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New to the field - literature advice needed


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#1 aerkenemesis

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Posted 13 April 2013 - 12:49 PM

Greetings!

I would like to introduce myself in this first post of mine with some background information.

I am a 28 year old male from Sweden, living in the capital city of Stockholm. I have a masters degree in mechanical engineering (robotics).

I have recently taken on a very intense interest in microbiology, this microbiological interest comes from my interest in organic gardening.

I am currently in the state that I pretty much understand what goes on in the soil and around the roots of the plants. I have cultures Lactic acid bacteria and bacterial/fungal soil samples from different forests.

This interest have intensified immensely over the last few months, to the point where I want to start learning more about microbiology on a more scientific level and also get me a small lab with a microscope as the top priority.

I am now turning to you, my fellow scientists. Please share with me your recommended literature for my particular situation. I think that at this point I want to take on a little more of a practical approach; learning the science as I go.

For now I want to:
- Evaluate the quality of my cultures
- Evaluate the methods of culturing I use
- Understand how to store my cultures and how it impacts them
- Understand to a greater extent how they affect my soil, the plants and organic matter

I realize that when I say culture you think of a glass platter with a few hundred microbes, what I actually mean is a pretty large jar of goo which I use as a soil inoculant.

I really hope to get some good replies, Thank You!

#2 aimikins

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Posted 13 April 2013 - 01:30 PM

these are very open-ended questions, and tough to answer. it would help if we understood more specifically what it is you are trying to accomplish.

what do you mean by "quality"?

as far as methods of culturing, what are you trying to enrich for?

what do you mean by "store"? are you talking about keeping for weeks, months, years?
"it is a miracle that curiosity survives formal education" -A.E.

#3 aerkenemesis

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Posted 13 April 2013 - 09:44 PM

these are very open-ended questions, and tough to answer. it would help if we understood more specifically what it is you are trying to accomplish.

what do you mean by "quality"?

as far as methods of culturing, what are you trying to enrich for?

what do you mean by "store"? are you talking about keeping for weeks, months, years?


By quality I mean concentration and diversity of beneficial bacteria and fungi. As for the moment I use my nose to make sure it smells "earthy" and not putrefying.

The current culturing methods I use is milk fermentation for LAB. For forest microbes I bury a box of carbohydrates (rice or macaroni) in the forest, wait for infection, ferment with sugar.

Storing it for years would not be necessary, months is a good thing though. As for now, I store it cool and dark in glass jars.

#4 aerkenemesis

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Posted 13 April 2013 - 09:54 PM

I think beneficial is kind of a stretch to describe, there are books about this subject. One in particular called Teaming with microbes by Dr. Elaine Ingham. She describes what is called the "Soil food web".

This Wikipedia article describes it pretty well. http://en.m.wikipedi...i/Soil_food_web

#5 pito

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Posted 14 April 2013 - 10:25 AM

Just wondering: why are you doing this?

If you don't know it, then ask it! Better to ask and look foolish to some than not ask and stay stupid.


#6 aerkenemesis

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Posted 14 April 2013 - 01:24 PM

Just wondering: why are you doing this?


I can't see why I would need a reason to take part of the seemingly classified literature that goes with this subject.

#7 pito

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Posted 14 April 2013 - 10:23 PM


Just wondering: why are you doing this?


I can't see why I would need a reason to take part of the seemingly classified literature that goes with this subject.

The literature I can understand, but I wonder what you really want to do?
Are you really going to try to inoculate your garden with it?

And do you have any basic microbiology books? Because I can give you some titles that are avaible online.
But I wonder how much you allready know.

If you don't know it, then ask it! Better to ask and look foolish to some than not ask and stay stupid.


#8 aerkenemesis

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Posted 14 April 2013 - 10:47 PM



Just wondering: why are you doing this?


I can't see why I would need a reason to take part of the seemingly classified literature that goes with this subject.

The literature I can understand, but I wonder what you really want to do?
Are you really going to try to inoculate your garden with it?

And do you have any basic microbiology books? Because I can give you some titles that are avaible online.
But I wonder how much you allready know.


Well I know close to nothing about microbiology, what I do know is how the bacteria, Protozoa, nematodes, fungi, algae etc. interact in the so called "soil food web".

My mission now is to learn about microbiology. First steps is to learn the general basics, next step is to focus more on the particular species of interest.

As I said, I already multiply bacteria in different ways according to guides and manuals created by researchers in the area. I want to know exactly what I am doing, what I am multiplying, how I can do it better, evaluate the produce etc. This means learning microbiology so that I can research it on a more scientific level.

Answering your question, yes I do inoculate my garden with it. The plants THRIVE! The idea behind it is that I feed the soil (microbes) with organic matter which they consume rather than salt based chemicals which are used in a conventional feeding regime. The predator-pray relationship between the microbes leads to the destruction of for example nitrifying bacteria - which release mineralized nitrogen in the form of ammonium or nitrate, which the roots of the plant can utilize.

I'd be thrilled to take part of the information you mentioned. The books I've read does not cover specifics about the organisms; it is more like overviews of the interactions between them. It does not even mention any specific species.

#9 pito

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Posted 14 April 2013 - 11:16 PM




Just wondering: why are you doing this?


I can't see why I would need a reason to take part of the seemingly classified literature that goes with this subject.

The literature I can understand, but I wonder what you really want to do?
Are you really going to try to inoculate your garden with it?

And do you have any basic microbiology books? Because I can give you some titles that are avaible online.
But I wonder how much you allready know.


Well I know close to nothing about microbiology, what I do know is how the bacteria, Protozoa, nematodes, fungi, algae etc. interact in the so called "soil food web".

My mission now is to learn about microbiology. First steps is to learn the general basics, next step is to focus more on the particular species of interest.

