Research Overview

Nevertheless, the earth’s geosphere is a kingdom for insects and microbes, which are omnipresent and constantly in motion, residing within the subsurface. As a matter of fact, one gram of soil can contain a few billion microorganisms. Some of these microorganisms in the ground interact with the soil minerals and release enzymes through the hydrolysis of carbon and nitrogen. The released enzymes precipitate calcium carbonate with the available calcium source, forming a natural biocement (calcite). The precipitated biocement will enhance the strength of the geomaterial through bridging and bonding particles and reduce the soil permeability through pore clogging. 

Inspired by the process of natural biocementation, the microbially induced calcite precipitation (MICP) process emerged as a sustainable method to biocement poorly graded geomaterials for various geotechnical engineering applications. During the MICP treatment, the urease-producing bacteria ‘Sporosarcina pasteurii’ with a high specific urease rate is commonly employed to catalyze the urea’s hydrolysis to produce ammonium and carbonate ions. In the availability of the calcium source, the biochemical reaction precipitates the calcium carbonate within the soil pores, thereby altering the hydro-mechanical performance. Because of these advantages, biocementation has been beneficial in several field applications such as groundwater remediation, erosion control, ground strengthening, minimizing leaks from a carbon-sequestrated aquifer and slope stabilization.

However, during the MICP treatment, the precipitated biocement on the soil solids also covers already attached bacteria to the grains. This leads to bacteria inactivation for the reaction with chemicals in the pore fluid. This phenomenon is called bacterial encapsulation, where the accumulated calcium carbonate limits the urea hydrolysis rate. Capturing the encapsulation phenomenon requires interdisciplinary knowledge of biology, chemistry, hydraulics, and mechanics to understand the coupled bio-chemo-hydro-mechanical (BCHM) mechanisms. This is because the flow, transport, reaction and deformation processes within the soil mass influence the cementation levels obtained during biocementation. However, understanding the BCHM processes is challenging and time-consuming on a laboratory scale. 

Consequently, a numerical model is essential to comprehend the MICP process and its individual and coupled effects. Although there are numerical models representing the mechanisms controlling biocementation, they usually consider reaction kinetics unaffected by the encapsulation phenomenon. This results in inappropriate predictions in calcite production to a greater extent. At the same time, the biochemical reaction rate kinetics, accounting for the influence of bacterial encapsulation on the urea hydrolysis rate, are not available in the state-of-the-art. Therefore, the current study paved the way for developing an accurate model that includes bacterial encapsulation effects. In this study, the authors Mr. Pavan Kumar Bhukya, Ms. Nandini Adla, and Prof. Dali Naidu Arnepalli from the Department of Civil Engineering, Indian Institute of Technology Madras, Chennai, India, have developed a coupled BCHM model to capture the encapsulation phenomenon during biocementation. The developed numerical model incorporated the negative influence of encapsulation on the rate of biocement precipitation. Above and beyond, the authors captured the encapsulation phenomenon and its coupled effects. It was found that the encapsulation phenomenon significantly influenced the amount of calcite precipitation. The authors suggested that similar simulations must be performed by including encapsulation’s influence on the reaction rate to represent realistic conditions of the MICP treatment process. The present study enhanced the mathematical framework and paved the way for an improved numerical modelling scenario for future research.

Dr. Xuerui Wang, who is a research scientist at the Site Selection Department, Society for Plant and Reactor Safety (GRS) gGmbH, Braunschweig, Germany, confirmed the importance of this study with the following comments: “Sustainable stabilization techniques, such as microbially induced calcite precipitation (MICP) are indispensable to replace chemical soil stabilization practices. The study conducted by Prof. Arnepalli’s research group developed a coupled bio-chemo-hydro-mechanical (BCHM) model focusing on understanding the encapsulation phenomenon during biocementation. Their study highlighted the necessity of considering encapsulation and its influence on the bio-chemo-hydro-mechanical behaviour during MICP treatment. Besides, the study innovatively attempted to include micro-scale parameters such as maximum calcite crystal size into the BCHM modelling framework. The presented results also quantified the effect of encapsulation on the calcium carbonate content, which is an essential outcome of the MICP treatment. Overall, it is an excellent study and provides insights into the mechanism of encapsulation at play when the biocementation initiates in the pore spaces of the soil.”

Here is the link to the Tech-Talk:

https://tech-talk.iitm.ac.in/soils-cemented-biologically-and-environmentally-friendly-way/

Here is the original link to the paper:

https://www.sciencedirect.com/science/article/pii/S1674775523003426 

• Tech-Talk Article 2: Bioengineering the Geomaterials: The Role of Bacterial Adhesion

The need for sustainable engineering practices has become demanding as the global community works toward achieving the United Nations’ Sustainable Development Goals (SDGs). This has increased the emphasis on environmentally friendly engineering solutions that utilise natural processes.

Most civil engineering infrastructure (i.e., buildings, roads, dams) are often constructed on the soil or rocks (known as geomaterials) that make up the earth’s subsurface. These geomaterials, while essential, sometimes fall short in their natural state, lacking the strength and permeability needed for robust construction. To address this problem, ground stabilisation methods are employed to improve the engineering behaviour and meet design standards. Though effective, traditional ground stabilisation methods can be resource-intensive and environmentally harmful, prompting the need for more sustainable and eco-friendly alternatives.

One such pioneering alternative method is biocementation, a process that utilises microbial activity to improve the properties of geomaterials. Microorganisms are plentiful on the ground we walk on. Certain microorganisms, particularly bacteria, can naturally interact with soil minerals and induce the precipitation of calcium carbonate – a natural cementing agent. By leveraging these microbial processes, we can sustainably improve soil strength and reduce permeability. Microbially Induced Calcite Precipitation (MICP) is one of the most widely used biocementation techniques, which utilises the bacteria Sporosarcina pasteurii to hydrolyse urea, leading to the precipitation of calcium carbonate (biocement). The precipitated biocement fills the pores between soil particles and improves engineering behaviour. Consequently, the MICP has several applications in ground stabilisation, plugging leaks in carbon geo-sequestrated aquifers, subsurface barriers, and mitigating erosion.

