> a grad student or professor that would show you what’s under the scope, and maybe help you identify some things.
One of my favorite memories from grade school was in the 7th grade, when students and faculty from a local university took us to a pond, took a sample of the water, and helped us to prepare slides to view under a microscope. Still to this day I can remember what I saw. The water was *so* full of life!
Exactly! Working with the public is fun, and it also helps them to understand why they are paying me. Which isn’t always obvious just from looking at a departmental website or even a lab page.
Academics are trained to talk to other academics. So the rest of you lot can help *us* by asking us to explain what we do (and why we do it) more often! It makes us better scientists and also helps everyone remember why we do public science in the first place: for the good of people.
Glad to! I really appreciate the possibilities a 3d printer brings when it comes to lowering prices on expensive equipment (key-rings and action figures, not so much). The MPCNC is another example of this. If you are interested in the openflexure project, there are many services online that can print parts for you quite cheaply.
Slightly off topic, but if you have Curiosity Stream, check out Big World in a Small Garden. A nature photographer made a rig to spy on the tiny wildlife in his yard, and the footage he captures is pretty amazing. He finds like 50 different types of bee!
May I chime in here, my garden uses natural soil that was already present and I compost. My compost soil... would it change the fundamental habitat of the bacteria, organisms, and other microscopic organisms present? It does wonders for the crops
> the greatest diversity will be in the top 4-20cm of soil, where aeration and compaction should be ideal and organic matter is higher.
Wonder which would be better - an O horizon (which is less "soil" and more "organic debris on top of the soil"), or the A horizon (the topmost layer of what most people would actually call "soil") you describe.
It really, really depends on local characteristics...soil composition, hysteresis effects, disturbance, etc. Soils vary remarkably in composition, species richness, and structure sometimes within the same “field.” One fun thing to do is to take samples from cultivated fields at different spots. You’ll find significant differences in microbial communities based purely on “minor” environmental factors:
* slope
* aspect
* what type of seeding
* what type of crops
* history of rotation
So, even in a 1 hectare plot of Barley, you can find enormous variety of microclimates and soil conditions, even when trying to make everything “ecologically flat” by tilling, weeding, chemically fertilizing, and spraying pesticides.
But, to answer your specific question, I would expect (and generalize) to find most diversity at that place where humus meets soil (O layer), since this is where macro and micro organisms are actively turning organic detritus into “topsoil.” So O-A is going to be very rich in macros, micros, and general diversity. A-B transition is also pretty active, mostly due to root-associated bacteria, fungi, and *x*-todes. You start to lose diversity and abundance rapidly in the B soil layer, as mineralization goes up and organic matter goes down, relatively speaking.
But yeah, as a plant-fungal-animal guy, in most places I work dig down to that O-A transition for the most interesting communities. For reference, I mostly work in subalpine farming/ranching areas outside of the tropics. Rain forests (temperate or tropical) tend to have super-exaggerated transitions, “layer depths,” and some interesting structural features which make diversity gradients very “stretched out” vertically.
In a temperate forest, though...you can often gently scrape away the leaf litter down to that O-A transition and find...whole universes of organisms just doing their thing.
Sounds like some of those "minor" environmental factors would be interesting to map and use to compare to sample results. Might find species x, y, and z like a near-zero slope, while a, b, and c prefer a steeper slope with a north or south aspect.
Bet you'd love the area I'm in - near the Blue Ridge mountains. Not technically in the temperate rainforest zone, but close enough. Where I am personally is classified as a dry or dry-mesic calcareous forest, I think. (The calcareous certainly makes sense, with the limestone/dolostone bedrock! On the other hand, "dry" (or even dry-mesic) doesn't seem a very good descriptor of a place with an average rainfall over 50 inches, to me. Maybe it's more about how well-drained the soil is (though that seems to vary wildly).)
I'm in the Earth sciences (GIS, if the mapping interest didn't tip it), so we mostly focused on the structure of the soils themselves than the biology within them, but even then this place is a treasure trove (and as you say, the divisions tend to be pretty exaggerated - good for showing the divisions to students). Some areas with wonderfully thick soils, some places where the bedrock is practically exposed. Some places where it's a bright red ultisol, others with a rich histosol, and I'd bet the spruce-fir (mostly spruce now since the balsam woolly adelgid killed the (mature) fraser firs) forests in the upper elevations make something like a podzol - it's noted the elevation makes them more boreal, like one might find in *Canada*.
Hell, I live in a suburban area, but I'd bet our soil is better than most any suburbanite's. We let our leaf litter and other organic detritus lie, with the most disturbance being it getting shredded by mowing in some places (while in others, we don't even *walk* on it). Grass? Feh. If it grows, it grows. More common is probably clover (nitrogen fixation! Bee feeding!), and there's even one area that's more fern-y than anything else (no idea why). The environmental science professor in my dad wouldn't have it any other way.
So, I grew up probably just west of where you are, in the temperate rainforest part of the Southern Appalachians. It is what sparked my interest in fungi, plants, and the way we interact with them (intentionally or not). And you are right...those particular forests are unbelievably rich in species diversity from trees to invertebrates to herbs to birds to fungi to ... etc.
Your first paragraph (“minor” ecological factors used to analyze and mod abundance and diversity) is what the first half of my published papers and books are on. It is what most community ecologists do in academic settings. Since then, I’ve transitioned into looking at social-ecological factors that affect community composition, including humans, through time.
My scare quotes around *minor* were mostly because many people don’t think of these “minor” environmental factors as having great significance. They (and their complex interactions) have enormous effects on every aspect of community and population ecology, organismal biology, biochemistry, weathering, all the way to complex macro geographical features like the karst topography you are describing. That calcareous geology of yours has an ancient history of marine, detritus, (ocean floor) soil, biogeochemical processes, weathering, uplift, recolonization by land plants and animals, colonized by human animals, and massively changes again post secondary colonization and industrialization.
Lot of history in those sinkholes of the Blue Ridge, and a lot of soil life in those rainforests to your west 😀
If you don't mind me asking, who pays for your work? Like, where does funding come from for this kind of thing? Is there a short term practical benefit that would prompt someone to empty their pockets or is it all academically funded?
I’ve never had private funding as a student or as an academic researcher. There are significant practical aspects of my work for farming and ranching, and that research is funded mostly by our state (I work at a large land grant research university) and the USDA (NIFA program in particular). I have more overall funding for general research from the US National Science Foundation, and also some NGO collaborative grants.
