SOM Lecture 7

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Animalia – rodents, worms, insects Plantae – plants Fungi – molds, mushrooms, Mycorrhizae Protista – algae, protozoa, slime molds Monera - bacteria, actinomycetes Kingdoms of Living Organisms:

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Classification of Microbes

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3 Ameba Flagellate Ameboid Protozoan Ciliate Microfauna (0.002 - 0.2 mm) Mesofauna (0.2 - 2.0 mm) Tardigrade Nematode Woodmite Springtail Macrofauna ( 1- 20 mm) Larva of a Beetle Isopod Megafauna (> 20 mm) Earthworm Important Soil Fauna

NUMBERS AND BIOMASS OF SOIL-INHABITING INVERTEBRATES: 

5 NUMBERS AND BIOMASS OF SOIL-INHABITING INVERTEBRATES TYPE OF ORGANISM NO. M -2 KG. HA -1 PROTOZOA 10 9 -10 10 20-200 NEMATODA (EELWORMS) 10 6 -10 7 10-150 ACARINA (MITES) 10 3 -10 5 5-150 COLLEMBOLA (SPRINGTAILS) 10 3 -10 5 5-150 EARTHWORMS 10-10 3 100-5,000 OTHERS 10 2 -10 4 10-100

NUMBERS AND BIOMASS OF SOIL MICROORGANISMS IN SOIL: 

6 NUMBERS AND BIOMASS OF SOIL MICROORGANISMS IN SOIL TYPE OF ORGANISM NO. M -2 KG. HA -1 BACTERIA 10 13 -10 14 400-5,000 ACTINOMYCETES 10 12 -10 13 400-5,000 FUNGI 10 10 -10 11 1,000-15,000 ALGAE 10 9 -10 10 10-500

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Vertebrates (backbone): Burrowing animals: Moles, mice, shrews, gophers, rabbits, etc. (aeration, structure, fertility, plant damage) Mix soil with burrowing Hasten decomposition Create macropores Can have major effects on soils & plants Animalia: Rodents, Worms & Insects

SOIL INVERTEBRATES IMPORTANT IN ORGANIC MATTER BREAKDOWN: 

17 SOIL INVERTEBRATES IMPORTANT IN ORGANIC MATTER BREAKDOWN EARTHWORMS -OLIGOCHAETES MILLIPEDES -DIPLOPODA WOODLICE -ISOPODA MITES -ACARINA INSECTS -INSECTA SPRINGTAILS -COLLEMBOLA TERMITES -ISOPTERA ANTS -HYMENOPTERA BEETLES -COLEOPTERA FLY LARVAE -DIPTERA CATERPILLARS -COLEOPTERA

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B. Invertebrates (no backbone): Arthropods 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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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 2. Gastropods Eat decaying vegetation (slugs, snails)

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Arthropods

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3. Annelids Earthworm ( Lumbricidae spp.) most important component of macrofauna (up to 80% of biomass). - Very important in soil structure; - 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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Earthworms Stimulate microbial activity Mix and aggregate soil Increase infiltration Improve water-holding capacity Provide channels for root growth Bury and shred plant residue

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Earthworms (3 niches)

Organic matter decomposition - Everyone is involved: 

Organic matter decomposition - Everyone is involved Earthworms Mix fresh organic materials into the soil Brings organic matter into contact with soil microorganisms Corn leaf pulled into nightcrawler burrow Millepede Ants Soil insects and other arthropods Shred fresh organic material into much smaller particles Allows soil microbes to access all parts of the organic residue

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SOIL LIFE

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4. Nematodes Important as population regulators and nutrient concentrators - Nearly microscopic roundworms - Common in 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

Organic matter decomposition Everyone is involved: 

Organic matter decomposition Everyone is involved Protists and nematodes, the predators Feed on the primary decomposers (bacteria, fungi, actinomycetes) Release nutrients (nitrogen) contained in the bodies of the primary decomposers Bacteria-feeding nematode Predatory nematode

