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  1. The Real Scoop on Dirt SAFS "More organization and complexity exist in a handful of soil than on the surface of all the other planets combined.” *************************************Edwin O. Wilson Harvard University

  2. http://www.soilfoodweb.com So what lives in soils? • “The soil is alive and the diversity is enormous. One square foot of soil has an array of small invertebrates, mites, arachnids... hundreds, or even thousands of species, many of which are still unknown to science.” E.O.Wilson

  3. Protozoa feed on bacteria and fungi 10 million /m2 (3 to 20 g/m2) Nematodes (round worms) feed on bacteria, fungi, protozoa and plant roots 10 million /m2 in grassland soils, 30 million /m2 in woodland soils Enchytraeids (pot worms) feed on dead plant material 200-000 /m2 in grassland (50-35 g/m2) Tardigrades (water bears) 50 to 500 /m2 Pauropoda 20 to 2000 /m2 Molluscs (Slugs and Snails) feed on rotting vegetation (+ a few carnivorous species which eat other molluscs) approx. 15 /m2 in grassland soils, 450 /m2 in woodland soils

  4. Symphyla • feed on fungi • up to 1000 /m2 in grassland soils, 3000 /m2 in woodland soils • Isopoda (Woodlice) • feed on fungi, and dead plant material • 500 to 1500 /m2 in grassland soils, 3000 /m2 in woodland soils • Diplopoda (Millipedes) • feed on fungi, and dead plant material • approx. 20 /m2 in grazed grassland, 100 /m2 in ungrazed grassland, 100+ /m2 in woodlands • Chilopoda (Centipedes) • feed on insects an other soil arthropods • approx. 120 /m2 in grassland, 150+ in woodlands • Aranaea (Spiders) • feed on other arthropods • 480 /m2 in Moorlands, 200 /m2 in pasture

  5. Acari (Mites) • feed on everything • 100,000 to 600,000 /m2 woodland soils • Collembola (Springtails) • feed on fungi and bacteria • 40,000 to 70,000 /m2 in grassland soils, 500-000 /m2 in coniferous woodland • Coleoptera (Beetles) • up to 2000 to 3000 /m2 in ungrazed grasslands, considerably lower in arable soils. • Hymenoptera (Ants) • feed on other arthropods and plants secretions • important soil movers

  6. Today’s topics • Taxonomy • Aravalli, She and Garrett. 1998. Archaea & the new age of microorganisms. • The n-dimensional ecological niche • Silvertown, J. 2004. Plant coexistence and the niche. • Soil food webs and crazy soil critters!

  7. Taxonomy = naming and classifying organisms into groups that share similar characteristics • Taxon = a taxonomic group or level • Taxa = plural of taxon • Linneaus (1707-1778) • Systema Naturae • Physician - studied medicinal plants • Father of taxonomy Linneaus- check this for more info on Linneaus http://www.ucmp.berkeley.edu/history/linnaeus.html

  8. Linneaus’ hierarchy • Imperium ("Empire") - the phenomenal world • Regnum ("Kingdom") - the three great divisions of nature at the time - animal, vegetable, and mineral • Classis ("Class") - subdivisions of the above, in the animal kingdom six were recognized (mammals, birds, amphibians, fish, insects, and worms) • Ordo ("Order") - further subdivision of the above - the class Mammalia has eight • Genus- further subdivisions of the order - in the mammalian order Primates there are four. e.g. Homo • Species - subdivisions of genus, e.g. Homo sapiens. • Varietas ("Variety") - species variant, e.g. Homo sapiens europaeus.

  9. Binomial nomenclature Genus species King Philip Came Over For Games Saturday Taxonomy of Fido • Kingdom • Class • Order • Genus • Species Phylum Note addition Family http://www.blackwellpublishing.com

  10. The problem of common names - this fish is a: Look ma, I think I caught a snake … • Pickerel • Pike • Snake • G嚇da (Swedish) • tika obecn� (Czech) • kinoje (Ojibwe) • Esox lucius • Northern pike • Common Pike • Great Northern Pike • Jack • Jackfish • Northern

  11. Oh, naaaa …. its just a squirrel • This is for you, Joey and John! http://vernix.org/new/images/squirrels/ I couldn’t resist!!

  12. Robert Whitaker - 1969 5 kingdoms Plantae, Animalia, Protista, Fungi, Monera Karl Woese - 1978 3 domains Bacteria, Archea, Eukarya Linnaeus - 1700’s 2 kingdoms Plantae, Animalia Ernst Haeckel - early 1900’s 3 kingdoms Plantae, Animalia, Protista Back to taxonomy … what were those groupings anyway?It depends on who you ask …

  13. The 5 Kingdoms • Based on morphology, reproduction, metabolism, etc. • In general, the height up the “tree” represents time

  14. The 3 Domains Bacteria Eucarya Archea Plantae Fungi Animalia • Based on molecular structure of 16S or 18s subunits of ribosomal RNA Proteobacteria Cyanoobacteria Euryarchaeota Crenarchaeota Animalia Chloroplasts Mitochondria Adapted from McGraw-Hill Pub.

