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Bioremediation of Soils in Afrrica

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1 Bioremediation of Soils in Afrrica
Africa-US Network of Centers of Excellence in Water & Environmental Science & Technol. Bioremediation of Soils in Afrrica Ramble O. Ankumah. Ph.D. Tuskegee University 1

2 Overview of Soil As Media For Biological & Chemical Reactions
1. Soils contain solids and fluids 2. The solids are various inorganic and organic compounds 3. The fluids are liquids (water being the solvent) and gases 4. The volume of the components of agricultural soils at optimum soil moisture for plants is approximately as follows:


4 Field View of Soil a. Soil vs. Regolith
Regolith: Unconsolidated material above bedrock: Quite universal 1. Can be negligible (shallow) or hundreds of feet thick 2. May be material weathered from underlying rock or might have been transported by H2O or wind and deposited upon the bedrock or upon other material covering bedrock.


6 Soil Colloids and Their Importance in Soil Function
Colloidal Materials in Soils I. Clay Minerals II. Soil organic Colloid (Humus) 


8 Clay Minerals Types of Clay Minerals 1. Layer Silicates
2. Hydrous oxides of Iron and aluminum 3. Amorphous Clays


10 Oxides, Hydroxides and Oxyhydroxides
Hydrous Oxides of Iron and Aluminum pH Dependent and variable Amphoteric i.e. can have positive or negative charges Positive charge under low pH Negative charge under high pH (0-4mmolc/100g)




14 Soil Colloids: Organic Colloids
pH Dependent and variable Structure has Carboxylic(–COOH), Phenolic, and hydroxyl (-OH) groups. Dissociation of this groups at various pH results in negative charge. Charge always negative (150 and 550 cmolc/kg)




18 Carbon Cycle on Soil Organic Matter (SOM)
A. Organic Constitution of Plants: Divided into six broad categories 1. Cellulose -most abundant % 2. Hemicellulose % 3. Lignin % 4. Water soluble fraction (simple sugars, amino acids, and aliphatic acids) %

19 Carbon Cycle: Assimilation/Mineralization
5. Ether and alcohol soluble (Waxes, fats oils resins and a number of pigments) 6. Protein (have N and S) 7. Mineral Component-usually estimated by ashing % As plant ages the content of water soluble fraction decreases and the percentage of cellulose, hemicelluose and lignin rises.

20 Carbon Cycle: Assimilation/Mineralization
B. Carbon Assimilation 1. Organic Matter serves two functions a. Provides energy b. Supplies C for new cell materials Products: CO2, CH4, organic acids, Alcohol

21 Carbon Cycle: Assimilation/Mineralization
Assimilation: Process of converting substrate to protoplasmic carbon Most microbial cells contain 50% Under aerobic conditions 20-40% of substrate C is assimilated and remainder released as CO2. Fungal flora more efficient in C transformation than other groups and releases less CO2.

22 Carbon Cycle: Assimilation/Mineralization
Fungi and actinomycetes more efficient than Bacteria. During Decomposition Fungi 30-40% C metabolized is used to form new mycelium. Actinomycetes 15-30% Aerobic Bacteria less efficient, assimilates to 5-10% Anaerobic Bacteria 2-5% assimilated

23 Carbon Cycle: Assimilation/Mineralization
Immobilization: Assimilation of inorganic substrates into complex organic molecules. Determined by utilization of nutrients elements for cell synthesis. Magnitude is proportional to net microbial cells or filament formed and is related to C assimilated by a factor governed by C:N, C:P, C:K, or C:S ratio of the newly generated protoplasm.

24 Carbon Cycle: Assimilation/Mineralization
C. Decomposition and CO2 Evolution: Most important function of microbial flora is decomposition of organic matter and release of CO2. Degradation is a property of organotrophs (heterotrophs).

25 Carbon Cycle: Assimilation/Mineralization
D. Process in Organic Matter Transformation. 1. Plant and animal constituent disappear under influence of microbial enzyme. 2. New microbial cells are synthesized. 3. Certain end products of the breakdown are excreted to the surroundings.

