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Light energy

CO Plant + O

Soil organisms HO Herbivoreprimary consumer NH Kinds, roles and inter- NO Carnivore (secondary, relationships mineral higher level consumer)

Kiyoshi Tsutsuki Saprophytes (decomposer) http://timetraveler.html.xdomain.jp Soil animals, soil microbes Importance of saprophytic organisms

Organisms in surface soil Biomass of soil organisms (some t / Plant roots ha) is almost equivalent to the yield of crops harvested annually Mammals from the land, or to the weight of Soil animals domestic animals bred on the land. Soil microbes Biomass of soil organisms /1 ha reaches several tons: 5/ ha, 0.5kg / m2

Role of soil to the crowd What soil owes to the crowd of soil organisms: of soil organisms: Moisture, Oxygen, Temperature, Decomposition of organic matter, Mineral nutrition, Supply of emission of carbon dioxide, liberation organic matter of mineral nutrients Creation of soil structure Supply of fertile plant growth environment

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Macrofauna Animals sized >2mm or 10mm Soil animals Earthworms, Enchytraeina, ants, Millipede, Centipede, etc. (soil fauna) Population of earthworms : 3000-250,000 /10a, 3-250 /m2

Function of earthworms Charles Darwin

Amount of soil passing through “The Formation of the body of earthworm : Vegetable Mould through the Action of 4t / 10a annually Worms, with the Observation of their In 30-50 years, all the soil in the Habits” (1881) plowed layer passes through the Japanese translations: body of earthworms. S. Yata (1949), H. Watanabe 200 t / 4 t = 50 years (1994)

Functions of soil animals: Clods of the feces of earthworms Eating and crushing plant remains and Baybay, Leyte, Philippines animal feces

• Decomposability of plant remains increases after eaten and crushed by soil animals. • Animal feces are first eaten and decomposed by the larva of insects (eg. Dung beetles and flies).

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Organic matter decomposition by Mesofauna soil animals Size: 0.2-2 mm 10 mm Collembola (spring tails), mites, nematodes Temperate region: Arthropods and earthworms Population: Collembola and mites: 50,000-80,000 /m2 in Tropics and subtropics: Termites forest floors. Sub-boreal needle forest: Nematoda: (saprophytic, predatory, parasitic) Enchytraeina 1.30 million /m2 in the forest, 50,000-80,000 /m2 in cultivated lands.

Microfauna Size: < 0.2mm Protozoa: Amoeba, Ciliates, Flagellate

Collembola ()

Collembola () Oribatid ()

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Isopoda, sow bug () Prostigmata ()

Lithobius () Larva of millipede

Larva of Diptera (flies) Enchytraeina ()

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Pratylenchus penetrance ()

Pratylenchus penetrance ()

Nematodes isolated from OUAVM fields.

Lumbricus rubellus Amynthus agrestis

Length: 8-20 cm Collected from compost Length: 6-10 cm Collected from compost Living depth: 10-50 cm Living depth: 10-25 cm

Population of soil animals / m2 Kitazawa, 1976

Needle Mulberry Upland kinds forest field field Soil microbes Macrofauna 73 16 19 Enchytraeina Bacteria, Actinomycetes, (103 150 6.5 3.7 Collembola Fungi, Algae (103 76 5.0 9.3 Mites (103 53 8.1 5.8 Nematodes (105 13 7.0 1.4

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Classification of organism by the Classification of organism by method to obtain carbon. the method to obtain energy. From organic matter.... From the light ...... organotrophs, heterotrophs Photosynthetic organisms From the chemical compounds, such as From carbon dioxide ..... methane, hydrogen sulfide, hydrogen gas, etc. ... lithotrophs, autotrophs Chemosynthetic organisms

Classification of organisms according to Classification of organisms according to the types of metabolism the types of metabolism

Types of metabolism Members of the group autotrophic, Autotrophic, Higher plants, algae, Photosynthetic Chromatiales bacteria, Chlorobiales bacteria photosynthetic Heterotrophic, Animals, fungi, actinomycetes, heterotrophic, Chemosynthetic most of bacteria chemosynthetic Autotrophic, Ammonium oxidizing bacteria (Nitrosomonas), autotrophic, Chemosynthetic Nitrite oxidizing bacteria (Nitrobacter), chemosynthetic Iron bacteria, heterotrophic, Hydrogen bacteria, photosynthetic Sulfur oxidizing bacteria (Thiobacteria) Heterotrophic, Purple bacteria Photosynthetic (Rhodobacteria, Blastochloris)

Function of soil microbes Mineralization of organic matter • Mineralization of organic matter Organic • Secretion of soil enzymes CO2 • Decomposition and purification of matter harmful organic matter Microbes NH4 • Symbiotic relationship with plants 2- • Antagonism (competition) with disease HPO3 causing germs 2- SO4

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Decomposition and purification Secretion of soil enzymes of harmful organic matter • Cellulase • Trichloloethylene Remaining % Remaining • α-Glucosidase • PCB • β-Glucosidase • Dioxin • Protease • Pesticides • Phosphatase days • Lipase Direct decomposition and co-metabolism

