Soil Biota and Organic Residue Decomposition Methods

Description about Soil Biota and organic residue decomposition methods

1. What is Soil ?????? “A dynamic natural body on the surface of the earth in which plants grow, composed of mineral and organic matter and living organisms .” - Buckman & Brady “Soil is a mixture of organic matter , minerals, gases, liquids, and organisms that together support life .” - Joffe and Marbut

2. Composition of Soil The basic components of soil are minerals, organic matter, water and air. The typical soil consists of approximately 45% mineral, 5% organic matter , 20-30% water, and 20-30% air. These percentages are only generalizations at best. In reality, the soil is very complex and dynamic.

3. Out of 5% Organic Matter : Humus – 80% Roots - 10% Organisms- 10%

4. Soil Biota Soil biota is a collective term that encompasses all organisms that spend a significant portion of their life cycle within a soil profile , or at the soil-litter interface. It is also known as edaphon or soil life . They constitute soil food webs and contribute to nutrient cycling, which is important for plants.

5. Classification of Soil Biota Soil Biota / Soil Organism Flora Fauna Macro flora Micro flora Macro fauna Micro fauna

6. Macro flora Micro flora Macro fauna Roots of Higher Plants Bacteria Actinomycetes Fungi & Algae Moles Ants Earthworms Micro fauna Protozoa Nematodes

7. Microflora Why important ? Most crucial life forms in soils They generate their energy by breaking down complex organic tissue , thereby freeing vital nutrients for other plants. Without these critters, these nutrients could be locked up indefinitely in complex organic compounds.

8. Bacteria

9. BACTERIA Single celled organisms Greater number of organisms present than all others combined Two categories : a) Heterotrophic & b) Autotrophic bacteria Heterotrophic - a. derive energy by consuming complex organic debris ( leaves,roots,plants or animal tissue) b.releases ammonium for plants Autotrophic – a. oxidize inorganic materials ( sulfer , iron, carbon, ammonia) b. releases nitrate and nitrite c. producing complex organic nutritive compounds from simple organic sources by photosynthesis

10. Examples : Chromatrum Chlorobium Rhodopseudomonas Nitrobacter Nitrosomonas Thiobacillus Bacillus Pseudomonas

11. Functions / Role of Bacteria in Soil: Bacteria bring about a number of changes and biochemical transformations in the soil and thereby directly or indirectly help in the nutrition of higher plants growing in the soil. The important transformations and processes in which soil bacteria play vital role are: decomposition of cellulose and other carbohydrates, ammonification (proteins ammonia), nitrification (ammonia-nitrites-nitrates), denitrification (release of free elemental nitrogen), biological fixation of atmospheric nitrogen (symbiotic and non-symbiotic) oxidation and reduction of sulphur and iron compounds. All these processes play a significant role in plant nutrition.

12. Geosmin Ray Fungi

13. Actinomycetes Single-celled organisms slightly larger than bacteria (fine, thread-like) Decompose complex organic materials in later stages in conversion to humus. Capable of producing antibiotics Also known as Ray Fungi. Examples : Streptomyces

14. FUNCTIONS OF ACTINOMYCETES IN SOIL

15. 1. Degrade/decompose all sorts of organic substances like cellulose, polysaccharides, protein fats, organic-acids etc. 2. Organic residues / substances added soil are first attacked by bacteria and fungi and later by actinomycetes , because they are slow in activity and growth than bacteria and fungi. 3. They decompose / degrade the more resistant and indecomposable organic substance /matter and produce a number of dark black to brown pigments which contribute to the dark colour of soil humus. 4. They are responsible for earthy / musty odour / smell of freshly ploughed soils. 5. Many genera species and strains ( eg. Streptomyces if actinomycetes produce/ synthesize number of antibiotics like Streptomycin, Terramycin , Aureomycin etc.

