Soil ORGANISMS

Global Soil Biodiversity Initiative website

KINGDOMS OF LIFE

Eukaryotes have cell membranes and nuclei All species of large complex organisms are eukaryotes, including animals, plants and fungi, although most species of eukaryotic protists are microorganisms. Prokaryotes lack nucleus bacteria Protists: eukaryotic microorganisms that don’t form tissues

Organic portion composed of: 5% 10% 85% Humus & decomposing organic litter

Living organisms <5% Fresh residue <10% Photo credit: Collohmannia sp. Roy A. Norton, State University of New York at Syracuse File name: M8 Mites and Leaf Stabilized organic matter (humus) 33% - 50% Decomposing organic matter (active fraction) 33% - 50%

The divisions of the 5%: 40% bacteria and actinomycetes

BACTERIA Photo credit: Michael T. Holmes, Oregon State University, Corvallis File name: PBUT

Bacterial biomass dominates : grassland and agricultural landscapes Fungal biomass dominates: Forests

bacteria

Bacteria Abundant in rhizosphere Four FUNCTIONAL GROUPS: Tiny (1 μm width), one-celled Single cell division In lab: 1 can produce 5 billion in 12 hours (In real world limited by predators, water & food availability) Abundant in rhizosphere Four FUNCTIONAL GROUPS: Decomposers Mutualists : partner with plants Pathogens Chemoautotrophs

Some terms: Autotrophs: can make organic compounds from inorganic compounds Heterotrophs: feed on others to make organic compounds Chemosynthetic: get energy from inorganic chemical reactions Photosynthetic: get energy from sun Aerobes: use aerobic respiration (need oxygen as electron acceptor) Anaerobes: use inorganic or organic compounds for electron acceptor

Decomposers Organic chemicals in big complex chains and rings Bacteria break bonds using enzymes they produce Create simpler, smaller chains

Mutualists e.g., Nitrogen-fixing Bacteria Nodules formed where Rhizobium bacteria infected soybean roots. File name: Nods on Beans.jpg 277K (Also C-2 at 580K shows whole box.) Photo credit: Stephen Temple, University of Minnesota, St. Paul. (NRCS may use this image for educational purposes.) File name: Nods on beans

Root nodules

Chemoautotrophs Get energy from OTHER THAN CARBON compounds From N, S, Fe, H

Actinomycetes Are bacteria but grow like fungi Filamentous but morphology varies Adaptable to drought Important at high pH Usually aerobic heterotrophs Break down wide range of organic compounds Produce geosmin (smell of “fresh soil”)

40% other Microflora Protozoa Algae Fungi

PROTOZOA Ciliates Amoeba Flagellates Largest of the three Move by means of hair-like cilia Eat other protozoa and bacteria Amoeba Also large Move by means of a temporary foot (pseudopod) Flagellates Smallest of the three Move by means of a few whip-like flagella.

Protozoa Flagellates Amoeba Ciliates Eat bacteria & protozoa

protozoa Unicellular Heterotrophic Form symbiotic relationships Eat bacteria, fungi Form symbiotic relationships e.g., flagellates in termite guts; digest fibers Require water Go dormant within cyst in dry conditions

Function of protozoa Make nutrients plant-available Release excess N from the bacteria they eat Regulate bacteria populations Compete with pathogens

PROTOZOA bacteria Sand protozoa File name: Testate amoeba LR.jpg, 179K Credit: Elaine R. Ingham, Oregon State University, Corvallis

Flagellate File name: vorticella prot LR.jpg, 278K Credit: Elaine R. Ingham, Oregon State University, Corvallis.