In the MICP treatment, the bacterial concentration is the major element that releases enzymes by hydrolysing urea, thereby contributing to significant precipitation (CaCO3). Therefore, the amount of biomass plays a substantial role in the effectiveness of the process, but it is influenced by phenomena such as biomass encapsulation and bacterial attachment. Typically, bacterial encapsulation initiates during precipitation, as precipitated biocement covers the attached biomass surface, leading to the inactivation of bacteria for the reaction with chemicals in the pore fluid, thus limiting the urea hydrolysis rate. The attachment of bacteria is another significant phenomenon, which transfers the mass of bacteria from a suspended state in water to an attached state onto the solid grains, which is crucial for biocementation. Without attachment, the bacterium could flush out of the system, resulting in lower calcite precipitation rates. Therefore, a fundamental understanding of biomass encapsulation and attachment is essential for ensuring the efficiency of MICP treatments, even at field scales.

In order to fundamentally understand the MICP treatment and its related mechanisms, knowledge of biology (B), chemistry (C), hydraulics (H), and mechanics (M) is essential. Therefore, considering the complexity of the problem and difficulty in understanding interactions at a laboratory scale, the numerical models are valuable for predicting and optimising the process with relevant physics (i.e., bio-chemo-hydro-mechanics, BCHM).

In a previous study, the authors, Mr. Pavan Kumar Bhukya, Ms. Nandini Adla, and Prof. Dali Naidu Arnepalli from the Department of Civil Engineering, Indian Institute of Technology (IIT) Madras, Chennai, India, had come up with a numerical model to evaluate the rate of bacterial encapsulation, its effect on the precipitated biocement content and permeability. The authors proved that considering the bacterial encapsulation effect on urea hydrolysis rate was necessary and influenced the amount of calcite (calcium carbonate) precipitation.

In the present study, the authors, Mr. Pavan Kumar Bhukya and Prof. Dali Naidu Arnepalli, have focussed on the role of bacterial attachment, developing a BCHM model that takes into account simple and sophisticated attachment rate models which include constant, exponential, gamma, and colloidal models.

The study examined the influence of different bacterial attachment models on biomass distribution and the resulting biocement content. While most research tends to focus on accurately capturing calcite distribution, the bacterial profile plays a crucial role in determining the correctness of these predictions. If bacterial concentrations are misrepresented, the resulting calcite distribution may not reflect the actual physical process. Therefore, it is essential first to calibrate (measure) bacterial distribution to ensure that the attachment rate accurately represents the actual attachment process. Without proper calibration, inaccurate predictions of biomass attachment could have significant consequences, particularly in large-scale applications, if not for laboratory-scale investigations.

With this as a prime goal, the present study developed a numerical model to evaluate the influence of the bacterial attachment models on the BCHM behaviour during the biocementation process. A workflow was also proposed to calibrate (measure) the parameters of all the attachment rate models from suspended bacterial profiles. It was found that the gamma and colloidal attachment theories reasonably predicted the experimental response of suspended biomass distribution and calcite content for the considered test case. However, constant and exponential attachment models overpredicted the calcium carbonate content. All the attachment rate models predicted the permeability changes accurately.

The study underscores the potential applications, future developments of the BCHM model, and adoption of an attachment model to address geotechnical and geoenvironmental engineering problems. This study also reveals that using a constant attachment model for all scenarios will not suffice for reasonably capturing biomass distribution and calcite content. The research highlighted that choosing the suitable bacterial attachment model is critical for accurate predictions in soil bio-cementation. Incorrect model choices can lead to significant errors in estimating calcite content and soil strength. The study also highlights the importance of considering various factors, such as injection strategy, bacterial concentration, and soil properties, to refine attachment models and enhance their predictability. In the future, the authors feel that the work should be extended for several field-scale injection strategies to better predict attached biomass concentration and calcite content. Overall, the study highlights the importance of selecting the correct attachment model to enhance predictability and effectiveness in soil biocementation.

Dr. David Landa Marban, a researcher from the Energy and Technology Division, NORCE Norwegian Research Centre, Bergen, Norway, acknowledged the importance of the work done by the authors with the following comments: “Microbially induced calcite precipitation (MICP) is a bio-geochemical process with promising applications, such as sustainable geomaterial stabilisation. The effectiveness of MICP is fundamentally governed by bacterial attachment, as the bacteria on soil grains significantly contribute to enzyme concentration. These enzymes catalyse the biochemical reaction of urea hydrolysis, resulting in calcium carbonate precipitation, also known as biocement. The study by Prof. Dali Naidu Arnepalli and his Ph.D. student Pavan Kumar Bhukya presents a comprehensive MICP mathematical model, focusing on the bacterial attachment process. By evaluating various bacterial attachment models and their impact on calcite precipitation, the study underscores the importance of selecting an appropriate model to accurately predict attached biomass concentration and biocement content. The results quantify the influence of these models on bacterial and calcium carbonate profiles by comparing them with experimental data. Additionally, the study recommends specific models for different subsurface conditions. In summary, this research provides valuable insights into the bacterial attachment mechanisms that initiate biocementation within soil pore spaces.”

Here is the link to the Tech-Talk:

https://tech-talk.iitm.ac.in/bioengineering-the-geomaterials-the-role-of-bacterial-adhesion/

Here is the original link to the paper:

https://www.sciencedirect.com/science/article/pii/S0266352X2400497X