16. Fungi Heterotrophic organisms capable of decomposing highly-resistant and complex organic compounds . Dominant flora when pH is less than 5 Examples: Aspergillus, Penicillium, Yeast, Moulds etc. also… mycorrhizae fungus ( Both ecto and endo mycorrhizae)

17. FUNCTIONS OF FUNGUS IN SOIL

18. 1. They plays important role in the degradation / decomposition of cellulose, hemi cellulose, starch, pectin, lignin in the organic matter added to the soil. 2. Lignin which is resistant to decomposition by bacteria is mainly decomposed by fungi. 3. They also plays important role in soil aggregation and in the formation of humus. 4. Some soil fungi are parasitic and causes number of plant diseases such as wilts, root rots, damping-off and seedling blights eg. Pythium, Phyiophlhora , Fusarium, Verticillium etc. 5. Number of soil fungi forms mycorrhizal association with the roots of higher plants ( symbiotic association of a fungus with the roots of a higher plant) and helps in mobilization of soil phosphorus and nitrogen eg. Glomus, Gigaspora , Aculospora , (Endomycorrhiza) and Amanita, Boletus, Entoloma , Lactarius (Ectomycorrhiza).

19. Algae Simplest green plant (needs sun and water) Blue-Green Algae most common Aids in adding organic matter Example: Anabaena, Nostoc etc.

20. Whereas microflora are affected by the ambient temperature and moisture, MACROFLORA tend to form in response to climate, parent material, and slope conditions.....

21. Macroflora Grasses Shrubs Trees Roots of plants

22. Functions: Produce an array of complex organic materials (leaves, roots, stems, bark, wood, seeds) —affect soil chemistry, water retention, pH, organic matter, etc. Aid in rock weathering and soil formation Protect soil from erosion

23. Micro fauna Protozoa: Protozoa are single-celled animals that feed primarily on bacteria , but also eat other protozoa, soluble organic matter, and sometimes fungi. They are several times larger than bacteria - ranging from 1/5000 to 1/50 of an inch (5 to 500 µm) in diameter. They eat bacteria, protozoa release excess nitrogen that can then be used by plants and other members of the food web. Example: Amoebae

24. What Do Protozoa Do? Protozoa play an important role in mineralizing nutrients , making them available for use by plants and other soil organisms. Bacteria eaten by protozoa contain too much nitrogen for the amount of carbon protozoa need. Bacteria and other organisms rapidly take up most of the ammonium, but some is used by the plant. Another role that protozoa play is in regulating bacteria populations .

25. Nematodes: Microscopic, unsegmented, threadlike worms Omnivorous nematodes – feed on decaying organic matter, most common soil nematode Predaceous nematodes – prey on soil bacteria, fungi, algae, other nematodes Parasitic nematodes – infest plant roots,nearly all field, vegetable crops & trees are affected Examples: Meloidogyne, Heterodera , Rotylenchulus , Xiphinema

26. Characteristics & Functions: More complex than protozoa Dine on decomposing organic matter , living soil animals, living plant roots Destructive to crops

27. Macro fauna Moles Ants Earthworms Moles Ants Earthworms

28. Common Functions: Feed on animal/plant residues Burrowing and scooping of soil Aerate/stir the soil Increases water infiltration Improves root penetration Production of sticky materials which helps in soil aggregation

29. Scooping by Moles Burrowing by Ants Burrowing by Earthworms

30. Arthropods Mites Spiders Scorpions Millipeds & Centipeds Termites Mites Spiders Centipedes

31. Gastropods Slugs Snails Slugs Snails

32. Functions: Feed on decaying plant vegetation Aerate soil Can be pests feeding on living plant materials

33. Soil Viruses & Viroids Non living nucleic acids surrounded by protein coat. Difficult to detect Viroid – no protective coat w/ RNA Virus – protective coat w/ RNA or DNA

34. Microbial Consortium A microbial consortium is two or more microbial groups living symbiotically . Consortiums can be endosymbiotic or ectosymbiotic . The concept of consortium was first introduced by Johannes Reinke in 1872 . The term preceded to the term symbiosis that was introduced into biology some years later.

35. Example: The developed microbial consortium consists of five microbes viz., Bacillus polymixa , Pseudomonas flourescens , Trichoderma harzianum , Azotobacter chroococcum , and Bacillus mycoides , isolated from rhizosphere of citrus grown on smectite rich alkaline black clay soils .

36. Characteristics of microbes present in microbial consortia ? Microbes( for example Bacteria ) should be compatible to each other . They should not create obstruction for the growth of each other. Having more multiplication rate . Should not generate any toxic compounds in the soil.

37. Microbial Consortium

38. What is the difference between a consortium and a mixed culture? The main important word here is " association " (association without any harm) and these microbes conducted a common function more effectively and efficiently than on an individual population basis. Such associations may be termed microbial consortia. Consortium is function base, mixed culture is functionally independent .

