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Old 07-18-2012, 04:48 PM   #1
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Beneficial Soil Microbes: Bacteria, Archea, Fungi, Protozoa

Greetings and respect,

It seems like every product geared to the organic gardener these days has a list of beneficial bacteria, archea or fungus on the packaging. When we brew our teas, compost our veggie scraps, or add mycorrhizae to a prepared hole, we are trusting that these beneficial microbes are going to do something ... this is a list of what these things actually do.

I was gifted a similar list of the known consortium in a specific brand of growing supplement. It was a good starting point. However, I took the list a little further than what was on that piece of paper.

This is not a complete list of all beneficial microbes... I've just started, with mostly bacteria. With some help, this could turn out to be a pretty comprehensive list of beneficial bacteria, archea, fungi, perhaps protozoa, and what they do.

If it's on the side of a bottle being sold as "beneficial" I would definitely like to see it on this list.

·
Actinobacteria- Actinobacteria are known for the important role they play in soil ecology. Some Actinobacteria form branching filaments, which somewhat resemble the mycelia of the unrelated fungi, among which they were originally classified under the older name Actinomycetes. Most members are aerobic, but a few, such as Actinomyces israelii, can grow under anaerobic conditions. They produce a number of enzymes that help degrade organic plant material, lignin, and chitin. As such, their presence is important in the formation of compost (1). Actinobacteria include many families...
The family Mycobacteriaceae of Actinobacteria has a single genus, Mycobacterium, which contains several pathogenic species causing diseases such as leprosy and tuberculosis.
The family Streptomyceteae of Actinobacteria comprises several organisms found in the soil. They are rarely pathogenic. In contrast, several species of the genus Streptomyces produce antibiotics (2).
The Frankia family of Actinobacteria works in a symbiotic relationship with many non legume plants as nitrogen fixing bacteria.

· Bacillus amyloliquefaciens- Bacillus amyloliquefaciens, are known for their catabolic (metabolic pathways that break down molecules into smaller units and release energy) properties and degradation of complex macromolecules. It also synthesizes a natural antibiotic protein barnase (think of this stuff like a ninja star, ripping through the DNA of viruses) and other secondary metabolites for use as biocontrol of plant pathogens (3).

· Bacillus circulans- A Decomposer, it secretes a variety of polysaccharide-degrading enzymes (32) (The most abundant polysaccharide in nature is cellulose followed by hemicelluloses and chitin.). B. circulans produce chitinanse , that are useful in the degradation of insoluble substrate chitin. B. circulans are similar to Bacillus megaterium, except this strain is very heat-resistant which causes fermentation of cereals in canned meat foods. They cause souring but no gas production. (33)

(Chitin can be found in a wide range of organisms. Chitin forms a polymer that allows it to function as a load-bearing component of the skeletal materials of many lower animals, for example the exoskeleton of arthropods (including insects and crustaceans). Chitin is also found in coelenterates, nematodes, protozoa, mollusks and the cell walls of many fungi. Chitin is almost always associated with other structural components like protein and glucans (Gooday,1990).)

· Bacillus Laterosporus- plant growth-promoting rhizobacteria (PGPR), shown to have toxicity to larvae of the mosquito.(4) The larvicidal activity of B. laterosporus was associated with spores and crystalline inclusions. The toxicity of the entomopathogenic strains of Bacillus thuringiensis subsp. Israelensis (Mosquito Dunks) and Bacillus sphaericus against mosquitoes is associated with protein crystal production (also). Also, sold all over the web as a toenail fungus fighting (5) and/or a colon cleansing (7) Pro-biotic. Has been used for it properties of microbial metal accumulation( biosorption ).(10)


· Bacillus Licheniformis- is a PGPR bacterium commonly found in the soil and on bird feathers. It has an ability to degrade the feathers, other non-digestable proteins (11), and cellulose. (12). used to treat ornamental plants to protect them from fungal pathogens. B. licheniformis is also used to produce the polypeptide antibiotic bacitracin. (13)Bacillus Licheniformis Final Risk Assessment
· Bacillus megaterium- PGPR, It is considered aerobic. It is found in soil and considered a saprophyte (i.e. any organism that lives on dead organic matter, as certain fungi and bacteria. Also called saprobe.)(14). B. megaterium is used as a soil inoculant in agriculture and horticulture (15), is also a Cytokin producer(16). Bacterial species capable of producing cytokinins may increase the level of cytokinins in root tissues. In turn, this may have an impact on plant growth.

