Biofilms: Formation, Composition, and Impact on Energy Infrastructure

In many environments, microbial behaviour is shaped by interactions with both surrounding fluids and solid interfaces. Attachment to surfaces provides access to nutrients, stability, and protection from external stressors. Over time, attached cells can proliferate and recruit additional microorganisms, leading to the development of structured communities. These communities exhibit properties that differ markedly from those of free-living cells. Understanding this form of organization is essential for interpreting microbial activity in both natural and engineered systems. 

Table of contents:  

• What are biofilms?  

• How are biofilms built?  

• What are biofilms composed of? 

• Why are biofilms relevant for the energy infrastructure? 

• What are corrosive biofilms? 

• Biofilm monitoring 

• Conclusion on microbial biofilms in energy infrastructure

What are biofilms? 

Biofilms are highly organized, surface-associated microbial communities in which cells are embedded within a self-produced matrix of extracellular polymeric material (EPS). This matrix anchors the microorganisms to biotic or abiotic surfaces and creates a distinct microenvironment that differs from the surrounding bulk fluid. In contrast to the traditional view of microorganisms as individual, free-floating (planktonic) cells, it is now well established that the majority of microbial life in natural, industrial, and clinical settings exists in the form ofbiofilms. These structures can develop on a wide variety of surfaces, including rocks and sediments in natural ecosystems, plant and animal tissues, pipelines, and metal infrastructure. 

Scanning electron micrograph of a multispecies biofilm composed of bacteria and archaea (Dengler et al, 2023).

Growth within a biofilm confers several advantages compared to a planktonic lifestyle. The extracellular matrix and community structure provide enhanced protection against environmental stressors such as desiccation, antimicrobial agents, disinfectants, hydrodynamic shear, and predation. Additionally, the close spatial arrangement of cells within biofilms promotes metabolic cooperation, nutrient exchange, and coordinated behaviour mediated by cell-to-cell signalling mechanisms such as quorum sensing. Through these combined benefits, biofilms support long-term persistence and adaptability, making them the dominant and most successful form of microbial organization on Earth. 

What are biofilms composed of? 

Biofilms are complex and heterogeneous systems made up of microbial cells embedded within a matrix of non-living material. Together, these components form a stable, surface-associated community with properties that differ from those of free-living microorganisms. 

Microbial cells 

The cellular component of a biofilm can range from a single species to highly diverse, multispecies communities. Biofilms commonly include: 

• Bacteria and archaea, which often dominate biofilm structure and metabolism 

• Fungi, algae, and protozoa, which may contribute to nutrient cycling, structural support, or predation 

Within a biofilm, cells are exposed to steep gradients of nutrients, oxygen, and metabolites. As a result, microorganisms in different regions of the biofilm can exhibit distinct physiological states, gene expression profiles, and metabolic roles, even when they belong to the same species. 

Extracellular polymeric substances (EPS) 

A defining feature of biofilms is the presence of extracellular polymeric substances (EPS), which form the structural and functional framework of the community. EPS is produced by the microorganisms themselves and creates a hydrated, three-dimensional matrix that embeds the cells and binds the biofilm together. In most biofilms, EPS accounts for the majority of the total biomass. 

The EPS matrix is composed of several key macromolecules, each contributing specific functions: 

• Proteins, including enzymes and structural proteins, which support biofilm architecture and mediate biochemical reactions 

• Polysaccharides (sugars), which support structural integrity and adhesion and serve as protectors during desiccation periods 

• Nucleic acids, including extracellular DNA (eDNA), which enhances mechanical stability, promotes adhesion, and enables horizontal gene transfer as well as RNA, which is increasingly recognized for roles in structural integrity and regulatory processes 

Through these components, EPS enables attachment to surfaces, cohesion between cells, retention of nutrients and water, and protection against environmental stressors such as antimicrobial agents, disinfectants, and toxic compounds. 

Fluorescence in situ hybridization micrograph of a multispecies biofilm showing archaeal cells (green) and bacterial cells (red) distributed within the biofilm matrix. 

Secondary compounds and environmental materials 

In addition to cells and EPS, biofilms often contain a range of secondary compounds and incorporated materials that influence their physical and chemical properties. These may include: 

• Metal sulfides, frequently occur as metabolic byproducts by anaerobic microorganisms like sulfate reducers 

• Mineral precipitates, formed through microbial activity or chemical reactions within the biofilm 

• Particles derived from the surrounding environment, such as corrosion products, sediments, or organic debris 

The accumulation of these materials can modify biofilm structure, alter local chemistry, and affect interactions between the biofilm and underlying surfaces, particularly in industrial and infrastructure settings. 

Heavy metal sufide deposit in surface gas infrastructure impacted by MIC

How are biofilms built? 

Biofilm formation is a dynamic and regulated process that involves a sequence of developmental stages. These stages are influenced by surface properties, environmental conditions, and microbial physiology, and they allow microorganisms to transition from a free-living to a surface-associated lifestyle. 

