Environmental Microbiology

microbial % of Earth’s biomass

50%

Isolation in pure culture

extracting and growing a single microorganism from its environment for detailed study in a controlled laboratory setting.

Biofilms

Assemblies of bacterial cells adhered to a surface and enclosed in an adhesive matrix

Biofilm matrix

typically a mixture of polysaccharides

Why might bacteria form biofilms?

self defence, so cells can remain in a favourable niche or so cells can live in close association

What bacteria forms a biofilm in the lungs of cystic fibrosis patients?

Pseudomonas aeruginosa

c-di-GMP

microbial hormone which controls biofilm formation

direct isolation

extraction of microbes from the sample by filtration or addition of eluent to release from solid matrix. Dilutions and plating are carried out.

conditions required for direct isolation

Medium and incubation conditions selective for the desired organism

What is direct isolation important for?

detailed, controlled studies and biotechnology applications

enrichment culture

microbes are extracted in the same way as they are for direct isolation, and enriched. They are then diluted and plated out.

What is enrichment culture used for?

isolation in biotech and risk assessments.

agar shake-tube method

dilution of mixed cultures in tubes of molten agar. Used for anaerobic bacteria

direct counting

Uses a grid. Cover slip over microscope slide means there’s a known volume under the cover slip

issues with direct counting

• live and dead cells not easily distinguished

• small cells overlooked

• precision difficult

• low density suspensions hard to count

• motile cells need immobilising

• debris may be counted as cells

Viable Cell Counts aka plate counts

Used to measure the living and reproducing microbial population in a sample. The spread-plate or pour-plate method is used. Sample should be diluted before plating for accuracy

Most Probable Numbers (MPN)

Serial dilution in liquid medium until final tube shows no growth to estimate microbial numbers. Used in routine sampling like food or wastewater analysis.

How is purity checked when using most probable numbers?

By microscopy, colony characteristics, and growth in other media

Oligotrophs (autochthonous microbes/k strategists)

Microbes that grow continuously with low rates of activity. Have nutrient uptake enzymes with low specificity and high affinity.

Copiotrophs (zymogenous microbes or r strategists)

Microbes that primarily exist in a resting phase with brief periods of activity. Their nutrient uptake enzymes have high specificity but low affinity.

arthrobacter

oligotrophs but undergo cell rounding and reduction in growth

Streptomyces

copiotrophs but have metabolically active spores

Viable but Nonculturable Bacteria (VBNC)

Live in state of very low metabolic activity, can’t grow on standard media. Morphologically smaller with reduced nutrient transport, respiration and macromolecule synthesis.

Why do VBNC arise?

In response to stress eg nutrient or osmotic stress

why do VBNC have major implications for public health?

They can become culturable once resuscitated meaning bacterial strains thought to be extinct may be uncovered

antibiotic hunting

streaking a suspected AB producer across one side of a plate. After incubating so antibiotic permeates the agar, the plate is cross-streaked with test organisms and incubated again. Zones of inhibition may be observed

Antibiotic Susceptibility Testing by dilution methods

Determines minimum inhibitory concentration (MIC) of an antibiotic against a specific organism. Successful ABs are effective at low concentrations

Designing antibiotics through genome mining

Sequencing bacterial genomes allows conversion of sequences into proteins in silico. Potential metabolic pathways can be constructed and antibiotics to target these pathways are designed

Microbial leaching

low grade ore dumped and sulphuric acid added. Emerging liquid is enriched in dissolved metals and transported to a precipitation plant. Bacterial oxidation of Fe (II) ions is critical as Fe (III) ions can oxidise metals in the ores.

Contamination of groundwater with uranium

Geobacter and Shewanella reduce water soluble U⁶⁺ to insoluble U⁴⁺

Bioremediation

Using prokaryotes to completely degrade organic pollutants, such as crude oil spills, to less harmful substances like carbon dioxide.

aerobic oxidation of petroleum products

Carried out by diverse range of bacteria, fungi, cyanobacteria and green algae. Best at optimal inorganic nutrient concentration and temperature

xenobiotic compounds

Synthetic chemicals eg pesticides and polychlorinated biphenyls. Most degrade slowly and are common in toxic waste.

Xenobiotic compounds and microbes

Some compounds can be used by microbes as electron donors or carbon sources eg Burkholderia aerobically dechlorinates pesticide 2,4,5-T.

Polyhydroxyalkanoates (PHAs)

Linear polyesters used as storage compounds by bacteria. Degraded by PHA depolymerase in some bacteria, aerobically producing CO₂ and water or anaerobically producing CO₂ and CH₄