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, 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

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 „ and toxic metal protection „ FungusFungus benefitsbenefits „ source of energy and carbon „ competitive advantage „ IncreasedIncreased soilsoil stabilizationstabilization Mycorrhizae means “ 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 NematodesNematodes RolesRoles ofof nematodesnematodes inin soilsoil

„ FeedFeed onon ,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 „ abundant „ water dependent „ diverse range of feeding strategies: „ parasites „ Bacterial and fungal feeders „ predators or other www.barc.usda.gov R. P. Esser „ omnivores SpecializedSpecialized nematodenematode mouthpartsmouthparts

bacteria

omnivore 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 „ 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, 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 inin soilsoil

„ ShredShred organicorganic materialmaterial „ StimulateStimulate microbialmicrobial activityactivity „ MixMix microbesmicrobes withwith theirtheir foodfood „ MineralizeMineralize plantplant nutrientsnutrients „ EnhanceEnhance soilsoil aggregationaggregation „ Burrow,Burrow, increaseincrease infiltrationinfiltration „ ControlControl pestspests „ MayMay alsoalso bebe pestspests FrassFrass

Excrement of soil (frass) provide nutrients for other soil organisms SpringtailsSpringtails (Collembola)(Collembola)

„ FungalFungal andand nematodenematode grazinggrazing „ Protect crops from pathogens „ UbiquitousUbiquitous –– 100,000/m100,000/m2 „ FoodFood sourcesource forfor manymany predatorspredators

Fercula = springing organ MitesMites (Acari)(Acari)

„ PredatorsPredators „ FungalFungal feedersfeeders „ Decomposers:Decomposers: shredshred plantplant D. E. Walter, C. Meacham materialmaterial

A. Hornor

R. Norton D. E. Walter R. Norton PseudoscorpionPseudoscorpion

„ Top predator of soil „ Crytozoans – living under rocks, logs, bark „ Numerous in tropics and subtropics „ Prey on small arthropods, nematodes and enchytraeids http://www.arachnology.org/ PotPot wormsworms ((EnchytraeidsEnchytraeids))

„ AnatomicallyAnatomically similarsimilar toto earthwormearthworm „ 600600 knownknown speciesspecies „ DecomposeDecompose plantplant remainsremains withwith highhigh microbemicrobe populations,populations, earthwormearthworm casts,casts, grazegraze onon fungalfungal hyphaehyphae „ FrassFrass isis enrichedenriched withwith nutrientsnutrients EarthwormsEarthworms (Annelids)(Annelids)

Manure worm a.k.a. Red Wiggler (Eisenia fetida) Epigeic = surface litter Nightcrawler (Lumbricus terrestris) Castings Anecic = deep burrowing