NRES322 5

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Chapter 5: Organisms and Their Residues Homework: See handout

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General classification of soil organisms: Animalia - animals Plantae - plants Fungi - fungi Protista - protozoans, nematodes Monera - bacteria, actinomycetes

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Animalia: A. Vertebrates: Burrowing animals: Moles, mice, shrews, gophers Functions: Mix soil with burrowing Hasten decomposition. Create macropores. Can have major effects on soils

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Animalia: B. Invertebrates 1. Arthropods Organism Function Beetles Primary consumer: transport and mixing of organics Ants Primary consumer: transport and mixing of organics; movement of B horizon to surface. Centipedes Predator; minor role in soil formation

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Animalia: B. Invertebrates 1. Arthropods (cont.) Organism Function Millipedes Saprophageous (feed on dead organic matter). Transport and mixing. Springtails Primary consumer: affect soil structure Mites Saprophageous; very important in numbers; affect soil structure Gastropods Eat decaying veg (slugs, snails)

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Animalia: B. Invertebrates Organism Function 2. Annelids Earthworms; very important in soil strucure, 1o breakdown Earthworm (Lumbricidae spp.) most important component of macrofauna (up to 80% of biomass). -Sensitive to pH and moisture -Casts are enriched in N and P; major role in mixing organic matter -2 million/ha in beech forest, 10 million/ha in pasture. None to few in acid soils.

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Animalia: B. Invertebrates - earthworms Lumbricidae terrestris Originated in Europe Uncommon in North America before European settlement. Major effect upon forest floor and soil organic matter in North America, especially in riparian areas (fisherman throw away bait) Now considered a major problem in many ways, including native plants

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Animalia: B. Invertebrates - earthworms - now a major environmental problem http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TC7-4MSR76S-3&_user=1450828&_coverDate=05%2F31%2F2007&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000052773&_version=1&_urlVersion=0&_userid=1450828&md5=ae933a255de3b357369f15b0076ff3b5 http://news.nationalgeographic.com/news/2003/01/0102_030102_earthworms.html http://www.sciencenews.org/20021130/fob5.asp http://apps.caes.uga.edu/news/storypage.cfm?storyid=1894

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Animalia: B. Invertebrates Nematodes Important as population regulators and nutrient concentrators -Nearly microscopic roundworms -Common in mull and grassland soils; some in forest soils -Can be parasites (roots) or predators (on bacteria, fungi) -Fumigation often improves tree growth; may be due to reduction of parasitic nematodes

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II. Plantae (Plants) Roots: 30-40% of plant mass Root hairs (single cell) Rhizosphere: zone within 1 mm; chemically changed, high bacterial concentrations W. Cheng and colleagues have shown that rhizosphere organisms decompose soil organic matter and mobilize nutrients from it

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III. Soil Microflora Many ways to classify One useful way is into these two major groups based on how they get energy: Autotrophic: Use sunlight of inorganic chemical reactions for energy Heterotrophic: Use organic compounds for energy

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III. Soil Microflora Fungi: molds, mushrooms, yeast, rusts Heterotrophic Tolerate low pH (most important in decomposition in acid forest soils (bacteria are acid-sensitive)

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III. Soil Microflora Fungi: molds, mushrooms, yeast, rusts Can be beneficial (even essential): Decomposers of OM Mycorrhizae “fungus root”symbiotic

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III. Soil Microflora Fungi: Mycorrhizae Symbiotic with plant roots - essential to growth in many cases (e.g., pines) Aid in taking up water and nutrients (especially P), and they get carbohydrates in return

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III. Soil Microflora Fungi: Mycorrhizae Two basic kinds: Ectomycorrrhizae: Penetrate only outer cell layers of root and only intercellular spaces (Fig 5.4) Form a sheath/mantle of mycelium on fine roots called Hartig Net Common in trees (pines, spruces, larches, D. fir, oak, birches, beeches, hickory, cottonwood, eucalyptus, aspen

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III. Soil Microflora Fungi: Mycorrhizae Two basic kinds: 2. Endomycorrhizae: Penetrate host cells and change root morphology (monopodal, bifurcate, corroloid Vesicular arbuscular mycorrhizae (form vesicles inside host cells - storage) Occur in many plants including some trees

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Protista: protozoans, algae, and slime mold Protozoa: Consume decomposing organic matter, bacteria, and fungi 1-celled organisms, motile (cilia or flagellum) eat bacteria, fungi Cause of several human diseases (malaria, sleeping sickness, dysentary)

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Protista: protozoans, algae, and slime mold Algae Carrry on photosynthesis (autotrophic) Not decomposers Green, blue-green (the latter now called cyanobacteria) fix N

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Monera: bacteria and actinomycetes

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Monera: bacteria and actinomycetes Bacteria: Single-celled rod or spherical, 1-2 µm 1 tsp = 100,000,000 bacteria = 1,000,000 actinomycetes Three subdivisions based on how they handle oxygen Anaerobes: Live only in the absence of O2 Facultative: Can live in either the presence or absence of O2 Aerobes: Live only in the presence of O2

