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113-423: The Sippewissett Salt Marsh houses a diverse, laminated intertidal microbial mat around 1 cm thick. The mat is characterized by regular influx of sea water, high amounts of sulfide and iron, and the production of methane. The mat contains four or five distinctly colored layers. The color of each layer can be attributed to the microbial community composition and the biogeochemical processes they perform at each of

226-454: A reef -like build-up rather than by "falling" out of the water, and this build-up has been at least influenced and perhaps sometimes caused by the actions of microbes. Stromatolites , bioherms (domes or columns similar internally to stromatolites) and biostromes (distinct sheets of sediment) are among such microbe-influenced build-ups. Other types of microbial mat have created wrinkled "elephant skin" textures in marine sediments, although it

339-487: A bacterium first became an endosymbiont of an anaerobic archean and then fused with it to become one organism. If such endosymbiosis was an important factor, microbial mats would have encouraged it. There are two known variations of this scenario: Microbial mats from ~ 1,200  million years ago provide the first evidence of life in the terrestrial realm. The Ediacara biota are the earliest widely accepted evidence of multicellular animals. Most Ediacaran strata with

452-586: A biofilm depends highly on the different species present. The EPS matrix consists of exopolysaccharides , proteins and nucleic acids. A large proportion of the EPS is more or less strongly hydrated, however, hydrophobic EPS also occur; one example is cellulose which is produced by a range of microorganisms. This matrix encases the cells within it and facilitates communication among them through biochemical signals as well as gene exchange. The EPS matrix also traps extracellular enzymes and keeps them in close proximity to

565-452: A biofilm depends on competence stimulating peptide (CSP). CSP also functions as a quorum-sensing peptide. It not only induces biofilm formation, but also increases virulence in pneumonia and meningitis. It has been proposed that competence development and biofilm formation is an adaptation of S. pneumoniae to survive the defenses of the host. In particular, the host's polymorphonuclear leukocytes produce an oxidative burst to defend against

678-578: A biofilm exopolysaccharide released immotile aggregates at high initial velocities, enabling the bacteria to recolonize fresh surfaces and cause infections in the hosts efficiently. Hence, biofilm dispersal is more complex than previously thought, where bacterial populations adopting distinct behavior after biofilm departure may be the key to survival of bacterial species and dissemination of diseases. Biofilms are usually found on solid substrates submerged in or exposed to an aqueous solution , although they can form as floating mats on liquid surfaces and also on

791-446: A biofilm is thought to make it harder to treat the infected lungs of people with cystic fibrosis. Early detection of biofilms in wounds is crucial to successful chronic wound management. Although many techniques have developed to identify planktonic bacteria in viable wounds, few have been able to quickly and accurately identify bacterial biofilms. Future studies are needed to find means of identifying and monitoring biofilm colonization at

904-575: A biofilm was recorded after spine surgery. It was found that in the absence of clinical presentation of infection, impregnated bacteria could form a biofilm around an implant, and this biofilm can remain undetected via contemporary diagnostic methods, including swabbing. Implant biofilm is frequently present in "aseptic" pseudarthrosis cases. Furthermore, it has been noted that bacterial biofilms may impair cutaneous wound healing and reduce topical antibacterial efficiency in healing or treating infected skin wounds. The diversity of P. aeruginosa cells within

1017-523: A calcified state which is more difficult to remove. Removal techniques can also include antimicrobials . Dental plaque is an oral biofilm that adheres to the teeth and consists of many species of both bacteria and fungi (such as Streptococcus mutans and Candida albicans ), embedded in salivary polymers and microbial extracellular products. The accumulation of microorganisms subjects the teeth and gingival tissues to high concentrations of bacterial metabolites which results in dental disease. Biofilm on

1130-418: A combination of competition and co-operation. Since the metabolic capabilities of bacteria (what they can "eat" and what conditions they can tolerate) generally depend on their phylogeny (i.e. the most closely related groups have the most similar metabolisms), the different layers of a mat are divided both by their different metabolic contributions to the community and by their phylogenetic relationships. In

1243-503: A commonly used biofilm model organism since it is involved in different types of biofilm-associated chronic infections. Examples of such infections include chronic wounds, chronic otitis media, chronic prostatitis and chronic lung infections in cystic fibrosis (CF) patients. About 80% of CF patients have chronic lung infection, caused mainly by P. aeruginosa growing in a non-surface attached biofilms surround by PMN . The infection remains present despite aggressive antibiotic therapy and

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1356-555: A dormant state. Microbial mats that live in tidal zones, such as those found in the Sippewissett salt marsh , often contain a large proportion of similar microorganisms that can survive for several hours without water. Microbial mats and less complex types of biofilm are found at temperature ranges from –40 °C to +120 °C, because variations in pressure affect the temperatures at which water remains liquid. They even appear as endosymbionts in some animals, for example in