· Bacillus pumilus- is aerobic, spore-forming bacillus commonly found in soil. Bacillus pumilus strain GB34 is used as an active ingredient in agricultural fungicides. Growth of the bacterium on plant roots prevents Rhizoctonia and Fusarium spores from germinating. (17) EPA Factsheet on B. pumilus GB34


· Bacillus polymyxa 9A- capable of inhibiting the growth of Verticullium dahlia (wilt).(8)

· Bacillus papillae - The spore-forming bacteria Bacillus papillae and Bacillus lentimorbus will infect and kill white grubs and Japanese Beetles in turf.

· Bacillus stearothermophilus- These aerobic bacteria grow in warm temperatures. For this reason it is called a "thermophile" which means heat loving. These bacteria are among the most abundant in warm compost piles, and participates in the denitrification of farmers' expensive NO3 fertilizers to volatile NO2 or N2 yet its exact role in this process has not been thoroughly explained(18). Spores of bacteria allow the bacteria to survive harsh conditions until the time when the bacterium can thrive and reproduce (6).

· Bacillus subtilis- known also as the hay bacillus or grass bacillus, classified as an obligate aerobe, though recent research has demonstrated that this is not strictly correct (20). Found in fresh horse and cow manure (19). Effective biological pesticide against fungi and bacteria that cause scab, powdery mildew, sour rot, downy mildew, and early leaf spot, early blight, late blight, bacterial spot, and walnut blight diseases. Bacillus subtilis QST713 EPA Fact Sheet


· Clostridium nitrophenolicum – anaerobic, they have been isolated from soil, sediment, decomposing biological material and the lower gut of mammals. Have diverse metabolic capabilities and are known to possess strong nitroreductase (reduction of nitrogen-containing compounds) properties. Was found to be capable of degrading p-nitrophenol (pNP) at a concentration of 0.5 mM under anaerobic conditions as revealed by HPLC analysis (21).

· Cyanobacteria- AKA. Blue-green algae- Nitrogen fixation, carbon fixation. (9)

· Microbacterium sp. – Bioemulsifier, also, used to remove heavy metal contamination from hazardous industrial waste (31).


· Nitrobacter winogradskyi - It can grow in both aerobic and anaerobic conditions with nitrate as its electron acceptor during anoxic conditions. They play a key role in the nitrogen cycle by converting nitrite to nitrate. As it interacts with ammonium oxidizing bacteria which also play a key role in the nitrogen cycle. Ammonium oxidizing bacteria initiate nitrification, in which nitrite is the end product. Nitrobacter winogradskyi then proceeds to oxidize nitrite to nitrate. (22)

· Pseudomonas citronellolis - It was first isolated from forest soil, under pine trees, in northern Virginia. Capable of degrading isoprenoid compounds (23). Pseudomonas citronellolisis a potential candidates for biodegradation of low density polyethylene (LDPE) (24)


· Pseudomonas stutzeri – single polar-flagellated, soil bacterium first isolated from human spinal fluid. It is a denitrifying bacterium, and strain KC of P. stutzeri may be used for bioremediation as it is able to degrade carbon tetrachloride. It is also an opportunistic pathogen in clinical settings, although infections are rare (24).

· Rhizobia - are soil bacteria that fix nitrogen (diazotrophs) after becoming established inside root nodules of legumes (Fabaceae). Rhizobia require a plant host; they cannot independently fix nitrogen. In general, they are Gram-negative, motile, non-sporulating rods (30).