Ciliate File name: ciliate2 LR.jpg 294K Credit: Elaine R. Ingham, Oregon State University, Corvallis

Amoeba bacteria amoeba Photo credits: (brown photo) No. 35 from Soil Microbiology and Biochemistry Slide Set. 1976. J.P. Martin, et al., eds. SSSA, Madison, WI (blue photo) Michael T. Holmes, Oregon State University, Corvallis. (We never used this in the Primer.) File names: (blue photo) AMOE (brown photo) SSSA35 bacteria amoeba

Soil-Dwelling “Vampires” Vampyrellids Vampyrellids are a group of amoebe that eat fungi by drilling round holes through the fungal cell wall and consumes the fluid inside. In this picture, they attack Gaeumannomyces graminis, the fungus that causes “take-all disease” in wheat. File name: vampraid.jpg, 451K (Also: E-4 at 1500KB, shows whole Bug Biography.) Photo credit: Homma, Y. et al. 1979. Phytopathology 69:1118-22. (Photo is in the public domain.) Group of amoebe that drill holes in fungus and consume liquid

Archaea ( ar-KEY-ah) A recent discovery: 1970s Woese and Fox: Divided bacteria into “normal” and “extremophiles” (archaeabacteria) Changed classic “tree of life” Bacteria Archaea Eukaryotes

Very similar to bacteria in shapes and size and reproduction Differences: Cell membranes contain lipids Not chitin (like fungi) Not cellulose (like plants) Genes of archaea are more similar to eukaryotes than to bacteria Can use a lot of various substances for energy

Importance Role in carbon cycle Photoautotrophs, chemoautotrophs, photoheterotrophs, chemoheterotrophs Many can survive in extreme environments (enzymes); heat, cold, salt, low pH Many are methane-producers: Swamp gas, cow farts Sheer numbers: Combined marine and soil archaea make them the most abundant organism on earth

Importance in Soil Role in N cycle Decomposition Ammonia oxidizers Important anaerobic decomposers Important in extreme environments where bacteria do not fluorish

algae Filamentous, colonial, unicellular Photosynthetic Most in blue-green group, but also yellow-green, diatoms, green algae Need diffuse light in surface horizons; important in early stages of succession Form carbonic acid (weathering) Add OM to soil; bind particles Aeration Some fix nitrogen

Fungi Break down OM, esp important where bacteria are less active attack any organic residue Most are aerobic heterotrophs chemosynthetic: adsorb dissolved nutrients for energy

Grow from spores into branched hyphae Hyphal strand divided into cells by septa that allow flow of liquids between cells Masses of hyphae grow together in visible threads called mycelia

Advantages over bacteria: They can grow in length Rate: 40 μm / min (bacterium travels 6 μm in its life) Don’t need a film of water to move Can find new food sources Transport nutrients great distances Produce enzymes that break down complex compounds Can break down lignin (woody compound that binds cellulose), shells of insects, bones Can break down hard surfaces

Clever, clever adaptations! Infecting a nematode Hypha twists back on itself and catches a nematode, hyphal cells swell and kill nematode then enter body and suck out nutrients Oyster mushroom Emits toxic drops from hyphal tips which touch nematode, immobilize it and hyphae enter body and remove nutrients Trap arthropods or protozoa and digest them

Mycorrhizae: symbiotic absorbing organisms infecting plant roots, formed by some fungi normal feature of root systems, esp. trees increase nutrient availability in return for energy supply plants native to an area have well-developed relationship with mycorrhizal fungi Can extend the effective surface area of tree’s roots by 700-1000 x

Mycorrhizal structure Mycorrhizae Tree root Photo credit: Randy Molina, Oregon State University, Corvallis. File name: M4 Fungi LR.jpg, 328K Fungal hyphae Mycorrhizal structure

Ectomycorrhizal Endomycorrhizal Grow close to root surfaces Hardwoods and conifers Penetrate and grow inside roots Vegetables, annuals, grasses, shrubs, perennials, softwoods

Ectomycorrhizae Photo Credit: USDA, Forest Service, PNW Research Station, Corvallis, Oregon. File name: Ectomy~1

Arbuscular Mycorrhizae (AM) File name: VAM LR.jpg 205K Photo Credit: Elaine R. Ingham, Oregon State University, Corvallis.

