Soil Bacteria – The Myth of Identification & Management

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Robert Pavlis

Bacteria are a vital part of soil and the health of plants, so it is no wonder that there is a lot of talk about keeping soil bacteria healthy, increasing their numbers, having the right kind of bacteria, and so on. It only makes sense that if bacteria are important for plants, gardeners should (a) know more about them and (b) learn to manage them properly.

Unfortunately, along with good practical information, you will also find quite a few soil bacteria myths. The one I’d like to discuss today deals with the idea that you can figure out which type of bacteria you have. Armed with this information, you can then manage the populations to increase the ones that are most beneficial for your plants.

Soil bacteria staring back at you under a microscope
Soil bacteria staring back at you through a microscope

Soil Bacteria and Dr. Elaine Ingham

Dr. Elaine Ingham has become synonymous with the Soil Food Web. Her teachings include many good ideas about keeping soil healthy. She is a proponent of compost, and adding organic material to soil. She promotes the idea that microbes in the soil are very important for developing good soil structure.

Unfortunately, Dr. Ingham then takes these ideas to a ridiculous extreme. She recommends gardeners should look at the microbes with a microscope, and with this device, they will be able to identify the various bacteria in soil. Once you know which bacteria you have in your soil you can take steps to manage the herd, and increase the right ones which would make the growing conditions more favorable for your plants. She goes on to suggest that different plants need different populations of bacteria and gardeners can learn to customize their soil.

Growing Great Tomaotes, by Robert Pavlis

Here is a quote from the advertisement for one of her courses where a full day is dedicated to identifying microbes: “Get the necessary training to identify the bacteria, fungi, protozoa, and nematodes that drive the health and well being of our plants” (ref 1, Soil Foodweb with Dr. Elaine Ingham).

I have no problem with the idea that microbe types in soil are important, and that their ratios might change over time, and that such changes influence plant growth. This is all very true.

What I have a problem with is the idea that anyone can control this situation in a quantitative way. To do this you need to be able to identify the current bacterial types that you have, and then influence their populations to make them more suitable for you plants.

Note: Added March 28, 2016. A couple of comments left at the end of this post said that Dr. Ingham does not promote the identification of species. 

The commenters can’t imagine where I got such an idea. So I went back and looked at a lot of the promotion from Dr. Ingham, and looked at several online videos. In every case she talks about the ‘identification of microbes’. In the video she clearly differentiates between various types of bacteria, and nematodes and talks about the importance of identifying these various types, and how this can be learned using a microscope. Clearly she expects you to do much more than just count total bacteria and total nematodes as one commenter said.

From her web site: “we will develop a wider and wider base of knowledge as more people encounter all the myriad of organisms that exist in soil.  Which in turns leads to a better understanding of what exactly is in different soils, in different climates, and with different organic matter and plants.” Sounds like a lot more than just counting bacteria, fungi, protozoa and nematodes!

Microbe Science for Gardeners Book, by Robert Pavlis

The Soil Food Web also talks a lot about ‘increasing diversity’ of microbes. If you don’t know which species you have how can you know that your methods are increasing diversity? You can’t, which would lead a reader to think they are doing much more than just counting total bacteria.

I think this is a case of misleading the reader/viewer about her courses. I don’t think it is intentional.

What about the rest of this post? If identification of species is not the goal, are the comments still valid? I think they are. The post is mostly about gardeners using the information gained from the microscope.

I have just finished reviewing the book Teaming with Microbes, a gardeners Guide to the Soil Food Web and they say the following about using a microscope “when it comes to the microorganisms, we will be the first to admit that you will not be able to determine precisely what is in your soil, even with a powerful microscope.“ This comment comes from two strong proponents of the Soil Food Web, Jeff Lowenfels & Wayne Lewis. I agree with their conclusion.

Update Aug 2023: I just received a copy of The Compost Tea Brewing Manual, by Dr. Ingham. Under the section Compost Tea Organisms, she says, “Currently, a combination of selective media, enzymes and finger printing can serve to determine whether 20 specific beneficial species are present or not. In this way, you can determine whether your tea includes the beneficial organisms that you need.” Notice that microscopy is NOT included as one of the methods used to identify the bacteria in compost tea. She clearly agrees with the conclusion in this post, but continues selling the courses anyway. 

