V. Soil and Plant Microbes / VI. Biofuels from Microbes

• Importance of Microbes

  • Microbes play crucial roles in maintaining the health of natural and managed ecosystems.

  • They are important in biogeochemical cycles, such as the carbon and nitrogen cycles.

  • In ecosystems, microbes function as producers, consumers, and decomposers.

• Soil Environment

  • Soil is a very complex environment (physical, chemical, biological).

  • It's important to consider the soil environment at the microhabitat level.

• Soil Organisms

  • Includes micro-organisms (bacteria, fungi, actinomycetes, protozoans, viruses, nematodes, metazoans, algae) and macro-organisms (insects, earthworms, plant roots and seeds, soil animals).

  • Soil communities can include over 4000 species per gram.

  • Microorganism distribution varies with soil depth. Estimates are conservative as most soil microbes cannot be grown in culture.

• Microbial biomass in soil

  • For surface soil, estimates include approx. 670 lb/acre of bacteria and approx. 703 lb/acre of fungi.

• Competition among soil microbes

  • Competition is intense in the soil environment; many microbes have antagonistic relationships.

  • They compete for organic and inorganic nutrients; active microflora keeps nutrient levels low.

  • Interactions include parasitism, predation, and antibiosis (production of antibiotics).

  • Almost all medicinal antibiotics used today come from soil-borne actinomycetes, bacteria, and fungi. Little is known about antibiotic production levels or function in the natural soil environment.

• Rhizosphere

  • The thin layer or volume of soil immediately surrounding the plant root.

  • Nutrients (exudates like organic acids, amino acids, sugars, polysaccharides) leach into the rhizosphere soil from the roots.

  • Microbial activity is intense due to this nutrient input. The microflora is diverse.

  • Fungistasis (soils naturally preventing fungal germination) is overcome in the rhizosphere due to nutrient input.

  • Similar phenomena occur in the spermosphere (soil surrounding a seed).

  • Significant C transfer from plants to the soil (10-40% of fixed C) occurs in the rhizosphere. This is analogous to gut microflora.

  • Benefits of the rhizosphere microflora for the plant:

    • Make minerals (N, P, K, Fe) available to the plant.

    • Secrete chemicals (plant hormones) that influence root growth.

    • Create an environment favoring the growth of beneficial microbes.

    • Protect the plant root from pathogenic microbes.

• Symbiotic Relationships of Roots and Microbes

  • Relationships are beneficial for both partners.

  • Not all parasites are pathogens; parasitism is a nutritional term, while a pathogen damages the plant. Some parasites can be beneficial.

  • Nitrogen-Fixing Root Nodules:

    • Found in legumes.

    • Involves the soil bacterium Rhizobium.

    • Rhizobium invades legume roots and forms root nodules. They enter via root hairs and an infection thread, developing into bacteroids within enlarged host cells.

    • Discovered by Beijerinck in 1887.

    • This symbiotic relationship benefits both: Rhizobium obtains nutrients, and atmospheric nitrogen is fixed and made available to the plant.

  • Mycorrhizae ("fungus root"):

    • Symbiotic relationship involving plant roots and fungi.

    • The fungi obtain nutrients from the root.

    • The plant benefits from more efficient uptake of water and nutrients, especially phosphorus.

    • Benefits include increased mineral/water uptake, nutrient storage/release, increased tolerance to stress (salinity, metals, infertile soil), and disease resistance.

    • Two main types:

      • Endomycorrhizae: Fungus penetrates root cortical cells, forming arbuscules (arbuscular mycorrhizal fungi). The fungus is inside the root cells. These are ancient relationships, found in 400 Ma fossils.

      • Ectomycorrhizae: Fungus is located between the root cells. They take materials leeched from the cell. Hosts include conifers and some broadleaf trees (oaks, beech, willow).

    • Rhizobium bacteria fix nitrogen while Mycorrhizae fungi do not. This statement is True.

• Plant Pathogenic Microorganisms

  • Include Phytoplasma (EM), Nematodes (LM), Bacteria (EM), Fungi (LM), and Viruses (EM).

  • Examples of plant disease symptoms include Bacterial wilt (e.g., banana), Rust fungus (e.g., oats), Tobacco mosaic virus, and Soybean cyst nematode.

• Virulence factors that help pathogens attack plants

  • Plant cell wall-degrading enzymes.

  • Toxins.

  • Plant growth regulators (hormones).

  • High molecular weight polysaccharides and glycoproteins.

  • Molecules that suppress plant defense responses.