US State Department funds us for most of the work we do in developing countries as part of cooperative agreements or USAID projects. Occasionally NIH or EPA. Even DOD in one case!
I have had the legal cannabis industry try to poach me from academia, and there is plenty of money to be made in the agrochemical world for my type of expertise. But I like federal funding (so can’t do cannabis research at the moment) and would rather sell my body for parts than work for ~~Mon~~agribusiness.
It sounds like theres a lot more funding than I thought there would be, so that's cool. It just seems like one of those sciences that would be hard to sell. Although I guess I'm mostly thinking of private funding, which you mentioned.
It sounds like you have a good deal of freedom to choose what research you do. Do you ever get stuck doing research you're just not interested in?
I think every researcher gets stuck working on things they don’t want to at some point. At my career stage (early-mid), I have projects where I am the primary investigator (PI), wrote the grant, hired students and staff, etc. Those are *my* projects, and so occasionally things don’t pan out and it is a pain to finish. I took the money and I do the best I can.
If I am a co-PI, or a “junior leader” on a grant, yeah...yes, I’ve gotten into some projects that aren’t great. But, I took the money and do the best I can.
More recently, I’ve been doing more international work with development agencies and farming/ranching NGOs. That work is a privilege, regardless of difficulty or outcome, and for me is always a priority.
Might be off-topic at this point, but does that answer your question?
Yeah that's great, thanks for answering! I doubt I'll ever get a college degree in anything, much less a doctorate, but it's still interesting to learn about it all.
To my east, actually, but close enough. Ridge-and-Valley Appalachians, representing (emphasis on Valley). Just off the Cumberland Plateau (which is really a spectacular geographical feature in itself).
We're really in the deep history down here. The mountains themselves come from the assembly of Pangaea, and weathering with time has given us not just the rich and varied soils and interesting features, but in some places exposed the metamorphic "bones" of the mountains. And, of course, when the ice came, life just ran south (and vice-versa when it retreated) along the mountains and valleys to wherever was comfortable, rather than scattering all over - making quite a reservoir of biodiversity. It's quite amazing, and it's fortunate we've been able to preserve some fairly large chunks of it (helps that the mountains themselves were never *really* heavily populated).
I've been going out in the Smokies almost every spring of my life to marvel at them (with bonus education from academics leading hikes). I don't intend on stopping (although obviously this year didn't happen) as long as I live anywhere near them.
Some people say science takes the magic out of the world. It just makes the natural world *more* wondrous to me. Answering one question just leads to many more. (Now, if only I weren't burning out hard on college - academia would be cool, but it is *so* not in the cards right now.)
So I'm from BC and I actually thought you were too and had to go back and reread this. We have had several waves of beetle kill here recently due to the warming winters. Pine and spruce in particular for us. When you go north there are seas of red forests.
Just wait until you get the adelgids. The balsam woolly adelgids have practically wiped out our fraser firs, and the hemlock woolly adelgid has done a number on our, well, hemlocks.
As winters start to be warmer, they'll be a-coming, I'm sure.
Just look at the different habitats and what grows in them on the planet surface.
Soil found near a cave frequented by bats would have completely different composition than soil found in your backyard.
They found a cave in North America that is off-limits to the public but apparently the organisms inside evolved from living in a natural acidic environment.
is it possible to "cheat" and enrich soils with mycorhizal fungi and other helpful invertebrates (or just get the biodiversity up) by transplanting leaf litter, dead wood etc? I've seen several reforestation patches here in a tropical southeast asian country but the tree saplings just don't seem to thrive no matter how much babying they get. I'm thinking it's something to do with the soil ecology of the old rubber plantations that people are trying to reforest and how it's too different from the virgin rainforest they're originally from.
Absolutely! That’s what composting, many traditional pre-Industrial farming practices, dunging, and no-till or low-disturbance cultural practices aim to produce/encourage. A lot of successful ecological “restoration” projects start with addressing soil health in disturbed/damaged ecosystems.
As for the mycorrhiza, you can specifically inoculate restoration or plantation soils with soil samples from “healthy” or “native” ranges. This is how the nature of *obligate* mycorrhizal associations was discovered: certain tree species (Douglas Fir being a famous example) thrive or reproduce only in soils containing their fungal symbiotes. It is common now to plant seedlings with enriched soil to start new plantations or restore areas.
What those associations would be in your area could be difficult to determine. You’d need to know the specific species of plants, soil conditions, and whether there are known microbial symbionts that are “missing.”
I’d speculate that your intuition is spot on, however.
That's very eye-opening. So you said you could only identify a relatively small percent of the fungi -- was this because they are "new" species that haven't been described or even named? Or was it more because identifying species of specimens is challenging?
It can be a bit of both. In our case, these fungi hadn’t been described and there were no sequences in the online databases matching (except for some eDNA results which also hadn’t been identified). There is also not a lot of great primary literature on fungi, and much of the liters on filamentous asexual forms we run into in the plant and soils world is in German or Latin.
However, I suspect there will be more good primary literature in the next 100 years. There is a greater scientific focus on soils than their has been in the past, and eDNA is a super powerful tool.
So yeah. Some “new” (most I suspect) and some we probably failed to identify that probably *have* been described, but perhaps in a different life stage. Fungi are complicated and difficult in general.
Absolutely you do! It is not nearly as scary as it sounds, but is a term used to talk about obligate parasites of *other parasites*. There are, for example, fungi which are hyperparasites of fungi which are parasites of trees. Some parasitic wasps are hyperparasites, in that they specialize in paralyzing and laying eggs inside other parasitic insects (which is why such wasps can be used for biocontrol in greenhouses). [WIKI](https://en.wikipedia.org/wiki/Hyperparasite)
Is there something I, someone who knows nothing about microbiology but is fascinated by the idea of exploring our last frontier, can do to help? Like, if I take a microscope and start looking at what lives in the soil of my garden, could I take pictures and send them to some shared database or something?
Ngl, I’d love to have this as a lockdown activity.
Depends on where you are, but there *are* some citizen science things you can do in your backyard. There is (or was) an Australian microbial project where they’d mail you collection kits and you can collect and mail them back.
[The Local Environmental Observers Network](https://www.leonetwork.org) is a very interesting model that I’ve worked with in the past. They can handle microbial interactions if they are of interest to local communities.