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Comparison of bacteria, actinomycetes, and fungi Bacteria Actinomycetes Fungi Numbers highest intermediate lowest Biomass --- similar biomass --- largest Competitiveness most least intermediate for simple organics Fix N 2 Yes Yes No Aerobic/Anaerobic both mostly aerobic aerobic Moisture stress least tolerant intermediate most tolerant Optimum pH 6-8 6-8 6-7 Competitive pH 6-8, all soils >8, dry high pH <5, dominate low Competitiveness soils pH soils

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Many ways to classify One useful way is into these two major groups based on how they get energy; Autotrophic : Use sunlight & inorganic chemical reactions for energy Heterotrophic : Use organic compounds for energy Fungi: Molds, Mushrooms, & Mycorrhizae

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Heterotrophic Tolerate low pH (most important in decomposition in acid forest soils because bacteria are acid-sensitive and do not perform well in acid systems) Decomposers of OM Mycorrhizae “fungus root” - 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 Molds, Mushrooms, Yeast, Rusts

Organic matter decomposition Everyone is involved: 

Organic matter decomposition Everyone is involved Fungi Grow more slowly and efficiently than bacteria when organic matter is added to soil Able to degrade more complex organic molecules such as hemicellulose, starch, and cellulose. Give other soil microorganisms access to simpler molecules that were protected by cellulose or other complex compounds. Soil fungus Fungus on poplar leaf Tree trunk rotted by fungi

Fungi and Soil Structure: 

Fungi and Soil Structure Fungal hyphae (threads) help hold soil granules together Fungal exudates (goo) help cement soil particles together Fungi absent - Soil structure is not maintained when immersed in water Active Fungi Present – Soil structure is maintained when immersed in water

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Symbiotic relationship between plants (roots) & soil fungi Plant provides fungus with energy (C) Fungus enhances soil resource uptake Widespread – Occurs ~80% angiosperm spp All gymnosperms Sometimes an obligate Relationship Mycorrhizae

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Two basic kinds of Mycorrhizae: Ectomycorrrhizae: Penetrate only outer cell layers of root and only intercellular spaces 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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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 Arbuscule in plant cell

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No mycorrhizae With mycorrhizae

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Microorganisms Fungi PSU Em facility Trichoderma Aspergillus Fusarium D.C. Straney K.J. Kwon-Chung Travis & Gugino - PSU

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Protozoa: Consume decomposing organic matter, bacteria, and fungi 1-celled organisms, motile (cilia or flagellum) Cause of several human diseases (malaria, sleeping sickness, dysentery) Algae: Carrry on photosynthesis (autotrophic) Not decomposers Green, blue-green (the latter now called cyanobacteria) fix N Protista: Algae, Protozoa & Slime Molds

Organic matter decomposition Everyone is involved: 

Organic matter decomposition Everyone is involved Bacteria Population increases rapidly when organic matter is added to soil Quickly degrade simple compounds - sugars, proteins, amino acids Have a harder time degrading cellulose, lignin, starch Cannot get at easily degradable molecules that are protected Bacteria on fungal strands Spiral bacteria Rod bacteria

Bacteria: 

Bacteria Services Decomposition of OM Nutrient cycling Nitrogen fixation Nitrification Denitrification Disease Suppression Breakdown of hard to decompose compounds

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

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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 Chemoautotrophs: use inorganic chemical reactions

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Nitrifying bacteria One of the most important autotrophic bacteria are nitrifying bacteria, who convert ammonium (NH 4 + ) to nitrite (NO 2 - ) and nitrate (NO 3 - ): 2NH 4 + + 3O 2 --------> 2NO 2 - + 4H + + 2H 2 O Nitrosomonas 2NO 2 - + O 2 -------> 2NO 3 - Nitrobacter Some Important Chemoautotrophs

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Sulfur oxidizing bacteria Another important chemoautotroph is the Genus Thiobacillus ; most important of chemoautotrophic mineral oxidizers (elemental sulfur and sulfide minerals). For elemental S: 2S + 3O 2 + 2H 2 O -------> 4H + + 2SO 4 2- Thiobacillus thiooxidans One important reaction carried out by these bacteria is the oxidation of pyrite, FeS 2 , which occurs commonly in mine spoils by Thiobacillus thiooxidans and Thiobaccillus ferroxidans: 4FeS 2 + 150 2 + 2H 2 O  2Fe 2 (SO 4 ) 3 + 4H + + 2SO 4 2-

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Some Important Heterotrophs 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 ( mineralization ) Nitrogen fixers: Convert N 2 gas in the atmosphere to ammonium (NH 4 + ) 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% N 2 gas but plants cannot utilize it because of the strong triple bond.

