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PROGRAM | Biological Sciences

The Microbiome of Concrete and Naturally Occurring Carbonate Minerals

By: Erik Kiledal Chair: Julie Maresca


Concrete is a common material—second only to water in global annual use—that poses many challenges for inhabiting organisms due to high alkalinity and salinity, desiccation, and exposure to extreme temperatures. Like most environments, concrete is inhabited by microbes; however, little was known about these communities of microbes, how they change over time, or how they are affected by the materials used to produce the concrete. Microbes can have beneficial, deleterious, or neutral relationships with concrete depending on their physiological and metabolic properties, nutrient availability, and environmental conditions. Deleterious microbial relationships with concrete have historically received the most attention, although beneficial relationships have recently gained increased appreciation. These beneficial relationships are of particular interest for concrete production, repair of existing concrete, or even production of “self-healing” concrete. However, most bacteria likely have little to no effect on concrete. The same cannot be said of the harsh concrete environment’s effects on microbes, which impose strong selective pressures favoring (poly-) extremophilic organisms.

Identifying how microbial communities are affected by chemical and physical changes to concrete could provide a means of monitoring concrete “health” by, for instance, identifying microbial bioindicators of concrete degradation. In Chapter 3, the potential of microbes to serve as bioindicators of concrete structural health is tested with a two year time series of microbial community samples from concrete cylinders prone to alkali-silica reaction (ASR) damage, and cylinders mitigated against that reaction. In addition to identifying multiple microbial bioindicators of ASR, this study showed that a large portion of the concrete microbial community originates from precursor materials used in the concrete’s production, and that the community decreases in diversity over time despite seasonally increased diversity in warmer months.

While the cylinder series analyzed in Chapter 3 determined microbial community composition in the first years after concrete is poured, Chapter 4 explores the microbial communities in older existing structures. Chapter 4 provides insight into the heterogeneity of concrete microbiomes across a diverse sample set representing concrete of different ages, mix designs, geographic locations, and sampling protocols. Shotgun metagenomic sequencing was applied in Chapter 4, providing insight into the functional capabilities in the community. High quality metagenome assembled genomes (MAGs) were assembled for 43 organisms providing further insight into adaptations required for life in concrete.

Chapter 4 presents a study of microbial communities in natural analogs of manufactured concrete, namely calcrete and aragonite. While these analogs have considerably different chemical composition, they are nevertheless cementitious materials and could be of particular benefit to concrete bio- production and repair work, as the microbes present in these materials are thought to be at least partially responsible for the formation of these materials. The aragonite samples were collected from a Kentucky stream adjacent to surface coal extraction activities, while the calcrete samples were obtained by different collaborators from two regions in Puerto Rico. Differences in the calcrete communities from North and South coast sites in Puerto Rico were identified, which may explain differences observed in the samples. While considerable differences were observed in the communities from concrete, calcrete, and aragonite, the shared taxa identified may be suitable candidates for concrete bio-repair. Extrapolated metagenomes from 16S rRNA amplicon data identified organisms possessing metabolic pathways suitable for bio-repair.

Most of the work in this dissertation focused on sequence-based analysis of microbial communities in concrete, but Appendix A includes work with individual bacterial strains isolated from concrete and subsequently characterized with physiological assays and long-read genomic sequencing.

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