Decoding the Secret Lives of Subsurface Microbes Inhabiting Gas Storage Sites

Carbon capture and storage is increasingly pursued as a viable means to reduce greenhouse gas emissions in the atmosphere. The subsurface is host to microbial life down to great depths, and the injection gasses carbon dioxide, hydrogen sulfide, and dihydrogen can serve as a source of nutrients and energy that support microbial growth (Fig. 1). Biological response to gas injection was detailed by the IPGP team (Trias et al., 2017), which found that during the pilot studies at Carbfix1, the injection of carbon dioxide into a low-temperature target formation resulted in an increase in abundance of microbes associated with iron-oxidation and carbon dioxide fixation. It was hypothesized that the dissolution of basalt via acidification by gas injection liberated, among others, iron that microbes were using as an energy source, while assimilating carbon dioxide.

Figure 1: Microbial dynamics inside of a geothermal aquifer

The S4CE team at UBO is expanding this work by reconstructing profiles of microbial function over time and across multiple monitoring wells at different distances from the injection site. This is done using metagenomics, which relies on analyzing patterns in gene content to reconstruct metabolic maps that can be used to predict microbial function (Fig. 2). This method examines the genome content of each organism in a sample, a genome being the entire genetic blueprint of a single organism, or the sum of its DNA needed to build and maintain itself. An organism’s genome reveals its total metabolic potential, showing all of the genes, pathways, and cycles it is capable of utilizing, written using combinations of nucleotides (A,T,C,G). A sample from the environment is composed of many individual genomes and genetic material derived from many organisms, and can include bacteria, viruses, archaea, and also eukaryotic organisms like protists and fungi. The sum total of all the genetic material present in a given sample from all of the organisms in that sample is the metagenome.

Metagenomics, the study of metagenomes, often relies on 1. read-based analysis, which looks at marker gene abundance often as indicators of prevalent metabolisms and 2. assembly-based analysis, which uses patterns in read abundance and sequence composition to piece individual genomes back together, resulting in metagenome-assembled genomes, or MAGs.

Metagenomics can tell us about:

  1. Previously undetected life (diversity) missed by other analyses that rely on marker genes
  2. The genetic capabilities of a microbial community and how they are changing over time
  3. Which organisms match to which metabolic pathways present

UBO is generating MAGs using 33 groundwater samples from the Carbfix1 pilot site taken between the years 2008 and 2019, and 6 samples from the Nesjavellir aquifer taken during the period of 2018-2019.

Figure 2: Metagenomics workflow for Carbfix1 and Nesjavellir groundwater samples

While metagenomics can further our understanding of the metabolic capability in a community, the limitation of DNA-based methods is that they cannot distinguish the capability of an organism from what function it is actually carrying out at a given time, under a set of environmental parameters, and at a certain rate. Microbes are often adapted to switch between physiologies to maximize chances of survival, and can have multiple pathways to fulfill the same function under different conditions. How and when are questions that cannot be answered based by an organism’s genetic code alone. To validate hypothesis derived from metagenomics, organisms isolated from the July 2019 sampling campaign to Carbfix1 and Nesjavellir are being grown in the lab (Fig. 3).

UBO is establishing a collection of nearly 100 isolates from Carbfix1 and Nesjavellir groundwaters and will soon be sequencing marker genes to determine the identity of the isolates.

Figure 3: Growth of microbial species isolated from Well HK26 at the Carbfix1 pilot site

Authors: Ashley Grosche