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)