Investigation Toolbox
This page explains some of the common tools which are utilised to investigate the impacts of nutrient changes on heterotrophic bacteria!
What do we want to know about how bacterial communities are affected by nutrient availability? Here I explain the toolbox of skills that I acquired throughout my professional practice!
How can we investigate bacterial communities?
What is there?
To explore the total abundance of bacterial cells Flow Cytometry is an important tool. Flow cytometry is a technique which can be used to count and classify the bacterial cells in a sample. This provides a quick way to compare different treatments! Figure represents the results from some flow cytometry analysis, indicating that the number of bacterial cells is much higher in Treatment A! Figure B shows another feature of flow cytometry! It can be used to classify your cells dependent on their nucleic acid properties!
To learn more about the process of flow cytometry:
Who are there?
Sequencing of 16S rRNA genes and subsequent classification into operational taxonomic units (OTU) can allow us to explore how community composition is altered by nutrient availability! Because marine bacteria are very diverse, the illustration of the communty composition is often done at lower phylogenetic resolution, such as the family level. This gives us a great insight as to whether different conditions favour different bacterial families. This image demonstrates the application of bacterial community analysis. Here you can see the effect of differing nutrient availability between treatment A and B.
Following visualisation of data, multiple statistical analyses can be produced to search for significance in this difference. In this case, a SIMPER analysis was used to investigate what family is contributing to the difference.
What are they doing?
Gene expression is another important resource which can be used to investigate the utilisation of nutrients by heterotrophic bacteria. Measuring the differential gene expression can allow you to understand the different mechanisms of nutrient uptake that bacteria are utilising.
In this case, I used the KEGG database (Kyoto encyclopedia for genes and genomics). This is an online database which holds not only genetic and genomic information, but also information regarding systematic function of genes. Navigation of these sites can be complicated, but here I explain how the KEGG database can be used!
How to utilise the KEGG database to determine the function of a bacterial gene!
Why are these tools important?
Understanding how nutrient conditions alter bacterial growth and overall success, can have a knock on effect further up the food chain. Making flow cytometry a very useful tool.
As shown, community composition analyses can give us information regarding the changes in species presence. This can tell us which species are favouring which conditions!
Bioinformatics is one of the skills on the forefront of bacterial studies. Not only are genomics used to identify the species present, but the ability to see which specific genes are being utilised by parts of a community provides vital insight.