Microorganisms often come together to create incredibly tenacious, slime structures known as biofilms. These structures can attach to virtually any wet surface in any environment. The secret to a biofilm’s resilience lies in the ability of its members to work together and coordinate their activities. Biofilms are a fascinating and complex part of our everyday lives. In fact, they can be equally heroes and villains in our ongoing battle against many global issues.
What are Biofilms?
Biofilms are dense clusters of microorganisms wrapped in their own slimy matrix of extracellular polymeric substances (EPS). The EPS matrix – a mix of complex carbohydrates, proteins, lipids, and DNA – provides stability and protection to its inhabitants. It not only surrounds the microbial cells but also acts as a glue, binding them to moist surfaces and keeping the community intact.
Some biofilms contain just one microbial species, but most are a diverse mix of bacteria, archaea, algae, yeast, fungi, and protozoa. Mixed-species biofilms are more resilient than those made of a single microbial species. Biofilms form on natural substrates (e.g., rocks, sediments, plant roots, inside the human body), and man-made surfaces (e.g., pipes and medical implants).
Just like in any thriving community, communication is important for the microorganisms within a biofilm. They can “talk” to one another through chemical signals in a process known as quorum sensing. Biofilm microbes can cooperate with each other and respond to changes in their surroundings through quorum sensing.
Examples of Biofilms:
Drain Clogs: The sticky, unpleasant substance that clogs your drain is usually a biofilm. Microorganisms grow on drain lines and secrete EPS, creating a dense, slimy mass that can block water flow.
Slippery Rocks and Pebbles: If you have ever slipped on a slimy rock or pebble at the bottom of a lake or river, you have encountered a biofilm. These communities help break down organic matter and recycle nutrients in water bodies.
Pet Water Bowls: The thin, slimy film that forms inside your pet’s water bowl is also a biofilm. Microorganisms colonize the surface of the bowl and secrete EPS, creating a layer of slime that can harbour harmful pathogens.
Dental Plaque: Perhaps the most well-known biofilm is dental plaque. This sticky film that forms on our teeth is a complex mixture of microorganisms, EPS, and food particles. If left unchecked, plaque can lead to tooth decay, gum disease, and other oral health problems.
Biofilms in the mineral-rich waters of the hot spring.
Biofilms of iron bacteria appear as an oily sheen on the surface of water.
Why do Microbes form Biofilms?
Microbial biofilms exemplify the age-old adage, “United we stand”. These surface-bound structures help microorganisms to thrive in the most extreme environments. Scientists estimate that 80% of microorganisms form biofilms! This is not surprising, considering the benefits they provide for these organisms. The EPS matrix shields microbial cells from UV radiation, antimicrobial agents, extreme temperatures, and predators. This matrix also traps nutrients from the environment, which are shared by the community.
Biofilm cells are 10 to 1000 times more resistant to antibiotics than free-living cells. Thanks to the densely packed structure of biofilms, microbes can easily exchange antibiotic-resistant genes. The EPS matrix also makes it difficult for traditional antibiotics and biocides to reach and destroy the microbes in its fold.
Just like any good team, biofilm microbes play unique roles that contribute to the overall success of the community. Some scavenge for nutrients, while others secrete enzymes that break down toxic contaminants. Biofilm microbes also fight with one another for limited resources (e.g., space and nutrients); they produce antimicrobial substances that kill their competitors. Such competition shapes the structure of biofilm communities and has a notable effect on their activities.
The EPS matrix has varying levels of oxygen, acidity, and nutrients. This creates small pockets of environments with their own distinct set of conditions. Each micro-environment harbours microorganisms that are adapted to its unique conditions.
The Two-edged Sword of Biofilms
Biofilms are helpful in industry and contribute to countless processes that make life possible. However, they can become a nuisance, wreaking havoc on any surface they choose to colonize. We must be mindful of their destructive tendencies and take measures to control their growth and spread.
Biofilms in the environment and ecosystem
The cycling of key elements such as carbon, nitrogen, phosphorus, and sulfur through the ecosystem is essential for life to thrive. This process – known as biogeochemical or nutrient cycling – is carried out by microbial biofilms. Without nutrient cycling, life would not exist since these elements make up all organisms.
Biofilm microbes have different metabolic capabilities and therefore mediate various biogeochemical processes. They decompose plant matter and dead organisms, releasing carbon and phosphorus for plants’ and microorganisms’ use. Farmers love them, as they help increase crop yields and reduce the need for synthetic fertilizers.
