Soil as microbial habitat

1. MICROBIAL ECOLOGY

2. Organization of Ecosystems
Biosphere – thick envelope of life that surrounds the earth’s surface
• Made up of:
• hydrosphere (water)
• lithosphere (soil)
• atmosphere (air)
• Maintains and creates the conditions of temperature, light, gases,
moisture, and minerals required for life processes
• Biomes- particular climatic regions
• Terrestrial biomes- grassland, tropical rainforest, temperate and tundra.
• Aquatic biomes- freshwater biomes and marine biomes.

3. • Communities – the association of organisms that live together and
that exhibit well-defined nutritional or behavioral interrelationships
• Population – organisms of the same species within a community
• Habitat – the physical location in the environment to which an
organism has adapted
• Niche – overall role that a species, or population, serves in a
community; nutritional intake, position in the community, and rate of
population growth

4. Ecology (oicos – house, hold, logos - doctrine) - science about legitimacies of creation and
functioning of biological systems and their mutual relation with an environment.
The microecology is the science about places of invading of microorganisms and their
ecological links.
At learning a microbial ecology use the same concepts, as well as in a common ecology.
Main of them are the following: population - an elementary evolutional unit (structure) of
a definite species;
biotope - site, habitation of a population, for parasites - place of their localization in an
organism;
microbiocenosis - microbial assemblage, association, that is collection of populations of
different species of microorganisms, which dwell(live) in the defined biotope (for example,
in an oral cavity, reservoir);
Ecosystem - system, in which enters a biotope and microbiocenosis

5. • Is the study of numerous interrelationships between microorganisms
and the world around them;
how microbes interact with other microbes
how microbes interact with organisms other than microbes
and how microbes interact with the non-living world around them

6. From old times it is known, that the microorganisms are omnipresent that is
ubiquitous organisms.
Huge quantities of them meet in soil, water and air.
The environment of their habitation is plants, animal, man.
Everywhere bacteria are existed as microbiocenoses.
The modern microbial biocenoses were generated as a result of durable evolution.
Mutual relation (cohabitation) of different species of microbes among
themselves and with other forms of life are called symbiosis.

11. Types of symbioses
1. Neutralism - the populations, existing in one biotope do not stimulate and do not
oppress each other.
2. Mutualism - mutually advantageous cohabitation; one population synthesizes
materials (matter), which are the basis of power supply for another (for example,
legume bacteria and bean plants, aerobic and anaerobic bacteria in an organism of
the man).
3. Commensalism - such form of symbiosis, at which one of jointly living
populations extracts for herself advantage(benefit), but does not put a harm of
other population. The commensalism is characteristic for many inhabitants of
human body.

12. Types of symbioses
4. Antagonism - oppression of one population another. The microbes –
antagonists produce antibiotics, bacteriocines, fatty acids, which cause
destruction of bacteria or delay their reproduction.
5. Parasitism - such kind of symbiosis, at which one population (parasite) brings
harm to the host, and for itself has a benefit. The causative agents of bacterial,
virus and fungi illnesses concern to microbes - parasites.
6. Synergism- the interaction or cooperation of two or more organizations, substances,
or other agents to produce a combined effect greater than the sum of their separate
effects.

13. Soil is alive…
For example, in 1g of soil:
>100,000,000 bacterial cells
>11,000 species of bacteria
Also fungi and larger animals

14. Microflora of the soil
The soil is the major environment for a habitation of microorganisms.
The first bacteria, as well as all alive ones, have appeared in water. However in more later geological
periods, when on a surface of globe the soil was derived, it became main habitation of microorganisms and
main arena of their vital activity.
The amount of bacteria in one gram of soil can be very great - from 200 millions up to 10 billions.
Manured and ploughing ground are stocked with microorganisms most densely.
The soil of woods, moor, the sands of desert contain few microbes.
The most surface sphere of soil (crust by width of 2-3 mm) is very poor by microorganisms. A desiccation
and the solar rays perniciously influence them.
The ground mass of bacteria is on depth 10-20 cm.

