Microflora of Soil


Soil as the superficial land layer is the habitat of large amounts of plant and animal species as well as myriads of microorganisms organized into complex microbial communities.

All kinds of microbial representatives have the place of dwelling in the soil – bacteria, fungi, viruses, or protozoans.

  • The greatest amount of microbial cells is present at 10-30 cm of soil depth. Here the number of microorganisms per 1 g of soil (soil microbial counts) is usually in the range from 5-10*106 to 1*109 depending mainly on the soil type.
  • Cultivated soil contains much more microorganisms (up to 5*109 cells per gram) than the soil of fallow lands. In the soil area around plant roots known as rhizosphere the total number of microbes is closer to 10 billion per gram. As the result, it has been estimated that the ploughed land harbors more than 5 tons of microbial mass per 1 hectare.
  • Chernozem or black soil contains billions of microbial bodies per 1 gram, peaty and forest soils are also rich of microbial cells whereas clayey podsols and loose sands harbor significantly less amounts of microbes.
  • Overall, soil microbial counts strongly depend on soil structure, water contents, available nutrients, levels of aeration, and intensity of pollution with animal or human wastes.
  • Moving to the soil depth, the total number of microbes declines sharply. Only sporadic microbes are found at 2-4 meters deep. But in underground water, oil wells, or coal accumulations single microbes can be detected at depth of tens meters.

Soil bacteria

Microflora of Soil
Soil Microorganisms
  • It pertains to numerous bacterial orders – Actinomycetales, Pseudomonadales, Nitrosomonadales, Enterobacteriales, Rhizobiales, Bacillales, Clostridiales. The members of the latter two orders produce spores that stay in the soil for decades.
  • Photosynthetic microbial of phylum Cyanobacteria and moderate amounts of microscopical algae can be determined in the soil as well.
  • Besides bacterial agents, numerous fungi (more than 100 species) are found in soil as the resident habitants.

Soil protozoans

  • It comprises amoebas and the number of flagellated representatives inhabiting the outmost layers of soil with sufficient aeration and humidity.

Viral agents

  • A plethora of viral agents is also present in soil following their natural hosts – plant and animal cells, bacteria, fungi and protozoans.
  • They maintain the balance among the diverse microbial communities limiting their uncontrolled propagation.
  • On the other hand, viruses (e.g., bacteriophages) create the conditions for exchange of genetic material supporting lateral gene transfer between soil-dwelling microbial species.

Resident microflora plays a tremendous role in soil metabolism and maintenance of soil fertility.

Soil autotrophs (cyanobacteria, nitrosomonads, nitrobacter, chlorobium) produce organic matter from carbon dioxide. And vice versa, heterotrophic bacteria (e.g., actinomycetes, pseudomonads, bacilli) and fungi intensively decompose the remnants of plant and animal cells. They utilize lignin, cellulose, pectin and other biopolymers. All these microorganisms participate in humus formation thereby enhancing substantially the fertility of soil and fostering soil self-clearing.

The activity of anaerobic bacteria (e.g., clostridia) results in putrefaction of degrading organic substances.

In the same vein, soil microorganisms are totally implicated into the global biogeochemical cycling of essential elements such us nitrogen, carbon, sulfur or iron.

For instance, a lot of microbial agents (e.g., pseudomonads and bacilli) participate in ammonification of amino acids resulting in ammonia production; other bacteria (e.g., Nitrosomonas and Nitrobacter species) catalyze nitrification of ammonia into nitrates.

Furthermore, multiple bacterial genera present in soil (agrobacteria, flavobacteria, pseudomonads, bacilli, vibrios and others) perform denitrification, converting nitrates into gaseous nitrogen.

And finally, certain soil bacteria are capable of direct nitrogen fixation converting molecular nitrogen into ammonia. The members from Rhizobium genus exert nitrogen fixation in symbiosis with various leguminous plant species, whereas clostridia and azotobacter don’t need symbiotic support for the reaction. This chemical transformation has a positive impact on soil fertility.

