual tree involved; THEY WILL sort themselves out. (Think war of the Worlds)
Hopefully, the ‘horrifyingly bad’ species will not take over and kill the tree.
I have seen this happen… American chestnut, peach rust, citrus rust, invasion of the body snatchers…
I DO keep the nuclear options on hand. Judicious use of anti-everything. Better living through chemistry.
Someone elswhere said burn the dead tree. Even fire doesn’t kill everything, though. Sheep scrapies virus comes to mind. It is the same virus family as mad cow disease. THEY got it from feeding dead sheep materials to
cows in cattle feed; and then, into hamburgers.
Wow. Back to bonsai. As I said, this is way more complicated than it needs to be. You really dont need the innoculant. Good microbes will show up. The inoculation just helps some show up sooner. The proper ones help the trees, and grow into a sharing comunity. The rest just hang around and wait their turn to decay cellulose…
Oh, by the way, the endosymbiotic bacteria (mitochondria) in YOUR cells just show up to the game automatically, along for the ride! Couldn’t live without them! Human beings are just a mitochondria’s way of growing more mitochondria…
Haute Bonsai!
(My apology for the late night ramblings… Too much peach cobbler… but, hay, the mitochondria asked for it…)

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@KurtP OK! The pennies have been saved and the microscope purchased. Also, I have watched some online videos about how to prepare a soil sample for viewing. So, at this point I am learning to use the microscope and learning the procedure for conducting a survey of soil microbes. FUN! But I am not quite there yet.

The microscope I purchased is a trinocular microscope which allows taking images and video. Because I only use Linux machines at home the cameras that are compatible are actually more expensive than the microscope! :flushed: subsequently I don’t have any images or videos to share yet.

I have been re-innoculating three specific tree seedlings and comparing them with a control group of tree seedlings. They are all planted in the same sized pots, with the same aggregate mix and all six trees are the same species. All 6 seedlings have been innoculated once. 3 of the seedlings have been innoculated every other week for about one and half months so far.

What I have observed is that the reinoculated subjects by far have a greater bio-activity and biodiversity than the subjects that were only inoculated once. Since at this point I am only learning how to do a survey I really cannot say any numbers but my observations would seem to indicate that there is some effect on population and diversity.

Due to my lack of knowledge I cannot really identify the microbes I am seeing, I can only assert that I see greater numbers by far in Group A vs. Group B.

So now one of the things I am thinking about is what sort of bonsai soil mix would make a good habitat for soil life? Do we know about any studies or advice about that?

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Mr. @sparkytwobillion … 'So now one of the things I am thinking about is what sort of bonsai soil mix would make a good habitat for soil life? ’ …Thats the $24M question... everybody has an opinion. Most of them will work to some extent. My best guess; and, Im using …1:1:1 akadama:pumice:lava, mostly 1/8 to 1/4"(maybe up to 3/8 on larger trees)… Organic decomposing fertilizer, with a moss top dressing. Also, makes it easier to control your testing. More control, better data.

  1. Are you doing pines, or decideous. I see pines as
    more needy of benificials. I may be wrong. They all
    need it…
  2. Are you using organic decomposing fertilizer
  3. pH of your water should be in the 6.5–7.2 range. Slightly acid to neutral. I think it makes a difference. Hopefully no chlorine.
  4. Constant steady moisture and temp monitering.
    Microbiology… read up on how fungi and bacteria morphology differ— cell structure and size. Fixing a sample on a slide, and simple cell staining techniques. Makes it easier to see and ID. There are volumous tomes on microbe ID.
    Start simple. Fungi and bacteria lab manuals are available in used book stores.
    Also, keep good notes. This will be publishable…
    Organic material mixed in will make the job harder. I once found an ex-plosive color tag in a microscopic sample. Company the sample came from used tagged dino-mite. Nature always amazes me.
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  1. Cover/protect your soil if you use insectasides, fungal, or bacterial sprays… The microbes you are cultivating will thank you.
    (:thinking:… Edit time run out while I was editing…)

Staining and Identification. Good information! Up until now I have just been working on how to use the microscope and seeing them. The microscope arrived last week and I don’t even have my test tube rack yet. But identification and population are definitely the next steps.

Further, it has been years since I have had to keep a lab notebook. Between work, daily responsibilities, and all the vodka my doctor requires me to drink I have to relearn what needs to go in the lab notes.

Publishable? Eh … not from an amature, but it might be helpful to others and it might be enough for a real scientist to pick it up and do an actual research project. Personally, at this point I’m just having a bunch of fun looking at little creepy crawlies and learning to use a microscope.

As a side note, one of the materials I use in my bonsai mix is diatomaceous earth. In the samples I kept seeing these beautiful mineral structures. It finally dawned on me that I was looking at ancient diatom shells. In a small way, breath taking, and just really cool!


Keeping track of moisture and temperature had not occurred to me but now that you bring it up that sounds like an important detail. Would it be enough to take those measurements when I take the sample or would this need to be a daily measurement? I’m always poking around my trees every day so doing it daily wouldn’t be a burden.

The trees being tested are 6 “bloodleaf” maples.

The fertilizer is Alaska Morbloom Organic Fertilizer 0-10-10 and Alaska Fish Emulsion Organic Fertilizer 5-1-1 depending on the time of year. Right now I am feeding them 0-10-10 and will be keeping that up until just before spring.

The water Ph is about 6.2 averaged over 5 samples on 5 different days. Also, I have an inline filter that takes out the chlorine and chloramines. Home testing kits I have used don’t detect any chlorines or chloramines after I installed the filter so I would assume that very little actually gets through the filter.

One thing that I find surprising is the number of multicellular creatures in the A group. Nematodes, tardigrades and arthropods all living in the soil where as they have not yet been observed in the B group.