15. The microflora of soil includes hundreds of species of bacteria, viruses, protozoa, actinomyces and
fungi.
It is various species of putrefactiving, nitrifying, denitrifying, nitrogen-fixing bacteria.
The most often inhabitants of soil are the representatives of genus Azotobacter, Nocardia, and
Clostridium.
Many bacteria of genus Rhisobium, Nitrosomonas, Nitrosospira, Nitrobacter, Pseudomonas are very
often found.
Almost always there are denitrifying bacteria (B.denitrificans), ammonifying microbes (Urobacillus
pasteurii, Urobacillus leybii), numerous iron bacteria and sulphur-bacteria.
All of them play the great role in a turnover of materials in a nature, improve productivity of our fields,
provide life on the Earth.
The microorganisms of soil take an active part in all processes of transformation of materials and energy:
synthesis of a biomass, biological nitrogen fixation, fermentation, denitrification of the cycle sulfur,
iron lactas, phosphorum, carboneum and other elements.

16. SOILS AS AN ENVIRONMENT FOR MICROORGANISMS
A soil scientist would describe soil as weathered rock combined with organic matter and
nutrients.
An agronomist would point out that soil supports plant life.
However, a microbial ecologist knows that the formation of organic matter and the growth
of plants depend on the microbial community within the soil.
Microbial activities can lead to the formation of minerals such as dolomite; microbial
activity also occurs in deep continental oil reservoirs, in stones, and even in rocky
outcrops. These microbes are dependent on energy sources from photosynthetic protists
and nutrients in rainfall and dust.

17. A typical soil habitat contains a mixture
of clay, silt, and sand along with soil
organic matter.
Roots, animals (e.g., nematodes and
mites), as well as chemoorganotrophic
bacteria consume oxygen, which is
rapidly replaced by diffusion within the
soil pores where the microbes live.
Soil Habitat

18. The Composition of the Lithosphere
• Soil is a dynamic, complex ecosystem with a vast array of microbes,
animals, and plants.
• Lichens – symbiotic associations between a fungus and a
cyanobacterium or green algae
• produce acid that releases minerals from rocks
• Humus – rich moist layer of soil containing plant and animal debris being
decomposed by microbes
• Rhizosphere – zone of soil around plant roots contains associated
bacteria, fungi and protozoa
• Mycorrhizae – symbiotic organs formed between fungi and certain plant
roots

19. What Are Microbes Doing For Plants?
• Providing nutrition
• Mycorrhiza – absorb water and nutrients
• Nitrogen fixation– rhizobacteria
• Decomposition of dead material into plant usable
• Store nutrients in their cells
• Preventing pathogens
• Bacteriocins and antibiotics
• Competition
• Molding the architecture of the soil
• Aeration
• Aggregates that enhance water retention

20. What does the plant do to encourage the microbiota?
• Secretes small molecules such as sugars and amino acids, peptides
• Far more life in the rhizosphere than away from it.
• A large part of the plants energy stores are secreted into the soil.
• Protection: allows some bacteria to live in plant cells.

21. Food sources of Soil Microbes

22. Bacteria
• -are more dominant group of microorganisms in the soil and equal to
one half of the microbial biomass in soil.
• Population 100,000 to several hundred millions for gram of soil -
Autochthonous - Zymogenous groups.
• Majority are Heterotrophs. (Common soil bacteria - Arthrobacter,
Bacillus, Clostridium, Micrococcus).

23. Plant Growth Enhancing by Bacteria
• Certain strains of the soil bacteria Pseudomonas fluorescens have anti-fungal
activity that inhibits some plant pathogens.
• P. fluorescens and other Pseudomonas and Xanthomonas species can increase plant
growth in several ways.
• They may produce a compound that inhibits the growth of pathogens or reduces
invasion of the plant by a pathogen. They may also produce compounds (growth
factors) that directly increase plant growth.
• In the future, farmers may be able to inoculate seeds with anti-fungal bacteria, such
as P. fluorescens, to ensure that the bacteria reduce pathogens around the seed and
root of the crop.

24. • - intermediate group between bacteria and fungi. Numerous and widely
distributed in soil.
• Abundance is next to bacteria. 104 - 108/g soil.
• 70% of soil actinomycetes are Streptomyces.
• Many of them are known to produce antibiotics. (e.g. S. antibioticus)
• Population increases with depth of soil.

