How Modern Science Reveals Stone Biofilms
Beneath the surface of ancient stone buildings, a silent battle between microorganisms and history rages on, revealed only through the lens of cutting-edge genetic science.
When we admire historic stone buildings, we see monuments to human achievement. To scientists, however, these stone surfaces tell another story—an epic tale of microscopic colonization, community building, and gradual decay. For centuries, the true complexity of these microbial cities remained hidden, their inhabitants largely unknown. Today, Next Generation Sequencing (NGS) is pulling back the curtain on this invisible world, revolutionizing our understanding of stone biodeterioration while presenting new scientific challenges 1 .
Biofilms are highly organized communities of microorganisms that function as barriers and create stable internal environments for cell survival. These aggregates represent a predominant form of microbial life that is ubiquitous in natural ecosystems 2 .
On historic stone buildings, these biofilms are more than just unsightly stains—they are sophisticated microbial networks accelerating the degradation of our cultural heritage. The formation of biofilms on stone follows a predictable sequence:
Planktonic bacteria attach to stone surfaces through weak physical forces
Cells secrete sticky polymers, cementing their attachment
Microorganisms form complex three-dimensional structures
In 2017, a groundbreaking study employed NGS to analyze biofilm communities on three degraded siliceous stone church façades in central Rio de Janeiro 1 3 6 . This research would demonstrate both the power and limitations of genetic analysis for cultural heritage preservation.
The research team approached the complex microbial communities using sophisticated genetic analysis:
Biofilms were carefully collected from three different church façades—two located in areas with intense vehicular traffic, and a third surrounded by trees and further from pollution sources
The team utilized the Illumina metabarcoding system to sequence the V4 region of the bacterial rRNA gene
Sequences were analyzed using two different reference databases—Greengenes and Silva—to compare taxonomic identification
This systematic approach allowed for an unprecedented look into the diversity of microbial life thriving on these stone surfaces.
The NGS analysis revealed fascinating patterns in the stone biofilm ecosystems:
| Sample Location | Dominant Bacteria | Dominant Fungi | Environmental Factors |
|---|---|---|---|
| Church 1 (granite) | Actinobacteria | Yeast-like Basidiomycetes & Ascomycetes | Intense vehicular traffic |
| Church 2 (augen gneiss) | Actinobacteria | Yeast-like Basidiomycetes & Ascomycetes | Intense vehicular traffic |
| Church 3 (granite) | Gammaproteobacteria | Yeast-like Basidiomycetes & Ascomycetes | Surrounded by trees, less traffic |
The data revealed that local environment influences community composition more than stone type. The tree-surrounded church biofilm showed greater dissimilarity from the others, suggesting microenvironmental conditions play a crucial role in shaping these microbial communities 1 3 .
Perhaps most surprisingly, 22.8% of fungal Operational Taxonomic Units could not be assigned to any known fungal taxon, highlighting significant gaps in our understanding of stone-inhabiting fungi 1 .
| Advantages and Drawbacks of NGS for Stone Biofilm Analysis | |
|---|---|
Advantages
|
Drawbacks
|
The Rio de Janeiro church study demonstrates the sophisticated tools required for cutting-edge biofilm research. Here are the essential components that made this analysis possible:
| Research Tool | Function in Biofilm Analysis |
|---|---|
| Illumina® Metabarcoding System | High-throughput DNA sequencing of entire microbial communities |
| V4 rRNA Gene Region | Target for bacterial identification and diversity analysis |
| ITS Primers | Genetic markers for fungal identification and classification |
| Greengenes Database | Reference database for classifying bacterial sequences |
| Silva Database | Alternative reference database for sequence classification |
| UNITE Database | Specialized database for fungal identification |
| Principal Components Analysis | Statistical method for visualizing community differences |
Each tool plays a critical role in decoding the complex biofilm ecosystems. The choice of analytical pipeline significantly influenced the results, with two major classes and many genera identified only by the pipeline using the Greengenes database but not the Silva database 1 3 . This underscores the importance of using multiple approaches when studying complex microbial communities.
Next Generation Sequencing has revolutionized our understanding of stone biodeterioration, transforming us from passive observers to informed interpreters of these complex microbial cities. The technology allows conservation scientists to identify not just the obvious players, but the entire microbial network responsible for stone decay.
As we move forward, the challenge lies in standardizing methodologies and expanding reference databases—particularly for understudied fungi.
With more complete information, scientists can develop targeted, effective conservation strategies that protect our architectural heritage at the most fundamental level.
The hidden world on our walls is finally revealing its secrets, and with this knowledge, we stand a better chance of preserving humanity's stone legacy for generations to come.