Microorganisms with macro potential

September 29th, 2023

Exploring biomineralising microbes for in-situ and ex-situ long-term carbon storage

Project duration: July 2023–June 2026

Image: Adapted from a cropped version of Figure 6in ‘Microbe-Mediated Extracellular and Intracellular Mineralization: Environmental, Industrial, and Biotechnological Applications’, published in Adv. Mater. 2020, 32, 1907833.  (https://doi.org/10.1002/adma.201907833) by Qin, W., Wang, C.-y., Ma, Y.-x., Shen, M.-j., Li, J., Jiao, K., Tay, F. R., Niu, L.-n.; used under CC BY 4.0.

Project lead

veena nagaraj

Dr Veena Nagaraj

Research scientist


Yongqiang Chen, Richard Schinteie, Hafna Ahmed, James McLaughlin, Joanna Strzelecki, Yen Truong, Anna Kaksonen, David Midgley and Linda Stalker.


Biomineralising microorganisms (e.g., cyanobacteria) contribute significantly to carbon sequestration and storage through the formation of carbonates in sediments and geological structures such as stromatolites and limestone rocks. Under natural conditions, carbon storage in these reservoirs is a slow process.

In recent years there’s been increasing interest in biomineralising microorganisms, primarily focused on creating construction materials. But despite showing potential for both in-situ and ex-situ applications (e.g., in subsurface rocks and as engineered microbial structures), the use of biomineralising microbes and their biofilms in carbon sequestration and storage is yet to be explored. While we do know that some microbes and communities biocalcify more rapidly than others, and certain types of rocks are more reactive with CO2, there are still significant gaps in knowledge.

What’s missing is a fundamental understanding of how to optimise the process of biomineralisation for accelerated carbon sequestration and safe, permanent storage. There’s an opportunity to fill that knowledge gap and harness powerful biotechnology IP with commercial appeal across a wide variety of sectors including energy, mining, construction and environment/conservation. Cultivating native microbes from subsurface environments and microbialites may be the breakthrough required to make large-scale biomineralisation a reality. 


We aim to identify the most rapidly biocalcifying microbes and biofilms, their metabolic pathways, community composition, and interactions with their environment, and then develop biological methods and technology to rapidly accelerate mineral carbonation processes, , via introduction into subsurface rock samples (in-situ) and engineered microbialite formations (ex-situ).

Microbialites are a novel model ecosystem as a carbon sink but, given they form 3.5-billion-year-old living fossils in Western Australia that act as ‘carbonate factories’, they are an untapped resource for mineral carbonation. Our approach is also unique in investigating the use of in-situ and ex-situ mineral carbonation strategies with microbial biomineralisation as the common denominator. The reasoning is simple; microbes survive in all environments including extreme conditions.

Initially, we’ll simulate environmental conditions for both applications in the lab. To achieve the highest possible carbonation rates and preserve the integrity of rock materials with in-situ carbonation, we’ll determine the optimal microbial communities, concentrations and exposure times, and the most appropriate rocks in which to introduce microbes. With ex-situ carbonation we’ll use the inherent nature of cyanobacteria and other biomineralising microbes to build biostructures that can accelerate the natural process of biomineralisation. While this is novel and fundamental research, successful methods and technology for in-situ and ex-situ biomineralisation have high commercial appeal, and value, to many different industry sectors. Moreover, together with the work of other CarbonLock FSP colleagues, this would place CSIRO at the forefront of negative emissions technology.


During in-situ experiments, there’s a chance rapid biofilm formation (without carbonation) may cause fractures in the rock samples to become clogged, possibly impacting the integrity of the rock material. Selecting strains of microbes and biofilms with rapid yet controllable biocalcification rates should overcome this issue.

In the ex-situ component of the research there are work safety concerns. Microbialites are mainly constituted by cyanobacterial biomineralisers, which can be potentially harmful if inhaled or ingested. We’ll address this by isolating strains from microbialite formations in designated physical containment labs and working with the appropriate personal protective equipment.

Scalability may also be an issue, given field trials will require permits for research in high-conservation natural environments. As an alternative, we’ll pivot to pilot-scale experiments in purpose-built facility. This is a complex project involving integration across interdisciplinary fields. A major component is dependent on lab work for cultivation and experimentation so contamination of microbe and biofilm communities or technical issues are possible. Given the depth of experience in the project team, these should be minimal.


Carbfix (2014). In situ mineral carbonation using captured CO2 emissions from a geothermal plant.

Dosier et al. (2019). Biocementation method and system.

Jones, T. R., Poitras, J., Gagen, E., Paterson, D.J., & Southam, G. (2023). Accelerated mineral bio-carbonation of coarse residue kimberlite material by inoculation with photosynthetic microbial mats. Geochemical Transactions, 24(1), 1.  https://doi.org/10.1186/s12932-023-00082-4