1. Advanced Microbiology MICROBIAL ECOLOGY

2. Population, Guilds, and Communities In nature, individual microbial cells grow to form populations. Metabolically related populations are called guilds, and sets of guilds interact in microbial communities. Microbial communities in turn interact with communities of microorganism and the environment to define the entire ecosystem. Microbial Ecology Microbial Ecosystems

3. Environments and Microenvironment Microorganism are very small and their habitats are likewise very small. The microenvironment is the place in which the microorganism actually lives. Microorganism in nature often live a feast-or-famine existence such that only the best-adapted species thrive in a given niche. Cooperation among microorganism is also important in many microbial relationships. Major resources and conditions that govern microbial growth in nature Resources Carbon (organic, CO 2 ) Nitrogen (organic, inorganic) Other macronutrients (S, P, K, Mg) Micronutrients (Fe, Mn, Co, Cu, Zn, Mn, Ni) O 2 and other electron acceptor (NO 3-, SO 42-, etc) Inorganic electron donors (H 2, H 2 S, Fe 2+, etc) Conditions Temperature: cold – warm - hot Water potential: dry – moist – wet pH: 0 – 7 – 14 O 2 : oxic – microoxic – anoxic Light: bright light – dim light - dark Osmotic conditions: freshwater – marine - hypersaline Microbial Ecology

4. Microbial Growth on Surface and Biofilms Oftentimes microorganism grow on surfaces enclosed in biofilms- assemblages of bacterial cells attached to a surface and enclosed in adhesive polysacharides excreted by the cells. Biofilms trap nutrients for growth of the microbial population and help prevent detachment of cells on surfaces present in flowing system. Why do bacteria form biofilms? 1. Type of defense 2. Allows cells to remain in a favourable niche 3. Allow bacterial cells to love in close association with each other 4. The typical way bacterial cells grow in nature Microbial Ecology

5. Formation of a Bacterial Biofilm

6. Microbial Ecology A biofilm of iron oxidizing prokaryotes on the surface of rocks in the iron-rich Rio Tinto, Spain. Photomicrograph of a DAPI-stained biofilm that developed on a stainless steel pipe. Note the water channels.

7. Terrestrial Environments The soil is a complex habitat with numerous microenvironments and niches. Microorganisms are present in the soil primarily attached to soil particles. The most important factor influencing microbial activity in surface soil is the availability of water, whereas in deep soil (the subsurface environment) nutrient availability plays a major role. Microbial Ecology Soil and Freshwater Microbial Habitats A soil aggregate composed of mineral and organic components, showing the localization of soil microorganisms.

8. Freshwater Environments Typical freshwater environments are lakes, ponds, rivers, and springs. The predominant phototrophic organisms in most aquatic environments are microorganisms. In oxic areas cyanobacteria and algae prevail, and in anoxic areas anoxygenic phototrophic bacteria dominate. Most of the organic matter produced is consumed by bacteria, which can lead to depletion of oxygen in the environment. BOD is a measure of the oxygen-consuming properties of a water sample. Microbial Ecology

9. Marine Habitats and Microbial Distribution Marine waters are more nutrient deficient than many freshwaters, yet substantial numbers of microorganisms exist there. Many of these use light to drive ATP synthesis. In terms of prokaryotes, species of the domain Bacteria tend to predominate in oceanic surface water whereas Archaea are more prevalent in deeper water. The dominant phototroph in subtropical open oceanic waters are prochlorophytes. Microbial Ecology Marine Microbiology

10. Percentage of total prokaryotes belonging to either the Archaea or the Bacteria in North Pasific Ocean Water. Microbial Ecology

11. Deep-Sea-Microbiology The deep sea is a cold, dark habitat where high hydrostatic pressure and low nutrient availability prevails. Bacteria isolated from depths below 100 m are Psychrophilic (cold-loving) 2-3 o C. Some are extreme Psychrophiles. Deep-sea microorganism must also be able withstand the enormous hydrostatic pressures associated with great depths. Some organisms simply tolerate high pressure; they are called barotolerant. By contrast, others actually grow best under pressure; these are called barophilic. In even deeper water (10,000 m) extreme (obligate) barophiles can be found. For example, the bacterium Moritella, isolated from the Mariana Trench (Pasific ocean, >10,000 m depth), 700-800 atm. Microbial Ecology

12. Hydrothermal Vents Hydrothermal vents are deep-sea hot springs where volcanic activity generate fluids containing large amounts of inorganic energy sources that can be used by chemolithotrophic bacteria. Two major types of vents have been found. Warm vents emit hydrothermal fluid at temperature of 6-23 o C. Hot vents, referred to as black smokers because the mineral-rich hot water forms a dark cloud precipitated material upon mixing seawater, emit hydrothermal fluid at 270-380 o C. Deep-sea hydrothermal vents are habitats where primary producers are chemolitotrophic rather than phototrophic. Some vents contain nitrifiying, hydrogen-oxidizing, iron-, and manganase-oxidizing bacteria, or methilotrophic bacteria. Microbial Ecology