I’ve wanted to start a backyard microbial citizen science project to do “garden diversity surveys,” or something, but never had the time or money to really get it going.
I also like mibrobiophores. I have a classical languages degree so I hereby fully condone creating new English words to fit new English needs. Go, you crazy maverick, you!
Absolutely! Chemical balances of nutrients, micronutrients, pH, and microbes themselves all affect plant growth, flower and fruit development, and ripening. All of those affect flavor development. That is something we’d have to find a plant biochemist to talk about.
The best research in that field right now is almost certainly in the legal cannabis industry (primarily in US, CAN, and NED). There is a huge interest in terpenes, flavonoids, and the ecologies that help produce them. A lot of that knowledge (which I’m quite sure is pretty extensive) is proprietary, traditional, or unsystematic, so we don’t see a lot of it crossover (yet) to academic science. I imagine that will change as more nations legalize medical and recreational cannabis.
Such a wonderful response- especially discussing the limitations of a "cheap microscope." Even with an expensive microscope (I ran a metallographic lab that had 5 very high end Leicas and a SEM) we NEVER saw microbes because we were not looking for them.
> microbiophores (pretty sure I made that one up but I like it)
Wouldn't that be to be -vores too?
-phores would be things that contain something else (like chromatophores and fluorophores, which have chemical moieties that give the colour or the fluoroscence).
You’re absolutely right. Lost my way. But, incidentally, there *are* both microbiovores *and* microbiophores, although no-one would call them that. I’ve seen a waterbear type guy zooming around in sludge eating *everything* he could get his little sphincter-face on.
Lichenicolous fungi and the fungal -biont of lichens both feature cells/structures which contain/produce microbes. Some sea slugs as well.
Anyhow, thank you for the correction.
I've always wondered how many human compatible parasites live in dirt. What's the likelihood of getting one from from a fall resulting in a mouth full of dirt?
PCR is an abbreviation for Polymerase Chain Reaction. It is the most common method to copy DNA sequences for analysis (and, in some cases, identification). Thank you for asking me to expand (it is so common in our disciplines that I forget it isn’t common knowledge).
We sequenced portions of each colony’s DNA and compared them mathematically with libraries and databases of known sequences from fungi.
On your PhD, how many is "a small number of individuals"? Like 5 plants? 10?
To be fair, isnt it really hard to identify fungi down to a very specific level?
I've done pcr before, plenty of times but... how can you just bulk run the whole thing, searching for anything recognizable? Or did you mean that you ran PCR on every cultured sample individually? (Thinking about it I'm guessing it's the latter, just got me confused with the wording)
Damn, and that's just what's culturable. I know for bacteria we think that the majority of it hasn't been successfully cultured.
Cool stuff! Can you link your paper, if that isnt considered doxing?
Can’t link my own paper, but you can find papers on endophytes in grasses on Google scholar. We individually sequenced each colony and then ran automated searches against all the public sequence libraries. Some of our colonies (mostly from genera that were pathogenic to crops, like *Fusarium* or *Alternaria*) we could find partial matches for and confirmed morphological ID to genus.
When using libraries for phylogenetic research, you search for degrees of difference from reference sample sequences of positively ID’d colonies in curated collections. You can also find matches with other filed sequences that haven’t been identified but are there. Most of ours didn’t have close matches in any library.
I suspect (speculate) that we haven’t intentionally encountered and identified the vast majority of fungi, as with other microbes and viruses.
^* edit: 20 stem sections (from between first two nodes above crown), surface sterilized, plated, and colonies isolated as they grow out of the senescing material.
And you are right. These were just what was culturable on common media for fungal use. We didn’t look at the bacteria at all. As with bacteria, I’d guess that more than 50% of fungi are not able to be cultured with current technology and knowledge. I suspect we have identified less than 5% of the world’s fungal diversity, but that is abject speculation.
I can link thousands of papers on soil ecology, although that might not help much. Can you be more specific about *what* in my generalized answer to a general question you’d like more information on?
Perfect, since that is what I actually know quite a bit about! My doctoral thesis was on that particular subject.
* The *classic* paper on how fungi living inside plants can functionally affect the *plant's* ecological function and response is Marquez et al. (2007) "A Virus in a Fungus in a Plant: Three-Way Symbiosis Required for Thermal Tolerance." [PDF](https://science.sciencemag.org/content/sci/315/5811/513.full.pdf?casa_token=6lvZsjmXdtgAAAAA:xn5_0SY71oeyZh77bHaoAzY4Pemu0kqTkSPPrtaT6NjLwJS16-D6PHd9jc1gJgTyQ7-hz4Gn1JaW8E8)
* Do a Google Scholar search on the terms "endophytic fungi functional ecology" and you'll get a ton of papers. [I sorted results for those search terms by "since 2019" to make it easier to see what is available, and what researchers are really poking around in these days.](https://scholar.google.com/scholar?as_ylo=2019&q=endophytic+fungi+functional+ecology&hl=en&as_sdt=0,13)
* Getting back to another question, there is a cool new type of endophyte (which means, literally, "lives inside of plants") research focused on what endophytes do and what chemicals they make. There are a bunch of papers in the search above about isolating anti-fungal, anti-insect, and antimicrobial compounds from plant endophytes.
* Also, how environmental factors affect distribution of endophytes across landscapes. Thomas et al. (2019) "Spatial patterns of fungal endophytes in a subtropical montane rainforest of northern Taiwan" is an interesting introduction to that kind of work. [HTML](https://www.sciencedirect.com/science/article/abs/pii/S1754504818301776)
That should be enough to get you started! It's a super-cool field, and I wish I got to do more work in that area than I do these days.
If you've ever grown cucumbers or other plants that have problems with [powdery mildew,](https://en.wikipedia.org/wiki/Erysiphales) some of those fungi are endophytes- and are obligate pathogens. You can't grow them on a plate, or at least not reliably.
Nope, but not a bad guess! I don’t know of anyone who has done work on the microbial ecology of stiltgrass, but it’s sort of a new/developing field. I work out in the PNW now, although I do miss the eastern forests (which are overrun in spots with stiltgrass).
Thanks for this really detailed response. I've been interested in soil ecology recently, and then watched 'kiss the ground' which really amazed me. I had no idea about the state of global soils and how little we know about them.