• Plant Disease Resistance

  • Plants lack T cells, B cells, antibodies, and phagocytic cells.

  • They have evolved various mechanisms to defend against pathogen attack.

  • Defense mechanisms include:

    • Production of anti-microbial compounds called phytoalexins.

    • Production of enzymes that degrade pathogen cell walls.

    • Production of structural barriers to pathogen colonization, such as stomatal closure and lignification. Plant cells produce wall material that becomes lignified to resist pathogen penetration. Lignification resists pathogen enzymes.

    • Rapid death of infected cells, known as the hypersensitive response.

  • Plant cells have receptors that recognize Pathogen-associated molecular patterns (PAMPs), similar to innate immunity in animals. Examples of plant receptor analogs include NOD, TOLL, and RIG.

  • Examples of PAMPs recognized by plants:

    • Bacteria: Peptidoglycan, LPS, Flagellin.

    • Fungi: Chitin, Mannans, Ergosterol.

    • Viruses: Double-stranded RNA.

  • The Zig-Zag model describes the ongoing evolutionary arms race between plants and pathogens, involving plant recognition of PAMPs versus pathogen suppression and evasion.

  • Stomata allow for gas exchange (CO2 in, O2 and water vapor out) but also serve as entry points for bacterial pathogens into the leaf.

    • Stomatal closure is a defense; plant receptors perceive flagellin, causing stomata to close.

    • However, pathogens can produce effector molecules like coronatine, which cause stomata to reopen.

  • Plant populations show significant genetic variation for disease resistance. Plant breeders utilize this variation to develop resistant plants.

  • Genetic engineering tools are now used to create plants with new types of resistance.

VI. Biofuels from Microbes

• Environmental Microbiology and Biofuels

  • Microbes can be utilized to produce biofuels.

  • Discussed types include Biogas (Methane), Bioethanol, and Biodiesel.

• Biogas (Methane)

  • Produced from materials like manure, sewage, and plant material.

  • Process involves anaerobic digestion by a consortium of microbes. Methanogenic archaea are responsible for producing the methane gas (CH4).

  • Often an important energy source in the developing world.

  • Methane can also be recovered from landfills.

• Bioethanol

  • Ethanol is a fermentation product.

  • Saccharomyces cerevisiae (yeast) is critical in brewing (anaerobic ethanol production).

  • Corn-based ethanol is considered a short-term solution, as the energy output typically only breaks even with energy input.

  • Cellulosic Ethanol production utilizes biomass feedstock like plant residues and energy crops.

  • The process involves pretreatment (to make cellulose accessible) and fermentation.

  • Generation 1 Biofuel: Ethanol produced from corn and yeast.

  • Generation 2 Biofuel: Ethanol or butanol produced from cellulose and yeast or bacteria.

• Biodiesel

  • Generation 3 Biofuel: Produced by photosynthetic algae or cyanobacteria exposed to sunlight and CO2. These organisms produce fats internally, which are then extracted using a chemical solvent and refined into biodiesel. An example is Botryococcus brunii, which can contain over 50% oil.

  • Generation 4 Biofuel: Uses genetically engineered photosynthetic cells that produce and secrete fats when exposed to sunlight and CO2, allowing for direct refining into biodiesel.

• Degradation of Lignocellulose

  • Efficient degradation of lignocellulose (tough plant fiber) is important for biofuel production. Lignocellulose is difficult to digest and a poor nitrogen source.

  • Two natural examples of systems with microbes specialized in lignocellulose degradation are the termite gut and the cattle rumen.

  • Termite Gut: Termites are important for recycling woody biomass but also cause significant damage to timber structures. They thrive on wood as their sole food source. They rely on a diverse symbiotic gut microflora (protozoa, bacteria, archaea) to digest wood and provide nutrients. The gut is an anaerobic environment. Significant methane (CH4) is released during digestion. Few of these microbes have been cultured. Some gut bacteria can fix nitrogen. Each termite species has a distinctive microflora. Protozoa in the hindgut often contain endosymbiotic bacteria (Pseudotrichonympha grassii). Sequencing their genomes allows researchers to study their metabolic pathways. Termite microbiology research could contribute to biofuel breakthroughs.

Cattle Rumen: Shows many similarities to the termite gut in terms of microbial activity. It is an anaerobic environment with very high microbial concentrations (bacteria/archaea, protozoa, fungi, phage). Microbes degrade plant fiber and ferment sugars to produce volatile fatty acids (VFAs), which provide energy for the animal. Significant CH4 is also released. The microbes themselves are digested by the animal, providing protein and vitamins.