They carry out nitrogen fixation and denitrification, which are necessary for the cycling of nitrogen in ecosystems. Among the many microorganisms in biofilms, Nitrosomonas and Nitrospira play a prominent role in converting nitrogen from its reduced state (ammonia) to its oxidized form (nitrate). This process is called nitrification, and it provides one of the most important nutrients for plant growth – nitrate. Plants absorb and use nitrate as a building block for essential molecules like proteins and nucleic acids.
These nitrifying bacteria take on another important role in water bodies and waste management. They improve water quality by removing ammonia, which is toxic to fish and other aquatic creatures.
Microbial mats are complex biofilms that are made of many coloured layers. Each layer contains microorganisms that perform distinct roles in nutrient cycling. Microbial mats are self-reliant ecosystems because they contain most of the biogeochemical cycles. They are a few millimetres to several centimetres thick and grow at the water-sediment interface of aquatic systems.
Microbial mats also inhabit harsh environments such as hot springs, hot deep-sea vents, desert soils, permafrost of polar regions, and hypersaline lakes.
In coastal environments, the top layers of microbial mats are often home to Cyanobacteria. These organisms provide oxygen and nourishment to the rest of the mat through photosynthesis and fermentation.
Just below this layer are the aerobic heterotrophs that depend on their upstairs neighbours for oxygen and organic molecules. They return the favour by supplying Cyanobacteria with carbon dioxide, which they need for photosynthesis.
Further down, we find methanogens, sulfate reducers, and denitrifying microbes, which require little or no oxygen to grow. It is incredible how they have adapted to life at the bottom of the microbial mat and a testament to the remarkable diversity of the biofilm communities.
But biofilms cause several environmental and ecological problems, such as marine biofouling. Biofouling is the growth of microbes, algae, plants, and small marine creatures (e.g., barnacles and mussels) on underwater objects. It is a major headache for the shipping, naval, and oil and gas industries; experts say that it costs the maritime industry a staggering 30 billion dollars a year!
Microbes first create a slimy layer on submerged surfaces that bigger marine creatures can attach to. Biofouling causes corrosion, engine stress, and increased cleaning time for ships and maritime infrastructure. When biofoulers latch onto a ship’s hull, they increase the vessel’s drag in water and slow its speed, leading to more fuel usage and carbon dioxide emission.
High levels of carbon dioxide (CO2) in the atmosphere increase photosynthesis rates in plants. As plants use more CO2, they make more carbohydrates, develop thicker leaves, and absorb less water and key nutrients. However, thick leaves prevent the exchange of gases and water loss through transpiration. Also, nutrient deficiency can reduce the quality and yield of food crops.
Marine biofouling is also a means through which species travel to new habitats. These alien species can harm local organisms through competitive and predatory activities, or parasitism. This can lead to immense changes in ecosystems, affecting vegetation, animals, and even people.
Biofilms and the fate of environmental pollutants
The EPS matrix works like a sieve, capturing toxic pollutants like microplastics, hydrocarbons, and heavy metals. These pollutants accumulate in the matrix where they are broken down by the biofilm community into less harmful substances or are bound to the cell walls of microbes in a process called biosorption.
Biofilms provide microbes with the ability to withstand and break down pollutants. This is all thanks to their teamwork involving quorum sensing and the high transfer rate of genes involved in biodegradation. Scientists are increasingly using biofilms to clean up contaminated environments and treat wastewater. For example, the oil-eating bacterium, Alcanivorax borkumensis, helps clean up spills in our oceans. It also forms biofilms on plastics and can help remove low-density polyethylene (LDPE) plastics from landfills. Meanwhile, Rhodococcus, Pseudomonas, and Nocardia form powerful biofilms that are effective at eliminating persistent organic pollutants (POPs) from sediments and groundwater.
Persistent organic pollutants (POPs) are chemicals that can remain in the environment for decades without breaking down. POPs (e.g., pesticides, flame retardants) can build up in tissues as they move through the food chain, leading to serious health problems in humans and animals.
Nowadays, bioelectrochemical systems like Microbial Fuel Cells employ biofilm-forming microbes to clean up polluted waters and create sustainable energy. These technologies can remove organic substances from wastewater, recover excess nutrients from effluents, or even desalinate seawater, while generating electricity or gas fuels like hydrogen or methane.
Sometimes, biofilms can become a source of pollutants. The pollutants trapped in the EPS matrix can spill back into the environment through biofilm detachment or gradual leaching. This can drastically affect the ecosystem and serves as a reminder of the unforeseen harm associated with biofilms.
