Soil Biota

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    Soil BiotaSoil Biota

    Actinomycetes: Features Belong to the order Actinomycetales

    Single celled and produced slender, branched filamentswhich develop into a mycelium in all soil genera except for the

    genusActinomyces.

    Actinomycetes: Features Individual filaments or hyphae are similar to fungal filament

    but are less broad, usuallyy 0.5 to 1.0 mm in diameter.

    Produce single ,pairs or chains of asexaul spores known as

    conidia on the hyphae .

    Few of the soil inhabitants bear their spores in a specializedstructure known as asporangium

    Actinomycetes: Features Usually saprophytes

    Competitive advantage seems to be in dry soil, high pH,

    warm

    Temperatures and high organic matter environments.

    LikeBacillus tend to exist in spores.

    Have aerial mycelium

    Actinomycetes: Features Have extensive branching

    Growth in liquid culture merely results in turbidity.

    Common Actinomycetes in Soil 1. Streptomyces

    Long chains of spores formed on filaments growing above

    the medium

    Species very numerous in soil and many produce antibiotics.

    Streptomyces are G+ and are oxidative organotrophs.

    Common Actinomycetes in Soil They make up about 90% of the actinomycete isolations from soil.

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    They produce well developed compact branched mycelium and

    compact colonies on agar plates.

    Mycelium does not divide into segments but gives rise to conidia

    Reproduction is by production of aerial spores and by mycelial

    fragmentation.

    Common Actinomycetes in Soil Colonies on agar media tend to be tough and have a leathery

    consistency, and resist destruction by mechanical force.

    They are the causal organisms of of potato scab, S. scabies

    Many streptomyces produce antibiotics, variously

    antibacterial, antifungal, anti-algal or anti-tumor.

    Common Actinomycetes in Soil The also produce geosmin which is responsible for the smellof freshly plowed soil.

    Chitin hydrolysis is often frequently encountered among

    many species ofStreptomyces

    Common Actinomycetes in Soil 2. Nocardia

    Second most abundant, about 10 to 30%

    They are aerobic and gram-positive. Mesophilic actinomycetes

    Filaments unstable, fragmenting into bacteria-like units;

    filaments do not usually grow above medium and spores are rarely

    produced.

    Common Actinomycetes in Soil The colonies ofNocardia and true bacteria bear a marked

    resemblance to one another in general features and in consistency.

    Some species are well documented for the metabolism of

    paraffins, phenols, steriods and pyrimidines.

    Common Actinomycetes in Soil 3. Micromonospora

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    Third most frequently encountered, and forms less than 1-

    15% of actinomycetes growing on solid media.

    Filaments do not grow above medium; single spores

    produced in and on surface of medium

    Colonies are slow growing in most media

    Common Actinomycetes in Soil Each hyphae is between 0.3-0.8 mm in diameter, while the

    spores are oval to round and are produced at the terminus of the

    specialized conidiophores.

    Micromonospora strains decompose chitin, cellulose,

    glucoides and hemicelluloses

    Common Actinomycetes in Soil 4. Thermoactinomyces

    Very similar to micromonospora

    Single spores formed on filaments above and within medium.

    Spores resistant; all species thermophilic

    Very common in heating compost heaps

    Common Actinomycetes in Soil 5. Streptosporangium

    Spores formed in sporagia or in chains on the filament above

    the media

    Colony appearance similar to Streptomyces

    Activity and Function

    The develop far more leisurely than most fungi and bacteria. Not effective competitors and are not prominent when

    nutrient levels is high and the pressure of competition is great.

    Actinomycetes are heterotrophic feeders, and their presence

    is therefore conditioned by the availability of organic substrates.

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    Activity and Function Activity and Function Utilization of carbon sources include simple and highly complex

    organic molecules from organic acids,and sugars to polysaccharides

    proteins, lipids and aliphatic hydrocarbons.

    Cellulose is decomposed by many species in pure culture, but rate ofdecomposition is slow.

    Many strains have the capacity to synthesize toxic metabolites.

    Activity and Function

    They participate in a number of processes which include

    a. Decomposition of certain resistant components of plant and

    animal tissues. They are usually effective competitors only when

    resistant compounds remain

    b. Formation of humus through the conversion of plantremains and leaf litter into the types of compounds native to the soil

    organic fraction.