  15. X-ray crystallography image of ribosome structure University of California, Santa Cruz • 16s rRNA of 3 spp. • Universal • Similar function • Changes slowly • Can be compared between organisms McGraw Hill Pub.

  16. Dendrogram of 3 domains Bacteria Archea Eucarya McGraw-Hill Pub. And this brings us back to Aravalli, She and Garrett, Archaea & the new age of microorganisms

  17. Why were these authors so excited? IUPUI Dept. of Biology • Archea are no longer just extremeophiles!!! • They’re ubiquitous!!! • Will this change our thinking on: • how food webs work? • how organisms are related? • how microbial communities are organized? • how soil communities are organized?

  18. And this brings us to the concept of an ecological niche • Grinnell (1917) - the sites where organisms of a species can live • Elton (1927) - the function performed by the species in the community • Gause (1934) - intensity of competition determines overlap of niche • Hutchinson (1957) - a region (n-dimensional hypervolume) in a multi-dimensional space of environmental factors that affect the welfare of a species

  19. Species that need the same resources must compete They either coexist or one will die out http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookpopecol.html

  20. General theory has been - to coexist, spp. must use resources in slightly different way • Time of resource use • Diurnal, crepuscular, or nocturnal feeding • Early or late spring nesting for owls/hawks • Particular part of resource used • Seeds versus nectar versus leaves of a plant • Large versus small seeds • Area of tree canopy used by bird spp. (MacArthur) • More or less efficient use of same resource • Both maples and paw paw need sunlight, but paw paw need less

  21. So how do so many spp. of plants coexist? (Silvertown) If plants all use same few resources, why so many spp.? • Two possibilities: • Niche model is wrong • Plant niches ARE different (we just don’t know enough to know HOW they differ) • Conclusion --> differences have not been studied sufficiently • Not asking the right questions (4 tests of niche separation) • Studies should test all 4 of these when determining how plants use resources to see if niche model applies equally to plants • One difference = mycorrhizae • And that takes us right back to ……soil communities

  22. http://www.soilfoodweb.com

  23. Communities rule! The amount of decomposition was greater with soil macrofauna than without • Fig. 3. Total remaining litter mass of entire microcosms as a function of total predicted litter mass remaining. Data points represent individual microcosms either without macrofauna (open circles) or with macrofauna (i.e., millipedes, earthworms or both; solid diamonds). Hättenschwilerand Gasser 2005

  24. And diversity matters for tough biodegrabables! Fig. 1. Litter mass of individual species predicted from monocultures of the respective species and animal treatments. (Left) Data from the three more slowly decomposing species are shown. (Right) Data from the more rapidly decomposing species. Hättenschwilerand Gasser 2005

  25. Roles of soil critters: • Decomposition • Nitrogen fixation • Mineralization • Primary production

  26. (Soil around plant roots) (Nitrogen!) http://nicholnl.wcp.muohio.edu/naturalsystems/dirtlectures/DirtOne.html

  27. Thanks to Dr. Nancy Nicholson for the following images and fun facts!

  28. Nematodes and fungi - an “inversion of the animal-eat- plant relationship” Background • Nitrogen is inert in the atmosphere, so doesn’t mix with soil • Nitrogen in soils is a limiting factor for plant growth • Nematodes and fungi abound in healthy soils - both are essential for healthy plants because they retain nitrogen (and other nutrients) in soils once it has been captured by nitrogen-fixing bacteria • The nematode - fungus relationship keeps nitrogen from going back to the atmosphere as a gas (methane)

  29. Capture mechanisms of fungi • Paralyzing toxins (see <-- Hohenbuehlia) • Traps - numerous designs but mainly sticky • lethal lollipops • sticky nets • sticky spores • sticky rings • constricting rings (really scary!)

  30. Fast Food... those Golden Arches should be so efficient... Catenaria spores germinating on an infected nematode Myzocyctium spores inside a nematode

  31. Sticky spores adapted to being eaten by bacterivore nematodes

  32. Arthrobotrys, the fungus with it all!

  33. The deadly constricting rings - rings rupture along line of weakness as nematode crawls through - moisture from the soil causes them to swell and … the fastest food in the west!

  34. More deadly rings

  35. Phragmospores of some nemtode-trapping fungi germinate as constricting rings if nematodes are present

  36. And yes, there is the usual relationship of animal-eat-plant. Above right, a nematode avoids the paralytic toxin of the oyster mushroom and feeds on fungal tissue

  37. Nealson, 1999 Cyanobacteria in tufa mounds, Mono Lake, CA • pH = 10 • hypersalinity Siberian permafrost core - frozen 1 million years

  38. Nealson, 1999 Halobacteria in salt crystals Salt mounds in Dead Sea Salt ponds near Sn Francisco Bacteria in stomachs of invertebrates in amber

  39. Population distribution by county 1800 - 1990 • Percent of land in farms by county 1850 - 1987