Soil Miroorganisms (why we love microbes)Love and MicrobesBiodiversity of Fungi and BacteriaMetabolism Bacteria Actinomycetes: Filamentous bacteria Fungi Fungal hyphae and resting spores - ChlamydosporesBiological control of plant pathogenic fungi by - antibiosis - parasitismFungal cells that swell and contract around the nematodeFungal parasitism of nematodesFungal parasitism of weevilsProtozoaProtozoaNematode head structures indicate trophic groupNematodes AlgaeDetermining microbial biomass and activity Most bacteria (99%) cannot be culturedColonization by microbesFormation of biofilms on wet surfacesPlant associated microbes Epiphytic growth on apple blossom by Erwinia bacteria Fire Blight pathogen Photos by Mark WilsonFungal movement - Mycelia BridgingMycelia Bridging Spread across touching leaves, across soil pore gapsRoot zone activity The RhizosphereRhizophere: zone of soil influenced significantly by the root, usually 2mmMycorhizosphere Extension of Rhizosphere concept Exudates from hyphae of mycorrhizal fungi selectively increase some bacterDecomposing organic matter Bacteria and fungi are inside-out stomachsFungal dynamics of leaf decompositionDecomposition of surface and buried leaf litter by fungi and bacteriaDecomposing millipedeLigninFungi - Decomposition of Organic MatterHumic Acid – Difficult to DecomposeOxidation – Reduction ReactionsSoil Miroorganisms(why we love microbes)Ecological Agriculture TESC 2-14-06Steve ScheuerellLove and Microbes• Halophiles• Thermophiles• Mesophiles• Psychrophiles•…Lavies, 1993Soil Food Web – Microbial LoveMicrobial diversityFrom: Soil Biology PrimerColeman and Crossley, 1996Coleman and Crossley, 1996Biodiversity of Fungi and BacteriaColeman and Crossley, 1996Metabolism• Extremely resistant resting stages• Rapid reproduction potential in response to food and environment• In decomposition colonize easy to degrade substrates, especially with tillage• Ability to use diverse substrates– some only catalyzed by bacteria, e.g. nitrifying• Heterotrophic (parasitic or saprophytic) or Autotrophic – Photoautotrophic- energy from sunlight– Chemoautotrophic- energy from oxidation of inorganic substratesKennedy et al, 2004Bacteria• “free living” usually attached to a surface• Symbiotic can be within or on another organism• Transform, solubilize, mineralize, fix, decompose, base of food chainActinomycetes: Filamentous bacteriaActinomycetes, such as this Streptomyces, give soil and compostits "earthy" smell from geosmins a type of terpene.Soil Microbiology and Biochemistry Slide Set. 1976. J.P. Martin,et al., eds. SSSA, Madison, WI From: Soil Biology PrimerFungiFungus beginning to decompose leaf veins in grass clippings.Soil Microbiology and Biochemistry Slide Set. 1976. J.P. Martin, et al.,eds. SSSA, Madison WI.From: Soil Biology PrimerFungal hyphae and resting spores -ChlamydosporesPaul and Clark, 1989Biological control of plant pathogenic fungi by -antibiosis - parasitismBelanger and Avis, 2004Belanger and Avis, 2004Fungal cells that swell and contract around the nematodeBW Ch 11 Fig 11.22Fungal parasitism of nematodesFlint and Dreistadt, 1998Fungal parasitism of weevilsFlint and Dreistadt, 1998Protozoa• Single celled that capture and engulf their food• Larger than bacteria• Three groups: Amoebas, ciliates, flagellates• 10,000-100,000 individual per gram• 20-200 kg.ha• Most prey on bacteria and can influence nitrogen availability like nematodes• Found in rhizosphereProtozoaColeman and Crossley, 1996Nematode head structures indicate trophic groupNematodes Predatory in general bacteria, fungi algae, protozoa, other nematodes and insect larvae (biological control of corn rootworm) Release nutrients from feeding on bacteria and fungi  bacteria contain more N than nematodes need can account for 30-40% of N released Beneficial but some plant parasiticRKN of beanAlgae• 1 to 10 billion per m2or 10,000 to 100,000/g• 10 - 500 kg/ha• Are eukarotes (nuclear membrane)• Photosynthesize, so found on surface of soil• Produce OM, polysaccharides• Important form mat on soil surface, microbiotic crusts in desert and lichens (with fungi)Diatoms, one type of soil algaeDetermining microbial biomass and activityPaul and Clark, 1989Microbial PopulationsDirect MicroscopyActive Bacterial Cells = GreenTotal Bacterial Cells = BlueCulturable Populations Plate CountsColony forming units(CFU)Most bacteria (99%) cannot be cultured• How do we know?– Direct counts and genetic diversity (DNA assessment)A ton of microscopic bacteria maybe active in each acre of soil.Bacteria dot the surface of strands of fungal hyphae.From: Soil Biology PrimerWeaver, 1919Decomposition of Organic MatterKennedy et al, 2004Coleman and Crossley, 1996Colonization by microbesFormation of biofilms on wet surfacesAtlas and Bartha, 1996InternalInternalRhizosphereRhizospherePhyllospherePhyllosphereMicrobial Habitats of PlantsMicrobial Habitats of PlantsKennedy et al, 2004Leaf Surface Bacteria - EpiphytesPlant associated microbesEpiphytic growth on apple blossom by Erwinia bacteriaFire Blight pathogenPhotos by Mark WilsonFungal movement - Mycelia BridgingMycelia Bridging Spread across touching leaves, across soil pore gapsRoot zone activityThe RhizosphereRhizophere: zone of soil influenced significantly by the root, usually 2mmIn this photo, sand grains are bound to a root by hyphae from endophytes (fungi similar to mycorrhizae), and by polysaccharides secreted by the plant and the fungi, demonstrating the rhizosphere.From: Soil Biology PrimerJerry Barrow, USDA-ARS Jornada Experimental Range, Las Cruces, NM.Paul and Clark, 1989MycorhizosphereExtension of RhizosphereconceptExudates from hyphae of mycorrhizal fungi selectively increase some bacterial populationsDecomposing organic matterBacteria and fungi are inside-out stomachsPaul and Clark, 1989Fungal dynamics of leaf decompositionAtlas and Bartha, 1996Coleman and Crossley, 1996Decomposition of surface and buried leaf litter by fungi and bacteriaDecomposing millipedeLavies, 1993Chitin exoskeletonresists decompositionStarchCelluloseChitinGlucosePaul and Clark, 1989LigninPaul and Clark, 1989Fungi - Decomposition of Organic MatterAnimal ManureWoodAtlas and Bartha, 1998Humic Acid – Difficult to DecomposePaul and Clark, 1989Kennedy et al, 2004Kennedy et al, 2004Oxidation – Reduction