39. Artificial Culturing of MC : Why ????? In agricultural eco-system, microorganisms have vital role in fixing/ solubilizing/mobilizing/nutrient recycling. These microorganisms occur in soils naturally, but their populations are often scanty . In order to increase the crop yield, the desired microbes from rhizosphere are isolated and artificially cultured in adequate count and mixed with suitable carriers or as they are in suitable combinations (Microbial consortium) by artificial culturing. These are known as biofertilizers or microbial inoculants.

40. Nutrient Recycling in Soil (Biofertilizers) They are broadly classified into three groups. 1. Nitrogen Fixing Microbes (NFM) 2. Phosphorus Solubilizing Microbes (PSM) and Phosphate Mobilizing Microbes (VAM) and 3. Potash Mobilizing Microbes ( Frateuria aurentia )

41. Nitrogen fixing microbes(Bacteria): Nitrogen-fixing bacteria, microorganisms capable of transforming atmospheric nitrogen into fixed nitrogen (inorganic compounds usable by plants). More than 90 percent of all nitrogen fixation is effected by these organisms, which thus play an important role in the nitrogen cycle. Three types: a. Free living (BGA/Cyanobacteria) b. Asymbiotic ( Azotobacter , Beijerinckia & Clostridium ) c. Symbiotic ( Rhizobium, Azo- & Brady rhizobium )

42. PSM & VAM(AM) Phosphate Solubilizing Microorganism : a) Bacillus polymixa b) Bacillus megaterium c) Pseudomonas striata d) Bacillus subtilis e) Aspergillus sp. f) Penicillum sp.

43. VAM(AM) An arbuscular mycorrhiza ( endomycorrhiza ) is a type of mycorrhiza in which the fungus (AM fungi or AMF) penetrates the cortical cells of the roots of a vascular plant. Two major structures : a) vesicle & b) arbuscle Vesicular arbuscular mycorrhizal fungi belong to class Zygomycetes . Example: a) Glomus aggregatum b) Glomus albidum c) Glomus ambisporum They act as P mobilizing microorganisms .

44. Potash Mobilizing Microbes ( Frateuria aurentia ) Zinc and Sulphur Solubilizing Bacteria ( Thiobacillus spp ) Manganese solubilizer ( Pencillium citrinum )

45. Organic Residues When organic waste , such as food and garden litter, is subject to biological treatment the remaining product can be referred to as organic residue . The organic residue should no longer be considered as a waste product, but rather as source that should be manufactured and utilized in the best possible way. So, organic waste that has been transformed into a new product after being subject to aerobic or anaerobic biological treatment such as biogas residues, compost and sewage & sludge, known as Organic Residues . Organic Wastes Biological Treatments Organic Residues

46. Use of organic residues in agriculture The use of organic residues is not novel. Historical records show that the ancient Greeks and Romans were familiar with the decay processes that occurred spontaneously in stacks of plant matter or animal wastes. Soil has been amended with compost made from garden waste for centuries, but in more recent years organic residues from source-separated household waste and wastewater treatment have gained more attention. All organic residues contain substantial amounts of organic material which, when added to the soil, will increase the humus content, increase the water holding capacity and improve soil structure. A good soil structure is important for root penetration, and for adequate drainage and aeration .In addition to organic material, organic residues contain several important plant nutrients such as N, P, K and Mg . Amendment with organic matter will also increase microbial activity in the soil, which in turn improves nutrient availability to the roots.

47. Components of Organic Residue

48. Organic residue nature and composition

49. Major Composition: Compound Range (%) 1. Cellulose 20-30 2. Hemicellulose 10-30 3. Lignins 10-30 4. Proteins 1-15 5. Fats & Waxes 1-8

50. Decomposition of various organic compounds Different organic residue(plants and animals) contain different groups of organic compounds. So different groups of compounds have their different ease of decomposition. General decomposition method: Lignin, fats, waxes, cellulose & Hemicellulose(very slowly decomposed) Crude protein, Simple proteins, sugars, starches etc.( rapidly decomposed) Increasing in decomposition

51. When we add fresh organic residue to soil….what happen ?????????? Three separate process occur simultaneously: Plant and animal tissue constituents disappear under the influence of microbial enzymes and appears new biological tissue, new microbial cells bringing about an increase in soil of proteins, polysaccharides & nucleic acids. Breakdown of so formed organic compounds by different group of microorganisms and release of different essential plant nutrients like N,P,S etc. into the soil or immobilization takes place by a series of specific reactions. Formation of resultant compounds to microbial action from the original organic residues and also due to microbial synthesis.