1469-488: A few centimeters in thickness, of which only the top few millimeters are oxygenated. Underwater microbial mats have been described as layers that live by exploiting and to some extent modifying local chemical gradients , i.e. variations in the chemical composition. Thinner, less complex biofilms live in many sub-aerial environments, for example on rocks, on mineral particles such as sand, and within soil . They have to survive for long periods without liquid water, often in

1582-461: A few survive in deserts. A few are found as endosymbionts of animals . Although only a few centimetres thick at most, microbial mats create a wide range of internal chemical environments, and hence generally consist of layers of microorganisms that can feed on or at least tolerate the dominant chemicals at their level and which are usually of closely related species. In moist conditions mats are usually held together by slimy substances secreted by

1695-540: A form of sexual interaction, favored under conditions of high cell density and/or stress where there is maximal opportunity for interaction between the competent cell and the DNA released from nearby donor cells. This system is optimally expressed when S. mutans cells reside in an actively growing biofilm. Biofilm grown S. mutans cells are genetically transformed at a rate 10- to 600-fold higher than S. mutans growing as free-floating planktonic cells suspended in liquid. When

1808-407: A highly purified effluent. Slow sand filters are used in water purification for treating raw water to produce a potable product. They work through the formation of a biofilm called the hypogeal layer or Schmutzdecke in the top few millimetres of the fine sand layer. The Schmutzdecke is formed in the first 10–20 days of operation and consists of bacteria , fungi, protozoa , rotifera and

1921-556: A host body's immune system. A biofilm usually begins to form when a free-swimming, planktonic bacterium attaches to a surface. Biofilms are thought to have arisen during primitive Earth as a defense mechanism for prokaryotes, as the conditions at that time were too harsh for their survival. They can be found very early in Earth's fossil records (about 3.25 billion years ago) as both Archaea and Bacteria, and commonly protect prokaryotic cells by providing them with homeostasis, encouraging

2034-408: A layer of photosynthesizing purple bacteria that could tolerate oxygen; and oxygen-free, H 2 S -dominated lower layers of heterotrophic scavengers, mainly methane-emitting and sulfate-reducing organisms. It is estimated that the appearance of oxygenic photosynthesis increased biological productivity by a factor of between 100 and 1,000. All photosynthetic reactions require a reducing agent , but

2147-657: A middle purple layer inhabited by photosynthesizing purple bacteria. Some other mats have a white layer inhabited by chemotrophic sulfur oxidizing bacteria and beneath them an olive layer inhabited by photosynthesizing green sulfur bacteria and heterotrophic bacteria. However, this layer structure is not changeless during a day: some species of cyanobacteria migrate to deeper layers at morning, and go back at evening, to avoid intensive solar light and UV radiation at mid-day. Microbial mats are generally held together and bound to their substrates by slimy extracellular polymeric substances which they secrete. In many cases some of

2260-400: A range of aquatic insect larvae. As an epigeal biofilm ages, more algae tend to develop and larger aquatic organisms may be present including some bryozoa , snails and annelid worms. The surface biofilm is the layer that provides the effective purification in potable water treatment, the underlying sand providing the support medium for this biological treatment layer. As water passes through

2373-428: A result of the growing commercial potential, there have been applications for and grants of patents relating to the growing, installation and use of microbial mats, mainly for cleaning up pollutants and waste products. Biofilm Aggregate of microorganisms in which cells that are frequently embedded within a self-produced matrix of extracellular polymeric substances (EPSs) adhere to each other and/or to

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2486-523: A result, microbial mats began to produce the atmosphere we know today, in which free oxygen is a vital component. At around the same time they may also have been the birthplace of the more complex eukaryote type of cell , of which all multicellular organisms are composed. Microbial mats were abundant on the shallow seabed until the Cambrian substrate revolution , when animals living in shallow seas increased their burrowing capabilities and thus broke up

2599-804: A short time (by geological standards) the build-up of dead microorganisms would have created an ecological niche for scavenging heterotrophs , possibly methane-emitting and sulfate-reducing organisms that would have formed new layers in the mats and enriched their supply of biologically useful chemicals. It is generally thought that photosynthesis , the biological generation of chemical energy from light, evolved shortly after 3,000  million years ago (3 billion). However an isotope analysis suggests that oxygenic photosynthesis may have been widespread as early as 3,500  million years ago . There are several different types of photosynthetic reaction, and analysis of bacterial DNA indicates that photosynthesis first arose in anoxygenic purple bacteria , while