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Monera: bacteria and actinomycetes Bacteria: Two major subdivisions based on how they get energy: Hetertrophs: Live on dead organic matter Autotrophs: energy from sunlight or chemical reactions Photoautotrophs: use sunlight Chemautotrophs: use inorganic chemical reactions

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Monera: bacteria and actinomycetes Bacteria: Autotrophs Some Important Chemautotrophs Nitrifying bacteria One of the most important autorophic bacteria are nitrifying bacteria, who convert ammonium (NH4+) to nitrite (NO2-) and nitrate (NO3-): 2NH4+ + 3O2 --------> 2NO2- + 4H+ + 2H2O Nitrosomonas 2NO2- + O2 -------> 2NO3- Nitrobacter

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Monera: bacteria and actinomycetes Bacteria: Autotrophs Some Important Chemautotrophs Nitrifying bacteria Very pH-sensitive (don't live below pH 5) Since they produce acid, they are self-limiting. However, nitrification has been observed in very acidic forest soils. Nitrification in these cases may be accomplished by hetertrophic nitrifiers; or in microsites

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Monera: bacteria and actinomycetes Bacteria: Autotrophs Some Important Chemautotrophs Sulfur oxidizing bacteria (not in chapter 5) Another important chemautotroph is Genus Thiobacillus; most important of chemautotroph mineral oxidizers (elemental sulfur and sulfide minerals). For elemental S: 2S + 3O2 + 2H2O -------> 4H+ + 2SO42- Thiobacillus thiooxidans

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Monera: bacteria and actinomycetes Bacteria: Autotrophs Some Important Chemautotrophs Sulfur oxidizing bacteria (cont.) One important reaction carried out by these bacteria is the oxidation of pyrite, FeS2, which occurs commonly in mine spoils by Thiobacillus thiooxidans and Thiobaccillus ferroxidans: 4FeS2 + 1502 + 2H2O  2Fe2(SO4)3 + 4H+ + 2SO42-

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Monera: bacteria and actinomycetes Bacteria: Heterotrophs Include: 1. Decomposers 2. Nitrogen-fixing bacteria Decomposing bacteria Both aerobes and anaerobes Very important for nutrient cycling: convert nutrients from solid phase to ions which go into soil solution

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Monera: bacteria and actinomycetes Bacteria: Heterotrophs Decomposers Both aerobes and anaerobes Very important for nutrient cycling: convert nutrients from solid phase (litter) to ions which go into soil solution

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Monera: bacteria and actinomycetes Bacteria: Heterotrophs Nitrogen fixers: Convert N2 gas in the atmosphere to ammonium (NH4+) in the nodules of roots in certain plants Very important source of N for soils and vegetation, especially in unpolluted areas – soils have no mineral N source! The atmosphere is 78% N2 gas but plants cannot utilize it because of the strong triple bond: N = N Nitrogen fixers take energy from host plants and convert this N to usable form using nitrogenase enzyme More on this important process later in the class

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Monera: bacteria and actinomycetes Bacteria: Heterotrophs Nitrogen fixers: Two subdivisions of nitrogen fixers: Non-symbiotic N2 fixers: Exist as free bacteria, but get energy from nearby organisms (plant rhizosphere, lichens) Symbiotic N2 fixers: live in plant roots, get energy from plant carbohydrates (heterotrophic)

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Monera: bacteria and actinomycetes Symbiotic N fixers include both bacteria and actinomycetes Rhizobium bacteria: Associated with the root nodules of legumes (e.g., Lupine, clover, alfalfa, soybean). Can fix up to 300 kg ha-1 yr-1 (atmospheric deposition = 1-25).

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Monera: bacteria and actinomycetes Symbiotic N fixers: both bacteria and actinomycetes Frankia spp. actinomycetes: Various tree and shrub species (Alnus, Myrica, Elaeagnus, Ceanothus, Cuasarina) (More on actinomycetes below). These are more important than legumes in forests. Can also fix up to 300 kg ha-1 yr-1 (atmospheric dep = 1-25).

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Monera: bacteria and actinomycetes Symbiotic N fixers: Frankia actinomycetes: Excessive N fixation has been shown to cause nitrification, nitric acid formation, nitrate leaching, and soil acidification in red alder

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Monera: bacteria and actinomycetes Free living N-fixers Do not need a host plant Usually fix much less than symbiotic fixers Aerobes: Azotobacter, A. beijerinckia, (hetero) Anaerobes: Clostridium, (most common) Blue-gree algae (Cyanobacteria). Often associated with plant roots; present in cryptogamic/biotic crusts. Believed to be first fixers 2-3 billion years ago.