Bacteria in Soil

Bacteria in soil carry out some very important functions. Some are nitrogen fixers which convert the nitrogen in the air, N2, into ammonia, nitrite and eventually nitrate, so plants can use the nitrogen. The decomposers are a large group of bacteria that decompose organic matter. This process releases nutrients for the plants and improves soil structure.

Bacterial pathogens cause diseases in plants. We don’t really want them around, but they are part of nature and play an important role. Normally, the good bacteria out compete the pathogens, and keep their numbers low enough so they don’t cause a problem.

Find out more about the bacteria found in compost at Compost Microbes – Good for the Soil?

Bacteria Species in Soil

How many species of bacteria exist in soil? You would think the question would have a simple answer, but the honest truth is that scientists don’t know. Most species of bacteria have not been identified which means no one knows how to identify them.

Estimates range between 2,000 and 8.3 million species of bacteria per gram of soil (ref 2).

Identifying bacteria is so complicated that the experts use approximation techniques to figure out the number of species. It is impossible to sit down in front of a microscope and figure out which species you have. For a glimpse at how soil scientists try to estimate bacteria communities see reference 3 .

A study (ref 4, Toward a Census of Bacteria in Soil) compared soil from Alaska and Minnesota and used computer models to identify species of bacteria because doing real identification was impossible. They found several thousand species, and 20% were endemic. So the soil bacteria from these two regions were quite different from one another.

The bottom line is that no one is able to identify bacteria species by looking at a soil sample. If the experts can’t do it, gardeners can’t do it – even if they take Dr. Ingham’s course.

Types of Bacteria

OK, so you can’t identify soil bacteria at the species level, maybe you can identify them as ‘classes’ of bacteria?

You can certainly see some bacteria cell structure under a microscope, and you can form classes of bacteria based on physical structure; rods, spheres, spirals etc., but that does not really tell you anything useful about which ones you want in the garden.

You can’t differentiate aerobic from anaerobic bacteria, based on physical appearance. You also can’t differentiate between beneficial and pathogenic bacteria. Identifying a bacteria as belonging to one or the other of these classes is critical to Dr. Ingham’s methods for the management of soil bacteria, and especially for the creation of compost tea.

You can count the number of bacteria you see, but I don’t know how accurate that is for a soil sample.

The average gardener can learn very little about the bacteria in soil by looking at a soil sample under a microscope.

Professional Labs

Let us assume that I have convinced you that you can’t identify the bacteria yourself. You then have the option of using one of the labs Dr. Ingham recommends on her web site, to do this identification for you.

Here is what one of them says “Complete Food Web Test (done by SFWNY) – Quantifies total and active bacteria, total and active fungi, and presence/absence of protozoa” , ref 5 Soil Foodweb Inc – Identifying Organisms. Your results will give you 4 numbers plus a yes/no for protozoa! Remember this is a ‘complete’ test, but it does not provide any information about the identification of bacteria. Odd – maybe the testing lab never took Dr. Ingham’s course??

So even the recommended professional labs don’t try to identify species, aerobic vs anaerobic, or even beneficial vs pathogenic.Why? It’s too complicated.

Managing Bacteria in Soil

The idea that someone can take a light microscope and find out critical information about their soil bacteria is ridiculous. You can certainly see bacteria, and you might be able to count some of them. That information is not very useful.

Even if you could get the information, what would you do with it? I don’t see how you would know which bacteria you should grow for each of your plants? No such table exists. How does this change for each plant you own? Nobody knows. We don’t even know which bacteria live in your soil!

Adding more organic matter will increase the number of bacteria – you don’t need to measure them to know this. Bacteria automatically increase in numbers when you supply a food source. Having active bacteria in soil is a good thing even if you don’t know which species you have. You don’t need a microscope.

In this discussion I have focused on bacteria in soil, but all of the comments also apply to bacteria in compost tea. Except for counting bacteria, a microscope will not help you to qualify your compost tea herd. Besides, there is no current evidence compost tea works any better than just compost.