2712-428: A surface such as a tooth or rock, and may include a single species or a diverse group of microorganisms. Subpopulations of cells within the biofilm differentiate to perform various activities for motility, matrix production, and sporulation, supporting the overall success of the biofilm. The biofilm bacteria can share nutrients and are sheltered from harmful factors in the environment, such as desiccation, antibiotics, and

2825-476: A surface. A biofilm is a syntrophic community of microorganisms in which cells stick to each other and often also to a surface. These adherent cells become embedded within a slimy extracellular matrix that is composed of extracellular polymeric substances (EPSs). The cells within the biofilm produce the EPS components, which are typically a polymeric combination of extracellular polysaccharides , proteins , lipids and DNA . Because they have

2938-449: A three-dimensional structure and represent a community lifestyle for microorganisms, they have been metaphorically described as "cities for microbes". Biofilms may form on living (biotic) or non-living (abiotic) surfaces and can be common in natural, industrial, and hospital settings. They may constitute a microbiome or be a portion of it. The microbial cells growing in a biofilm are physiologically distinct from planktonic cells of

3051-568: A wet environment where sunlight is the main source of energy, the uppermost layers are generally dominated by aerobic photosynthesizing cyanobacteria (blue-green bacteria whose color is caused by their having chlorophyll ), while the lowest layers are generally dominated by anaerobic sulfate-reducing bacteria . Sometimes there are intermediate (oxygenated only in the daytime) layers inhabited by facultative anaerobic bacteria. For example, in hypersaline ponds near Guerrero Negro (Mexico) various kind of mats were explored. There are some mats with

3164-491: Is a common cause of death in CF patients due to constant inflammatory damage to the lungs. In patients with CF, one therapy for treating early biofilm development is to employ DNase to structurally weaken the biofilm. Biofilm formation of P. aeruginosa , along with other bacteria, is found in 90% of chronic wound infections, which leads to poor healing and high cost of treatment estimated at more than US$ 25 billion every year in

3277-563: Is a long tube with three hook attachments that are used to attach to each other or to a surface, enabling a community to develop. Hyperthermophilic archaeon Pyrobaculum calidifontis produce bundling pili which are homologous to the bacterial TasA filaments, a major component of the extracellular matrix in bacterial biofilms, which contribute to biofilm stability. TasA homologs are encoded by many other archaea, suggesting mechanistic similarities and evolutionary connection between bacterial and archaeal biofilms. Hydrophobicity can also affect

3390-434: Is considerable interest in industrial uses of mats, especially for water treatment and for cleaning up pollution . Microbial mats may also be referred to as algal mats and bacterial mats. They are a type of biofilm that is large enough to see with the naked eye and robust enough to survive moderate physical stresses. These colonies of bacteria form on surfaces at many types of interface , for example between water and

3503-437: Is dominated by Lyngbya and Oscillatoria species The green layer is also composed of green sulfur bacteria which oxidize sulfur during their growth and are strict photolithotrophs. The pink layer extends 3 mm below the green layer. The color is due to the presence of carotinoids which are the primary pigments of the phototrophic purple sulfur bacteria. Amoebobacter, Thiocapsa, Chromatium, and Thiocystis are among

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3616-470: Is easier for other marine organisms such as barnacles to attach. Such fouling can reduce maximum vessel speed by up to 20%, prolonging voyages and consuming fuel. Time in dry dock for refitting and repainting reduces the productivity of shipping assets, and the useful life of ships is also reduced due to corrosion and mechanical removal (scraping) of marine organisms from ships' hulls. Stromatolites are layered accretionary structures formed in shallow water by

3729-473: Is hard to eradicate due to the complexity of its aggregation structure, and it has a significant contribution to developing aggressive medical complications, increase in hospitalization rate, and cost of treatment. The development of E. coli biofilm is a common leading cause of urinary tract infections (UTI) in hospitals through its contribution to developing medical device-associated infections . Catheter-associated urinary tract infections (CAUTI) represent

3842-795: Is highly different from that of planktonic and biofilm cells. Hence, the dispersal process is a unique stage during the transition from biofilm to planktonic lifestyle in bacteria. Dispersed cells are found to be highly virulent against macrophages and Caenorhabditis elegans , but highly sensitive towards iron stress, as compared with planktonic cells. Furthermore, Pseudomonas aeruginosa biofilms undergo distinct spatiotemporal dynamics during biofilm dispersal or disassembly, with contrasting consequences in recolonization and disease dissemination. Biofilm dispersal induced bacteria to activate dispersal genes to actively depart from biofilms as single cells at consistent velocities but could not recolonize fresh surfaces. In contrast, biofilm disassembly by degradation of