Detachment – the breaking up and dispersal of cells from the biofilm community – is the last phase of the biofilm lifecycle. Various factors can lead to this separation. These include shear pressure, predation, and human interventions with antibiotics or biocides. Environmental conditions like changes in pH, temperature, salinity, and oxygen levels also play a role.
Biofilms as agents of corrosion and corrosion control
Microbial biofilms are gaining more interest as an alternative to traditional anti-corrosion methods. This is because they are cost-effective and more environmentally friendly. Beneficial biofilms can suppress corrosion in metals like copper, steel, and aluminium in four different ways:
- Aerobic bacteria (require oxygen to survive), can prevent corrosion by removing oxygen through aerobic respiration. Oxygen plays an important role in metal corrosion.
- Some bacteria produce antibiotics that can stop the growth of metal-eating microbes. For example, Bacillus brevis produces gramicidin, an antibiotic that curbs steel corrosion by halting the growth of metal-corroding bacteria like Desulfosporosinus orientis and Leptothrix discophora.
- Many microorganisms like Bacillus subtilis and Fusobacterium nucleatum, produce biodegradable corrosion inhibitors, such as polyaspartate and gamma-polyglutamate. Coating metal surfaces with these substances can prevent corrosion.
- Competing microbes like nitrate-reducing bacteria (NRB) can suppress sulfate-reducing bacteria (SRB) which corrodes metals by producing hydrogen sulfide. Creating an environment that promotes the growth of NRB (e.g., through nitrate addition), can prevent SRB from carrying out their damaging activities.
Biofilms can cause major issues in many industries, particularly the water sector. Pipe walls in drinking water distribution systems often contain these close-knit communities. They corrode pipes and reduce the efficiency of heat exchangers, which can affect drinking water quality.
Iron-oxidizing bacteria (e.g., Gallionella ferruginea), sulfate-reducing, and sulfur-oxidizing microbes are mainly responsible for this corrosion. Other microorganisms like Leptothrix sp. (a manganese-oxidizer) and Geothrix fermentans (an iron-reducing bacteria) are also known to speed up steel corrosion in such systems.
Biofilms in the recovery of natural resources
Crude oil
Microbial-enhanced oil recovery (MEOR) involves injecting a mixture of microbes along with nutrients (e.g., fermentable carbohydrates) needed for their growth into oil reservoirs. These microorganisms grow, form biofilms, and produce gases, together with other metabolic products like enzymes, acids, solvents, and biosurfactants, that boost oil recovery by making oil flow easily. Species of Clostridium, for example, produce acetone, hydrogen gas, and butanol, while the archaeon, Methanobacterium, generates methane as an end-product of fermentation. These gases and solvents can displace additional oil and force it to the wellbore. With the help of special enzymes, some bacteria can convert heavy crude oil into light crude, which is less viscous and therefore easier to extract.
Researchers say MEOR can recover up to half of the residual oil in a reservoir following traditional extraction procedures.
Like any deep subsurface environment, oil reservoirs are home to many biofilm-forming microorganisms that are adapted to the high-pressure, high-temperature, and low-oxygen conditions. Among these microscopic inhabitants are sulfate-reducing bacteria and archaea. These microorganisms produce hydrogen sulfide that corrodes pipeline and “sours” oilfields. Reservoir souring significantly lowers the quality and value of crude oil and poses serious risks to oilfield workers. Hydrogen sulfide – the primary culprit behind the rotten-egg stench of sour oil – is both highly explosive and extremely toxic. It spontaneously ignites at high temperatures and inhaling high concentrations can be fatal.
Metallic minerals
Extracting metals from low-grade ores, mine tailings, polluted habitats, and e-wastes can be an expensive and environmentally destructive process. Fortunately, bioleaching – a technique where biofilm-forming microbes are used for metal extraction – is faster, cheaper, and much more environmentally friendly.
Bioleaching is a natural process that has been happening for billions of years through the activities of acidophilic bacteria, archaea, and fungi. These microbes can thrive in acidic environments with pH values below 3.0 and break down sulfide minerals to release metals. Prominent strains of acidophilic bacteria used for bioleaching include Acidithiobacillus thiooxidans and Leptospirillum ferriphilum. These microbes dissolve pyrite to release iron and other metals such as copper while producing sulfuric acid.
Mines are by nature harsh environments. They are hot, humid, and contain abrasive particles, noxious gases, and corrosive chemicals. But some microorganisms can thrive in these extreme environments, making the most of the unique resources. It is no wonder that equipment and machinery quickly corrode if not managed properly, leading to safety and environmental issues.