26 Carbon Cycle: Assimilation/Mineralization
E. Decomposition of Soil Organic Matter Rate of CO2 release during mineralization of humus varies with soil type Factors governing humus decomposition are a. Organic Matter Level in soil b. Cultivation

27 Carbon Cycle: Assimilation/Mineralization
c. Temperature d. pH e. Depth f. Aeration

28 Carbon Cycle: Assimilation/Mineralization
Fresh substrates sometimes accelerate and sometimes reduce humus decomposition. Enhancement is known as priming. 2-5% C present in humus can be mineralized per annum. Cultivation enhances O. M. Decomposition.

29 Carbon Cycle: Assimilation/Mineralization
E. Breakdown of Added Carbonaceous Materials: Factors affecting breakdown of added organic materials. a. Type of material b. Temperature c. O2 d. pH e. Inorganic nutrients f. C/N ratio of plant tissue

30 Carbon Cycle: Assimilation/Mineralization
Nitrogen is the key substrate for microbial growth and hence organic matter breakdown. If the N content is high and the substrate is easily metabolized, organism satisfies N needs from this source. If substrate is poor in N, decomposition is slow, and C mineralizes will be stimulated by the supplement.

31 Carbon Cycle: Assimilation/Mineralization
F. Mineralization of the Materials and C:N Ratio. 1. During mineralization of the compounds containing little N, the C:N ratio tends to decrease with time. 2. This results in gaseous loss of C while N remains in organic combinations for as long as C:N ratio in wide.

32 Carbon Cycle: Assimilation/Mineralization
3. Thus % of N in residue continues to rise as decomposition progresses. 4. Curve approach approximately ratio of 10:1. 5. C:N ratio of soil is roughly 10:1 6. Microbial cells have C:N ratio between 5 to 15 parts C to 1 parts N. approximately 10:1.

33 Carbon Cycle: Assimilation/Mineralization
Arrangement of plants in order of decreasing rate of Mineralization. 1. Sweet Clover % 2. Alfalfa % 3. Red Clover % 4. Soybeans % 5. Millet % 6. Flax % 7. Corn Stalks % 8. Sudan Grass % 9. Wheat % 10. Oat Straw %

34 Carbon Cycle: Assimilation/Mineralization
Low N content or a wide C:N ratio is associated with slow decay. Example: Incorporation of a residue having a wide C:N ratio. 1. Microbes will develop to the extent of available N and other inorganic nutrients. 2. All immediately available N will be

35 Polysacharides: Cellulose: Introduction
Insoluble polymer of β(1-4) linked glucose The most abundant organic carbon material in nature Molecular weight appox. 20, million Most bugs hydrolyze α-linkages Because it occurs with other materials and is resistant to degradation it impedes enzymatic attack


37 Cellulose: Introduction
Generally animals don't metabolize it. Older plant tissues have a lot of it. Cotton fibres about 90% cellulose. About 14,000 isolates can degrade it. Bugs degrading it need supply of N. Decomposition faster under aerobic conditions when N-fertilizers are applied.

38 Factors Affecting Cellulose Degradation
Occurs from freezing to 65 C, Slow in frozen state Thermomophiles optimum Mesophiles C, tolerate C Psychrophiles < 20 C Most soil microbes are mesophiles Cellulose not available as source of energy Slow type of release, conversion to glucose is very slow.

39 Microbiology of Cellulose Degradation
Microbes growing on it don't grow fast on cellulose. Ability to degrade cellulose is common in fungi but unusual with bacteria and actinomycetes. Fungi Degrading Cellulose: Aspergillus, Fusarium, Chaetomium, Phoma Bacteria: Most popular is Cytophaga, Pseudomonas spp.

