AnAn IntroductionIntroduction toto SoilSoil EcologyEcology NovemberNovember 8,8, 20042004 AllisonAllison HornorHornor MostMost imagesimages inin slidesslides from:from: Dr.Dr. JaniceJanice ThiesThies RelativeRelative sizesize ofof soilsoil organismsorganisms FungalFungal hyphaehyphae Microbes on a root surface BacteriaBacteria BacteriaBacteria adheredadhered toto rootroot surfacesurface RootRoot hairhair FungalFungal hyphaehyphae SoilSoil BacteriaBacteria KingdomKingdom BacteriaBacteria • ProkaryotesProkaryotes •• FewFew diagnosticdiagnostic featuresfeatures •• ClassifiedClassified atat firstfirst onon metabolicmetabolic capabilities,capabilities, nownow onon 16S16S rRNArRNA sequencesequence •• Saprophytes,Saprophytes, pathogens,pathogens, autotrophs,autotrophs, andand symbiontssymbionts BacterialBacterial cellcell NN == nucleoidnucleoid CWCW == cellcell wallwall CM=CM= cellcell membranemembrane RR == 70S70S ribosomeribosome FF == flagellumflagellum PP == piluspilus FiFi == fimbriaefimbriae InIn == inclusioninclusion MeMe == mesosomemesosome BacteriaBacteria onon thethe headhead ofof aa pinpin BiosphereBiosphere 22 FailedFailed becausebecause ofof highhigh COCO2 levelslevels ForgotForgot aboutabout thethe soilsoil microbes!microbes! Weren’tWeren’t ableable toto recreaterecreate aa functioningfunctioning soilsoil environmentenvironment BacteriallyBacterially mediatedmediated nitrogennitrogen transformationstransformations NitrogenNitrogen FixationFixation NN2 inin thethe atmosphereatmosphere andand NHNH4 inin thethe lithospherelithosphere areare thethe majormajor NN poolpoolss NN2 mustmust bebe “fixed”“fixed” byby prokaryotesprokaryotes intointo ammoniaammonia toto bebe usedused forfor metabolicmetabolic processes.processes. NN isis aa primaryprimary constituentconstituent ofof proteinsproteins andand nucleicnucleic acidsacids,, thereforetherefore essentialessential forfor life.life. SoybeanSoybean rootroot nodulesnodules BacteriaBacteria provideprovide thethe plantplant withwith mineralizedmineralized NN PlantPlant providesprovides thethe bacteriabacteria withwith aa sourcesource ofof CC TypesTypes ofof Symbioses:Symbioses: AgriculturalAgricultural Trifolium pratense (red clover) – Rhizobium (bacterium): important forage crop Pisum sativum (pea) – Glycine max (soybean) – Rhizobium Bradyrhizobium (bacterium): (bacterium): important important crop crop, forage, oil production, soybeans, etc. TypesTypes ofof Symbioses:Symbioses: AgriculturalAgricultural Azolla (aquatic fern) - Anabaena azollae (cyanobacterium): important in rice cultivation D. Dalton Inga (tropical tree) - Rhizobium (bacterium): Important canopy tree for shade grown coffee, could contribute significant N Jatun Sacha agroforestry station, Ecuador TypesTypes ofof Symbioses:Symbioses: TreesTrees Alnus rubra (red alder) – Frankia (bacterium): important sucessional species in forests Casuarina equisetifolia (tropical tree) – Frankia (bacterium): common in the Carribean TypesTypes ofof Symbioses:Symbioses: UnusualUnusual Lobaria pulmonaria (lichen) – Nostoc (cyanobacterium): important in forest ecosystems Sesbania rostrata (legume) – Rhizobium (bacterium): stem nodules that can also photosynthesize InoculantsInoculants J. Thies PhD thesis 1987 SoilSoil FungiFungi RolesRoles ofof fungifungi inin thethe soilsoil SoilSoil aggregateaggregate stabilitystability IncreasedIncreased nutrientnutrient availabilityavailability forfor plantsplants (Mycorrhizal(Mycorrhizal symbiosis)symbiosis) NutrientNutrient sourcesource forfor otherother soilsoil organismsorganisms DecomposersDecomposers (especially(especially inin forestforest systems)systems) SomeSome areare predatory!predatory! SoilSoil aggregateaggregate stabilitystability SoilSoil aggregateaggregate FungalFungal hyphaehyphae Glomalin: chemical produced by some fungi that acts as a glue in aggregates SoilSoil aggregateaggregate FungalFungal hyphaehyphae MycorrhizalMycorrhizal SymbiosisSymbiosis MainMain types:types: EctoEcto--,, EEndondo-- PlantPlant benefitsbenefits improved nutrient status protection from desiccation and salts pathogen and toxic metal protection FungusFungus benefitsbenefits source of energy and carbon competitive advantage IncreasedIncreased soilsoil stabilizationstabilization Mycorrhizae means “fungus root” Pine seedling roots Mycorrhizal hyphae Increased surface area for nutrient uptake Paul and Clark, 1994 IonIon diffusiondiffusion DiffusionDiffusion coefficientscoefficients - -6 2 -1 NONO3 == 1010 cmcm secsec + -7 2 -1 NHNH4 == 1010 cmcm secsec 3- -8 2 -1 POPO4 == 1010 cmcm secsec ConcentrationConcentration 3- NONO3-- >>>> POPO4 EnhancedEnhanced nutrientnutrient uptakeuptake withwith mycorrhizaemycorrhizae EctomycorrhizaeEctomycorrhizae “short“short--roots”roots” ofof pinepine EctoEcto == “outside”“outside” rootroot D.M. Sylvia EndomycorrhizaeEndomycorrhizae EndoEndo == “inside”“inside” rootroot D.M. Sylvia EndomycorrhizaeEndomycorrhizae EndomycorrhizaeEndomycorrhizae ArbusculesArbuscules insideinside ofof aa plantplant cellcell –– increasedincreased surfacesurface areaarea forfor nutrientnutrient exchangeexchange Kinden and Brown, 1975 BenefitsBenefits ofof inoculationinoculation NematodeNematode trappingtrapping fungifungi hyphae constrict using water pressure, then digest the nematode NematodesNematodes RolesRoles ofof nematodesnematodes inin soilsoil FeedFeed onon bacteria,bacteria, fungifungi andand protprotoozoazoa ControlControl bacterialbacterial numbersnumbers andand populationpopulation structurestructure ReleaseRelease largelarge amountsamounts ofof NN whilewhile feedingfeeding andand uponupon deathdeath HelpHelp maintainmaintain plantplant availableavailable NN PlantPlant andand animalanimal parasitesparasites NematodesNematodes vermiform animals small (300 to 500µm in size) ubiquitous to all soils abundant water dependent diverse range of feeding strategies: plant parasites Bacterial and fungal feeders predators or other www.barc.usda.gov R. P. Esser nematodes omnivores SpecializedSpecialized nematodenematode mouthpartsmouthparts bacteria omnivore plants PlantPlant pathogenicpathogenic nematodenematode StyletStylet forfor piercingpiercing plantplant cellcell wallwall BacterialBacterial FeederFeeder 66 lipslips createcreate aa currentcurrent toto bringbring bacteriabacteria intointo theirtheir mouthsmouths ScanningScanning electronelectron micrographmicrograph ofof bacterialbacterial feedingfeeding nematodenematode FungalFungal feedingfeeding nematodenematode Smaller stylet than plant feeding nematodes PredatoryPredatory nematodenematode LargeLarge recurvedrecurved “tooth”“tooth” aidsaids inin capturingcapturing preyprey PredatoryPredatory nematodenematode ProtozoaProtozoa ProtozoaProtozoa EukaryotesEukaryotes UnicellularUnicellular animalsanimals NoNo cellcell wall,wall, cancan rapidlyrapidly formform cystscysts WidespreadWidespread inin soilsoil andand waterwater NeedNeed waterwater filmsfilms forfor activityactivity LargeLarge proportionproportion ofof soilsoil biomassbiomass SexualSexual andand asexualasexual reproductionreproduction TypesTypes ofof ProtozoaProtozoa FlagellatesFlagellates CiliatesCiliates AmoebaeAmoebae TestateTestate NakedNaked FlagellatesFlagellates Smaller than ciliates Live in freshwater and soil Phagotrophic (eat bacteria) Saprotrophic (eat decaying organic matter) Parasites of animals Trypanosoma, Giardia, Leishmania CiliatesCiliates Motile by means of numerous cilia Organized into a coordinated locomotor system Phagotrophic: eat flagellates Live in freshwater, soil, rumen (animal intestinal systems) Paramecium C. Jones I = ingestion P = production R = Respiration E = ExcretionR = respiration P = Production E = excretion NN mineralizationmineralization AmoebaeAmoebae PrincipalPrincipal consumersconsumers ofof bacteriabacteria inin soilsoil RegulateRegulate populationpopulation sizesize andand compositioncomposition AccelerateAccelerate turnoverturnover ofof soilsoil biomass/OMbiomass/OM MaintainMaintain plantplant availableavailable NN PreventPrevent pathogenpathogen establishmentestablishment FoodFood sourcesource forfor fungi,fungi, nematodes,nematodes, othersothers CauseCause diseasedisease (trypanosomes)(trypanosomes) -- parasitesparasites http://www.bms.ed.ac.uk/research/others/smaciver/Amoeba4.gif NakedNaked AmoebaeAmoebae http://www.micrographia.com Motile by means of pseudopodia Reproduce by binary fission (like bacteria) Phagotrophic Fresh water and soil Amoeba and Entamoeba and slime molds Animal parasites (amoeboid dysentery) Giant amoeba up to 1 mm diameter TestateTestate amoebaeamoebae CommonCommon inin forestforest soilssoils “test”“test” isis constructedconstructed outout ofof mineralsminerals www.micrographia.com PseudopodiaPseudopodia comecome outout thethe endend toto feedfeed VampyrellidVampyrellid amoebaeamoebae EatEat fungifungi ImportantImportant inin thethe controlcontrol ofof soilsoil--borneborne fungalfungal pathogenspathogens PuncturePuncture hyphaehyphae andand feedfeed onon cellularcellular contentscontents Rotifer:Rotifer: eatingeating algaealgae http://www.microscopy-uk.org.uk/mag/imag97/feeder1.jpg WaterWater Bears:Bears: ((TardrigradaTardrigrada)) FeedFeed onon algae,algae, fungi,fungi, OM,OM, bacteria,bacteria, plantsplants SomeSome preyprey onon nematodes,nematodes, protozoaprotozoa PreyedPreyed uponupon byby amoebae,amoebae, nematodes,nematodes, fungi,fungi, mitesmites andand spidersspiders ArthropodsArthropods RolesRoles ofof ArthropodsArthropods