52. Organic residue cycle

53. Influence of applied fresh organic materials on the loss of Soil Organic Matter

54. Stages of Organic residue decomposition Stage 1 : Decomposition of easily degradable substances , partial conversion to CO2 and body tissue. Stage 2 : Cellulose and other carbohydrates utilized with further loss in weight. Formation of new body tissue part of previous biomass mineralized. Stage 3 : Further decrease in cellulose, initiation of lignin decomposition & further loss in weight of biomass. Stage 4 & Successive stages : Further cycling of plant residues . About one-third of the carbon will be at the end of growing season.

55. Enzymes involved : Urease : Breaks the urea in water and soils to CO2 & Ammonium ion. Protease : Breaks the protein into amino acids Cellulase : Breaks the cellulose into small chain of sugar units. Lignase : Degrades lignin compounds of decomposed materials. Hemicellulase : Breaks hemicellulose compounds or organic materials. Phosphatase : making phosphorus(P) available to plant. Sulphatase : making Sulphur(S) available to plant. PME : Pectic acid and methanol from Pectin. PG : Galacturonic acid from Pectin compounds.

56. Simple Products of Decomposition Soil Conditions Simple end products of Decomposition 1. Under aerobic condition(Well aerated soil) CO2, ammonium ion, nitrate ion, H2PO4 ion , sulphate ion, H2O, resistant residues and other essential plant nutrients Ca, Mg, Fe, Mn, Cu, Zn etc. 2.Under anaerobic condition(Waterlogged soil) CH4(swamp gas), some organic acids like lactic acid, propionic acid, butyric acid etc. Toxic gas like Hydrogen Sulphide(H2S) and Ethylene and the resistant humus substance.

57. Factors affecting organic residue decomposition : Temperature ?? Soil moisture ?? Soil reaction ?? Nutrients ?? Soil texture ?? Type of vegetation ?? Other factors like presence or absence of toxic chemicals, excessive amount soluble salts and organic phytotoxins etc. ??

58. Decomposition of Water Soluble Organic Substances

59. Sugar and other water soluble organic nitrogen compounds are subjected to decomposition first as depicted below:

60. Water soluble organic nitrogenous compounds like protein, amides etc. are subjected to break down as more plant available forms Ammonium ions & Nitrate ions through the process of ammonification an nitrification and also forms gaseous nitrogenous compounds. Ammonification : Organic N Compounds polypeptides amino acids ammonia or ammonium ions

61. Nitrification : In this process, the so formed ammonia and ammonium salts are converted to nitrate ions in the form of inorganic nitrogen intermediate nitrate ions formation as follows( 2 steps )

62. Ammonification (Ammonifiers ): Bacillus, Pseudomonas Nitrification (Nitrifying bacteria) : Nitrosomonas, Nitrobacter Nitrococcus Denitrification (Denitrifies): Achromobacter , Pseudomonas, Bacillus, Micrococcus

63. Decomposition of Water Insoluble Organic Substances

64. Protein The protein molecule is composed of a long chain amino acids having general structure H2N CHRCOOH where R may be a hydrogen atom, a single methyl group, a short carbon chain or a cyclic structure. In a protein molecule, amino acids are linked together by peptide bonds ( CO-NH) Action of protease enzyme by hydrolizing of those bonds

65. DECOMPOSITION OF PROTEIN RESIDUE

66. Enzymes : exopeptidases Endopeptidases Microorganisms : Bacillus Pseudomonas

67. Cellulose Cellulose is a carbohydrate composed of glucose units bound together in a long, linear chains by Beta-linkages at carbon atoms 1 and 4 of the sugar molecule . A number of polysaccharides like xylans , polyuronides etc. are also associated with the cellulose of the plant wall cell. They are called as cellulosans .