· Rhodococcus erythropolis - The genus Rhodococcus is a diverse group of bacteria commonly found in many environments from soil to seawater. They are Gram-positive, high G+C content, coryneform bacteria belonging to the order Actinomycetales. Many strains of Rhodococcus bacteria show remarkable metabolic versatility, including their ability to degrade a variety of xenobiotic compounds such as polychlorinated biphenyls (PCBs). Some strains are known to produce biosurfactants and still others are source of useful enzymes such as phenylalanine dehydrogenase and endoglycosidases. Because of these characteristics, Rhodococcus bacteria are assumed to be industrially important (25). Rhodococcus erythropolis C2, which is able to degrade several kinds of fossil fuel, was isolated from soil samples (26).


· Rhodospirillum rubrum - and other Purple Non-Sulfur Bacteria (PNSB) can be found in natural setting such as pond water, mud or a sewage sample. Capable of nitrogen fixation, produce vitamins and other organic molecules, biomass production, perform photosynthesis and ATP formation.

· Rhodopseudomonas palustris - R. palustris is a PNSB and has been found to grow in swine waste lagoons, earthworm droppings, marine coastal sediments and pond water. Capable of nitrogen fixation (27).


· Streptomyces griseoviridis – Streptomyces griseoviridis Strain K61 is a soil bacterium that can prevent certain disease-causing fungi from infecting plants. It is not expected to harm humans, other non-target organisms, or the environment. Steptomyces griseoviridis Strain k61 EPA Fact Sheet.

· Gliocladium virens – Gliocladium virens is a naturally occurring, ubiquitous soil saprophyte found throughout the United States in various soil types. This common soil fungus has been shown to suppress a variety of soilborne plant pathogens, including Pythium spp., Rhizoctonia solani, and Sclerotium rolfsii that cause damping-off, root rots, and various other seedling diseases on a wide variety of host plants (28).

· Trichoderma harzianum strain T-22 - There are many natural antagonists that keep disease organisms under suppression. Members of the genus Trichoderma are filamentous fungi that can be isolated from many soil types. They are part of a healthy soil environment with numerous species found worldwide. A few select strains of T. harzianum have been shown to suppress plant pathogens. However, they are limited in the scope of plants they protect and the pathogens they control. For example, one strain can control Pythium and grow in cooler soils, while another can control Rhizoctonia and colonizes the root system.
To overcome these limitations, researchers at Cornell University produced a hybrid strain that had enhanced attributes of the parents. The strain, T-22, protects the root system against Fusarium, Pythium and Rhizoctonia on a number of crops including corn (field, sweet, silage), soybeans, potatoes, tomatoes, beans (green and dry), cabbage, cucumbers, cotton, peanuts, turf, trees, shrubs, and other transplants and ornamental crops. T-22 is able to grow in a range of soil types at temperatures above 50F. Because of its superior attributes, T-22 has been commercially developed as one of the first biofungicides (29)


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Old 07-18-2012, 06:52 PM   #2
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Toes,
Very interesting. Thanks for posting this. -granger
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Old 07-19-2012, 08:04 PM   #3
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Great read....
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Old 07-19-2012, 09:33 PM   #4
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Please note that Actinomycetes is a 'very' outdated term for Actinobacteria which reflects the fact that they are bacteria and not fungi. Streptomyces is a part of this group.

They are actually mostly aerobic (AFAIK) at least the soil ones which we are interested in.

I'm wondering what made you use the term 'bacteria/archaea'. I'm the only one I know of to use the combination this way,

Just curious...
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Old 07-20-2012, 04:51 AM   #5
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thx for posting, really interesting information
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Old 07-20-2012, 07:33 AM   #6
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Originally Posted by MM
I'm wondering what made you use the term 'bacteria/archaea'. I'm the only one I know of to use the combination this way,

Just curious...
You're an inspiration I suppose...
I've got a list of Endo and Ecto mycorrhizae, I will be doing those next.

Thank you for your support.



I hope that everyone will feel free to post examples of your favorite bennies and how they interact with our plants and us.

some soil critters/creepers are just as helpful to us as they are to our plants...

some of those little fuckers I wouldn't mess around with. forget getting them in my mouth, eyes, or open sores... (especially with a compromised immune system!)

We could make this a total list of bennies, what they do, which ones you need, and which ones are most beneficial.


Respect.
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Old 07-20-2012, 06:11 PM   #7
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If you proceed it is probably a good idea to research from more than one source of information for each species or group before posting. This would have revealed the information about Actinobacteria and Streptomyces being of that group.