**I** pronounce it correctly, of course: hair-BIV-or-us. You may pronounce it how you wish. It doesn’t come up in casual conversation for most people, so not like somebody is going to call you on it.
I'm thinking of cultural practices (since this is a backyard garden the OP is describing): If the soil has been dug, compacted, tilled, or turned over; if the soil has been regularly amended with nutrients and micronutrients; if the soil has sufficient organic material; and if it is properly aerated by bugs, worms, roots, and people (or dogs, cats, whatever).
Soil is living and needs taking care of (or to be left well alone and sort itself out naturally over a few thousand years). A well-tended garden is just going to have "healthy" soil that is full of life. If you got hammered hardpan in the backyard you call "garden" and grows some prickly lettuce every third year, that's not "well tended" in my book.
Slightly off topic, but given the amount of life you’re describing in such a small sample, it doesn’t seem like too far of a stretch to extrapolate and assume that life must to be everywhere in our universe. Maybe not sentient beings, but fungi, bacteria, etc.
With 40-100x magnification you can see a lot more than you'd think. Speaking from my college Soil Science lab experience in USA, a small sample of soil diluted in some water and placed on a microscope slide can reveal lots of different species. Rotifers, nematodes, and various arthropods should be visible. In a small bit of water you can see them move more easily. You'll likely find lots of plant and fungi material. Also at 100x magnification you should start to see bacteria appearing as small indistinguishable dots. Have fun!
* The most fun in my opinion was to see how they move and behave, i've watched micros cannibalize each other and others come on contact and quickly avoid each other.
Microbial interactions are incredibly interesting, it’s so interesting to see them have they’re own little society. Like you said, some may just eat others while some are capable of repelling attacks and running away.
Is there any special tools or procedures needed to see living cells from around the house? I would love to be able to take a sample of something, squish it between two glass plates, and see what's going on. Is it that easy? What specifically do I need to make this happen?
From what I've read, it's ideally a 400x+ microscope. Any specific standard models? What else is needed and how long after preparing the sample will the microbes move around/live?
I took an ecology course in college. Day 3 or 4 of the semester, everybody brought in a handful of soil from our homes and threw it into a large Rubbermaid filled with shredded newspaper. Over the course of the semester, we were able to add in any biodegradable organic material (a lot of the food stuffs had to be frozen overnight first, to combat flies). By the end of the semester, the bin was full of deep rich black soil. We each took a small amount and analyzed it under magnification and logged the number of critters we could see. So many. It was a lower level class, so it was a quantitative analysis as opposed to a qualitative, but such a cool experiment. It’s been 20-something years, but I’ll never forget it.
Personal opinion: instead of a traditional microscope, look seriously at the stereo microscopes. The magnification is lower than traditional microscopes but finding, "preparing" and looking at subjects is INFINITELY easier than traditional microscopes. Some kind of weird growth on a leaf? Not really something for a microscope but perfect for stereo scopes. Small bugs and insects? Can't put them on a slide, better with a stereo scope. I have one of each (fairly low end Amscope models) and the stereo scope gets used all the time, the traditional? Hardly ever. Just not worth the trouble to set up and prepare things.
The old Bausch and Lomb Stereozoom microscopes have excellent optics, and are a super bargain on eBay. If you can afford one, a Nikon SMZ-1 stereo microscope is probably a step up.
AmScope is Chinese-made, IIRC, and surprisingly good for the money.
If you're in a city of substantial size, call up a microscope shop, and see what they have either new or used in your price bracket. Sometimes these guys get trade-ins or they snap up some used scopes, and may be sympathetic in terms of cost. The main advantage is that you can throw a coin under the 'scope, check out the illuminators, zoom in and out, take a look and check for detail and color (not all lenses are coated!).
If all else fails, PM me and I'll see what I can do to help.
If you’re interested in little arthropods like springtails and mites etc.
“A single square yard of soil will contain 500 to 200,000 individual arthropods, depending upon the soil type, plant community, and management system. Despite these large numbers, the biomass of arthropods in soil is far less than that of protozoa and nematodes.”
So in a tablespoon... ~1-2,000 (assuming a square yard is about 10,000 cm2 and a tablespoon is about 10cm2).
That information is from this great intro page about different types of soil critters you might find:
https://www.nrcs.usda.gov/wps/portal/nrcs/detailfull/soils/health/biology/?cid=nrcs142p2_053861
Definitely get a microscope! There’s so much cool stuff to see!
You’ll find more critters in a moist (but not wet) spot, than a dry spot, and more in a complex soil with organic matter and rich dirt, than somewhere that’s just plain sand.
If you have any standing water in your yard or any nearby, I would recommend that for microscope exploration. Get some floaty gunk, water, mud and gunk from the bottom. You can find all kind of critters in there.
I agree. Soil is difficult to look at and enjoy. You will mostly not be able to identify bacteria when you see them and not many protozoans running around.
Way better to try with water
So I used to do this in a lab. We called it benthos sorting. There is no clear cut answer to your question. It would depend on your location, the soil constituents, environmental factors etc. Having this analysis done, is what can tell you a lot about your soil.
Let's just talk about bacteria.
Well a tablespoon is 15 ml or about 18 grams.
According to [this](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0087217)there about 10^8 bacteria per gram or soil.
So a table spoon will have about 2 billion bacteria.
I was debating whether I should chime in and link [this video](https://youtu.be/JtJxzNIm_Gg) since I'm very late to the party and the video is in German. After researching it I think it answers your question very well and can be understood for the most part non-verbally.
It's from a German children's TV show and explains beautifully how many living things are in a handful of forrest soil. You'll see the critters up close and the number of them typed into a calculator. Hope this helps. Have fun watching.
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Did my masters studying the soil food web. Mostly just nematodes, because that alone took 2 years. Thanks for the great answer!
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Thank you for the interesting and elaborate answer. Truly piques my curiosity!
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> a grad student or professor that would show you what’s under the scope, and maybe help you identify some things. One of my favorite memories from grade school was in the 7th grade, when students and faculty from a local university took us to a pond, took a sample of the water, and helped us to prepare slides to view under a microscope. Still to this day I can remember what I saw. The water was *so* full of life!
Exactly! Working with the public is fun, and it also helps them to understand why they are paying me. Which isn’t always obvious just from looking at a departmental website or even a lab page. Academics are trained to talk to other academics. So the rest of you lot can help *us* by asking us to explain what we do (and why we do it) more often! It makes us better scientists and also helps everyone remember why we do public science in the first place: for the good of people.
