The Real Scoop on Dirt "More organization and complexity exist in a handful of soil than on the surface of all the other planets combined.” *************************************

The Real Scoop on Dirt

"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

"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

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SAFS

“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

“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

So what

lives in soils?



http://www.soilfoodweb.com

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

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

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

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

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

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

Today’s topicsToday’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!

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!

Taxonomy = naming and classifying organisms into groups that share similar characteristics

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

Taxon = a taxonomic group or level

Taxa = plural of taxon

Linneaus (1707-1778) Systema Naturae Physician - studied

medicinal plants Father of taxonomy



http://www.ucmp.berkeley.edu/history/linnaeus.htmlLinneaus - check this for more info on Linneaus

http://www.ucmp.berkeley.edu/history/linnaeus.html

Linneaus’ hierarchyLinneaus’ 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.

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.

King Philip Came Over For Games SaturdayKing Philip Came Over For Games Saturday

Kingdom Class

OrderGenus

Species

Kingdom Class

OrderGenus

Species

Phylum

Family

Binomial nomenclatureGenus species



Taxonomy of Fido

http://www.blackwellpublishing.com

Note addition

The problem of common names - this fish is a: The problem of common names - this fish is a:



Northern pikeCommon PikeGreat Northern PikeJackJackfishNorthern

PickerelPikeSnakeG 嚇 da (Swedish)tika obecn� (Czech)kinoje (Ojibwe)Esox lucius

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TIFF (Uncompressed) decompressorare needed to see this picture.

Look ma, I think I caught a snake …

Oh, naaaa …. its just a squirrelOh, naaaa …. its just a squirrel

This is for you, Joey and John! This is for you, Joey and John!



I couldn’t resist!!

http://vernix.org/new/images/squirrels/

Back to taxonomy … what were those groupings anyway?

It depends on who you ask …

Back to taxonomy … what were those groupings anyway?

It depends on who you ask …

Robert Whitaker - 1969 5 kingdoms Plantae, Animalia,

Protista, Fungi, Monera

Karl Woese - 1978 3 domains Bacteria, Archea,

Eukarya

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

Linnaeus - 1700’s 2 kingdoms Plantae, Animalia

Ernst Haeckel - early 1900’s 3 kingdoms Plantae, Animalia, Protista

The 5 KingdomsThe 5 Kingdoms Based on

morphology, reproduction, metabolism, etc.

In general, the height up the “tree” represents time

Based on morphology, reproduction, metabolism, etc.

In general, the height up the “tree” represents time

The 3 DomainsThe 3 Domains Based on

molecular structure of 16S or 18s subunits of ribosomal RNA

Based on molecular structure of 16S or 18s subunits of ribosomal RNA

Bacteria Eucarya Archea

Pro

teo

bact

eria

Cya

noob

acte

ria

Ani

mal

ia

Fun

gi

Pla

nta

e

Ani

mal

ia Eur

yarc

haeo

ta

Cre

narc

hae

ota

Chloroplasts

Mitoch

ondria

Adapted from McGraw-Hill Pub.



X-ray crystallography image of ribosome structureUniversity of California, Santa Cruz

16s rRNA of 3 spp.•Universal•Similar function•Changes slowly•Can be compared between organisms

McGraw Hill Pub.

Dendrogram of 3 domainsDendrogram of 3 domainsBacteria EucaryaArchea

McGraw-Hill Pub.

And this brings us back to Aravalli, She and Garrett, Archaea & the new age of microorganisms

Why were these authors so excited?Why were these authors so excited?

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?

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?

IUPUI Dept. of Biology

And this brings us to the concept of an ecological niche

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

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

Species that need the same resources must compete

Species that need the same resources must compete

http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookpopecol.html

They either coexist or one will die out

General theory has been - to coexist, spp. must use

resources in slightly different way

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

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

So how do so many spp. of plants coexist? (Silvertown)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

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



http://www.soilfoodweb.com

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).

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).



Hättenschwiler and Gasser 2005

Communities rule!

The amount of decomposition was greater with soil macrofauna than without



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.

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.

And diversity matters for tough biodegrabables!

Hättenschwiler and Gasser 2005

Decomposition Nitrogen fixation Mineralization Primary production

Decomposition Nitrogen fixation Mineralization Primary production

Roles of soil critters:

http://nicholnl.wcp.muohio.edu/naturalsystems/dirtlectures/DirtOne.html

(Soil around plant roots)

(Nitrogen!)

Thanks to Dr. Nancy Nicholson

for the following

images and fun facts!

Thanks to Dr. Nancy Nicholson

for the following

images and fun facts!



Nematodes and fungi - an “inversion of the animal-eat- plant relationship”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)

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)

Capture mechanisms of fungiCapture 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!)

Paralyzing toxins (see <-- Hohenbuehlia) Traps - numerous designs but mainly sticky

lethal lollipops sticky nets sticky spores sticky rings constricting rings (really scary!)





Fast Food... those Golden Arches should be so efficient...

Fast Food... those Golden Arches should be so efficient...





Catenaria spores germinating on an infected nematode

Myzocyctium spores inside a

nematode



Sticky spores adapted to being eaten by bacterivore nematodes

Sticky spores adapted to being eaten by bacterivore nematodesQuickTime™ and a

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Arthrobotrys, the fungus with it all!

Arthrobotrys, the fungus with it all!





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!

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!



More deadly rings More deadly rings



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

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



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

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



Cyanobacteria in tufa mounds, Mono Lake, CA pH = 10 hypersalinity

Cyanobacteria in tufa mounds, Mono Lake, CA pH = 10 hypersalinity Siberian permafrost core -

frozen 1 million years

Nealson, 1999

Bacteria in stomachs of invertebrates in amber

Halobacteria in salt crystalsSalt mounds in Dead SeaSalt ponds near Sn Francisco

Nealson, 1999

Percent of land in farms by county 1850 - 1987

Percent of land in farms by county 1850 - 1987

Population distribution by county 1800 - 1990

http://biology.usgs.gov/luhna/images/pop/psmanim.gif








http://biology.usgs.gov/luhna/images/pop/popsanim.gif



Documents

The Real Scoop on Dirt "More organization and complexity exist in a handful of soil than on the surface of all the other planets combined.” *************************************