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Two subdivisions of nitrogen fixers: Non-symbiotic N 2 fixers: Exist as free bacteria, but get energy from nearby organisms (plant rhizosphere , lichens) Symbiotic N 2 fixers: live in plant roots, get energy from plant carbohydrates (heterotrophic) 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 y r-1 (atmospheric deposition = 1-25). Frankia spp. actinomycetes : Various tree and shrub species ( Alnus , Myrica , Elaeagnus , Ceanothus , Cuasarina ) These are more important than legumes in forests. Can also fix up to 300 kg ha -1 y r-1

Bacteria vs. Fungi: 

Bacteria vs. Fungi Bacteria are smaller than fungi and can occupy smaller pores and thus potentially have greater access to material contained within these pores. Bacteria are less disrupted than are fungi by tillage practices commonly used in agriculture.

Bacteria vs. Fungi: 

Bacteria vs. Fungi Fungi tend to be selected for by plant residues with high C/N ratios. Fungi have a greater influence on decomposition in no-till systems in which surface residues select for organisms that can withstand low water potentials and obtain nutrients from the underlying soil profile.

Bacteria vs. Fungi: 

Bacteria vs. Fungi Fungi often produce more cell wall than cytoplasmic material when starved for N, and thus can extend into new regions of the soil without requiring balanced growth conditions. The filamentous growth structure of a fungus permits it to access C in one location and nutrients in another.

Organic matter decomposition Everyone is involved: 

Organic matter decomposition Everyone is involved Actinomycetes The cleanup crew Become dominant in the final stages of decomposition Attack the highly complex and decay resistant compounds Cellulose Chitin (insect shells) Lignin Waxes

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Microorganisms Actinomycetes SSSA Univ of Iowa Paul R. August Streptomyces Travis & Gugino - PSU

Variable of SOM Decomposition: 

56 Variable of SOM Decomposition Detritivore Decomposition Microbial Decomposition Optimal Conditions for Detritivores and Primary Decomposers

Detritivore Decomposition: 

57 Detritivore Decomposition Detritivores decrease the size of OM parts and thus increase the surface area exposed to microbial decomposition. Detritivores include invertebrates such as ants, worms, termites, and grubs that chew or cut plant tissues and excrete them or store them below the soil surface. Examples are caterpillars that eat leaves and leaf-cutter ants that carry leaves them into their dens. Detritivores also include vertebrates that chew up and excrete plant or animal tissues or transport and store them below the soil surface. Examples include squirrels that bury acorns, and pack rats that store twigs and leaves in their burrows or nests. Animal excreta (manure) quickly decomposes into SOM because many of the complex bonds are already broken down by internal microbes and chemical actions in the animal.

Microbial Decomposition: 

58 Microbial Decomposition Primary microbial decomposition of OM begins with fungi and bacteria. Microbes may begin to decompose NHS before detritivore activity, but the rate increases after detritivore activity. Fungi are the only microbes that can break the strong bonds between lignin rings. Bacteria can break the simple bonds of NHS substances such as sugars, starches, carbohydrates (cellulose) and fats, but not lignin. Because all fungi and 70% of soil bacteria are aerobes, microbial decomposition is inhibited when the soil is devoid of oxygen (anaerobic).

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59 Optimal Conditions for Detritivores and Decomposers Presence of gaseous O 2 (periodic aerobic conditions)* Steady supply of available, easily-digestible OM or OC* Soil properties Adequate N, P and essential nutrients for microbes Normal soil temperature range (5° to 25° C)* Soil moisture of 9% or higher* Slightly acidic pH Low amounts of toxins, heavy metals, salinity Low bulk density Granular structure 10:1 C:N ratio for microbes * These increase the rate of decomposition