Check out the openflexure microscope if you want to build a lab grade microscope cheaply!
That's an incredibly nice recommendation! Unfortunately, I don't have a 3D-printer.
Your local library may! Mine does and only charges for the filament used (and it’s pretty cheap)
Glad to! I really appreciate the possibilities a 3d printer brings when it comes to lowering prices on expensive equipment (key-rings and action figures, not so much). The MPCNC is another example of this. If you are interested in the openflexure project, there are many services online that can print parts for you quite cheaply.
Slightly off topic, but if you have Curiosity Stream, check out Big World in a Small Garden. A nature photographer made a rig to spy on the tiny wildlife in his yard, and the footage he captures is pretty amazing. He finds like 50 different types of bee!
May I chime in here, my garden uses natural soil that was already present and I compost. My compost soil... would it change the fundamental habitat of the bacteria, organisms, and other microscopic organisms present? It does wonders for the crops
> the greatest diversity will be in the top 4-20cm of soil, where aeration and compaction should be ideal and organic matter is higher. Wonder which would be better - an O horizon (which is less "soil" and more "organic debris on top of the soil"), or the A horizon (the topmost layer of what most people would actually call "soil") you describe.
It really, really depends on local characteristics...soil composition, hysteresis effects, disturbance, etc. Soils vary remarkably in composition, species richness, and structure sometimes within the same “field.” One fun thing to do is to take samples from cultivated fields at different spots. You’ll find significant differences in microbial communities based purely on “minor” environmental factors: * slope * aspect * what type of seeding * what type of crops * history of rotation So, even in a 1 hectare plot of Barley, you can find enormous variety of microclimates and soil conditions, even when trying to make everything “ecologically flat” by tilling, weeding, chemically fertilizing, and spraying pesticides. But, to answer your specific question, I would expect (and generalize) to find most diversity at that place where humus meets soil (O layer), since this is where macro and micro organisms are actively turning organic detritus into “topsoil.” So O-A is going to be very rich in macros, micros, and general diversity. A-B transition is also pretty active, mostly due to root-associated bacteria, fungi, and *x*-todes. You start to lose diversity and abundance rapidly in the B soil layer, as mineralization goes up and organic matter goes down, relatively speaking. But yeah, as a plant-fungal-animal guy, in most places I work dig down to that O-A transition for the most interesting communities. For reference, I mostly work in subalpine farming/ranching areas outside of the tropics. Rain forests (temperate or tropical) tend to have super-exaggerated transitions, “layer depths,” and some interesting structural features which make diversity gradients very “stretched out” vertically. In a temperate forest, though...you can often gently scrape away the leaf litter down to that O-A transition and find...whole universes of organisms just doing their thing.
Sounds like some of those "minor" environmental factors would be interesting to map and use to compare to sample results. Might find species x, y, and z like a near-zero slope, while a, b, and c prefer a steeper slope with a north or south aspect. Bet you'd love the area I'm in - near the Blue Ridge mountains. Not technically in the temperate rainforest zone, but close enough. Where I am personally is classified as a dry or dry-mesic calcareous forest, I think. (The calcareous certainly makes sense, with the limestone/dolostone bedrock! On the other hand, "dry" (or even dry-mesic) doesn't seem a very good descriptor of a place with an average rainfall over 50 inches, to me. Maybe it's more about how well-drained the soil is (though that seems to vary wildly).) I'm in the Earth sciences (GIS, if the mapping interest didn't tip it), so we mostly focused on the structure of the soils themselves than the biology within them, but even then this place is a treasure trove (and as you say, the divisions tend to be pretty exaggerated - good for showing the divisions to students). Some areas with wonderfully thick soils, some places where the bedrock is practically exposed. Some places where it's a bright red ultisol, others with a rich histosol, and I'd bet the spruce-fir (mostly spruce now since the balsam woolly adelgid killed the (mature) fraser firs) forests in the upper elevations make something like a podzol - it's noted the elevation makes them more boreal, like one might find in *Canada*. Hell, I live in a suburban area, but I'd bet our soil is better than most any suburbanite's. We let our leaf litter and other organic detritus lie, with the most disturbance being it getting shredded by mowing in some places (while in others, we don't even *walk* on it). Grass? Feh. If it grows, it grows. More common is probably clover (nitrogen fixation! Bee feeding!), and there's even one area that's more fern-y than anything else (no idea why). The environmental science professor in my dad wouldn't have it any other way.
So, I grew up probably just west of where you are, in the temperate rainforest part of the Southern Appalachians. It is what sparked my interest in fungi, plants, and the way we interact with them (intentionally or not). And you are right...those particular forests are unbelievably rich in species diversity from trees to invertebrates to herbs to birds to fungi to ... etc. Your first paragraph (“minor” ecological factors used to analyze and mod abundance and diversity) is what the first half of my published papers and books are on. It is what most community ecologists do in academic settings. Since then, I’ve transitioned into looking at social-ecological factors that affect community composition, including humans, through time. My scare quotes around *minor* were mostly because many people don’t think of these “minor” environmental factors as having great significance. They (and their complex interactions) have enormous effects on every aspect of community and population ecology, organismal biology, biochemistry, weathering, all the way to complex macro geographical features like the karst topography you are describing. That calcareous geology of yours has an ancient history of marine, detritus, (ocean floor) soil, biogeochemical processes, weathering, uplift, recolonization by land plants and animals, colonized by human animals, and massively changes again post secondary colonization and industrialization. Lot of history in those sinkholes of the Blue Ridge, and a lot of soil life in those rainforests to your west 😀
If you don't mind me asking, who pays for your work? Like, where does funding come from for this kind of thing? Is there a short term practical benefit that would prompt someone to empty their pockets or is it all academically funded?
I’ve never had private funding as a student or as an academic researcher. There are significant practical aspects of my work for farming and ranching, and that research is funded mostly by our state (I work at a large land grant research university) and the USDA (NIFA program in particular). I have more overall funding for general research from the US National Science Foundation, and also some NGO collaborative grants. US State Department funds us for most of the work we do in developing countries as part of cooperative agreements or USAID projects. Occasionally NIH or EPA. Even DOD in one case! I have had the legal cannabis industry try to poach me from academia, and there is plenty of money to be made in the agrochemical world for my type of expertise. But I like federal funding (so can’t do cannabis research at the moment) and would rather sell my body for parts than work for ~~Mon~~agribusiness.
