Quantifying the Effect of Encapsulation on Microbial Mineralization Processes Using a Modified DNA Extraction Method
Year: 2026
Type: preprint
Abstract: Microbially-mediated mineral precipitation is important in the natural world and to a number of emerging climate, energy, and water technologies. Central to many microbial mineralization processes is the preferential accumulation of precipitates on microbial surfaces. In some systems, including ureolytic microbially-induced carbonate precipitation (MICP), precipitates may entomb cells in a process termed “encapsulation.” Encapsulation is known to greatly affect microbial systems, but understanding these relationships quantitatively has proven difficult, largely because nucleic acid extraction from encapsulated cells yields inconsistent results. Here, a demineralization protocol adapted from studies of natural microbialites is shown to recover genomic DNA from carbonate-encapsulated Sporosarcina pasteurii at yields indistinguishable from unmineralized cells and of sufficient quality for quantitative PCR. This method allows the degree of encapsulation to be expressed quantitatively as the amount of precipitate formed normalized to the estimated number of cells present, and allows growing populations to be tracked with increased precision. Simultaneous growth and mineralization experiments in mixed batch reactors suggest encapsulation-induced growth suppression at calcium concentrations of 250 mM, which are commonly employed in MICP under different physicochemical conditions. Variable rates of precipitate accumulation on cells, possibly stemming from local mass transport constraints, are proposed as a mechanism of calcium concentration-dependent growth suppression. Accordingly, mass transport principles are used to derive a reaction rate scaling function, allowing the observed growth and precipitation behavior to be replicated by a numerical model. These findings lay the groundwork for a more fundamental understanding of how encapsulation shapes microbial mineralization processes. Importance Some microorganisms have the ability to form minerals from dissolved ions, which often build up on microbial cells and biofilms. We use this phenomenon to answer key questions in geology and ecosystem science, and to engineer new solutions to environmental problems. When microorganisms become fully encased in precipitates, however, it can pose problems for extracting microbial DNA, which limits our biological understanding of these systems. In this study, we use a model calcium carbonate-precipitating bacterium to test a modified DNA extraction approach. This approach allows us to obtain high and reproducible yields of good-quality DNA even from completely encapsulated cells. We then show how this method can help us better understand the fundamental relationship between carbonate precipitation and cell growth.
Institution: University of Michigan
Language: English
Subfield: Environmental Engineering
Field: Environmental Science
Domain: Physical Sciences
Open Access status: green
OpenAlex ID: W7220835506