  1. Soil Food web with Dr. Elaine Ingham;
  2. Pyrosequencing enumerates and contrasts soil microbial diversity;
  3. Empirical and Theoretical Bacterial Diversity in Four Arizona Soils;
  4. Toward a Census of Bacteria in Soil;
  5.  Soil Food web Inc – Identifying Organisms;
  6. Photo source: Filter Forge
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Robert Pavlis

I have been gardening my whole life and have a science background. Besides writing and speaking about gardening, I own and operate a 6 acre private garden called Aspen Grove Gardens which now has over 3,000 perennials, grasses, shrubs and trees. Yes--I am a plantaholic!

100 thoughts on “Soil Bacteria – The Myth of Identification & Management”

  1. I’m not quite sure where this notion that you need to identify specific bacteria came from but I have not once heard her advocate for doing that.

    Dr. Ingham specifically says you don’t need to know specifics about the populations of bacteria or any of your microbiology. It’s the generalities, mostly of later succession than bacteria, that reveal information about your soil biology health. For instance, you don’t need to know which anaerobic bacteria are present in the soil, but you should most certainly know that ciliates tend to feed on anaerobic bacteria and as such their populations will be higher in a soil/compost/tea that has or is currently anaerobic. With nematodes you’re really just identifying mouth parts and a few other parts which distinguish them from each other. The anatomy of a root eating nematode, for instance, can be distinguished under a microscope from a bacteria feeding nematode.

    • If you read the article – it quotes Dr. Ingham’s promotion for the course “Get the necessary training to identify the bacteria, fungi, protozoa, and nematodes that drive the health and well being of our plants” – that’s where this idea comes from.

      • The identification is very rough — like good or bad bacteria or fungi. I think it’s widely acknowledged that identifying specific bacterial species is beyond the scope of any online class.

          • Diversity is really what you are looking for, in every dimension and trophic level. I don’t think I need to pay thousands for her course, but many without a deep background in managing ecology could.

  2. I am a gardener, have grown organically for 7 years, minimal till, own compost, manure, woodchips, municipal compost.
    The last few years of drought showed me my plants are not doing very well. I bought a simple microscope. Look what – bacterially dominated soil ++, with extremely limited nutrient cycling, very few protozoa, very few nematodes. The earth worm population and over ground biodiversity is reasonable, which led me to assume if it’s ok over ground, diversity must be OK under ground too. Not so.

    This is in line with the findings of the UN’s Soil Biodiversity report’s findings.

    I have since looked at all sorts of soil. Very sobering. Occasionally I come across soil ecosystems, that clearly have occupied niches.

    Finding and preserving these as a resource to regenerate our degenerated soils, and learning to cultivate conditions that support their survival in our garden and agricultural soils is one of the greatest challenges of our time.

    We all need soils. Our gardens are an important space to learn about this. A microscope can be a very useful resource for the neighbourhood.
    I took mine down to the farm where I buy much of my food. The farmer, organic for decades, showed me his somewhat yellow-looking wheat, and told me they can’t get reliable results. We looked through the microscope together, and at his different trial plots. Very revealing.
    No species identification needed.

    Is there a lot simplified in Dr Ingham’s teachings? Probably yes.
    Does it need combining with other knowledge? No doubt. John Kempf, whilst for farmers, has some fab resources that explain the basics of plant health. Equally relevant in my garden.

    Let’s all learn a lot more and quickly and share what we have been successful with. Ultimately our plants tell us what’s going well. Our wellbeing and future depends on it – let’s have a bit of fun in the process. A microscope is not a requirement for successful gardening, but a useful tool. There are plenty of free resources available, in addition to the above report with good photos, the European Commission has created fantastic soil atlases for different continents.

    All excellently and clearly referenced, as well as the UN report on soil biodiversity.

  3. You’ve been asking somewhere up there for studies showing that difference in fungal:bacterial ratios lead to measurables effects.

    Here’s one on carbon sequestration.

    There was also a really speaking graph, showing strong correlation between plant growth volume and fungal:bacterial ratios, in this video (from 23:10 to 24 something)

    I unfortunately do not have a direct link to the details of the study leading to this graph. Coming from a USDA researcher I tend to “trust” the integrity and method leading to these results, but It would sure be best to have access to the methodology.

    Sorry for my broken english, I’m a Frenchman =’p.

    Love your content, I learn a lot from your debunkings of myths as an amateur gardener.