Biofilm formation 

Biofilm development typically proceeds through several interconnected steps: 

1. Initial attachment Microbial cells first approach a surface through passive transport (e.g. diffusion or fluid flow) or active motility. At this stage, attachment is usually reversible and governed by weak physical and chemical interactions such as van der Waals forces, electrostatic interactions, and hydrophobic effects. Cell surface structures, including flagella, pili, and fimbriae, facilitate contact with the surface and enable cells to sense surface-associated conditions. 

2. Irreversible attachment Following initial contact, microorganisms strengthen their association with the surface by producing extracellular polymeric substances (EPS). The secretion of EPS anchors cells firmly to the surface and reduces the likelihood of detachment. This transition is often accompanied by changes in gene expression, including the downregulation of motility genes and the activation of pathways involved in matrix production and surface adhesion. 

3. Microcolony formation Once attachment becomes irreversible, cells begin to divide and form small clusters known as microcolonies. During this stage, additional microorganisms may be recruited from the surrounding environment, and cell-to-cell interactions become increasingly important. Quorum sensing and other signalling mechanisms allow cells to coordinate behaviour, regulate EPS production, and initiate collective metabolic activities. 

4. Maturation As microcolonies expand into larger aggregates, the biofilm develops into a complex three-dimensional structure. The continued production of EPS results in the formation of a matrix with water-filled channels that facilitate the transport of nutrients, gasses, and metabolic waste products. Gradients of chemical compounds form within the biofilm, creating distinct microenvironments that support a wide range of metabolic processes, including aerobic and anaerobic respiration, fermentation, and syntrophic interactions. 

5. Stabilization In its mature state, the biofilm reaches a dynamic equilibrium in which growth, cell death, matrix production, and detachment occur simultaneously. The structure is maintainedthrough ongoing microbial interactions and continuous EPS renewal, allowing the biofilm to persist over extended periods despite environmental fluctuations. 

Biofilm detachment 

Biofilms are not static but continuously release cells or cell aggregates back into the surrounding environment. Detachment plays a critical role in biofilm dispersal, population turnover, and colonization of new surfaces. 

• Active dispersal occurs when microorganisms intentionally initiate escape from the biofilm. This process often involves the enzymatic degradation of the EPS matrix and is regulated by environmental cues such as nutrient limitation or changes in oxygen availability. 

• Shear-induced detachment results from external physical forces, including fluid flow, turbulence, or mechanical stress, which can remove individual cells or small biofilm fragments. 

• Sloughing refers to the sudden release of large sections of the biofilm, typically caused by internal weakening of the matrix or strong external forces. 

Through these detachment mechanisms, biofilms can seed new environments and restart the biofilm life cycle elsewhere, contributing to their persistence and widespread distribution. 

Biofilm of sulfate-reducing bacteria isolated from an oil well displays dark aggregates incorporating metal sulfide precipitates.

Why are biofilms relevant for the energy infrastructure? 

Biofilms have a significant impact on the operation, maintenance, and longevity of energy-related infrastructure. Their ability to adhere to surfaces, persist under harsh conditions, and mediate chemical reactions makes them both a challenge and an opportunity for energy systems. The presence of biofilms can lead to material deterioration, structural damage, operational inefficiencies, and increased maintenance costs, but they can also be harnessed for beneficial purposes in engineered processes.  

Oil and gas systems In oil and gas pipelines, reservoirs, and storage tanks, biofilms are common and can cause several problems. Certain microorganisms, such as sulfate-reducing bacteria, produce hydrogen sulfide (H₂S) during metabolism, leading to souring, which degrades product quality and poses safety hazards. Biofilms can also contribute to pipeline plugging, reducing flow efficiency, and accelerate microbiologically influenced corrosion (MIC), which weakens metal surfaces and increases the risk of leaks or failures. These effects result in significant operational costs for monitoring, cleaning, and repair. 

Water distribution systems In drinking water networks, biofilms form on pipe surfaces and storage tanks, where they can harbor pathogenic microorganisms, including bacteria, viruses, and protozoa. The biofilm matrix protects these microbes from disinfectants, reducing the effectiveness of water treatment. Biofilm growth can also lead to clogging of pipes, changes in taste and odor, and localized corrosion, all of which compromise water quality and infrastructure integrity. 

Wastewater treatment systems Not all biofilms are detrimental; in engineered systems, they are intentionally exploited to enhance treatment efficiency. Biofilms are used in trickling filters, biofilm reactors, and anaerobic digesters to degrade organic matter, remove nutrients, and reduce pollutants. The EPS matrix and microbial diversity in these biofilms improve stability, resilience, and overall treatment performance. 

Economic and operational impact The presence of biofilms in energy infrastructure is costly. They accelerate material deterioration and corrosion, reduce operational efficiency, increase maintenance and cleaning requirements, and can cause unplanned downtime. Effective monitoring and management of biofilms are therefore critical to minimize damage, maintain safety, and optimize both natural and engineered systems in the energy sector.   