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“It finally dawned on me that I was looking at ancient diatom shells. In a small way, breath taking, and just really cool!”
Yes, nature is infinitely cool…!
You are seeing the MOVING large insects. MOST of the fungi and soil bacteria (order of magnitude smaller…) are non-motile. The stains are to be able to SEE them and distinguish from each other.
Look up the Gram stain. It’s complicted , but gives you information and a easy way to see the cells. Dont do the staining in your kitchen sink. The colors do NOT wash away. I have used ‘basic fushin stain in alcohol’ effectively to JUST see the organic, fungi and bacteria cells. There may be better simple stains. Unstained, you will not be able to see /distinguish the cells.
You need to FIX the sample to a glass slide. Place a wet sample on a slide and heat it to dry. Bic lighter works. Then stain, rinse, and dry. Bacteria need a 500 to 1000x magnification to see. An oil emersion 1000x occular would be handy. Drop of mineral oil between the slide and microscope 1000x objuctive.
Any newer, self focusing camera can be MOUNTED on the eyepiece, most give good photos… Get creative. You can buy widgets to mount. Most of them come with programs and USB cables. Even still shots of important finds, holding the camera up to the eyepiece, are usefull. Especially for ID. I’m not fully Linux friendly; program modules should be out there for a cheap camera…
Darwin was an amateur, too.
Keep notes. Well founded basic research INFORMATION applying to bonsai would be of interest to US. Even if it us just cool photos and odd observations. If compiled with others data, someday it will be seen as groundbreaking.
There IS mountains of information out there. Some applies to what WE do. Most, not. Store and compile usefully information.
Good hunting, an good luck. Remember, use gloves while staining, and wash your hands. Don’t take your work home with you…

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OK! I got my Gram Stain kit. I tried doing a couple of slides just going through the process. Much like someone’s first attempt at making a crepe, or a pancake it mostly failed. :slight_smile: Although I did manage to detect what I suspect are both Gram positive and negative single cell life forms.

For fixing the slides slide 1 I used a heat fixing technique. For slide two I used an alcohol fixing technique. I had similar results with both slides. I suspect because of my severe lack of practice at using Gram Stain. :slight_smile:

Be that as it may my petri dishes also arrived. I made a home made recipe growth medium. Gelatin, sugar and beef bullion.

I then prepared a soil sample from each subject and am now trying to culture the culturable microbes from each sample. I should know in about 3-4 days if my cultures worked. While I do not have an incubator I do have seedling heating pads. I placed the cultures on that so they should stay reasonably warm.

Aside from that I have been practicing with the microscope. I have learned to differentiate between non-living material in the sample and single cell microbes. Learning how to use the microscope at the highest magnifications (2500x and 1000x) using oil immersion has been tricky but worth it.

As a matter of fact today for the first time in my life I watched a bacterium go through its mitosis cycle at 2500x in all of its live action wonder. :slight_smile: Perhaps not as exciting as football but more exciting the cricket.

All of that aside, I am looking forward to examining the cultures and taking another pass with Gram staining. I should be getting a camera suitable for my microscope soon so there will be video and pictures coming!


I’m impressed. Your really into this…
As I said, start a lab notebook. Kinda like a diary. Keep you steps, mishaps, AND your observations by date.
One note, the live bacterium and fungi cultures CAN be quite hazardous. Carefully and safely discard, or kill them. Bleach, fire, or steam sterilize. There is a commercial compound, Tergisil (?) for keeping your work area disinfected. Isopropyl alcohol works, but is VERY flammable.
A alcohol lamp works for heat fixing. Or a small Bunsen burner (propane…).
If your microscope has a phase contrast attachment, you CAN see the live bacteria and fungi; fixing, staining helps look at the cell walls and internal structures.

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OK! I’ve been away for a while but I have been keeping up on this project. I can report some results.

The biological inoculants did not make a noticable difference in the apparent health of the trees.
Neither did they make any noticeable difference in the bio-activity nor the biodiversity of the soil mixture I am using.

I ran the experiment on 12 different trees all the same species. And two different soil mixtures, one akadama based and another swapping out diatomaceous earth for akadama.

I can tell you that the akadama based soil showed a greater biodiversity as well as greater bio-activity than the diatomaceous earth based mixture.

Again, the inoculant made no discernible difference with either soil mixture.

Your info is noted! Usefull.
Did any specific tree do better in the DE?.
Did you use biogold / organic fertilizer, or inorganic?
Did you utilize a top dressing to keep moisture up, or left the surface bare?
What’s your opinion of diatomaceous earth, and what size range did you use? What was your mix? I have DE, have not utilized it much yet.
This is such a weird spring. Really happy with my herd so far this year. Too bad the ROONA has shut down shows and meetings…

Sorry Kurt!

I got a new job and had to focus on that for a few days.

  • No tree did any better than another as far as I can tell. However, I have not examined the roots of any of the trees. So there may be something there of which I am unaware.
  • Over the winter I used Alaska Morbloom Concentrate 0-10-10. In spring when the leaf buds started to swell I switched to Biogold
  • The surface was bare on all trees.

My opinion of DE.

Mixture 1 was 1/3 DE 1/3 Organic Compost 1/3 50-50 mix of lava pebbles and pumice.

Mixture 2 was 1/3 Akadama 1/3 Organic Compost 1/3 50-50 mix of lava pebbles and pumice.

One of the things I noticed about the DE mixture is that it seemed more prone to inhibit water percolation which worried me a little. Given that the DE mixture also seems to NOT support the wider range of biodiversity in the soil I am backing off of DE. Now that the experiment is over all trees are in the Mixture 2.

The lower biodiversity makes sense as DE is sometimes used in gardening to hinder non-beneficial soil fauna. It is non-toxic and works by dehydrating small organisms.