    • I was not asking for studies that show “fungal:bacterial ratios lead to measurables effects”.
      The claim is that some plants grow better at one ratio than another, and that there is a benefit to adjusting your soil for particular plants.
      It is well known that soil quality improves with more organic matter and more microbes. This study concludes that “the increased abundance of fungi in both soils and the altered C cycling patterns in the F:B dominated soils highlight the significant role of fungi in litter decomposition and indicate that F:B ratios are linked to higher C storage potential.” That has never been under question.

      This study did not try to grow plants in different F:B ratios.

  4. Have you considered asking some of Dr. Ingham’s graduates what they think? How about the ones who have gone on to become professionals using the method? How about their customers in the ag industry? What do they think? Results speak louder than opinions.

    • Results speak louder than opinions – you are absolutely correct. That is why I would not ask some of Dr. Ingham’s graduates what they think?

      Instead I looked at the science.

        • I’d rather have results today than peer-reviewed facts in ten years.
          One of the fallacies of scientism is that if a thing has not been proven true, it must be considered to be false. This popular, misconceived attitude paradoxically runs against the current of true science, which has curiosity as its basis. To close doors in the name of “skepticism” is popular today, but it will not yield new knowledge. Mainstream science is always behind the curve in fields such as this, where innovators push the envelope. By the time this is tested, trialed, repeated, published and accepted there will be new pioneers blazing new trails and getting mocked for being unproven. But we can see for ourselves what works and what does not. There’s no need to wait.

          • ” if a thing has not been proven true, it must be considered to be false.” – that statement is not correct.
            if a thing has not been proven true, it must be considered unproven. Science does not say all unknown facts are false.

          • That is correct. If only more people would adhere to science! It’s more of a prevailing attitude, as I said.

  5. Dear Sir,

    1) But basic microscopes can identify specific bacteria, given the correct differential staining and other differential processes, such as the addition of hydrogen peroxide, or depriving of oxygen, for oxidase and catalase and aerobic differentials.

    2) These processes and techniques are not beyond the realm of learning in a few weeks, nor is the acquisition of the stains and other tools.

    3) There are certain bacteria and fungi that are known to harm certain plants.

    4) Whether we can then rid these bacteria by adding an ‘antibiotic’, or antifungal to the soil of some sort, or provide a specific nutritional element to the plant, is another question however.

    Your thoughts on my 4 points would be appreciated.

    All the best.

    • 1) The techniques being promoted for gardeners do not include staining – only viewing by light microscope. Also, staining helps to classify a type of bacteria, but it does not usually identify it. Remember that most soil bacteria have not even been named yet, so how can an armature identify it?
      Yes – certain bacteria and fungi harm plants.
      In theory we can control a problem, but this is usually beyond what a gardener can do.

    • Dear Sirs

      All the methods regarding identification of bacteria you have mentioned belong to the past.
      There is no way you can identify a Bacillus with 100% of certainty except with the use of gene sequencing that today you can get for nearly 100 dollars.

      Elaine Ingham was very important 20 years ago but today I don’t think she can contribute for this new biological agricultural revolution that is being used in nearly 30% of the farm land in Brazil, for instance.

      Compost Tea is a total waste of time as it reduces the biodiversity of the medium after 24 hours of favorable conditions to only bacteria.
      Compost Extract make much more sense and this is is why we are currently using along it with E.M. which contributes with anaerobic organisms which Elaine completely disregard.

      Sorry but I see this subject as a total waste of time to be discussed.

      Let’s move on.

      Jose Luiz M Garcia

      • What % of soil bacteria species have been identified?

        It is about 30% – so, no you can’t ID soil bacteria with a microscope.

        • Not species but functional groups. Beneficial fungi and bacteria generally have certain characteristics, as do anaerobic ones. Additionally, the presence of facultative anaerobic organisms such as rotifers and ciliates gives us a clearer picture of the condition of the soil. Yes there are plenty of beneficial anaerobic species as well, but as we cannot distinguish them, the goal of the SFW approach is to focus on aerobic species which do not include human or plant pathogens.

          • Yes you can classify bacteria into functional groups, but that is not what Dr. Ingram claim to teach in her classes.

            You still have the issue that once you classify and count them – how do you use this information in the garden?

          • I’m a bit confused on this format; it only gives me the option of replying to my own comment, not directly to yours.