Some microbial agents, e.g., thiobacilli, convert sulfur into sulfates, and other bacteria reduce them into hydrogen sulfide.

At the same time, the soil serves as the reservoir that may hold numerous pathogenic microorganisms discharged from their animal or human hosts.

In the case of poor sanitation, the most common is faecal pollution of the soil. In these situations, the soil contains pathogenic enterobacteria (salmonellae, shigellae and others) spread by faecal-oral route of disease transmission. Likewise, the soil may harbor microorganisms transmitted with dust by air-borne route (e.g., M. tuberculosis) or by direct contact (e.g., the agent of tularemia).

The viability of pathogenic microbes in soil is greatly variable. In general, the soil is not the beneficial medium for non-sporeforming bacteria albeit they may stay long there in special conditions.

As an example, mid survival time for Salmonella enterica var. Typhi is about 2-3 weeks, but its maximal survival period is near 12 months. Similarly, for shigellae these periods are 1-5 weeks and 9 months, for Vibrio cholerae – 1-2 weeks and 4 months, for M. tuberculosis – 13 weeks and 7 months, for brucellae – 0.5-3 weeks and 2 months.

By contrast, the spores of soil-dwelling bacilli and clostridiae can survive in the soil indefinitely long, at least for several decades. Thus, the contamination of tissues with soil can lead to severe wound clostridial infections like tetanus or gas gangrene, as well as it predisposes to anthrax in case of presence of B. anthracis spores.

As the soil is the natural habitat for many types of pathogenic fungi and actinomycetes, this maintains conditions for the development of actinomycosis and certain fungal infections (e.g., aspergillosis or various systemic mycoses).

In the same vein, the soil is an important part in the transmission of protozoan infections (e.g. leishmaniasis) and helminthic invasions (ascaridosis, toxocariasis, taeniasis, ancylostomiasis and many others).

Taking into account the substantial impact of soil on the communicability of human infections, the continuous monitoring of soil sanitary state is maintained with special emphasis on the control of enteric infections transmitted by fecal-oral route.

Biological contamination of soil is evaluated by assessment of the number of indicator bacteria and/or by direct determination of pathogenic bacteria in the soil.

Similar to water sanitary testing, indicator microorganisms of soil comprise total coliform bacteria (E. coli and other members of Enterobacteriaceae family) and enterococci.

Total coliform bacteria are determined by titration method, membrane filtration method, and by direct inoculation of various dilutions of soil specimens into lactose-containing agar media (e.g., Endo agar).

Enterococci are determined by the same methods but with special media for their culture.

Further assessment of soil sanitary conditions includes quantification of coliphages, enteroviruses, and spores of С. perfringens.

Finally, for direct determination of microbial pathogenic species in the soil the members of Salmonella and Shigella genera are detected. In this case, the soil specimens are inoculated into the selective media for their culture. After primary isolation, the bacteria are further identified by the number of serological, biochemical and molecular genetic tests.

As the result, the soil is regarded as clean without sanitary limitations if the total number of coliform bacteria is less than 10 cells per 1 g of soil specimen, and pathogenic Salmonella and Shigella species, as well as enterococci and enteroviruses, are not determined.

The excessive amounts of coliform bacteria (10 and more per 1 g of soil), the presence of enterococci and/or enteric pathogenic bacteria indicate fresh fecal pollution of soil and elevated risk of enteric infections.

Additional testing of soil microbial load includes the determination of soil microbial counts. It is equal to the total number of microorganisms present in 1 g of soil capable of forming colonies after the incubation at 28-30oC for 72 h.

The number of actinomycetes and fungi per 1 g of soil can be determined as well.

As all of these parameters are highly variable, the obtained results should be compared with the data characteristic for “clean soil” samples.


  1. https://www.sciencedirect.com/science/article/abs/pii/0740002086900146
  2. https://link.springer.com/protocol/10.1007/978-1-4939-9861-6_33