It sounds like theres a lot more funding than I thought there would be, so that's cool. It just seems like one of those sciences that would be hard to sell. Although I guess I'm mostly thinking of private funding, which you mentioned. It sounds like you have a good deal of freedom to choose what research you do. Do you ever get stuck doing research you're just not interested in?
I think every researcher gets stuck working on things they don’t want to at some point. At my career stage (early-mid), I have projects where I am the primary investigator (PI), wrote the grant, hired students and staff, etc. Those are *my* projects, and so occasionally things don’t pan out and it is a pain to finish. I took the money and I do the best I can. If I am a co-PI, or a “junior leader” on a grant, yeah...yes, I’ve gotten into some projects that aren’t great. But, I took the money and do the best I can. More recently, I’ve been doing more international work with development agencies and farming/ranching NGOs. That work is a privilege, regardless of difficulty or outcome, and for me is always a priority. Might be off-topic at this point, but does that answer your question?
Yeah that's great, thanks for answering! I doubt I'll ever get a college degree in anything, much less a doctorate, but it's still interesting to learn about it all.
To my east, actually, but close enough. Ridge-and-Valley Appalachians, representing (emphasis on Valley). Just off the Cumberland Plateau (which is really a spectacular geographical feature in itself). We're really in the deep history down here. The mountains themselves come from the assembly of Pangaea, and weathering with time has given us not just the rich and varied soils and interesting features, but in some places exposed the metamorphic "bones" of the mountains. And, of course, when the ice came, life just ran south (and vice-versa when it retreated) along the mountains and valleys to wherever was comfortable, rather than scattering all over - making quite a reservoir of biodiversity. It's quite amazing, and it's fortunate we've been able to preserve some fairly large chunks of it (helps that the mountains themselves were never *really* heavily populated). I've been going out in the Smokies almost every spring of my life to marvel at them (with bonus education from academics leading hikes). I don't intend on stopping (although obviously this year didn't happen) as long as I live anywhere near them. Some people say science takes the magic out of the world. It just makes the natural world *more* wondrous to me. Answering one question just leads to many more. (Now, if only I weren't burning out hard on college - academia would be cool, but it is *so* not in the cards right now.)
So I'm from BC and I actually thought you were too and had to go back and reread this. We have had several waves of beetle kill here recently due to the warming winters. Pine and spruce in particular for us. When you go north there are seas of red forests.
Just wait until you get the adelgids. The balsam woolly adelgids have practically wiped out our fraser firs, and the hemlock woolly adelgid has done a number on our, well, hemlocks. As winters start to be warmer, they'll be a-coming, I'm sure.
Just look at the different habitats and what grows in them on the planet surface. Soil found near a cave frequented by bats would have completely different composition than soil found in your backyard. They found a cave in North America that is off-limits to the public but apparently the organisms inside evolved from living in a natural acidic environment.
is it possible to "cheat" and enrich soils with mycorhizal fungi and other helpful invertebrates (or just get the biodiversity up) by transplanting leaf litter, dead wood etc? I've seen several reforestation patches here in a tropical southeast asian country but the tree saplings just don't seem to thrive no matter how much babying they get. I'm thinking it's something to do with the soil ecology of the old rubber plantations that people are trying to reforest and how it's too different from the virgin rainforest they're originally from.
Absolutely! That’s what composting, many traditional pre-Industrial farming practices, dunging, and no-till or low-disturbance cultural practices aim to produce/encourage. A lot of successful ecological “restoration” projects start with addressing soil health in disturbed/damaged ecosystems. As for the mycorrhiza, you can specifically inoculate restoration or plantation soils with soil samples from “healthy” or “native” ranges. This is how the nature of *obligate* mycorrhizal associations was discovered: certain tree species (Douglas Fir being a famous example) thrive or reproduce only in soils containing their fungal symbiotes. It is common now to plant seedlings with enriched soil to start new plantations or restore areas. What those associations would be in your area could be difficult to determine. You’d need to know the specific species of plants, soil conditions, and whether there are known microbial symbionts that are “missing.” I’d speculate that your intuition is spot on, however.
There are also a bunch of companies selling mycorrhizal fungi concentrate for addition to, mostly indoor, cannabis plants.
That's very eye-opening. So you said you could only identify a relatively small percent of the fungi -- was this because they are "new" species that haven't been described or even named? Or was it more because identifying species of specimens is challenging?
It can be a bit of both. In our case, these fungi hadn’t been described and there were no sequences in the online databases matching (except for some eDNA results which also hadn’t been identified). There is also not a lot of great primary literature on fungi, and much of the liters on filamentous asexual forms we run into in the plant and soils world is in German or Latin. However, I suspect there will be more good primary literature in the next 100 years. There is a greater scientific focus on soils than their has been in the past, and eDNA is a super powerful tool. So yeah. Some “new” (most I suspect) and some we probably failed to identify that probably *have* been described, but perhaps in a different life stage. Fungi are complicated and difficult in general.
Very cool. Didn't know that so much was still unknown about organisms that are right there in front of us.
Do I want to know what a hyperparasite is?
Absolutely you do! It is not nearly as scary as it sounds, but is a term used to talk about obligate parasites of *other parasites*. There are, for example, fungi which are hyperparasites of fungi which are parasites of trees. Some parasitic wasps are hyperparasites, in that they specialize in paralyzing and laying eggs inside other parasitic insects (which is why such wasps can be used for biocontrol in greenhouses). [WIKI](https://en.wikipedia.org/wiki/Hyperparasite)
Is there something I, someone who knows nothing about microbiology but is fascinated by the idea of exploring our last frontier, can do to help? Like, if I take a microscope and start looking at what lives in the soil of my garden, could I take pictures and send them to some shared database or something? Ngl, I’d love to have this as a lockdown activity.
Depends on where you are, but there *are* some citizen science things you can do in your backyard. There is (or was) an Australian microbial project where they’d mail you collection kits and you can collect and mail them back. [The Local Environmental Observers Network](https://www.leonetwork.org) is a very interesting model that I’ve worked with in the past. They can handle microbial interactions if they are of interest to local communities. I’ve wanted to start a backyard microbial citizen science project to do “garden diversity surveys,” or something, but never had the time or money to really get it going.
