Environmental Microbiology Introduction

1. Environmental Microbiology Introduction

2. Modes of Nutrition

3. Difference between Microbial ecology and Environmental microbiology. ‘Microbial ecology is the study of the behaviour and activities of bacteria in their natural environments’ ‘Environmental microbiology is the effect of microbes on the environment’

4. Laboratory conditions are ideal • plenty of nutrients and monoculture - no competition. • In the world outside the petri dish they can be exposed to: • changing nutrient levels, • oxygen, • pH, • temp, • very low nutrient levels • Competition.

5. Soil particle, an example of a microenvironment Distance is in mm. Concentrations O2 are in %

6. Soil particleAnaerobic at centre, microaerophiles further out, obligate aerophiles near the surface and facultative aerophiles throughout.

7. Ecological Role of Microorganisms

8. Winogradsky Column

9. Estimated that in some environments only 1% of the microbial species have been cultured. This figure comes partly from PCR screening for 16SRNA in samples directly from the environment without culturing. culture conditions for a particular organism hasn’t been ascertained one or two organisms may outgrow (they may even be numerically less important), because laboratory conditions suit them better one microorganism may need the presence of others to grow – Syntrophism. The growth of one organism depends or is improved by factors produced by another, this is often metabolic. This is very common and is probably the main reason.

10. Reminder about phylogenetics

11. Community analysis What are the advantages of community analysis for unculturable organisms?

12. Examples of Signature Sequences used for FISH

13. More restrictive sig seq’s have been made specific for a particular domain, genus or even species. The use of them is useful as they can rapidly place a new microbe in a group. The probes (labelled) can be reacted with bacteria bound to microscope slides and will only stick (hybridise) if there is a sequence match. They are seen under a microscope if a fluorescent dye is attached. This technique has been labelled FISH (fluorescent in situ hybridisation).

14. Multiple FISH Probes on Sewage Sample

15. Terrestrial Environments 1 Soil, rocks, lichens, mycorrhizae

16. Most soils are mineral soils – derived from bogs and marshes. Formation of soils – weathering of rock is by physical, chemical and biological processes. Most exposed rocks have algae, lichens or mosses on (or in) them. They produce organic matter which supports chemoorganotrophic bacteria and fungi. CO2 formed by respiration dissolves to form carbonic acid + organic acids which help dissolve rocks. Freeze thaw etc (Not in Ja!). Plants start to grow in crevices, and a raw soil develops. Plants die adding nutrients for more microbes, more minerals added make the soil more extensive. Eventually trees can grow. This process may take 100’s of years.

17. Profile of a Mature Soil

20. Organic Matter in soils After plant matter, bacteria and fungi are present at the next highest levels in terms of biomass. They actively decompose plant matter releasing the nutrients. Surface soils can have 108 – 109 cells per gram dry weight and fungal hyphae as several hundred metres of hyphae per gdw (gram dry weight). A single fungi can be very big. Some fungi (single organism) can cover a number of acres underground and have a mass measurable in tons. Estimated that only 10% (perhaps as low as 1%) of soil organisms have been cultured.

22. Types of Soils Tropical. Due to high temperatures, organic matter is decomposed rapidly and nutrients can be easily leached out of the soil by rain. Many tropical plants have roots that are shallow and penetrate the organic layer to get nutrients as they are released. Temperate. Decomposition is slower, so litter accumulates. Deep root penetration results in fertile soil, good for intensive farming. Temperate coniferous, acid limits decomposition, also they cause a bleached zone, due to liberation of metal ions. Bog soil. Wet anaerobic conditions lead to slow decomposition.

24. Lichens These are one of the first organisms colonising new environments. They are symbiotic associations of fungi with algae or cyanobacteria. Algae/Cyanobacteria present in a layer/lumps in the lichen. They photosynthesise and if cyanobacteria, usually fixes N2. Fungi gets fixed C and N, Algae/Cyano gets firm anchor with moisture, preventing it from drying up. Usually live in v. dry habitats. Grow very slowly from 1mm-3cm/year

25. Some different Lichens

27. Mycorrhizae These are root/fungus associations in soil. 95% of all plants are thought to form these symbioses. 5 mycorrhizal associations but broadly classed as two. Ectomycorrhizae – fungal cells form a sheath around the root and Endomycorrhizae - Fungal mycelium is embedded in the root.

28. Pine seedling With extensive Mycorrhizal mycelium

29. 6 month old pine Seedlings. Guess Which one was planted in sterile soil and which with mycorrhizae?

31. Rhizosphere • This is the region in the soil immediately adjacent to the roots • It is often high in nutrients/plant secretions. • The # microbes here can be high. • These microbes can aid in • absorbing nutrients by the root, • protecting the plant from pathogen • 3 promoting the formation of root/mycorrhizal • interactions. • Tri and tetrapartite associations can occur between plant, • mycorrhizae, nodulating bacteria and rhizosphere bacteria.

32. A- Seedlings bacterized with Bacillus sp.(UWI-3); B- control; C- Seedlings bacterized with Pseudomonas putida. Data supplied by Threesha Lawrence.

33. A- Potyvirus inoculated + bacterized with Pseudomonas putida; B- Potyvirus inoculated control; C- - Potyvirus inoculated + bacterized with Bacillus sp.Data supplied by Threesha Lawrence

34. A- Potyvirus inoculated + bacterized with Pseudomonas putida; B- Potyvirus inoculated + bacterized with Bacillus sp.; C- Potyvirus inoculated Control

35. Dr McLaughlin and Miss Lawrence believe that in this case the bacteria are aiding the plant in a number of ways. Stimulating the uptake of minerals from soil and stimulating (somehow?) the plants own defences against viruses. In the field (Not possible to use sterile soil) they get increased yield but not increased virus resistance.