Studying microbial communities

The field has come a long way since I first started studying microbial communities - dare I say - 20 years ago!

When I started out, I was using PCR (a technique that copies tiny amounts of DNA so we can study it) and cloning methods to get an idea of what microbes were present in microbial inoculant products, followed by Sanger sequencing (an early DNA-reading technology). In simple terms, we were trying to answer the question: who is actually living in this microbial community? But doing this was time-consuming, labour-intensive, and expensive - we could only read relatively small amounts of DNA at a time.

By the time I started my PhD in 2012, the field had moved on significantly with the more regular use of 16S rRNA gene metabarcoding - which was being called next-generation sequencing at the time. This technique works a bit like scanning barcodes in a supermarket: instead of identifying products, we identify bacteria based on a specific gene (the 16S rRNA gene) that all bacteria carry, but which differs slightly between species. This allows us to quickly build up a picture of which bacteria are present in a sample.

However, there’s an important limitation. Because this method specifically targets a bacterial gene, it only tells us about the bacterial members of a microbial community. Other microbes - such as fungi and yeasts - don’t have this gene, so they are effectively invisible to this approach. So while it’s an incredibly powerful and widely used method, in some situations we need something less selective if we want to understand the whole community.

Fast forward to today, and I’ve just had a great meeting with a sequencing provider to set up a compost metagenomics project. Metagenomics takes a different approach: rather than targeting one specific gene, we sequence all of the DNA in a sample. You can think of it as taking a full inventory of everything living in the soil, instead of just looking for organisms that carry a particular biological “barcode”.

This means that as well as bacterial members of the community, we should also be able to detect fungi - which are incredibly important members of the soil microbiome and play key roles in processes like nutrient cycling and organic matter breakdown.

The one thing that really struck me was the incredibly low cost now required to generate millions of DNA sequences from a single sample. The field has moved on so quickly in the last two decades - what once took weeks and significant funding can now be done faster, more comprehensively, and at a fraction of the cost.

It was a great meeting, and I’m really looking forward to getting started.