Environmental DNA, or eDNA, is the genetic material that organisms leave behind in their surroundings. Biofilms are communities of microorganisms that attach to surfaces and encase themselves in a protective matrix. Scientists have begun to utilize biofilms as natural collectors for eDNA. By examining the DNA trapped within these structures, researchers can identify the variety of organisms present in an ecosystem.
The Composition of Biofilms as eDNA Archives
A biofilm’s structure makes it a rich source of environmental DNA. These communities are composed of microorganisms like bacteria, algae, and fungi, held together by a self-produced substance called the extracellular polymeric substance (EPS) matrix. This sticky material allows the biofilm to adhere to submerged surfaces such as rocks, plant roots, and man-made structures.
The adhesive nature of the EPS matrix is key to its function as a DNA archive. As water flows over the biofilm, the matrix traps eDNA shed from a wide array of organisms. This includes genetic material from fish, amphibians, insects, and even mammals that have passed through the area. The DNA becomes entangled and preserved within the dense, protective layers of the biofilm.
This preservation capability offers an advantage over analyzing DNA from water samples alone. In open water, eDNA degrades relatively quickly due to exposure to ultraviolet light, microbial activity, and chemical reactions. The biofilm’s EPS matrix, however, creates a stable environment that protects the entrapped DNA. This stability means that a single biofilm sample can provide a more comprehensive and time-integrated record of the species present.
Methodology for Biofilm eDNA Analysis
The analysis of eDNA from biofilms begins with sample collection. Scientists gather biofilms from various surfaces depending on the research question, such as scraping biofilms from rocks or taking samples from pier pilings. The collected material is then preserved, often by freezing or in a special buffer solution, to prevent DNA degradation during transport to the laboratory.
Once in the lab, a key step is the extraction of DNA from the sample. The resilient EPS matrix must be broken down to release the genetic material held within. This requires specialized chemical protocols and commercially available kits designed to dissolve the matrix without harming the DNA itself.
After the DNA is extracted and purified, it is ready for analysis. A common technique is metabarcoding, which involves amplifying a specific gene region using the polymerase chain reaction (PCR). This amplified DNA is then sequenced using next-generation platforms, which can generate millions of DNA sequences simultaneously. These sequences are then compared against global genetic databases to identify the different species from which the eDNA originated.
Applications in Aquatic and Terrestrial Ecosystems
The use of biofilm eDNA is valuable for monitoring the health of aquatic ecosystems. In rivers and lakes, biofilms on stones and other submerged surfaces act as continuous samplers of the environment. By analyzing the DNA they accumulate, scientists can create a detailed inventory of the species present. This method offers a more integrated picture of biodiversity over time compared to traditional survey methods.
This technique is effective for detecting species that are rare, elusive, or invasive. Organisms that are difficult to find and capture through conventional means, such as netting or visual surveys, still shed DNA into their environment. Biofilms capture this genetic trace, allowing researchers to confirm the presence of these species without physically collecting them. This aids in the early detection of invasive species.
While most applications have focused on freshwater environments, the methodology is also being applied in marine and terrestrial settings. In oceans, biofilms on buoys or plastic debris can reveal information about local marine life. In soils, biofilms on plant roots and mineral particles can provide insights into the complex underground microbial and fungal communities.
Relevance in Industrial and Medical Fields
Beyond environmental science, analyzing eDNA from biofilms has applications in industrial settings. A common issue is biofouling, where biofilms accumulate on surfaces, causing operational problems like clogged pipes or contaminated equipment. By analyzing the eDNA from these biofilms, companies can identify the responsible microorganisms and develop targeted cleaning and prevention strategies.
Another industrial application is in the maritime industry. Biofilms that grow on ship hulls increase drag, which increases fuel consumption and operational costs. Analyzing the eDNA from these biofilms helps researchers understand which organisms are the primary colonizers in different marine environments. This knowledge aids the development of more effective anti-fouling coatings and maintenance procedures.
In the medical field, biofilm analysis is used to address infections associated with medical devices. Biofilms can form on implants like catheters and artificial joints, protecting bacteria from antibiotics and the patient’s immune system. Analyzing the eDNA from these biofilms allows clinicians to identify the microbial species causing the infection, which can guide more effective antibiotic treatments.