            Robert Pavlis says:
            April 30, 2021 at 11:59 am
            “Yes you can classify bacteria into functional groups, but that is not what Dr. Ingram claim to teach in her classes.”

            As a student of the SFW school I can verify that this is absolutely not the case. Dr. Ingham makes it very clear that we are by no means trying to ID species, only functional groups. Not sure how you got the wrong idea.

            “You still have the issue that once you classify and count them – how do you use this information in the garden?”

            The courses are more aimed toward training professional consultants and lab analysts to work in the agricultural sector, than for the home gardener, but the same principles can apply anywhere. Once you have an idea of the bacterial and fungal biomass (an application assists in the calculation based on your counts) as well as numbers of the different protist and nematode groups, you start to see where a soil is lacking in those groups and can work to fill in the gaps. There are minimum requirements for her standards of “biocomplete” soil and amendments. Certain numbers of each group must be met, as well as a certain fungal to bacterial ratio, depending on the desired crop.

          • “Dr. Ingham makes it very clear that we are by no means trying to ID species” – prove it. Link to one of her pages where she is promoting the technique and clearly points this out. All of the promotion I have ever seen claims to teach you the ability to ID microbes.

            Your last paragraph is very general. If you know A and B, you can improve your soil. But how? Lets see a clear defined methodology for this. And then provide some science to support the methodology.

            The reality is that the science community does not buy into the importance of trying to control various different populations of microbes. They don’t agree that it is important to have the right fungal to bacterial ratios. To date, I have yet to see a single study that shows some benefit from doing this kind of manipulation. But I am willing to look at the science.

            By the way, I have asked Dr. Ingham these same questions and got no response. She was unable to provide even one study to support the fungal/bacterial ratio benefit.

          • “Link to one of her pages where she is promoting the technique and clearly points this out. All of the promotion I have ever seen claims to teach you the ability to ID microbes.”

            I won’t link to one of her proprietary courses where this is taught, and you’d need to be a student to access it anyway. But you are confusing the level of identification. Can you show me where she says she can identify to species? No you cannot. She teaches ability to identify functional groups, she never promises more specificity than this. And simply promising to identify microbes, well that’s pretty vague. I could say look there’s a microbe, and we’ve now identified it.

            “Your last paragraph is very general. If you know A and B, you can improve your soil. But how? Lets see a clear defined methodology.”

            Again this is taught in the courses.

            “The reality is that the science community does not buy into the importance of trying to control various different populations of microbes. They don’t agree that it is important to have the right fungal to bacterial ratios. To date, I have yet to see a single study that shows some benefit from doing this kind of manipulation. But I am willing to look at the science.”

            There are plenty of Ph.D.’s working with us in the school who do buy into the science, but your skepticism is understandable. I did a quick search and found this. I’m sure there’s more but I’m not breaching any paywalls today.

          • “Can you show me where she says she can identify to species? ” – that is easy – all you have to do is read my post where it says:

            “Here is a quote from the advertisement for one of her courses where a full day is dedicated to identifying microbes: “Get the necessary training to identify the bacteria, fungi, protozoa, and nematodes that drive the health and well being of our plants” (ref 1, Soil Foodweb with Dr. Elaine Ingham).”

            That is a direct quote, “identify the bacteria”.

            If you read the link you posted, it says right near the beginning “Greenhouse plant-growth trials” – this is not a field trial. Just because soemthing works in pots in a greenhouse, does NOT mean it works in the field.

  6. What conclusions can you draw by looking at a microscope if you cannot make any difference between a bacteria, actinobacteria, etc… and quantify them ?

    I use microBIOMETER (r) which is much better and gives you a quantified amount and now you can also quantify the F:B relation.

    If you or anyone else want to learn how to do a real Biological Agriculture come to Brazil. Don’t forget that USA since last year is just number two in world soybean production. We know how to do things which doesn’t include Elaine’s mental masturbation.

  7. Enough of Elaine Ingham.
    I just can’t take all of this mental masturbation about Compost Tea and seeing some little guys moving on the microscope screen.
    There is no professionalism on that whatsoever.
    Keep Regenerative out of this subject.

