Soil Biota

Reading Assignment Soil Microbiology: An exploratory Approach

Chapter 4, 5,6 & 7

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. 6.

Reproduction of binary fission. 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

Energy Source a. Light as energy source - phototrophic b. Chemical as 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). Chemolithotrophs -Energy sources include NH4+, NO2-, Fe2+, S2-, S2O32-(Chemoautotrophs).

Groupings

3. Ecological Groupings i. Autochthonous (indegenous)- grow slowly in soils containing no 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 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 ribosomal RNA from genomic DNA using PCR

3. Sequence PCR product 4. Analyze data by computer analysis

Steps In Biodiversity Analysis of Microbial Community

1. Extract DNA 2. Ribosomal DNA obtained by PCR 3. Run Gel 4. Sequence and compare clones

Importance of Soil Bacteria

1. Higher amount in soil than counted in plate. 2. Most important group in soil. 3. Contain members that grow rapidly. 4. Cannot readily degrade lignin.

5. Important in reduction of inorganic compounds. 6. Most important in the degradation of synthetic biodegradable compounds 7. Most soil bacteria are heterotrophs. Few are autotrophs.

Importance of Soil Bacteria

Common Soil Bacteria. 1. Arthrobacter 2. Bacillus 3. Pseudomonas 4. Agrobacterium 5. Alcaligens 6. Corynebacterium 7. Micrococcus 8. Staphylococcus 9. Xanthomonas 10. Mycobacterium 11. Sarcina

-lot of unusual shapes; K strategist. -spore formers; R-strategists -tend to degrade a lot of things; R-strategists

-K-strategist, non-sporeforming -Highly underestimated

Acid fast, less common and small

significance

Common Bacteria in Soils

1. Pseudomonas G- , straight or curves rods with polar flagellata. Aerobic except denitrifying groups Organotrophic (most), few lithotrophic Some are pathogenic

Attack a wide range of organic substrates including sugars, amino acids, alcohols, and synthetic pesticides. Many species produce pigments in media especially iron media. Yield 3-15 % of colonies on agar Involved in may soil transformations

Common Bacteria in Soils

2. Arthrobacter Members of this genus are the numerically predominant bacteria in the soil as determined by plate counts Account for 5-60% of plate counts Numerically predominate in soil ( as determined by plate count) 40% of the total plate count .

Characterized by pleomorphism and Gram variability Slender, gram negative (G-) rod in early stage of growth. Very short gram positive (G+) rods and coccoid at later stage of growth Slow growers and poor competitors in the early stages of residue decomposition; K-strategist.

Common Bacteria in Soils

3. Bacillus: 7-67% , About 5-20 of the total bacterial count as determined by plate counting. Numbers quite high, about 106 to 107 or more/gram soil Gram negative (G-) to Gram positive (G+) variable rods Most species are motile

Common Bacteria in Soils

Heat resistant endospores are placed and sporulation is not repressed by exposure to air. Most are vigorous organothrophs Metabolism is strictly respiratory, strictly fermentative or both. Some species are facultative litotrophs that use H2 as energy source in

Common Bacteria in Soils

the absence of carbon. B. polyxyxa fixes N2 B. thuringiensis is pathogenic to some insect larvae and is widely used as a biological control agent. B.anthacis highly virulent animal pathogen -causes anthrax

Common Bacteria in Soils

B macerans used for netting flax Temp tolerance ranges from 5-70oC Tolerance to acid ranges from pH 2-8 Salt tolerance is as high as 25% NaCl

Common Bacteria in Soils

4. Clostridium Sporogenic species Most species are strict anaerobes Few are microaerophilic Plate counts show 103 to 107 cells/g soil

Genus of economic importance; its species are used commercially for the production of alcohols and commercial solvents. Several species, C. butyricum and C. pasteurianum are known to fix N2. Genus is widely distributed in soils, marine, and freshwater sediments; manures, and animal intestinal tract.

Pathogenic forms in this genus include C..tetani and C. botulinum. Part 15 Bergey's manual

Common Bacteria in Soils

5. Xanthomonas Uses O2 as the only electron acceptor Nitrates are not reduced Xanthomonas species are pathogenic to plants.

Common Bacteria in Soils

6. Other Soil Bacteria a. Azotobacter -aerobic organotrophic capable of fixing N2 symbiotically. b. Agrobacterium- Induces galls or other hypertrophies, such as hairy roots, on plants but does not fix N2.

Common Bacteria in Soils

c. Nitrobacter and Nitrosomonas are chemolititrophic general which cause nitrification in soil. NH4+ NO2NO2 NO3 d. Thiobacillus: sulfur compounds to SO42 S + 11/2O2 + H2O H2SO4