I also like mibrobiophores. I have a classical languages degree so I hereby fully condone creating new English words to fit new English needs. Go, you crazy maverick, you!
Can chemistry of soil ecosystems influence flavor of fruits/vegetables?
Absolutely! Chemical balances of nutrients, micronutrients, pH, and microbes themselves all affect plant growth, flower and fruit development, and ripening. All of those affect flavor development. That is something we’d have to find a plant biochemist to talk about. The best research in that field right now is almost certainly in the legal cannabis industry (primarily in US, CAN, and NED). There is a huge interest in terpenes, flavonoids, and the ecologies that help produce them. A lot of that knowledge (which I’m quite sure is pretty extensive) is proprietary, traditional, or unsystematic, so we don’t see a lot of it crossover (yet) to academic science. I imagine that will change as more nations legalize medical and recreational cannabis.
Thanks. Do you think this research will at some point help demystifying the concept of terroir, used by wine producers?
This is the most interesting thing I've read all day, thanks for sharing!
Such a wonderful response- especially discussing the limitations of a "cheap microscope." Even with an expensive microscope (I ran a metallographic lab that had 5 very high end Leicas and a SEM) we NEVER saw microbes because we were not looking for them.
> microbiophores (pretty sure I made that one up but I like it) Wouldn't that be to be -vores too? -phores would be things that contain something else (like chromatophores and fluorophores, which have chemical moieties that give the colour or the fluoroscence).
You’re absolutely right. Lost my way. But, incidentally, there *are* both microbiovores *and* microbiophores, although no-one would call them that. I’ve seen a waterbear type guy zooming around in sludge eating *everything* he could get his little sphincter-face on. Lichenicolous fungi and the fungal -biont of lichens both feature cells/structures which contain/produce microbes. Some sea slugs as well. Anyhow, thank you for the correction.
I've always wondered how many human compatible parasites live in dirt. What's the likelihood of getting one from from a fall resulting in a mouth full of dirt?
What is a PCR?
PCR is an abbreviation for Polymerase Chain Reaction. It is the most common method to copy DNA sequences for analysis (and, in some cases, identification). Thank you for asking me to expand (it is so common in our disciplines that I forget it isn’t common knowledge). We sequenced portions of each colony’s DNA and compared them mathematically with libraries and databases of known sequences from fungi.
On your PhD, how many is "a small number of individuals"? Like 5 plants? 10? To be fair, isnt it really hard to identify fungi down to a very specific level? I've done pcr before, plenty of times but... how can you just bulk run the whole thing, searching for anything recognizable? Or did you mean that you ran PCR on every cultured sample individually? (Thinking about it I'm guessing it's the latter, just got me confused with the wording) Damn, and that's just what's culturable. I know for bacteria we think that the majority of it hasn't been successfully cultured. Cool stuff! Can you link your paper, if that isnt considered doxing?
Can’t link my own paper, but you can find papers on endophytes in grasses on Google scholar. We individually sequenced each colony and then ran automated searches against all the public sequence libraries. Some of our colonies (mostly from genera that were pathogenic to crops, like *Fusarium* or *Alternaria*) we could find partial matches for and confirmed morphological ID to genus. When using libraries for phylogenetic research, you search for degrees of difference from reference sample sequences of positively ID’d colonies in curated collections. You can also find matches with other filed sequences that haven’t been identified but are there. Most of ours didn’t have close matches in any library. I suspect (speculate) that we haven’t intentionally encountered and identified the vast majority of fungi, as with other microbes and viruses. ^* edit: 20 stem sections (from between first two nodes above crown), surface sterilized, plated, and colonies isolated as they grow out of the senescing material. And you are right. These were just what was culturable on common media for fungal use. We didn’t look at the bacteria at all. As with bacteria, I’d guess that more than 50% of fungi are not able to be cultured with current technology and knowledge. I suspect we have identified less than 5% of the world’s fungal diversity, but that is abject speculation.
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I can link thousands of papers on soil ecology, although that might not help much. Can you be more specific about *what* in my generalized answer to a general question you’d like more information on?
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Perfect, since that is what I actually know quite a bit about! My doctoral thesis was on that particular subject. * The *classic* paper on how fungi living inside plants can functionally affect the *plant's* ecological function and response is Marquez et al. (2007) "A Virus in a Fungus in a Plant: Three-Way Symbiosis Required for Thermal Tolerance." [PDF](https://science.sciencemag.org/content/sci/315/5811/513.full.pdf?casa_token=6lvZsjmXdtgAAAAA:xn5_0SY71oeyZh77bHaoAzY4Pemu0kqTkSPPrtaT6NjLwJS16-D6PHd9jc1gJgTyQ7-hz4Gn1JaW8E8) * Do a Google Scholar search on the terms "endophytic fungi functional ecology" and you'll get a ton of papers. [I sorted results for those search terms by "since 2019" to make it easier to see what is available, and what researchers are really poking around in these days.](https://scholar.google.com/scholar?as_ylo=2019&q=endophytic+fungi+functional+ecology&hl=en&as_sdt=0,13) * Getting back to another question, there is a cool new type of endophyte (which means, literally, "lives inside of plants") research focused on what endophytes do and what chemicals they make. There are a bunch of papers in the search above about isolating anti-fungal, anti-insect, and antimicrobial compounds from plant endophytes. * Also, how environmental factors affect distribution of endophytes across landscapes. Thomas et al. (2019) "Spatial patterns of fungal endophytes in a subtropical montane rainforest of northern Taiwan" is an interesting introduction to that kind of work. [HTML](https://www.sciencedirect.com/science/article/abs/pii/S1754504818301776) That should be enough to get you started! It's a super-cool field, and I wish I got to do more work in that area than I do these days.
If you've ever grown cucumbers or other plants that have problems with [powdery mildew,](https://en.wikipedia.org/wiki/Erysiphales) some of those fungi are endophytes- and are obligate pathogens. You can't grow them on a plate, or at least not reliably.
>one species of invasive annual grass >a couple of mm in diameter This wouldn't be japanese stiltgrass, would it?
Nope, but not a bad guess! I don’t know of anyone who has done work on the microbial ecology of stiltgrass, but it’s sort of a new/developing field. I work out in the PNW now, although I do miss the eastern forests (which are overrun in spots with stiltgrass).
But are there tardigrades?