Just so everyone is aware Rhodopseudomonas palustris is a PNSB (purple non-sulphur bacterium). This is not made clear in the list above.
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Old 07-20-2012, 06:23 PM   #8
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I'm wondering what made you use the term 'bacteria/archaea'. I'm the only one I know of to use the combination this way,

Just curious..
because bacteria are dna organisms and archaea are rna organisms ( precursor to dna)?

microbeman, i'd really like someone who knows their stuff (unlike my noob self) to post a little about archaea. from what i've gleaned the archaea are wonderful additions to many microherds. they are even anaerobic.

some of the hardiest, most beneficial, prolific , ancient life forms on earth and not much posted on their usefulness. i use an archaea dominated mircoherd and they can reduce a rootball to humus in quick order. they are supposedly the best at chelating trace minerals making the supplements actually available to the plant. i use this culture to clean cigar smoke off my windshield (only cleaner i've found that works). they are used to clean up all types of toxic waste sites including oil spills.

i've had fungus and mold form on the top of growing mediums after adding molasses to water/feed my microherd. i spray a light mist of my archaea dominated culture on the fungus/mold and it is gone (eaten) in short order (one or two days max.). i have used the same culture with baking soda to thoroughly destroy and prevent powdery mildew infestations on budding plants without ruining the product and without having to shut down and sterilize and start from scratch a new garden.

just because organic supplements are added to a growing medium does not mean those supplements are available to the plant for nutrient uptake. little has been posted about the efficacy of chelating various organic supplements but if they aren't fixed they can actually do more harm than good.

biozome and sea-crop are two great sources of dormant archaea. it takes a month for them to be induced out of their hibernation state. once awakened one archaea multiplies into 20,000 archaea within one 24 hour period. these creatures are what i term tyrannosaurus rex/billy goat hybrids in respect to their ferocious ability to make organic supplements actually available to the plants nutrition uptake.

thks., idiit.
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Old 07-20-2012, 09:49 PM   #9
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I've posted previously on archaea so you might find something with a search.

Because they are visually identical (virtually) to bacteria the ubiquitousness [sic] of them has gone unnoticed for years.

Recent research has revealed that they are very common in soil and compost. I'm quite certain that they multiply along with bacteria in ACT. Just like bacteria they nitrify and I hypothesize they are a key player in mineralization (including predation) of plant nutrients.

Just like bacteria there are aerobic, anaerobic and facultative respirators.

http://www.sciencedaily.com/releases...0817103131.htm

http://www.innovations-report.com/ht...ort-69385.html
My hero Vigdis Torsvik forsaw this in the 80s (she is the true originator of direct microscopy microbe counts; [and the microbial nutrient loop])

http://www.ucmp.berkeley.edu/archaea/archaea.html

The use of archaea gathered from harsh environments is interesting but hardly seems necessary to me as probably the more useful ones are living in your back yard.

Like bacteria they multiply every 20 minutes so one can turn into way more than 20,000 in 24 hours. There are 1440 minutes in 24 hours or 72 twenty minute intervals. Consider that the first 20 minute interval only produces 2. The next 2x2=4; then 4x4=16;
then 16x16=256; then 256x256=65,536 This is in only 80 minutes.

This is why a decent ACT maker works so well. (And why it used to pay to open a savings account for a child)
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Old 07-20-2012, 10:02 PM   #10
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just because organic supplements are added to a growing medium does not mean those supplements are available to the plant for nutrient uptake. little has been posted about the efficacy of chelating various organic supplements but if they aren't fixed they can actually do more harm than good.
The amount of nutrients provided to plants in natural growing by 'nutrient fixing' is relatively minor compared to the active mineralization of nutrients via the predation of bacteria/archaea by protozoa, nematodes, rotifers...

Properly made compost or vermicompost cannot be over applied so long as there is drainage (pumice, perlite, sand, etc)
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Old 07-20-2012, 10:59 PM   #11
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If you proceed it is probably a good idea to research from more than one source of information for each species or group before posting. This would have revealed the information about Actinobacteria and Streptomyces being of that group.