    Activity and Function c. Transformation at high temperature particularly in the rotting

    and heating of green manures, hay, compost piles, and animal

    manures.

    d. Cause of certain soil-borne disease of plants ; for example,

    potato scab and sweet potato pox, for which the causal agents are

    S.scabies and S. ipomoeae, respectively.

    Activity and Function e. Cause of infections of humans and animals ; for example,

    Nocardia asteroides andN otitidis-caviarum..

    f. Possible importance in microbial antagonism and in

    regulating the composition of the soil community.- This role may be a result of the ability of many actinomycetes to excrete

    antibiotics or their capacity to produce enzymes that are responsible for lysis of fungi and

    bacteria.

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    Bacteria: Features 1.One-celled organisms, whose genetic material are not enclosed in a

    special nuclear material. About 4-5 mm (0.004-0.005mm)

    2. Lack nuclear membrane and thus are termed prokaryotic.

    3. Nucleoplasms not separated from cytoplasm. 4. Cell walls composed principally of peptidoglycans.

    5. Reproduction of binary fission. 6. Genetic exchange accomplished by conjugation and transduction. 7. Appendages called flagella. Many swim by means of whiplike

    Conjugation involves large transfer of genetic materials between donor and

    recipient cells in mating. Transduction involves direct genetic exchange of DNA by virus attacking bacteria

    (bacteriophage).

    Groupings 1 Energy Source

    a.Light as energy source -phototrophic

    b. Chemicalas energy source-chemotrohic

    2. Carbon Sources.

    a. CO2 as C source- Lithotrophic (autothrophic) b. Organic substrate as C source- Organotrophic (hterrotropjic)

    Groupings Photolitotrophs - Higher plants, algae, cyanobacteria, green sulfur

    bacteria. (Photoautotroph).

    Chemoorganotrophs - Require preformed organic nutrients as their

    energy and carbon sources (Heterotrophs).

    Chemolithotrophs -Energy sources include NH4+, NO2-, Fe2+, S2-,

    S2O32-(Chemoautotrophs).

    Groupings Photolitotrophs - Higher plants, algae, cyanobacteria, green sulfur

    bacteria. (Photoautotroph).

    Chemoorganotrophs - Require preformed organic nutrients as their

    energy and carbon sources (Heterotrophs).

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    Chemolithotrophs -Energy sources include NH4+, NO2-, Fe2+, S2-,

    S2O32-(Chemoautotrophs).

    Groupings 3. Ecological Groupings

    i. Autochthonous (indegenous)- grow slowly in soils containingno easily oxidizable substrates. Humus degraders.

    Indeginous populations may have resistant stages and endure long

    periods without being active metabolically, but at some time these natives

    proliferate and participate in the biochemical functions of the community.

    Groupings ii. Zymogenous grow very fast on fresh residues in soil.

    Opportunists.

    a. K-Selected Species - Adapted to livng under conditions

    of bountiful supply of energy. b. R-Selected Species -Live in uncrowded but physically

    restrictive environments.

    iii. Invaders or Allochthonous- These do not participate in

    community.

    Groupings activities. They enter with precipitation, disesed tissues, animal

    manure , or sewage sludge, and they may persist for some time in a

    resting form. They never contribute significantly to the various ecological

    transformations and interaction. Not widely used now

    New terms are now Oligotrophy and Copiothropy respectively

    Groupings 4. Morphological

    a. Cocci- Usually round, but may also be oval, elongated or

    flattened on one side.

    b. Bacillus

    c. Spirillum- Have distinctive helical shape like a corkscrew, their

    cell bodies are fairly rigid.

    d. Pleomorpism -Have may shapes, not just one in a life- time

    Groupings 5. Aeration Status

    a. Aerobes -O2 required

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    b. Anaerobes -O2 not required

    c. Facultative -Grows in the presence or

    absence of O2.

    Groupings 6. Cell Wall Chracteristics

    Gram-Positive:

    Plasma membrane is surrounded but thick cell wall

    Cells have peptidoglycan and teichoic acids

    Gram negative:

    Have thinner cell wall which is surrounded by outer cell membrane.

    Has peptidoglycan but lack teichoic acids.

    Conventional Taxonomy and GC ratios Guanine + Cytosine content of DNA

    G +C/A+T + G + C x 100%

    GC ratio vary over wide range from 20 to 80 %

    Generating Phylogenetic Trees from RNA

    sequences 1. Pure Culture

    2. Amplify genes encoding 16S