Symbiotic relationship with plants (1) Non-symbiotic nitrogen fixer bacteria

• Nitrogen fixation Proteobacteria group Symbiotic nitrogen fixation Cyanobacteria group Rhizobium, Cyanobacteria, Azolla Gram positive bacteria group Associative nitrogen fixation Bacterial nitrogen fixation Green sulfur bacteria group in the root zone of rice General Archaea group Pseudomonas, Alcaligenes

Root nodule bacteria (Rhizobium, Nitrogen fixation Bradyrhizobium, Azorhizobium) Grouped into Proteobacteria α

→ Symbiosis with legume plants and Ulmaceae plant, Parasponia phosphate Legume plants are grown in 25010ha of Nitrogenase land in the world, and 140 kg haof

+ nitrogen are fixed. NH4 → Glutamine→ Glutamic acid→ → Total agricultural land area in the world is Protein, Nucleic acid 140610ha, in Japan 5.110ha Ammonia assimilation enzymes

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Nitrogen fixation and the fertility of paddy field • Cyanobacteria in the paddy water. • Azolla • Sesbania as green manure grown on the ridges of rice field Cross section of root nodule. • Associative nitrogen fixing bacteria Soy bean root Bacteroid tissue in the rhizosphere of rice nodule Root nodules

Cyanobacteria (blue green algae) Have symbiotic relationships with Lichens and mosses, Azolla (Fern plant) Cycad family (Gymnosperm) Sesbania Gunnera (Angiosperm)

Actinomycetes (Frankia) Belongs to Gram positive bacteria. Forms root nodules with alder and Alnus firma as well as many other angiosperm trees in the temperate and tropic region.

Azolla

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Symbiotic relationship with plants (2) Mycorrhizal fungi Symbiosis with 70 % of terrestrial plants. Fungi residing in the surface layer or inside of roots. Help the absorption of phosphate and water. Arbuscular mycorrhizal fungi Alder trees in the wetland Ectomycorrhiza

Transfer of nitrogen from N fixing plants to other plants Mycorrhizal fungi in Timothy roots

Legume plants Gramineous plants

N2 CO2 Mycorrhiza

carbohydrates

N compounds 0.1 mm P Rhizobium

Antagonism with disease causing germs

Abundant and heterogenous microbial flora prevents the spread of disease causing germs. Bacillus subtilis controls the crop diseases. Microbial biomass in soil Pseudomonas bacteria prevent the seedling diseases of tomato. Non pathogenic Fusarium prevents various wilting and soft-rotting diseases of vegetables.

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Microbial biomass Total C and N, and biomass C contents in some Japanese soils.

Total C Total N Biomass C occupies 0.35.0 of total soil carbon. Kind of soils Texture (Mg/ha) (Mg/ha) (kg/ha)

Immature sand In mineral soils 2 3 , in volcanic ash soils S 9.4 0.86 32 0.31.0 in average. dune soil Light colored L 33.4 3.36 114 Numbers of microbes: 107109 / g soil ando soil ( 10 millions 1 billion /g ) Humic ando soil SiL 110 8.33 234 Brown forest soil CL 20.6 1.69 276

( Fungi occupy ca. 70 % in upland field, Dark red soil LiC 83.8 7.49 1,155 grassland, forest, and orchard field, while bacteria occupy 80 – 98 % of total microbes in Sakamoto and Hodono: SSPN, 46, 483-490 (2000) (Introduction to soil science, 2005) p.169 paddy soils.)

Methods of soil biomass 1. Direct counting determination Jones-Mollison method 1) Direct counting method Count and measure the microbes in soil suspension with hemo-cytometer. 2) Culture method Fluorescent immuno-staining 3) Biochemical method method Staining the specific bacterium by its fluorescent antibody.

3. Biochemical method 2. Culture method Chloroform fumigation method (applicable to all Dilution Plate Method (DP ) microbes) →fumigation-culture and fumigation-extraction Most Probable Number Method methods (MPN) ATP method (applicable to all microbes) Substrate Induced Respiration Phospho-lipid (applicable to all microbes) Method (SIR) Muramic acid, diamino-pimelic acid (for bacteria) Ergosterol (for fungi) Microcalorimeter (applicable to all microbes)

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2 Fumigated with chloroform

CO2 from Functions of soil microbial biomass biomass control 1) Decomposer of organic matter 2) Source and stock of soil nutrients Emission amount of CO of amount Emission days Effect of chloroform fumigation on the CO2 emission from soil.

Growth of crops and nutrients from microbial Nutrients in microbial biomass biomass and absorbed amounts by crops Relative % of nutrients contained in the microbial biomass of upland field. (Anderson and Domsch, 1980) Biomass Absorbed C N P K Ca nutrients nutrients Bacteria 25 4.5 1.5 0.8 0.4 Germany, upland 100 kg N/ha 40 kg N/ha Fungi 75 10.5 10.1 9.0 1.0 England, upland 17 kg P/ha 6.8 kg P/ha Total 100 15.0 11.6 9.8 1.4 Amounts of biomass nutrients in the field (kg/ha) England, pasture 56.8 kg P/ha 22.7 kg P/ha 108 83 70 11 Philippines, 44 – 156 40 – 100 paddy field Showing the balance of nutrient uptake by crops kg N / ha kg N / ha and nutrients supplied from microbial biomass.

Animals Human Crops, Forage

Feces CO2

Plant residue Inorganic nutrients Soil animals Vital point of Soil Soil organic microbes circulation matter

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