Just so everyone is aware Rhodopseudomonas palustris is a PNSB (purple non-sulphur bacterium). This is not made clear in the list above.
You are a fountain of knowledge, Microbe. I'll edit the the list to include the mistakes you have pointed out to me.

here's is something neat I found... Some types of Actinobacteria are responsible for the peculiar odor emanating from the soil after rain (Petrichor), mainly in warmer climates. The chemical that produces this odour is known as Geosmin. http://en.wikipedia.org/wiki/Actinobacteria
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Old 07-20-2012, 11:52 PM   #12
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thks. also mm. i read the links provided.

Quote:
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Archaea are divided into four recognized phyla, but many more phyla may exist. Of these groups, the Crenarchaeota and the Euryarchaeota are the most intensively studied. Classification is still difficult, because the vast majority have never been studied in the laboratory and have only been detected by analysis of their nucleic acids in samples from the environment.
Quote:
Enzymes from these thermophilic archaea also tend to be very stable in organic solvents, allowing their use in environmentally friendly processes in green chemistry that synthesize organic compounds
^http://www.sidepad.com/Archaea

Quote:
Quote:
Methanogens are usually coccoid (spherical) or bacilli (rod shaped). There are over 50 described species of methanogens, which do not form a monophyletic group, although all methanogens belong to Archaea.
Quote:
Methanogens are key agents of remineralization of organic carbon in continental margin sediments and other aquatic sediments with high rates of sedimentation and high sediment organic matter
^https://en.wikipedia.org/wiki/Methanogen

Quote:
Methanogenesis or biomethanation is the formation of methane by microbes known as methanogens. Organisms capable of producing methane have been identified only from the domain Archaea. Methanogenesis is the final step in the decay of organic matter.




again i'm a noob just wanting to get up to speed. it appears from what i've read that there are untold varieties of archaea (over 50 subspecies of just the methanogens category under the archaea umbrella) just like there are untold varieties of bacteria.

the type of extreme archaea that are found in sea water and the type found deep in volcanic vents are different than archaea found in or near the earth's crust. these thermophilic archaea are what needs to be re-indroduced to our growing mediums per what my limited capabilities can glean.

the fixing capacity of the different archaea subspecies appears to widely vary among different archaea subspecies.

the brix test measures total solids including sugar but does not to my knowledge isolate out the amount of trace mineral content found in the end product being farmed.

the trace minerals are essential to plant and animal health. pestilence is a big problem in my outdoor grows and i'm trying to make sure that my plants are nutritionally healthy as a pestilence preventive measure. i'm not seeing many trace mineral percentages being published by organic farmers yet it is accepted by the scientific community that the best way to get trace minerals into our system is by eating foods high in trace minerals thereby making us healthier and less susceptible to diseases, the same goes for the plants until we get product tested for trace minerals specifically we don't know if the trace minerals are available for uptake by the plants. this is where the whole efficacy of different micro organisms specifically the efficacy of certain archaea subspecies is what i'm addressing.
posted on the link on archaea post you provided by mistake
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Old 07-21-2012, 04:56 AM   #13
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The amount of nutrients provided to plants in natural growing by 'nutrient fixing' is relatively minor compared to the active mineralization of nutrients via the predation of bacteria/archaea by protozoa, nematodes, rotifers...
etc)
MM, I have read a study recently that said pretty much the opposite. I wish I could remember where. If I remember or find it again I'll post it. But in a nutshell the soil was analyzed and weighed and the plant was analyzed and the study showed a high percentage of the plant came from the air rather than the soil. I know it was surprising to me. I have heard of nitrogen fixing but I never thought it amounted to much. Now I'm as confused as ever, lol.

If it's not a bother could you point me in the right direction with sites? Thanks. Scrappy
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Old 07-21-2012, 06:47 AM   #14
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Scrappy' What do you mean 'air'? This has nothing to do with n utrient fixing bacteria. All the nutrients from microbes are related to soil.
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Old 07-21-2012, 06:50 AM   #15
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PS. The people cited on my page will lead you to lots of solid info or the two books I listed on this forum the other day.
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