SOIL BIO

• Soil organisms classified into two broad groups

  • Soil flora
  • Soil fauna
• Soil flora and fauna subdivided by size

  • Soil macroflora
  • Soil microflora
  • Soil macrofauna
  • Soil microfauna
• Soil organisms belong to six kingdoms (formerly five)
• Approximate life content of as little as ¼ tsp of fertile soil:
• Microorganisms


  Organisms too small to be seen without the aid of a microscope
• Nitrogen cycle


  When molecular N from the air is fixed by soil organisms and forms part of microbial, plant, and animal bodies, and from here, through processes of decomposition, N enters the bodies of soil organisms and humus and is recycled through plants and animals
• Carbon cycle


  The fixation or immobilization of carbon dioxide from the atmosphere and/or biosphere and its regeneration or return to the atmosphere through several microbial processes
• The Five (6) Kingdoms

  • Animalia
  • Plantae
  • Fungi
  • Protista
  • Monera
  • Monera: eubacteria
• Animalia


  • Large burrowing animals (moles, dogs, mice, rabbits, etc), earthworms, arthropods (mites, millipedes, insects, etc), gastropods (slugs and snails), and nematodes (microscopic, unsegmented worms) – also called threadworms or eelworms
• Plantae


  • Plants and algae
• Higher plants


  • The primary producers – the most important groups of organisms in the whole soil population
  • Dead plants contribute to the pool of soil OM which, in turn, provides food, energy, and nutrients to microorganisms and higher plants – a process of plant nutrient cycling
  • Continuous decay of plant roots adds OM to the soil, thereby changing the soil properties, viz. soil aggregation, CEC, water, and nutrient retention capacity, etc
  • Soil minerals combine with OM (a process called organo-mineral reactions) to stabilize soil structure
  • The area of high biological activity surrounding plant roots is called the rhizosphere
• Algae


  • Microscopic (mostly unicellular and growing in water) organisms that carry on photosynthesis
  • Simple chlorophyll-containing plants that live in a high-water environment
  • Are also considered primary producers like higher plants
  • Not important as decomposers but are producers of new photosynthetic growth: include green algae (Chlorophyta), yellow-green algae (Xanthophyta), and the golden-brown algae or diatoms (Bacillaryophyta)
  • What were once called blue-green algae are now reclassified into Kingdom Monera as Cyanobacteria (also called blue-green bacteria; grow in the aquatic environment)
  • Certain algae combine with fungi to form lichens
• Fungi


  • Organisms w/o the ability to use the sun's energy; feed on dead/living plant/animal tissue (saprophytes)
  • Dominate in acid soils
  • Entirely aerobic (live in larger pore spaces) and heterotrophic, they need an abundant supply of oxygen and OM in soil
  • Optimum pH between 4.5 and 6.5
  • Regarded as scavengers as they decompose in soil almost anything that resists breakdown by bacteria
  • One of the first visual evidence of decay is the appearance of fungal mycelia, a vegetative mass of tangled (branching) threadlike filaments (hyphae)
  • Fungi and actinomycetes are the most important agents of soil aggregation due to their threadlike hyphae that twine between soil particles and the gummy substances that they produce that glue the aggregates together
  • Because of their larger size, they make up the largest microbial biomass in the soil
• Fungi


  • Yeasts
  • Multicellular, filamentous molds, mildews, smuts, and rusts
  • Mushrooms – the fruiting body of a fungus whose hyphae feed on decaying material
• Common molds


  • Penicillium
  • Fusarium
  • Aspergillus
• Aspergillus flavus is a common mold growing on grains and nuts and produces aflatoxins – potent carcinogens as in moldy peanuts
• Plant diseases caused by fungi

  • Smuts and rusts on grains
  • Wilts
  • Scabs
  • Leaf spots in bananas
• Fungi that cause plant diseases

  • Verticillium spp – the wilt fungus
  • Rhizoctonia spp – soil-borne fungi, the "damping-off" fungi
• Mycorrhizae


  The term for fungi-root association; are fungi that form a symbiotic relationship with plant roots. They aid in transmitting nutrients and water to the roots and roots transmit substances to the fungi. Helps in the solubilization of phosphorus and its absorption.
• Types of mycorrhizae


  • Ectomycorrhizal fungi – "sheath (envelope) the host root but penetrate only the outer layers of the root cell walls
  • Endomycorrhizal fungi – their hyphae penetrate the host cells. Vesicular Arbuscular Mycorrhizae (VAM)
• Protista


