Workshop 1 - Microbial Ecology

Most life on the planet is microbial. Microbes are diverse, able to adapt to and grow/thrive/reproduce in diverse environments.

species richness = number of species present

species evenness = abundance of species.

Species richness and evenness can be measured by culture-independent or culture-dependent methods. Examples of culture-independent methods are 16S rRNAs, operational taxonomic units (OTUs) and metagenomics. Examples of culture-dependent methods depend on the method, conditions and ability to culture the particular microbes.

Microbiomes play a key role in the host’s physiology, development, immune function/defence, and nutrition. The microbiome may be important in protecting bees against pathogens, helping to prevent colony collapse disorder. Bees play a key role in pollination and food production. The core gut microbiome of worker honey bees contains 9 distinctive species with a characteristic distribution in the hindgut. The different microbial strains have different metabolic capabilities. There is transmission of a consistent gut microbiome across generations of bees.

The Shannon index (H) is one of the main methods of measuring diversity. A higher H value means the community is more diverse. A H value of 0 means there’s only 1 species present.

Colony forming units is an estimate of the number of cells in the original sample. The media and conditions bacteria are grown in must allow the bacteria to grow. Serial dilutions are used to plate the bacteria, colonies are counted after incubation and the cfu is calculated from here.

cfu/mL = number of colonies counted/(dilution factor x volume plated)

Sergei Winogradsky was a pioneering molecular microbiologist and microbial ecologist who carried out research on biogeochemical cycles (N, S) and chemosynthesis. He designed the WInogradsky column.

The Winogradsky column is an artificial microbial ecosystem which act as enrichment cultures depending on the substrates added. Gradients of oxygen and nutrients form and microbes grow in different zones according to their physiology.

Top of Winogradsky column = iron oxidising bacteria which require oxygen to oxidise Fe (II) to Fe (III).

2nd from top in Winogradsky column = cyanobacteria, produce oxygen by photosynthesis.

3rd from top in Winogradsky column = purple and green non sulphur bacteria which usually carry out anoxygenic photosynthesis. May be able to fix nitrogen.

3rd from bottom of Winogradsky column = purple sulphur bacteria, photosynthesise using sulphide or thiosulphate as an electron donor.

2nd from bottom of Winogradsky column = green sulphur bacteria, obligate anaerobes which carry out anoxygenic photosynthesis using H2, H2S and S as electron donors.

Bottom of Winogradsky column = sulphur reducing bacteria. Obligate anaerobes which produce sulphide.