As I said, I already multiply bacteria in different ways according to guides and manuals created by researchers in the area. I want to know exactly what I am doing, what I am multiplying, how I can do it better, evaluate the produce etc. This means learning microbiology so that I can research it on a more scientific level.

Answering your question, yes I do inoculate my garden with it. The plants THRIVE! The idea behind it is that I feed the soil (microbes) with organic matter which they consume rather than salt based chemicals which are used in a conventional feeding regime. The predator-pray relationship between the microbes leads to the destruction of for example nitrifying bacteria - which release mineralized nitrogen in the form of ammonium or nitrate, which the roots of the plant can utilize.

I'd be thrilled to take part of the information you mentioned. The books I've read does not cover specifics about the organisms; it is more like overviews of the interactions between them. It does not even mention any specific species.

Check your PM.

If you don't know it, then ask it! Better to ask and look foolish to some than not ask and stay stupid.


#10 aerkenemesis

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Posted 14 April 2013 - 11:19 PM

The plant controls the ratios of different microorganisms around its roots by excreting different sugars in different amounts; "selecting" what nutrients it consumes by controlling the amount of N-fixing, P-fixing org K-fixing bacteria/fungi. The nematodes and Protozoa "eats" the bacteria releasing the nutrients.

#11 hobglobin

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Posted 15 April 2013 - 01:39 AM

I'd say most important for plants are mycorrhiza fungi which you should not forget. You can detect them even with simple microscopy and suitable staining methods. Even quantification is possible with quite easy methods (e.g. percentage of roots with mycorrhiza).

Anyway your approach is quite challenging esp for a beginner as you work with an extreme complex and dynamic system which you have no idea when (or only when it's too late), how and why it changes. And you cannot control changes in terms quality and quantity and possible direction of changes, as you have no measures except the proper soil smell.

A more scientific approach would be to work with a standardisation (only one soil type with defined characteristics as I write below) and simplification (i.e. one or few MOs) so that you can tell which changes cause which results and then go to more complex experiments.

Don't forget that also other factors such as humidity, soil texture, pH, nutrient content and organic matter content highly influence plants, MOs and all other species in soil and that these factors also influence each other to a high degree (e.g. influences the pH value the availability of nutrients). You should consider to measure these values as far as possible (humidity regime, pH measurements).

For pH and nutrient measurements kits for gardeners are available, that you can get an idea about this and they are quite cheap.
For inoculation of soils with beneficial MOs also ready-made cultures are available that should support the fertility of soil. Esp. many organic gardeners use them to avoid synthetic fertilisers. You should check this (also to avoid double work Posted Image ).
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#12 aerkenemesis

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Posted 15 April 2013 - 05:38 AM

I'd say most important for plants are mycorrhiza fungi which you should not forget. You can detect them even with simple microscopy and suitable staining methods. Even quantification is possible with quite easy methods (e.g. percentage of roots with mycorrhiza).

Anyway your approach is quite challenging esp for a beginner as you work with an extreme complex and dynamic system which you have no idea when (or only when it's too late), how and why it changes. And you cannot control changes in terms quality and quantity and possible direction of changes, as you have no measures except the proper soil smell.

A more scientific approach would be to work with a standardisation (only one soil type with defined characteristics as I write below) and simplification (i.e. one or few MOs) so that you can tell which changes cause which results and then go to more complex experiments.

Don't forget that also other factors such as humidity, soil texture, pH, nutrient content and organic matter content highly influence plants, MOs and all other species in soil and that these factors also influence each other to a high degree (e.g. influences the pH value the availability of nutrients). You should consider to measure these values as far as possible (humidity regime, pH measurements).

For pH and nutrient measurements kits for gardeners are available, that you can get an idea about this and they are quite cheap.
For inoculation of soils with beneficial MOs also ready-made cultures are available that should support the fertility of soil. Esp. many organic gardeners use them to avoid synthetic fertilisers. You should check this (also to avoid double work Posted Image ).


Actually mycorrhizal fungi is indeed important but they mainly supply phosphorous to the plant, other MO supply other nutrients. As I said, I have the organic gardening bit down - it is the scientific explanations to what I am doing that I need to acuire. The books on the subject are very simplified in biological terms, that's why I feel the need to learn more of microbiology. At this point I don't feel the need to "prove" that different MO impact the plants in certain ways, there's already research done in that area. What I am interested in is to know what I feed the plants, exactly - and how to produce it, and why the guides on how to produce it is designed in the way they are, and how to impact the quality. Hence, again I need to learn about microbiology.

Using store bought MO kind of defeats the purpose, I'm interested in the biology - not in buying branded bottles with unknown content (yes, the manufacturers are very restrictive with declaring the contents of the bottles).

The goal is to not use any bottles at all, which I am very close to accomplish. I only use ONE store bought product and that is kelp extract, which I will produce myself as soon as the algae in my local sea starts to bloom (it won't be kelp but algae with similar nutritional content). The other bottled fertilizers I have made myself out of enzyme digested fish, fermented plants, fruits etc. They work well, in fact they work much MUCH better than inorganic fertilizers. The plants grow like crazy and are completely disease free!

I don't mean to be an ass but I came here to discuss the biology behind these methods, not whether to consider not using them. There are other forums with very knowledgeable people to discuss what works and what not, but not the biology at a higher level.

Thanks!

Edited by aerkenemesis, 15 April 2013 - 05:41 AM.


#13 Phil Geis

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Posted 17 April 2013 - 05:29 AM

I doubt yo';d recommend that we pursue engineering endeavors by just reading. Suggest you complete some appropriate courses in microbiology. At minimum you should learn aseptic technique, limitations of culture - esp. in soil application and the practical aspects of mycology.




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