Soil Microbiology

1. Soil Microbiology ENVIRONMENTAL MICROBIOLOGY

2. WHAT IS SOIL? • Soils are excellent culture media for the growth of many kinds of microorganism

3. Who is at home in the soil? Soils are excellent culture media for the growth of many kinds of microorganism

4. Size of Soil Organisms Macro or large (>2 mm) Meso or mid-size (2–0.2 mm) Micro or small (<0.2mm) Mite Earthworm Yeast Bacteria Alfalfa root Springtail

5. A single teaspoon of soil contains over 1,000,000,000 bacteria, about120,000 fungi and 25,000 algae. Number Biomass1 Organism per gram soil (lbs per (~1 tsp) acre 6”) Earthworms – 100 – 1,500 Mites 1-10 5 – 150 Nematodes 10 – 100 10 – 150 Protozoa up to 100 thousand 20 – 200 Algae up to 100 thousand 10 – 500 Fungi up to 1 million 1,000 – 15,000 Actinomycetes up to 100 million 400 – 5,000 Bacteria up to 1 billion 400 – 5,000 1 Biomass is the weight of living organisms

6. Microorganism in 1 acre of average fertility soil would weight as a medium sized-dairy cow • Bacteria • Fungi • Actinomycetes • Algae • Protozoa MOO!

7. The world of microorganisms in soil

8. Bacteria • Bacterial population of the soil exceeds other groups of microorganisms in number and variety. • Plate count yields 1-10% of the total count (as compared to direct microscopic counts). • Dominant genera : Arthrobacter, Pseudomonas, Agrobacterium, Flavobacteriumand Bacillus. • Animal pathogens : Clostridium, Bacillus, Coxiellaand Streptococcus • Plant pathogens : Agrobacterium, Erwinia, Corynebacterium, Pseudomonas andXanthomonas. • Different physiological groups are also present.

9. Where are the microorganisms located in the soil? • Usually the top 2-3 cms. • Commonly found close to root surfaces, in dead roots, on soil particles or amongst aggregates of soil particles. • Soils that are clayey have many bacteria because these soils have lot of small pores. • Sandy soil is less suitable habitat.

10. Infertile Soil Fertile Soil Sandy Soil Clay Soil

12. Soil factors that affect microorganism growth Spherical Bacteria • Organic matter • Aeration (oxygen) • Moisture and temperature • Soil fertility and pH

13. Rod-Shaped Bacteria

14. Organic matter in the soil • Organic matter = anything that contains carbon compounds that were formed by living organisms. • Dead forms of organic material - mostly dead plant parts (85%) • Living parts of plants - mostly roots (10%) • Living microbes and soil animals • Partly decayed organic matter is called humus Components of Soil Organic Matter

16. Microbial degradation or organic matter • Involves complex processes. Chemical alteration of organic matter, physical fragmentation and release of mineral nutrients. • The dead organic matter is colonized by microbes and degraded with help of microbial enzymes. • Macromolecules are broken down into simpler units and further degraded into constituent elements.

17. Organic matter decompositionEveryone is involved • Bacteria • Population increases rapidly when organic matter is added to soil • Quickly degrade simple compounds - sugars, proteins, amino acids • Have a harder time degrading cellulose, lignin, starch • Cannot get at easily degradable molecules that are protected Bacteria on fungal strands Spiral bacteria Rod bacteria

18. Effect of soil temperature • Microorganisms have been found growing in virtually all environments where there is liquid water, regardless of its temperature. • Microorganisms are found growing at the sub zero temperatures of Antarctic soil to temperatures as high as 115oC in deep sea hydrothermal vents.

19. General response of microorganisms to temperature and pH.

20. SOIL MOISTURE CONTENT • Availability of water (aw - known as water activity) is a critical factor that affects the growth of all cells. • aw pure water = 1 • range of m.o. = aw 1 to 0.7. • aw agricultural soils : 0.9 to 1.