68. DECOMPOSITION OF CELLULOSE COMPOUNDS

69. Cellulose decomposing bacteria: Aerobic : Angiococcus Cytophaga Polyangium Sporocytophyga Bacillus Achromobacter Cellulomonas Anaerobic: 1. Clostridium 2. Methanosarcina 3. Methanococcus

70. Hemicellulose Hemicellulose are water-insoluble polysaccharides . During breaking of hemicellulose, the production of single soluble sugars are found . They are first attack by microorganisms than that of cellulose compounds. Enzyme : Hemicellulase

71. Polysaccharides Oligosaccharides Simple Sugars Simple sugars CO2 + H20 Simple sugars Organic acids, alcohols etc. (hemicellulose) (‘Oligo’ means ‘few’)

72. Bacteria involved: Clostridium Bacillus Pseudomonas Fungi involved: Aspergillus Penicillium Actinomycetes involved: Streptomyces

73. Starch Starch is a polymer of glucose and it serves the plant as a storage product, and as such it is the major reserve carbohydrate. It is made up of 2 components : a) amylose & b) amylopectin Amylose has a linear structure of glucose units linked together by alpha-1, 4 glucosidic bonding. Amylopectin has a branched structure ( it is made up of glucose units linked together by alpha-1, 4 glucosidic bonding and it has side chains attached through alpha-1, 6 glucosidic bonding .

74. Starch maltose glucose Enzymes involved: Alpha-amylase Beta-amylase Alpha-glucoside Beta-glucoside amylase Alpha- glucosidase

75. Lignin Woody type of plants contribute large amounts of lignin. The lignin content of young plants is relatively low, but quantity increases as plant matures . The decomposition of lignin proceeds either in presence or absence of oxygen. Most of fungi ( sp. Basidiomycota group of fungus) can decompose lignin very effectively. Lignin is probably depolymerized to give simple aromatic substances such as vanillin and vanillic acid or possibly other methoxylated aromatic structures.

76. Figure 1 : Lignin Decomposition

77. Figure 2 : Lignin Decomposition

78. Figure 3: Lignin Decomposition

79. Examples of Lignin decomposing fungus : Puffballs Mushrooms Bird’s-nest fungi Stinkhorns Wood living fungus Aspergillus Penicillum

80. Others There are organic nitrogenous substances also carry sulphur( like cysteine, cystine etc.). These organic substances break down by the action of different microorganism through mineralization and covert them into inorganic sulphate ions . Organic compounds like phospholipids, phosphoproteins, nucleic acids, phytin and inositol hexaphosphate break down by the action of different microorganism through mineralization and covert them into inorganic phosphate ions . Fats are first broken down by microorganisms through the action of lipase enzyme and converted into glycerol and fatty acids .

81. Figure: Rate of decomposition of Organic Residue

82. Tenny and Waksman, 1929 USA

83. Changes in the nitrogen content of decomposing barley straw (From Alexander, 1977)

84. Changes in soil mineral N as a function of time, and addition of manure and straw

85. McClintok et all, 2007

86. Impact of organic residue towards C cycle :

87. C:N ratio What it is ?????? -A carbon-to-nitrogen ratio (C/N ratio or C:N ratio) is a ratio of the mass of carbon to the mass of nitrogen in a substance. Materials C:N ratio 1. Food wastes 15:1 2. Sewage & Sludge 16:1 3. Grass Clippings 19:1 4. Cow manure 20:1 5. Leaves & Foliage 40-80:1 6. Paper 150-200:1 7. Wood & Saw dust 300-700:1

88. As a general rule, an initial net mineralization (gain in mineral forms of the nutrients) will occur at C:N ratios < 20:1 C:P ratios < 200:1 C:S ratios < 200:1

89. 1 . Add high/wide C:N residue : microbial activity, CO2 long nitrate depression final N level 2. low/narrow C:N: microbial activity, CO2 no nitrate depression final N level

90. Organic Residue Vs Humus/ humic acid ??????

91. Formation of Humic Acid

92. Why it is relevant to Organic Farming ????

93. Conclusion Among soil microorganisms Bacteria plays a major role in decomposing organic residue. Organic residue decomposition is a step-wise process where simple sugar decompose first then followed by complex materials like cellulose, lignin etc. As the complexity of materials increases, population of bacteria in soil decreases. Organic Residue decomposition results in development of humus or humic acid pool in the soil.

94. References Das, D.K., 1997, Introductory Soil Science. Kalyani Publishers, New Delhi. Reddy, T.Y. and Reddi , G.H., 2014.Priciples of Agronomy. Kalyani Publishers, New Delhi. Subbarao, N.S., 1999, Soil Microbiology. Science Publishers, U.S. Google & Wikipedia