Higher fungi have basidium : club-shaped structure , bearing fruiting body toadstools, mushrooms, puffballs, bracket fungi

Fungi and Soil Quality Decompose carbon compounds Improve OM accumulation Retain nutrients in the soil Bind soil particles Food for the rest of the food web Mycorrhizal fungi Compete with plant pathogens Photo credit: No. 48 from Soil Microbiology and Biochemistry Slide Set. 1976. J.P. Martin, et al., eds. SSSA, Madison WI. File name: SSSA48

12% Earthworms (Macrofauna: > 1 cm long) ANNELIDS

earthworms Some 7000 species 3 categories: Epigeic (leaf litter/compost dwelling ) Endogeic (topsoil or subsoil dwelling ) Anecic (deep burrow drillers)

Giant Benefits to soil Move air in and out of soil Castings are rich in available nutrients Produce 10 lbs / yr

1 acre good garden soil: 2-3 million 1 acre forest soil: 50,000

Other Macrofauna (5%) and Mesofauna(3%) CHORDATES (vertebrates) mammals, amphibians, reptiles PLATYHELMINTHES (flatworms) ASCHELMINTHES (roundworms, nematodes) MOLLUSKS (snails, slugs) ARTHROPODS : (insects, crustaceans, arachnids, myriapoda)

vertebrates Squirrels, mice, groundhogs, rabbits, chipmunks, voles, moles, prairie dogs, gophers, snakes, lizards, etc. Contribute dung and carcasses Taxicabs for microbes

nematodes

NEMATODES File name: large todes LR.jpg, 262K Credit: Elaine R. Ingham, Oregon State University, Corvallis.

NEMATODES Bacteria feeder Fungal feeder Top left is the bacterial-feeding nematode, Elaphonema. Bottom right is a fungal-feeding nematode. Photo credits: (for both) Elaine R. Ingham, Oregon State University, Corvallis File names: BFTODE FFTODE Fungal feeder

Predatory Nematode File name: predatory tode LR.jpg 254K Credit: Kathy Merrifield, Oregon State University, Corvallis.

Root-feeding nematodes Upper left is the lesion nematode, Pratylenchus. Lower right is the root-feeding nematode, Trichodorus. File names: Upper Left: rootfeedingtode prat LR.jpg, 233K Lower right: rootfeedingtode trich LR.jpg, 184K Credits: Upper Left: Kathy Merrifield, Oregon State University, Corvallis. Lower right: Elaine R. Ingham, Oregon State University, Corvallis.

Fungal hyphal rings constrict when a nematode swims through. Nematode Trappers Fungal hyphal rings constrict when a nematode swims through. Some fungi make circular rings of hyphae. The rings constrict when a nematode swims through. Genus of this fungi is Arthobotrys. File name: Arthrobotrys.jpg at 265K. (Also: F-4 at 1600KB shows whole Bug Biography) Photo credit: George L. Barron, University of Guelph, Ontario.

Nonsegmented, blind roundworms > 20,000 species Eat bacteria or fungi or plants (stylet) And protozoa, other nematodes, algae Specialized mouthparts Can sense temperature and chemical changes

nematode

arthropods ¾ of all living organisms Exoskeleton, jointed legs, segmented body Insects Crustaceans Arachnids Myriapoda

Shredders Microbial taxis

Mites arachnids

Extracted from one ft2 of top two inches of forest litter and soil

Springtails Arthropods Spring or hop Detrivores 100,000 / m3 topsoil Invertebrates with external skeleton Spring or hop Detrivores 100,000 / m3 topsoil

Beetles Arthropods; order Coleoptera 400,000 species (40% of all known insect species) Some omnivores, some eat plants, fungi, some are carnivores Larvae (grubs)

pseudoscorpons Arachnid Carnivorous: eat larvae, ants, mites, flies Joint-legged invertebrate Carnivorous: eat larvae, ants, mites, flies

Feeding Habits Carnivores : parasites and predators Phytophages: eat above ground green plant parts, roots, woody parts Saprophages: eat dead and decaying OM Microphytic feeders: eat spores, hyphae, lichens, algae, bacteria

Movement existing pore spaces, excavate cavities, transfer material to surface improve drainage, aeration, structure, fertility, granulation

Rove beetles