21. Limiting aw for growth of certain procaryotes.

22. Soil pH • The pH or hydrogen ion concentration of natural environments varies from about 0.5 in the most acidic soils to about 10.5 in the most alkaline lakes. • Most free living prokaryotes can grow over a range of pH. • Depending on pH preferences microorganisms are classified into • acidophiles, neutrophiles and alkaliphiles.

24. Sources of N • Lightning • Inorganic fertilizers • Nitrogen Fixation • Animal Residues • Crop residues • Organic fertilizers

25. Forms of Nitrogen • Urea  CO(NH2)2 • Ammonia  NH3 (gaseous) • Ammonium  NH4 • Nitrate  NO3 • Nitrite  NO2 • Atmospheric Dinitrogen N2 • Organic N

26. Roles of Nitrogen • Plants and bacteria use nitrogen in the form of NH4+ or NO3- • It serves as an electron acceptor in anaerobic environment • Nitrogen is often the most limiting nutrient in soil and water. Nitrogen is a key element for • amino acids • nucleic acids (purine, pyrimidine) • cell wall components of bacteria (NAM).

27. NITROGEN CYCLE • AMMONIFICATION • NITRIFICATION • DENITRIFICATION • NITROGEN FIXATION

28. Nitrogen in the air nitrogen fixing plant eg pea, clover animal protein plant made protein dead plants & animals urine & faeces denitrifying bacteria root nodules (containing nitrogen fixing bacteria) decomposition by bacteria & fungi nitrates absorbed nitrates ammonia bacteria nitrites bacteria (nitrifying bacteria) www.worldofteaching.com

29. N2 N2O NH4 NO2 R-NH2 NO NO2 NO3

30. Ammonification or Mineralization N2 N2O NH4 NO2 R-NH2 NO NO2 NO3

31. Mineralization or Ammonification • Decomposers: earthworms, termites, slugs, snails, bacteria, and fungi • Uses extracellular enzymes  initiate degradation of plant polymers • Microorganisms uses: • Proteases, lysozymes, nucleases to degrade nitrogen containing molecules

32. Plants die or bacterial cells lyse  release of organic nitrogen • Organic nitrogen is converted to inorganic nitrogen (NH3) • When pH<7.5, converted rapidly to NH4 • Example: Urea NH3 + 2 CO2

33. Nitrification N2 N2O NH4 NO2 R-NH2 NO NO2 NO3

34. Nitrification Two step reactions that occur together : • 1rst step catalyzed by Nitrosomonas 2 NH4+ + 3 O2 2 NO2- +2 H2O+ 4 H+ • 2nd step catalyzed by Nitrobacter • 2 NO2- + O2  2 NO3-

35. Optimal pH is between 6.6-8.0 • If pH < 6.0  rate is slowed • If pH < 4.5  reaction is inhibited

36. Denitrification N2 N2O NH4 NO2 R-NH2 NO NO2 NO3

37. Denitrification • Removes a limiting nutrient from the environment • 4NO3- + C6H12O6 2N2 + 6 H20 • Inhibited by O2 • Not inhibited by ammonia • Microbial reaction • Nitrate is the terminal electron acceptor

38. Nitrogen Fixation N2 N2O NH4 NO2 R-NH2 NO NO2 NO3

39. Nitrogen Fixation • Energy intensive process : • N2 + 8H+ + 8e- + 16 ATP = 2NH3 + H2 + 16ADP + 16 Pi • Performed only by selected bacteria and actinomycetes • Performed in nitrogen fixing crops (ex: soybeans)

40. Azobacter Beijerinckia Azospirillum Clostridium Cyanobacteria Require the enzyme nitrogenase Inhibited by oxygen Inhibited by ammonia (end product) Microorganisms fixing

41. The nitrogen fixing bacteria are found inlumps on the roots called root nodules. The bacteria and the plant have a symbiotic relationship: the bacteria benefits by having food and shelter from the plant and the plant benefits by having nitrates produced by the bacteria. Roots of a legume plant (peas, beans and clover). www.worldofteaching.com