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Monera: bacteria and actinomycetes Actinomycetes 5-20 µm dia, 0.1 - 1 m long (filaments, but more similar to bacteria) Morphologically transitional from bacteria to filamentous fungi Unicellular, slender branced mycelium Numerically second only to bacteria Aerobic, like pH > 5 Active in decay of cellulose and other organics (hetero) Frankia genus active in nitrogen fixation (as noted above) Some produce antibiotics (exudates which kill bacteria)

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Viruses Non-cellular Non-living nucleic acids with a coating Diseases Prion: nucleic acids with no coat Viroid: no coat around RNA Virus: coat

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Optimum conditions for microbial activity Moisture near FMC pH: near 7 for bacteria; do not do well below pH 5 Temp: biological activity increases 2x as temp goes from 10 to 20 C Exceptions: Psychrophiles: can grow at <5 C, opt at 15 C Mesophiles: slight growth at 0 C, little growth >40 C, opt at 25-37 C Thermophiles: tolerate 45-75 C, opt at 55-65 (composters)

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Encouraging good microbes Inoculation Lime Minimize sterilization Maintain SOM Avoid contamination Avoid stress (drought, temp, etc)

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Controlling bad microbes Start with clean plants Sanitation Minimize mechanical damage Control water. Not too humid Control soil acidity Control infestations quickly (spray)

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Soil organic matter (SOM) Composition of SOM 40-50% C, then H, O, N, P,…. C-chains Humic substances: colloidal, amorphous, polymeric, dark-colored materials. Humus is composed of this; after extensive decomposition

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Soil organic matter (SOM) Composition of SOM Functional breakdowns of humus: Humic acid: soluble in NaOH, but not in HCl Fulvic acid: soluble in both Humin: insoluble in both SOM is very complex, from simple sugars to complex humic substances.

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Decomposition of SOM Activation energy: what it takes to push the reaction over the edge (fire is example) Energy needed to sustain the reaction Reaction Energy

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Decomposition of SOM Enzymes lower activiation energy by acting as Catalysts (substances which activate the reaction but are consumed by it) ( Insight on p. 150, Table 5-4 are examples of enzymes Products of decomposition: CO2, NH4+, H2PO4-, SO42-, Ca2+, K+, Mg2+, Na+, H2O Nutrients are converted from organic form (not useable by plants) to inorganic form (available to plants and microbes)

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Decomposition of SOM Products of decomposition: CO2, NH4+, H2PO4-, SO42-, Ca2+, K+, Mg2+, Na+, H2O Nutrients are converted from organic form (not useable by plants) to inorganic form (available to plants and microbes)

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Decomposition of SOM Factors affecting decomposition Moisture: too dry (aridisols) or too moist (histosols) Temperature: Nitrogen: Carbon to nitrogen ratio (C:N ratio) – a fundamental property of soils that relates to nitrogen status

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Mean Annual Temp Decomposition Litterfall Mean Annual Temp O Horizon mass Both litterfall and decomposition increase with mean annual temperature; however, decomposition increases more rapidly and thus O horizon mass decreases

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O Horizon mass Litterfall CO2 Litterfall CO2 Cold ecosystem Warm Ecosystem

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Other factors affecting the accumulation of soil organic matter: Texture: very important for SOM accumulation: surfaces adsorb (especially allophane and sesquioxides) pH: too low inhibits decomp Disturbance: ploughing is the best example (lost 40% SOM in Great Plains since agriculture). This allowed early settlers to grow crops w/o fertilizer; that is over now.

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C:N Ratio of Organic Organic Matter Compare the C:N ratio of decomposers (microbes) with that of the litter they must decompose

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C:N Ratio of Organic Organic Matter In order for soil microbes to decompose most litter types, they must initially incorporate N from the soil. Thus, inputs of high C:N ratio litter can cause N deficiency to plants unless accompanied by fertilization. As C is lost at CO2 gas, the C/N ratio of the litter decreases to a value ranging of about 20:1 N is released from decomposing litter (Figure 5-9)

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Nitrogen Cycling in Soil: C:N ratios of litter substrate is often much greater than in microbe bodies Therefore, microbes keep the N, release the C as CO2, thereby reducing the C:N ratio: Organic Substrate C:N = 12 to 200 Carbon Nitrogen CO2 Microbes C:N = 12

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Nitrogen Cycling in Soil: In order to consume very high C:N ratio material (such as wood), microbes may need to import ammonium (NH4+) from the soil This is called N immobilization It steals available N from plants! Organic Substrate C:N = 200 Carbon Nutrients CO2 Microbes C:N = 12 NH4+ Immobilization Plants X

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Nitrogen Cycling in Soil: Once microbes have satisfied their N demands, they release N as ammonium (NH4+) during decomposition as they continue to get energy from the organic C This is called N mineralization, and it provides available N to plants Organic Substrate C:N = 12 to 200 Carbon Nutrients CO2 Microbes C:N = 12 NH4+ Mineralization Plants

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C:N Ratio of Organic Organic Matter Organic matter plus microbe N NH4+ As a rule of thumb: At C:N >20:1, NH4+ is immobilized At C:N < 20:1, NH4+ is mineralized C:N >20:1 C:N < 20:1

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Biofuels – be aware of the limitations and dangers! See insight on page 153 The US farmland could produce about 1 quad of biofuels from crop residues US energy consumption is 100 quads per year. Removing more than 30% of crop residues could create problems with wind and water erosion (the dust bowl again?), not to mention greater fertilizer needs and potential loss of soil organic matter. Biofuel plantations could produce more than 1 quad Also, use excessive fuels now in southwestern forests for co-generation

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Organic wastes Animal manure Municipal sludge – application to land instead of dumping in water Composting

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