    • Dr Vinagre PhD, I don’t see what you have added to the conversation. I am not here to defend Dr. Ingham, her work can stand by itself. I think sometimes to get the big picture you have to look through a microscope especially if we are just at the beginning of understanding practices and methods that will make us all better stewards of the soil and the ability to perhaps make it healthy or at the very least mitigate some of the damage we have already done. Would you tell someone getting into astronomy not to buy a telescope but just to look up at the night sky? My advice to anyone is to buy the best microscope you can afford if you are seriously studying soil health because almost everything is in the details. The better look you get at anything, the far easier it is to fully understand. If we are talking soil health then something must be alive, I believe a microscope gives you that ability to see for yourself.

  8. It is important to be skeptical when anyone insists a home gardener needs their own microscope. Afterall, haven’t people been gardening and farming for centuries without microscopes? Indeed, they have; yet, there have also been many long standing challenges for gardeners and farmers struggling with fertility loss, amounting to nothing less than the degradation of soils, desertification of whole bioregions, and the collapse of agricultural systems. The common thread was their ignorance of the soil food web due to an inability to see it, monitor it, and manage it. They affectively had no tools for diagnosing soil food web problems, beginning with the most basic: the microscope.

    It is by the newfound knowledge of microbiological science, begun by the discovery of “microscopic animals” (thanks to the microscope) that we have books such as, “Teaming with Microbes”, “… Nutrients”, and “… Fungi” by Jeff Lowenfels, that home gardeners can become better educated about principles of good soil health. Afterall, someone needed a microscope to take all the nice pictures of bacteria, archaea, fungi, protozoa, nematodes, and microarthropods provided in Lowenfel’s books… without this, you would need your own microscope.

    To be sure it is a fallacy to believe you must identify individual species of bacteria when bacteria are only the bottom rung of the soil-food-web trophic ladder. Alone, bacteria are a dysfunctional population: You need all the rungs to climb to the top. The forest mustn’t be missed for the trees – the usefulness of the microscope is in observing populations of all microbes beyond just the bacteria. As we know, bacteria (and fungi) tie up nutrients, and we need protozoa and nematodes to ensure those nutrients’ cycles are completed in their return to plant available forms when they predate bacteria and poop them out, releasing nutrients in plant available form.

    Three major principles of SFW gardening that you’re overlooking here are Lowenfels’ principles 1-3, and these are regarding Fungi:Bacteria ratios: 1) Different plants prefer different F:B ratios, 2) Annuals prefer bacterial dominance, 3) Perenials prefer fungal dominance. Ingham emphasizes these same things in the beginning of her Foundation Course 1: how to recognize bacteria, fungi, protozoa, and nematodes using microscopy.

    By and large, Lowenfels and Ingham acknowkedge the pointlessness of home-gardeners IDing bacteria and emphasize IDing all microbes (not by species, but by ecological niche), confirming their presence in approximately healthy numbers relative to one another, thus confirming healthy diversity of the soil foodweb. As Lowenfels says, “Exact measuring is best left to the professionals” (“… Microbes” p. 118). He acknowledges the importance of having professional labs and the fact that every gardener need not be a professional microbiologist – they just need access to their advice. On the following page, he provides a lab test from Ingham’s lab in Corvallis, OR. He obviously values her work. Furthermore, he says, “… With the results of your own visual surveys and such microbiological lab tests, you will know what is active in your soil and… what isn’t there… But rest assured: whoever is missing can be activated by soil foodweb gardening techniques” (…, p.119). Thus, he still recommends having this analysis done. Sure you can garden by the SFW principles, never having gotten a lab test, and you’ll probably keep on track enough to grow some satisfying tomatoes, but if you want to become a professional SFW microbiologist, consider taking Ingham’s courses. Afterall, a $5500 fee for Ingham’s full course is not tailored to educate a home-gardener hobbyist – it’s for people who want to start labs and offer services to gardeners and farmers for whom such measures of soil analysis are impractical to do themselves.

    A good example of this professional/non-professional distinction of personal context is the regenerative farming movement. Professional farmer Richard Perkins of Ridgedale Permaculture Farm in Sweden uses a microscope to monitor his own SFW and teaches up-coming farmers how to do the same as a crucial tool for distinguishing regenerative farming practices from degenerative ones. It’s value is in enabling farms to troubleshoot their own fertility issues, and decentralize reliance on big-ag fertilizer solutions.

    So… do you need a microscope?
    Well, that depends… are you a gardener, or are you a professional regenerative farmer?


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