40 Cellulose Degradation: Microbiology
Actinomycetes: e.g. Streptomyces*, Norcodia*, Micromonospora. * Very versitile All cellulose degrading bacteria and actinomycetes can be isolated at pH 5.5. Montmorillonite reduces activity of cellulases. Cellulose exploited in industry by breaking and fermenting it to ethanol

41 Hemicellulose Chemistry:
Not a polymer of just glucose but a mixture of glucose, galactose, mannose, glucoronic acid, galactoronic acid, arabinose, and xylose. Hemicellose, generally 50 to 200 units. Polysacharide may exist as a linear chain as with cellulose. Usually branched.


43 Degradation of Hemicellulose
Only few sugars and uronic acids are common. These are: Pentoses (5 C sugars)-Xylose and Arabinose; Hexoses (6 C sugars)- Mannose, glucose, and galactose; Uronic acids-glucouronic acid and galactouronic acids.

44 II. Degradation of Hemicellulose
a. Easily degraded than cellulose; b. Hemicellulose disappears initially at a rapid rate and may be due to degradation of part which is physically available. c. Converted to CO2 and microbial cells.

45 Degradation of Hemicellulose: Factors
2. Factors Affecting Decomposition a. pH approximately 7 b. O2 limiting c. Age Older plant more resistant to decomposition. d. Availability of inorganic nutrients e.g. N

46 Microbiology of Hemicellulose Degradation
More microbes can degrade it; Microbes not specific, can degrade other things. Microorganisms Utilizing Hemicelloluse: 1. Bacteria Organism Substrate Bacillus Mannan, galactomannan, xylan Cytophaga Glactan Erwinia Xylan Pseudomonas Xylan Streptomyces Mannan, Xylan

47 III. Microbiology of Hemicellulose Degradation
2. Fungi Organism Substrate Alternaria Arabinoxylan, xylan Aspergillus Araban, arabinoxylan, mannan. Chaetomium Arabinoxylan Fusarium Araban, arabinoxylan Penicillium Araban, mannan


49 Lignin: Introduction a. Lignin is the third most abundant plant tissue
Most common in woody plants, i.e. about 15-35%. they are slowly degraded. Woody plants contribute most of the lignin which are degraded by the microflora.

50 Lignin : I. Introduction
b. Lignin is chemically complex and is found in cell walls and also in the middle lamella. c. Lignin can also be found in certain fungi and algae d. Not much known about the biochemistry of lignin degradation.


52 Lignin: Decomposition
a. Very resistant to degradation (enzymatic) b. Occurs in the presence of oxygen. c. Rate observed far less than cellulose, hemicellulose, and other carbohydrates. d. Well decomposed material has high percentage of lignin.

53 Lignin Decomposition e. Aerobic decomposition of corn stalks.
2/3 of total dry matter lost in 6 months and 1/3 of lignin in 6 months. f. Lignins of young tissues disappear more rapidly than mature plants. g. Lignin protects the decomposition of associated polysaccharides by mechanically separating the microorganisms from CHO.

54 Factors Affecting Rate and Extent of Lignin Decomposition.
1. Temperature Optimum temperature is 30oC No degradation less than 7oC or greater than 37oC. 2. Availability of nitrogen 3. Aeration 4. Plant residue undergoing decay Methoxy groups first-more under anaerobiosis and least under aerobic conditions

55 V. Microbiology of Lignin Degradation
Numbers of microbes capable of breaking down lignin are small. 1. Major microflora are Fungi Decomposition of lignin is primarily by fungi. color of the decayed substrate is indicative of the mode of attack.

56 Microbiology of Lignin Degradation
i. White-rot-Fungi: White rot-fungi are the most active lignin-degrading microorganisms. Their degradation leads to CO2 and H2O Species involved are mainly basidiomycetes (Phanerochaete sp., most studied) and a few ascomycetes.