Among the many causes of corrosion are sulfate-reducing microbes like Desulfovibrio desulfuricans and sulfur-oxidizing microbes like Acidithiobacillus thiooxidans. These microorganisms form tenacious biofilms on metal, steel, and concrete structures, causing damage. Sulfate-reducing microbes produce hydrogen sulfide, which is turned into sulfuric acid by sulfur-oxidizing microbes. This potent chemical not only corrodes metal and steel, but also attacks concrete support systems. Sulfuric acid reacts with calcium hydroxide in concrete to form gypsum, a mineral that causes cracking in concrete.
Biofilms in food processing
Cheese, beer, sourdough bread, and yoghurt owe their unique flavours and textures to biofilm microorganisms. With cheese, Lactic acid bacteria (LAB) ferment lactose in milk into lactic acid, which curdles the milk protein, casein. Lactic acid and other compounds produced by LAB create the complex flavours that we love in cheeses. Similarly, biofilms of yeasts and LAB help transform a mixture of flour and water into sourdough.
Biofilms are useful for fermenting foods and serve as a natural and sustainable way of preserving foods and preventing wastage. We can use beneficial microorganisms as biocontrol agents to increase the shelf life of fruits, vegetables, and grains. These helpful microbes produce antimicrobial compounds that prevent the growth of spoilage bacteria.
Biocontrol or biological control uses living organisms to manage pathogens, insects, weeds, and other pests.
However, food waste and the warm, moist conditions of the food processing environment create an ideal breeding ground for biofilms. Biofilms are difficult to remove when they form on processing equipment and utensils. They can speed up equipment corrosion which would require more cleaning time or costly repairs.
Because they are great insulators, biofilms can interfere with the heating and cooling methods often used in food processing. This can affect the quality of food and put consumers’ health at risk. Contamination of foods with biofilms can cause food-borne illnesses, which can be severe or even fatal. Scientists say that biofilms cause about two-thirds of all food-borne infection incidents!
Biofilm-forming bacteria capable of causing food-borne illnesses include Bacillus cereus that causes diarrhea and vomiting. This bacterium produces spores, which are heat-, chemical-, and radiation resistant. Campylobacter jejuni contaminates raw milk and poultry, bringing about gastroenteritis. Listeria monocytogenes can thrive even under acidic and poor oxygen conditions, and induces miscarriages in pregnant women. Salmonella enterica is the common cause of gastroenteritis and blood poisoning, while Enterohaemorrhagic Escherichia coli (EHEC) is associated with hemorrhagic colitis.
Biofilms in medicine and health
Biofilms also play vital roles in plant, animal, and human health. Take Bacillus subtilis, for example. This bacterium can help combat plant pathogens like the soil-dwelling fungus known as Fusarium. Even in our guts, biofilm microbes help us digest food, produce essential vitamins, defend against disease, and improve our mental health.
These surface-attached communities are also useful for testing new medications and antibiotics. In laboratories, scientists grow biofilms to measure how susceptible they are to various drugs. This strategy has already led to the development of new antibiotics, like teixobactin. By using biofilms to study drugs, scientists can imitate bacterial infections in the body, and gain valuable insights into how effective a drug is.
Interestingly, microbial biofilms are also being explored as potential solutions to infections. Take for example, the coating of urinary catheters with Lactobacilli biofilm. This can prevent colonization by pathogens like Escherichia coli, Staphylococcus aureus, and Pseudomonas aeruginosa. This trio is often associated with urinary tract infections. Likewise, lactic acid bacteria may be beneficial in wound healing. These bacteria can speed up tissue repair and prevent infection through their antibacterial activities.
Of course, not all biofilms are helpful. Experts say biofilms cause roughly 80% of human infections, and they are present in more than half of all chronic wounds, slowing down their healing. Pseudomonas aeruginosa is a troublesome biofilm-forming pathogen, often responsible for chronic wound infections.
In addition, medical devices (e.g., catheters, ventilators) and implants can become hosts to potentially harmful biofilm-producing bacteria like Staphylococcus aureus and Pseudomonas aeruginosa. Biofilm infections are challenging to treat because they are resistant to antibiotics and can evade the body’s immune system. In certain instances, surgery may be necessary to get rid of them.
Remarkably, Staphylococcus aureus causes roughly 70% of device-related infections!
