KANGAROO RAT BURROW BIOFILMS TO IMPROVE SOIL STABILITY: BIOFILM-INDUCED CEMENTATION AND MICROBIAL MECHANISMS

Duygu Aydin

doi:10.7273/000007317

Kangaroo rats (Dipodomys deserti) construct complex burrow systems in loose desert sand that remain stable under extreme environmental conditions due to the cementation effects of biofilms. Burrow biofilms, through their extracellular polymeric substances and filamentous structures, bind sand particles together and increase soil mechanical strength. Utilizing biofilm formations for soil improvement presents an environmentally sustainable alternative to traditional methods that rely on cement and chemical additives. As such, I investigated the mechanisms behind biofilm-induced cementation in kangaroo rat burrows and their application in soil improvement. This work included (1) characterizing microbial communities in kangaroo rat burrow sand and studying the influence of kangaroo rats on the burrow microbiome, (2) identifying the microbial species that are likely responsible for biofilm-induced cementation and assessing their potential contributions to mechanical strength of burrow sand. We collected samples from burrow ceilings of occupied burrows, abandoned burrows, and proximal surface sand in the Sonoran Desert, Yuma, AZ. The results of the first objective revealed that burrow sand exhibited greater bacterial richness and diversity compared to surface sand, with higher abundance of bacterial genera associated with nitrogen fixation, nitrification, and urea hydrolysis. The correspondence of bacterial taxa between burrows and kangaroo rats suggested that kangaroo rats influence the microbial composition of their burrow environment by introducing organic material and waste, resulting in increased species richness and bacterial diversity in the burrows. The second objective explored how different biofilms formed by different microbial species contribute to the strength in burrow sand. To address this, we quantified the tensile strength of pure and mixed biofilm cultures of burrow sand microbiota using the microcantilever technique to assess the potential influence of different species and their combinations on burrow sand tensile strength. The study identified key abundant microbial species, including the fungus Aspergillus tamarii and four bacterial species: Peribacillus frigoritolerans, Paenibacillus ehimensis, Bacillus sp., and Neobacillus niacini for testing. The tensile strength of mono-species biofilms varied, with A. tamarii exhibiting the highest tensile strength (67.3 ± 13.6 kPa) and N. niacini the lowest (9.45 ± 4.84 kPa). Dual-species biofilms exhibited synergistic or antagonistic effects depending on microbial combinations. Increasing species diversity in biofilms to five species resulted in a decline in tensile strength. These findings demonstrate that biofilms formed by different species can contribute to varying degrees of tensile strength in biofilm-induced cemented burrow sand, depending on species composition and interactions. Collectively, this dissertation improves our understanding of biofilm-induced cementation, drawing inspiration from naturally formed biocementation processes in kangaroo rat burrows and translating these insights into practical insights for soil improvement in engineering.

KANGAROO RAT BURROW BIOFILMS TO IMPROVE SOIL STABILITY: BIOFILM-INDUCED CEMENTATION AND MICROBIAL MECHANISMS

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