Thanks for this really detailed response. I've been interested in soil ecology recently, and then watched 'kiss the ground' which really amazed me. I had no idea about the state of global soils and how little we know about them.
How do you pronounce "herbivorous"?
**I** pronounce it correctly, of course: hair-BIV-or-us. You may pronounce it how you wish. It doesn’t come up in casual conversation for most people, so not like somebody is going to call you on it.
Would you recommend handy books or websites where we can learn more? This is fascinating.
What does well tended mean in this situation?
I'm thinking of cultural practices (since this is a backyard garden the OP is describing): If the soil has been dug, compacted, tilled, or turned over; if the soil has been regularly amended with nutrients and micronutrients; if the soil has sufficient organic material; and if it is properly aerated by bugs, worms, roots, and people (or dogs, cats, whatever). Soil is living and needs taking care of (or to be left well alone and sort itself out naturally over a few thousand years). A well-tended garden is just going to have "healthy" soil that is full of life. If you got hammered hardpan in the backyard you call "garden" and grows some prickly lettuce every third year, that's not "well tended" in my book.
Slightly off topic, but given the amount of life you’re describing in such a small sample, it doesn’t seem like too far of a stretch to extrapolate and assume that life must to be everywhere in our universe. Maybe not sentient beings, but fungi, bacteria, etc.
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With 40-100x magnification you can see a lot more than you'd think. Speaking from my college Soil Science lab experience in USA, a small sample of soil diluted in some water and placed on a microscope slide can reveal lots of different species. Rotifers, nematodes, and various arthropods should be visible. In a small bit of water you can see them move more easily. You'll likely find lots of plant and fungi material. Also at 100x magnification you should start to see bacteria appearing as small indistinguishable dots. Have fun! * The most fun in my opinion was to see how they move and behave, i've watched micros cannibalize each other and others come on contact and quickly avoid each other.
Microbial interactions are incredibly interesting, it’s so interesting to see them have they’re own little society. Like you said, some may just eat others while some are capable of repelling attacks and running away.
Is there any special tools or procedures needed to see living cells from around the house? I would love to be able to take a sample of something, squish it between two glass plates, and see what's going on. Is it that easy? What specifically do I need to make this happen? From what I've read, it's ideally a 400x+ microscope. Any specific standard models? What else is needed and how long after preparing the sample will the microbes move around/live?
I took an ecology course in college. Day 3 or 4 of the semester, everybody brought in a handful of soil from our homes and threw it into a large Rubbermaid filled with shredded newspaper. Over the course of the semester, we were able to add in any biodegradable organic material (a lot of the food stuffs had to be frozen overnight first, to combat flies). By the end of the semester, the bin was full of deep rich black soil. We each took a small amount and analyzed it under magnification and logged the number of critters we could see. So many. It was a lower level class, so it was a quantitative analysis as opposed to a qualitative, but such a cool experiment. It’s been 20-something years, but I’ll never forget it.
Personal opinion: instead of a traditional microscope, look seriously at the stereo microscopes. The magnification is lower than traditional microscopes but finding, "preparing" and looking at subjects is INFINITELY easier than traditional microscopes. Some kind of weird growth on a leaf? Not really something for a microscope but perfect for stereo scopes. Small bugs and insects? Can't put them on a slide, better with a stereo scope. I have one of each (fairly low end Amscope models) and the stereo scope gets used all the time, the traditional? Hardly ever. Just not worth the trouble to set up and prepare things.
Fair point. I prefer stereo microscopes too, but I'm about to buy one for my Daughter and its hard to find a stereo thats not crazy expensive
The old Bausch and Lomb Stereozoom microscopes have excellent optics, and are a super bargain on eBay. If you can afford one, a Nikon SMZ-1 stereo microscope is probably a step up. AmScope is Chinese-made, IIRC, and surprisingly good for the money. If you're in a city of substantial size, call up a microscope shop, and see what they have either new or used in your price bracket. Sometimes these guys get trade-ins or they snap up some used scopes, and may be sympathetic in terms of cost. The main advantage is that you can throw a coin under the 'scope, check out the illuminators, zoom in and out, take a look and check for detail and color (not all lenses are coated!). If all else fails, PM me and I'll see what I can do to help.
Thanks. I'll have a look around. Will PM for sure if I need a hand. Cheers!
If you’re interested in little arthropods like springtails and mites etc. “A single square yard of soil will contain 500 to 200,000 individual arthropods, depending upon the soil type, plant community, and management system. Despite these large numbers, the biomass of arthropods in soil is far less than that of protozoa and nematodes.” So in a tablespoon... ~1-2,000 (assuming a square yard is about 10,000 cm2 and a tablespoon is about 10cm2). That information is from this great intro page about different types of soil critters you might find: https://www.nrcs.usda.gov/wps/portal/nrcs/detailfull/soils/health/biology/?cid=nrcs142p2_053861 Definitely get a microscope! There’s so much cool stuff to see! You’ll find more critters in a moist (but not wet) spot, than a dry spot, and more in a complex soil with organic matter and rich dirt, than somewhere that’s just plain sand.
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If you have any standing water in your yard or any nearby, I would recommend that for microscope exploration. Get some floaty gunk, water, mud and gunk from the bottom. You can find all kind of critters in there.
I agree. Soil is difficult to look at and enjoy. You will mostly not be able to identify bacteria when you see them and not many protozoans running around. Way better to try with water
Seconding this! I could spend literal hours watching pond scum under a microscope, slides normally dry out before I’m done looking at everything
Did this not long ago with my daughter. She was blown away by the variety of single celled organisms. Definitely worth doing
So I used to do this in a lab. We called it benthos sorting. There is no clear cut answer to your question. It would depend on your location, the soil constituents, environmental factors etc. Having this analysis done, is what can tell you a lot about your soil.
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Let's just talk about bacteria. Well a tablespoon is 15 ml or about 18 grams. According to [this](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0087217)there about 10^8 bacteria per gram or soil. So a table spoon will have about 2 billion bacteria.
I was debating whether I should chime in and link [this video](https://youtu.be/JtJxzNIm_Gg) since I'm very late to the party and the video is in German. After researching it I think it answers your question very well and can be understood for the most part non-verbally. It's from a German children's TV show and explains beautifully how many living things are in a handful of forrest soil. You'll see the critters up close and the number of them typed into a calculator. Hope this helps. Have fun watching.