Enable Dark Mode!
Travel Stories: The golden age of microbial ecology

By Esteban Góngora, PhD Student at McGill University

Between August 14 – 19, 2022 I attended the 18th International Symposium on Microbial Ecology from the International Society for Microbial Ecology (ISME) held in Lausanne, Switzerland thanks to the support of the QCBS Excellence Award. ISME is the largest society in the field of microbial ecology and this edition of their symposium (ISME18) was a special one for various reasons. It was the first major in-person conference many of us took part in after a couple of years of virtual conferences. Second, this is a conference that is being held during what many are calling the “golden age” of microbial ecology.

Presenting my research at the 18th International Symposium on Microbial Ecology.

Given their small size, studying microbes has always been a challenging task. We cannot perform community counts the same way that animal or plant ecologists would, but there are still ways to get around this using methods like plate counting. With this method, we create a nutrient medium using agar, a gelatin-like polymer, where microbes can grow if their environmental conditions are met. This technique is similar to how test cages allow behavioural ecologists to study test animals under lab conditions.  Plate counting has been central to the history of microbiology and has helped humanity to treat many diseases by having a means to grow and study microbes. However, it is estimated that we can only grow around 1% of the total microbial diversity using plate counts. This is commonly referred to as the “great plate count anomaly” and it disproportionately affects the most interesting environments and species as these are the ones we know the least about.

With recent advancements and decreasing costs of “omics” technologies (these include metagenomics, single-cell genomics and transcriptomics, and proteomics, among others), we have been able to overcome the need to figure out a way to grow more microorganisms in the lab before being able to study their ecology and physiology. During a panel discussion at ISME18, one of the speakers mentioned that the cost of performing all experiments and characterization needed to describe a single microbial species is between 5000-10,000 USD while the cost of doing a metagenomics sequencing run which can give you genetic information of an entire ecosystem comprising tens and even hundreds of species is around 4000-7000 USD. We can even sequence samples in the field, which removes the need to preserve samples for processing back in the lab. We can study the microbiome of any environment for cheaper and the cost keeps going down at a rate faster than Moore’s law.

Setting up a sequencing run using the MinION field sequencer in the middle of the Arctic Ocean inside the CCGS Amundsen research vessel during its 2019 field season. We had just sampled deep-sea sediment near a methane seep and we used sequencing to see whether the microbial community around the seep has the genomic capability to metabolize the methane and other hydrocarbons released by the seep. Photo taken by Madison Ellis.

One fascinating thing that “omics” technologies are able to provide us is that we can describe new microbial species that no one has ever seen or grown before. Imagine if someone described a new bird species based only on sequencing data obtained by swabbing a rock in the middle of the Amazon without ever having seen or heard the bird. We have advanced so much in the field of microbial ecology thanks to this technology that we are able to tell the microbes life history without ever meeting them. There are still formal requirements to properly name a microbial species that require us to grow and isolate them, but researchers all over the world still recognize that we need to find a way to name these genomes, commonly referred to as metagenome-assembled genomes or MAGs. These MAGs obtained through sequencing currently have names such as HB2-32-21 (this is an actual placeholder name for a proposed genus I found on my high Arctic beach sediment samples for my PhD project that was found in beach sand in other parts of the world as well). This was an important topic discussed during ISME18 and a new naming system for MAGs that can provide names similar to the Linnaean system that is currently used for all domains of life was proposed. This new initiative is called SeqCode and it presents a promising idea to allow our traditional systems used to describe microbial diversity to be able to keep up with the recent advancements producing millions of TB of data that needs to be studied. By being able to name them we can start attempt to better understand the biodiversity of many fascinating environments we have not been able to properly study in the past.

This is a schematic of a MAG obtained from a sediment sample taken from a beach close to Resolute, NU in 2018 and classified as Rhodococcus fascians. By sequencing the beach sediment, we were able to obtain the genome of this bacteria and determine it can degrade alkanes. Additionally, it can also live on inorganic nutrients such as nitrate, sulfate, and carbon dioxide. The green boxes represent complete pathways and blue boxes represent incomplete pathways. Blue arrows represent aerobic processes and red arrows represent anaerobic processes. The schematic was created with Biorender.

I would like to end this post with a quote from one of the keynote speakers of ISME18, Dr. Kenneth Nealson. Dr. Nealson discovered a process known as quorum sensing which is a way in which bacterial cells can communicate with each other and, among other things, allow bacterial communities to control bioluminescence. When he was trying to publish his findings, a reviewer at PNAS told him: “I  [cannot] find anything wrong with the data, but the conclusion can not be correct – bacteria [do not] do this”. As wild as it seems right now to talk about describing organisms based only on DNA sequences on a computer screen, maybe this is another one of those “bacteria [do not]  do this” moments. I am looking forward to seeing what else will come from the golden age of microbial ecology and how it could spread to other parts of ecology. Maybe someday we will be able to actually describe a new bird species by swabbing rocks in the Amazon!

Dr. Nealson giving his keynote speech at ISME18 and telling the story of how he got rejected by PNAS when trying to publish his work on bioluminescence and quorum sensing. His manuscript was later published in the Journal of Bacteriology and now has more than 1500 citations.

About the author: Esteban Góngora is a PhD student in Microbiology working in Dr. Lyle Whyte’s research group at McGill University. Their research focuses on using state-of-the-art sequencing technologies to understand the microbial ecology of hydrocarbon bioremediation in the Arctic, with the goal of characterizing the microbial diversity of beaches across the Northwest Passage in order to understand if these microbes could potentially degrade hydrocarbons from a fuel spill. This is important as the Northwest Passage is slowly opening and brings with it a risk of a ship crashing and releasing all its fuel into the Arctic Ocean and the surrounding beaches.

Post date: December 01, 2023


Submit a Comment

Your email address will not be published. Required fields are marked *