25. Characteristics of Actinomycetes
• Similarities to bacteria
– Prokaryotic
– sensitive to anti-bacterials
– resemble bacteria in size, shape and gram-staining properties.
• Similarities to fungi
– shape and branching properties, spore formation
– Reproduction mechanism

26. Actinomycetes, such as this Streptomyces, give soil its
"earthy" smell.

27. Fungi
• More numerous in surface layers of well-aerated and cultivated soils-dominant in
acid soils.
• Common genera in soil are Aspergillus, Mucor, Penicillium Trichoderma, Alternaria,
Rhizopus.
• Algae – found in most of the soils in number ranges from 100 to 10,000 per g
• Decomposers – saprophytic fungi – convert dead organic material into fungal
biomass, carbon dioxide (CO2), and small molecules, such as organic acids. Like
bacteria, fungi are important for immobilizing, or retaining, nutrients in the soil.
• In addition, many of the secondary metabolites of fungi are organic acids, so they
help increase the accumulation of humic-acid rich organic matter that is resistant to
degradation and may stay in the soil for hundreds of years.

28. • Mutualists – the mycorrhizal fungi – colonize plant roots. In exchange for carbon from
the plant, mycorrhizal fungi help solubilize phosphorus and bring soil nutrients
(phosphorus, nitrogen, micronutrients, and perhaps water) to the plant.
• Pathogens or parasites, cause reduced production or death when they colonize roots
and other organisms. Root-pathogenic fungi, such as Verticillium, Pythium, and
Rhizoctonia, cause major economic losses in agriculture each year.
• Many fungi help control diseases. For example, nematode-trapping fungi that
parasitize disease-causing nematodes, and fungi that feed on insects may be useful as
biocontrol agents.

29. Fungi
• abundant after bacteria
• food sources for other organisms
• beneficial symbiotic relationships with plants or other organisms
• reduce crop residues
• biochemically process nutrients to improve the soil
Factors effecting growth of fungi
• quality as well as quantity of organic matter in the soil has a direct correlation to the
growth of fungi
• Fungi are abundant in acidic areas compared to bacteria
• Fungi also grows well in dry, arid soils (aerobic, or dependent on oxygen)

30. Algae
• Algae can make its own nutrients through a process known as photosynthesis
• distributed evenly wherever sunlight and moderate moisture is available
– do not have to be on the soil surface or directly exposed to sun rays
– can live below the soil surface as long as the algae has uniform temperature and
moisture conditions.
• Possess the character of symbiotic nitrogen fixation in association with other organisms
like fungi, mosses, and liverworts
• Association fix nitrogen symbiotically in rice fields.
• Plays important role in the maintenance of soil fertility especially in tropical soils.
• Add organic matter to soil when die and thus increase the amount of organic carbon in
soil

31. • Most of soil algae (especially BGA) act as cementing agent in binding soil particles and
thereby reduce/prevent soil erosion
• Mucilage secreted by the BGA is hygroscopic in nature and thus helps in increasing
water retention capacity of soil for longer time/period
• Soil algae through the process of photosynthesis liberate large quantity of oxygen in
the soil environment and thus facilitate the aeration in submerged soils or oxygenate
the soil environment
• Help in checking the loss of nitrates through leaching and drainage especially in un-
cropped soils
• They help in weathering of rocks and building up of soil structure

32. Soil Protozoa
• Unicellular – population ranges from 10,000 to 100,000 per g of soil.
• Most of the soil forms are flagellates, amoebae or ciliates.
• Derive their nutrition by devouring soil bacteria.
• Abundant in upper larger of the soil.
• They are regulating the biological equilibrium in soil.
• Ciliates –paramecia eat bacteria and each other
• Amoeba – feeds on bacteria and parmecia
• Release nitrogen from bacteria
• Protozoa can be split up into three categories: flagellates, amoebae, and
ciliates

33. Types of flagellates
• smallest members of the protozoa group, and can be divided
further based on whether
– Non chlorophyll-containing flagellates found mostly in soil and
flagellates that contain chlorophyll typically occur in aquatic
conditions.
– distinguished by their flagella

34. Amoeba
• larger than flagellates and move in a different way
• slug-like properties and pseudopodia
• does not have permanent appendages
Ciliates
• largest of the protozoa group
• move by means of short, numerous cilia

35. Importance of soil microorganisms
• Involved in nutrient transformation process
• Decomposition of resistant components of plant and animal tissue
• Role in microbial antagonism
• Participate in humus formation
• Predator to nematodes
• Surface blooming reduces erosion losses
• Improves soil structure
• Maintenance of biological equilibrium

36. Soil sample under microscope

37. Assignment (1 page each)
• Cold moist soil (Soils in cold environments; Arctic, Antarctic, or
alpine regions)
• Desert soil
• Geologically Heated Hyperthermal Soils (-found in such areas
as Iceland, the Kamchatka peninsula in eastern Russia,
Yellowstone National Park, and at many mining waste sites)
• State the Microorganisms found in each