13. Deep Sea Hot Springs: Hydrothermal Vents Microbial Ecology

14. Microbials Leaching of Ores Oxidation of copper ores by bacteria can lead to the solublelization of copper, a process called microbial leaching. Leaching is important in the recovery of copper, uranium, and gold from low-grade ores. Bacterial oxidation of iron in the iron sulfide mineral pyrite is also an important part of the microbial-leaching process because the ferric iron produced is itself an oxidant of ores. Microbial Ecology Microbial Bioremediation

15. Arrangement of a leaching pile and reactions involved in the microbial leaching of copper sulfide minerals to yield Cu o

16. Mercury and Heavy Metal Transformation A major toxic form of mercury is methylmercury. The latter can yield Hg 2+, which is reduced by bacteria to Hg o. The ability of bacteria to resist the toxicity of heavy metals is often due to the presence of specific plasmid that encode enzymes capable of detoxifying or pumping out the metals. Microbial Ecology Mechanism of Hg 2+ reduction to Hg 0 in Pseudomonas aeruginosa

17. Microbial Ecology Biogeochemical Cycling of Mercury

18. Biodegradation of Xenobiotics Xenobiotics are synthetic chemicals that are not naturally occuring subtance. Many chemically synthesized compounds such as insectiside, herbicides, and plastics are completely foreign to microorganisms but can often be degraded by one or another prokaryote nonetheless. Microbial Ecology Pathway of aerobic 2,4,5-T biodegradation

19. The Plant Environment Key microbial habitats on plants include the rhizoplane/ rhizosphere and the phyllosphere. – Rhizosphere is the region immediately outside the root; it is a zone where microbial activity usually high. – Rhizoplane is the actual root surface. – Phyllosphere is the surface of the plant leaf. – Phylloplane is the actual plant leaf surface Microbial Ecology Microbial Interaction With Plants

20. Lichen structure c A Lichen growing on a branch of a dead tree Microbial Ecology Lichens and Mycorrhizae Lichens are symbiotic associations between a fungus and an alga or corynobacterium. b Lichens coating the surface of a large rock a

21. Miccorrhizae are formed from fungi that associate with plant roots and improve their ability to absorb nutrient. Mycorrhizae have a great beneficial effect on plant health and competitiveness. ectomyorrhizae: fungal cells form an extensive sheath around the outside of the root with only little penetration into the root tissue itself. endomycorrhizae: the fungal mycelium becomes deeply embedded within the root tissue. Typical ectomycorrhizal root of the pine. Pinus rigida with Thelophora terrestis Seeding of Pinus contorta, showing extensive development of the absorptive mycelium.

22. Agrobacterium and Crown Gall Disease The crown gall bacterium Agrobacterium enters into a unique relationship with higher plants. A plasmid in the bacterium (the Ti plasmid) is able to transfer part of itself into the genome of the plant, in this way bringing about the production of crown gall disease. The crown gall plasmid has also found extensive use in the genetic engineering of crop plant. Microbial Ecology Crown Gall

23. Root Nodule Bacteria and Symbiosis With Legumes One of the most widespread and important plant-microbial symbioses is that between legumes and certain nitrogen fixing bacteria. The bacteria induce the formation of root nodules within which the nitrogen-fixing process occurs. The plant provides the energy source needed by the root nodule bacteria, and the bacteria provide fixed nitrogen for the growth of the plant. Legume root nodule bacteria play an important agricultural role because many important crop plants are legumes. Other nitrogen-fixing symbioses include the water fern Azolla and the nodule-forming Frankia. Microbial Ecology

24. Soybean root nodules. The nodules develop by infection with Bradyrhizobium japonicum. Microbial Ecology Effect of nodulation on plant growth. A field of unnodulated (left) and nodulated (right) soybeans plants growing in nitrogen-poor soil.

25. Stages in Root Nodule Formation 1. 2. 3. 4. 5. 6. Recognition of the correct partner on the part of both plant and bacterium and attachment of the bacterium to root hairs. Excretion of nod factors by the bacterium. Bacterial invasion of the root hair. Travel to the main root via the infection thread. Formation of modified bacterial cells, bacteroids, within the plant cells and development of the nitrogen fixing state. Continued plant and bacterial division and formation of the mature root nodule. Microbial Ecology

26. The Infection Thread and Formation of Root Nodules An infection thread formed by cells of Rhizobium leguminosarum Nodules from alfafa roots infected with with cells of Sinorhizobium meliloti