57 Microbiology of Lignin Degradation
a. Basidiomycetes-Agaricus, Armillaria, Fomes, Pleurotus, Coriolus etc. b. Ascommycetes: Xylaria, Libertella and Hypoxylon White rot fungi are thought to degrade lignin only in the presence of other degradable substrates which they use as primary energy source

58 V. Microbiology of Lignin Degradation
ii. Brown-rot Fungi. These degrade the polysaccharides associated with lignin and remove the CH3 subgroups, and R-O-CH3 side chains. This leaves the phenol behind which turn brown upon oxidation. Representative groups include Poria and Gloeophyllum

59 V. Microbiology of Lignin Degradation
iii. Soft-rot Fungi. Important in wet situations and appear to degrade hardwood lignin more effectively than soft woods. Representative groups are Chaetomium and Preussia 2. Aerobic bacteria e.g. Arthrobacter, Pseudomomas, Xanthomonas, Flavobacterium, and Micrococcus.

60 V. Microbiology of Lignin Degradation
3. Actinomycetes have been implicated e.g. Streptomyces and Norcardia. Actinomycetes and Bacteria such as Streptomyces and Norcardia and anaerobic G- bacteria such as Azotobacter and Pseudomonas , depolymerize the lignin structure and lower the molecular size.


62 VI. Biochemistry of Lignin Degradation:
4. To obtain energy and carbon from the transformation, the ring is opened and the cleavage products either enter the metabolic pathway or are used in biosynthesis. 5. Ring opening proceeds by 3 ways. A. Ortho fission B. Meta Ring Fission C Gentisic Acid Pathway

63 VI. Biochemistry of Lignin Degradation:
1. All 3 pathways require molecule O2. 2. Reason not much aromatic degradation in anaerobic environment. 3. Oxygenase involved is mainly dioxygenase i.e. in ortho Fission. 4. Meta Fission limited to alkyl substituted rings.



66 Soil Organic Matter (SOM)
Degradation of Plant Residues Mineralization of less resistant C compounds leads to CO2 Less resistant C compounds persist Rate of decomposition influenced by C/N ratio of material


68 Organic Matter Equilibrium
C = bm/k Where: C= The % of soil organic carbon in Equilibrium (tons/ha) b= The annual amount of fresh organic matter added (tons/ha) m= Conversion rate of fresh organic matter in to soil carbon (percent).

69 Organic Matter Equilibrium
k= the annual decomposition rate of the soil organic carbon (percent) a= the annual addition of organic matter (tons/ha) a = bm

70 b values Temperate Forest = 3-15 tons/ha Tropical Forest = 1-8 tons/ha
Temperate Praires = 1.5 tons/ha Tropical Savannas = tons/ha

71 k and m values k is primarily a function of temperature
Values range from 2-5 % in tropical forest to about 1.5 in tropical savannahs. Temperate forest values range from 0.4-1% m is about 30-50% per year




75 Organic Matter Effect 1. Direct physical/Chemical- soil structure and chemical properties 2. Direct biological Effect- Mineralization/Immobilization 3. Indirect Biological Effect- Alter/Modify physical and chemical processes

76 Organic Matter Management
1. Manipulate existing organic matter through tillage or soil drainage 2. Crop residue placement on or in soil and burning to enhance management operations

77 Organic Matter Mgt. 3. Augment in situ production using green manure, cover or sod crops 4. Amendment with organic matter sources such as animal waste and or compost




81 In Situ Production of Organic Crops
1. Legume crops 2. Green crops 3. Animal manure

82 Use of Enzyme Activity in Evaluation Bioremediation
Evaluation of the use of soil enzyme activities and microbial diversity in determining agricultural and environmental impacts of “soil quality”. Tillage Practices: Conventional vs Conservation Organic Farming




86 Bioremediation of Contaminated Soil-Approaches
Bioremediation strategy uses microbes, plants or microbial or plant enzymes to detoxify contaminants. Biodegradation Mineralization Cometabolism

87 Criteria for Bioremediation
Organisms must have catabolic activity to degrade contaminant at a reasonable rate Target contaminant must be bioavailable Site must have soil conditions conducive to microbial and plant growth

88 Bioremediation Strategies
Passive or intrinsic bioremediation Biostimulation Bioventing Bioaugmentation Landfarming Composting Phytoremediation

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