Corrosive Biofilms 

Corrosive biofilms are specialized microbial communities that accelerate the deterioration of metals through a process known as microbiologically influenced corrosion (MIC). MIC arises from the complex interplay between microbial metabolism, the chemical environment within the biofilm, and electrochemical reactions at the metal surface. Unlike uniform chemical corrosion, MIC is often localized, highly variable, and influenced by the structure and activity of the biofilm itself. 

Microorganisms involved in corrosion 

Several key microbial groups are commonly associated with corrosive biofilms: 

• Sulfate-reducing bacteria (SRB) produce hydrogen sulfide as a metabolic byproduct, which reacts with metal surfaces to form metal sulfides, directly promoting corrosion. 

• Methanogens, a group of archaea, generate methane and can participate in electron transfer processes that influence corrosion rates on metal surfaces. 

• Acetogens produce acetate and other organic acids that may accelerate corrosion chemically or by altering the local biofilm chemistry. 

Phase contrast microscopy image of methanogens as planktonic cells and in biofilm aggregates. Left: Epifluorescence microscopy showing the typical autofluorescence. Right: Phase contrast microscopy.

These organisms frequently coexist within biofilms, forming syntrophic consortia in which metabolic byproducts from one species support the activity of others. This cooperative metabolism often enhances the overall corrosive potential of the biofilm.

Mechanisms of microbiologically influenced corrosion 

MIC is a biological, but also an electrochemical process. It can occur through overlapping mechanisms: 

• Chemical MIC occurs when corrosive metabolic byproducts, such as sulfide or organic acids, chemically attack metal surfaces. 

• Electrical MIC involves the direct uptake or transfer of electrons between microorganisms and metal surfaces, effectively creating a biological “electrochemical cell.” 

Because of these mechanisms, MIC poses a significant challenge in pipelines, storage tanks, offshore platforms, and cooling systems, where it can cause structural damage, leaks, and costly maintenance. 

Biofilm Monitoring 

Effective monitoring of biofilms is essential for managing their impact on industrial and energy infrastructure, as well as for optimizing engineered processes such as wastewater treatment. Because biofilms are often invisible to the naked eye and can develop rapidly under favourable conditions, early detection and characterization are critical to prevent material deterioration, operational inefficiencies, and safety hazards. 

Physical monitoring methods 

Physical approaches involve direct or indirect measurement of biofilm presence, structure, and growth: 

• Coupons and probes are metal, or polymer surfaces inserted into pipelines or reactors to allow biofilm formation and subsequent analysis. 

• Sensors and imaging tools can measure biofilm thickness, density, or attachment in situ, providing real-time or periodic data on biofilm development. 

These methods are particularly useful for assessing the spatial distribution of biofilms and identifying localized hotspots where corrosion or fouling may occur. 

Metal sulfide precipitates on a submersed steel coupon caused by corrosion from a sulfate-reducing bacterium in an aqueous system. 

Chemical monitoring 

Chemical techniques detect biofilm activity by measuring metabolites or byproducts produced by microbial metabolism: 

• Sulfide, organic acids, and ammonia are commonly monitored to assess the activity of corrosive microorganisms. 

• Corrosion products, such as metal sulfides or oxides, provide indirect evidence of microbiologically influenced corrosion (MIC) within pipelines or storage tanks. 

Chemical monitoring allows operators to identify early signs of biofilm-induced material degradation and to implement mitigation strategies before significant damage occurs. 

Microbiological and molecular techniques 

Advanced microbiological methods provide detailed information on biofilm composition, structure, and metabolic potential: 

• Microscopy enables visualization of biofilm architecture and cell density. 

• Culturing techniques allow isolation and characterization of specific microbial species. 

• DNA-based methods, including quantitative PCR (qPCR) and high-throughput sequencing, provide precise identification of microbial populations, including unculturable organisms. 

• Metabolic activity assays measure processes such as respiration, sulfide production, or enzyme activity to assess biofilm functionality. 

Recent advances in real-time sensing technologies and molecular tools are improving the speed, sensitivity, and accuracy of biofilm detection. These innovations allow for continuous monitoring in pipelines, reactors, and water systems, supporting proactive management of harmful biofilms and reducing operational risks and maintenance costs. 

Conclusion 

Biofilms represent the predominant mode of microbial life, characterized by surface attachment, structural organization, and collective behaviour. Their complex composition and dynamic development enable microorganisms to persist under diverse and often harsh conditions. In energy and industrial infrastructure, biofilms play a dual role: they can drive essential engineered processes, but they also contribute to material degradation and microbiologically influenced corrosion. Understanding biofilm formation, composition, and activity, along with effective monitoring strategies, is therefore critical for managing their impact, mitigating risks, and ensuring the reliability and longevity of energy systems.