  • Protozoa and slime molds (the main phyla of the Protista kingdom)
• Protozoa


  • Unicellular organism, without a true cell wall
  • Ingest bacteria, fungi, other microbes, nematode larvae, eggs, and even smaller protozoa
  • Different protozoan classes are named for their methods of movement in the soil water; amoeboid moving by pseudopodia, flagellar moving by whiplike units, and ciliate moving by hairlike cilia that "wave"
  • They help to control other microbes but also cause many animal problems: sleeping sickness, severe diarrhea, amoebic dysentery, malaria, etc.
• Monera


  • Prokaryotic or archaebacteria
• Bacteria


  • Simple, unicellular (rod-shaped) microorganisms; the most numerous in the soil (up to 100M organisms may live in one tsp of soil but with the least biomass; most dominant in non-acid soils; growth results in an increase in number; the genera Bacillus, Pseudomonas, Azotobacter, Arthrobacter, Aerobacter and Agrobacterium – are the most abundant in soil. The 1st two genera have the largest number of species present in soil
• Types of bacteria


  • Autotrophic (self-nutritive) – manufacture their own food from CO2 as plants do
  • Heterotrophic – derive their food (C) and energy directly from organic substances
• Nitrification


  1. Nitrosomonas

  2. Nitrobacter

  3. NH4+ -> NO2- -> NO3-
• Symbiotic N2-fixing bacteria


  • Rhizobia (singular- Rhizobium) which fixes atmospheric N2 in plant root nodules
  • Frankia spp. are soil microbes responsible for nodulation in non-leguminous plants like Alnus, Eleagnus, Casuarina, and Coriaria
• Biological N2 fixation


  N2 -> NH3 (catalyzed by nitrogenase)
• Non-symbiotic N2-fixing heterotrophic bacteria

  • Azotobacter and Clostridium – the latter are anaerobic, so they develop best in poorly drained, acid soils
• Associative N2-fixation


  • Undertaken by bacteria in association with most Graminae, e.g., rice, corn, sugar cane, and pasture grasses; does not form nodules. Example Azospirillum brasilense in BioN
• Plant diseases caused by bacteria

  • Wildfire of tobacco
  • Blight of soybeans, rice, and peas
  • Slippery skin of onions
  • Moko of bananas
  • Wilt of carnations, corn and tomatoes
  • Soft rot of fruits
• Human diseases caused by bacteria

  • Bacterial food poisoning (Salmonella)
  • Typhoid fever
  • Rheumatic fever
  • Cholera
  • Dental caries
• Cyanobacteria


  • Formerly blue-green algae, free-living N-fixers thriving in aquatic environments; their source of energy is sunlight
• Actinomycetes


  • Have antibiotic properties
  • Morphologically and taxonomically related to both fungi and bacteria
  • Particularly tolerant of dry soils, thrives in more alkaline or high-temperature conditions
  • The source of numerous beneficial antibiotics, e.g. Streptomyces (also imparts the characteristic smell of damp, well-aerated soil)
  • Many species produce chemicals that stop the growth of other microbes, a phenomenon called antagonism
  • Some produce musty tastes and odors in waters
  • A few species cause plant diseases as potato scab (Streptomyces scabies)
  • Aid in the decomposition of O.M., esp, cellulose and other resistant organic molecules
  • Like fungi, they aid in the development of water-stable soil structures by secreting non-water-soluble gummy substances
• Microbial classification based on oxygen requirements

  • Aerobes – need molecular oxygen as an electron acceptor
  • Anaerobes – grow only without molecular oxygen; are inactive in the presence of oxygen
  • Facultative anaerobes – those which grow and develop with or without oxygen
• Microbial classification based on temperature and pH adaptation

  • Psychrophiles – the cold lovers – those which grow at temperatures below 5° C, but have optimum temperatures near 15-20 °C
  • Mesophiles – those which grow between 20 and 40°C
  • Thermophiles – the heat lovers – those that proliferate higher than 45°C
  • Acidophilic – acidic medium lovers
  • Alkaliphilic – alkaline medium lovers
  • Halophiles – salt-loving bacteria
• Microbial classification based on energy and carbon requirements for cell synthesis

  • Heterotrophs – derive their energy from oxidation of complex organic compounds
  • Autotrophs – utilize C from CO2 for cellular synthesis
• Heterotrophs further classified into

  • Photoheterotrophs – derive energy from sunlight; C from O.M.
  • Chemoheterotrophs – derive their energy and nutritive carbon from O.M.
• Autotrophs further classified into

  • Chemoautotrophs – derive their energy from oxidation of inorganic substances such as N, S, or Fe
  • Photoautotrophs – derive their energy from sunlight
• Environmental factors influencing microbial activity

  • Water
  • Temperature
  • Aeration
  • Reaction (pH)
  • Light
  • Food
  • Energy rich material
  • Soil factor
  • Microbial association