Unfortunately, plants are not immune to biofilm-forming microorganisms either. These tenacious microbes can take over plant leaves, stems, and roots, causing various infections. Xanthomonas campestris is one of the earliest known bacterial plant pathogens. It invades and forms biofilms in the xylem of crucifer crops (e.g., cabbage, broccoli, and cauliflower) resulting in black rot diseases. Xylella fastidiosa, another biofilm-forming bacterium that infects plants, is transmitted by insects that suck on xylem sap. This bacterium is responsible for citrus variegated chlorosis (CVC) in sweet oranges and Pierce’s disease in grapevines.
Concluding Remarks
Biofilm microbes have truly mastered the art of communication and teamwork! These allow them to form tenacious structures that can survive even the toughest conditions. Biofilms have both fascinating and fearsome qualities; on one hand, they have numerous applications in industry, but on the other, they are at the heart of many global problems, causing major financial losses worldwide.
Despite the challenges they present, emerging technologies like spatial omics, 3D bioprinting, and microfluidics are expanding our understanding of the dual nature of biofilms, and how it affects everything from human health to our environment. Continued research and innovation can reveal the hidden potential within these resilient communities. These could lead to new ways to make use of their abilities, and also help us tackle some of the most significant challenges that face our world today.
References
- Cámara, M., Green, W., MacPhee, C. E., Rakowska, P. D., Raval, R., Richardson, M. C., … & Webb, J. S. (2022). Economic significance of biofilms: a multidisciplinary and cross-sectoral challenge. npj Biofilms and Microbiomes, 8(1), 42.
- Carrascosa, C., Raheem, D., Ramos, F., Saraiva, A., & Raposo, A. (2021). Microbial biofilms in the food industry—A comprehensive review. International Journal of Environmental Research and Public Health, 18(04), 2014.
- Carvalho, F. M., Mergulhão, F. J., & Gomes, L. C. (2021). Using lactobacilli to fight Escherichia coli and Staphylococcus aureus biofilms on urinary tract devices. Antibiotics, 10(12), 1525.
- Flemming, H. C., Wingender, J., Szewzyk, U., Steinberg, P., Rice, S. A., & Kjelleberg, S. (2016). Biofilms: an emergent form of bacterial life. Nature Reviews Microbiology, 14(9), 563-575.
- Kip, N., & Van Veen, J. A. (2015). The dual role of microbes in corrosion. The ISME journal, 9(3), 542-551.
- Mahgoub, M. A., Abbass, A. A. G., Abaza, A. F., & Shoukry, M. S. (2022). Probiotic lactic acid bacteria as a means of preventing in vitro urinary catheter colonization and biofilm formation. Journal of the Egyptian Public Health Association, 97(1), 30.
- Mekky, A. F., Hassanein, W. A., Reda, F. M., & Elsayed, H. M. (2022). Anti-biofilm potential of Lactobacillus plantarum Y3 culture and its cell-free supernatant against multidrug-resistant uropathogen Escherichia coli U12. Saudi Journal of Biological Sciences, 29(4), 2989-2997.
- Muhammad, M. H., Idris, A. L., Fan, X., Guo, Y., Yu, Y., Jin, X., … & Huang, T. (2020). Beyond risk: bacterial biofilms and their regulating approaches. Frontiers in microbiology, 11, 928.
- Nikolova, C., & Gutierrez, T. (2020). Use of microorganisms in the recovery of oil from recalcitrant oil reservoirs: Current state of knowledge, technological advances and future perspectives. Frontiers in microbiology, 10, 2996.
- Prieto-Barajas, C. M., Valencia-Cantero, E., & Santoyo, G. (2018). Microbial mat ecosystems: Structure types, functional diversity, and biotechnological application. Electronic Journal of Biotechnology, 31, 48-56.
- Qian, P. Y., Cheng, A., Wang, R., & Zhang, R. (2022). Marine biofilms: diversity, interactions and biofouling. Nature Reviews Microbiology, 20(11), 671-684.
- Saravanan, P., & Balachander, N. (2023). Anti-inflammatory and wound healing properties of lactic acid bacteria and its peptides. Folia microbiologica, 1-17.
- Tsai, W. H., Chou, C. H., Huang, T. Y., Wang, H. L., Chien, P. J., Chang, W. W., & Lee, H. T. (2021). Heat-Killed Lactobacilli Preparations Promote Healing in the Experimental Cutaneous Wounds. Cells, 10(11), 3264.
- Wu, B., Xiu, J., Yu, L., Huang, L., Yi, L., & Ma, Y. (2022). Research advances of microbial enhanced oil recovery. Heliyon, e11424.
- Xu, D., & Gu, T. (2015). The war against problematic biofilms in the oil and gas industry. J Microb Biochem Technol, 7, 124.