3955-409: Is known as development, and is the stage in which the biofilm is established and may only change in shape and size. The development of a biofilm may allow for an aggregate cell colony (or colonies) to be increasingly tolerant or resistant to antibiotics . Cell-cell communication or quorum sensing has been shown to be involved in the formation of biofilm in several bacterial species. Biofilms are

4068-471: Is likely that they acquired many of these sub-systems from existing mat organisms, by some combination of horizontal gene transfer and endosymbiosis followed by fusion. Whatever the causes, cyanobacteria are the most self-sufficient of the mat organisms and were well-adapted to strike out on their own both as floating mats and as the first of the phytoplankton , which forms the basis of most marine food chains . The time at which eukaryotes first appeared

4181-567: Is made up of green sulfur bacteria belonging to the genus Prosthecochloris , though this layer is not always present. Below the mat is iron sulfide-rich sediments and remnants of decaying mats. The top 1 mm of the green layer is often gold due to the dominant cyanobacteria and diatom species. Specific cyanobacteria identified are Lyngbya , a sheeted cyanobacterium, and Nostoc and Phormidium , which are filamentous cyanobacteria, and Spirulina spp. Diatom species identified include Navicula . Below this top gold layer extends 5 mm and

4294-481: Is much faster in responding to pathogen induced infection, and may be able to deflect pathogens before they are able to establish themselves. Plants increase the production of lignin, reinforcing cell walls and making it difficult for pathogens to penetrate into the cell, while also cutting off nutrients to already infected cells, effectively halting the invasion. They produce antimicrobial compounds such as phytoalexins, chitinases, and proteinase inhibitors, which prevent

4407-516: Is non-existent or negligible: very harsh environments, such as hyper-saline lagoons or brackish estuaries, which are uninhabitable for the burrowing organisms that broke up the mats; rocky "floors" which the burrowers cannot penetrate; the depths of the oceans, where burrowing activity today is at a similar level to that in the shallow coastal seas before the revolution. Although the Cambrian substrate revolution opened up new niches for animals, it

4520-404: Is often facilitated within bacterial and archaeal biofilms and can leads to a more stable biofilm structure. Extracellular DNA is a major structural component of many different microbial biofilms. Enzymatic degradation of extracellular DNA can weaken the biofilm structure and release microbial cells from the surface. However, biofilms are not always less susceptible to antibiotics. For instance,

4633-462: Is still uncertain: there is reasonable evidence that fossils dated between 1,600  million years ago and 2,100  million years ago represent eukaryotes, but the presence of steranes in Australian shales may indicate that eukaryotes were present 2,700  million years ago . There is still debate about the origins of eukaryotes, and many of the theories focus on the idea that

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4746-400: Is toxic to organisms that are not adapted to it, but greatly increases the metabolic efficiency of oxygen-adapted organisms — for example anaerobic fermentation produces a net yield of two molecules of adenosine triphosphate , cells' internal "fuel", per molecule of glucose , while aerobic respiration produces a net yield of 36. The oxygenation of the atmosphere was a prerequisite for

4859-583: Is toxic to organisms that are not adapted to it. Microbial mats would have been separated into oxidized and reduced layers, and this specialization would have increased their productivity. It may be possible to confirm this model by analyzing the isotope ratios of both carbon and sulfur in sediments laid down in shallow water. The last major stage in the evolution of microbial mats was the appearance of cyanobacteria , photosynthesizers which both produce and use oxygen . This gave undersea mats their typical modern structure: an oxygen-rich top layer of cyanobacteria;

4972-436: Is usually available about those for which only the hard parts are usually preserved. Microbial mats help to preserve soft-bodied fossils by: The ability of microbial mat communities to use a vast range of "foods" has recently led to interest in industrial uses. There have been trials of microbial mats for purifying water, both for human use and in fish farming , and studies of their potential for cleaning up oil spills . As

5085-629: The United States . In order to minimize the P. aeruginosa infection , host epithelial cells secrete antimicrobial peptides , such as lactoferrin , to prevent the formation of the biofilms. Streptococcus pneumoniae is the main cause of community-acquired pneumonia and meningitis in children and the elderly, and of sepsis in HIV-infected persons. When S. pneumoniae grows in biofilms, genes are specifically expressed that respond to oxidative stress and induce competence. Formation of

5198-485: The oxygenic photosynthesis seen in cyanobacteria and much later in plants was the last to evolve. The earliest photosynthesis may have been powered by infra-red light, using modified versions of pigments whose original function was to detect infra-red heat emissions from hydrothermal vents. The development of photosynthetic energy generation enabled the microorganisms first to colonize wider areas around vents and then to use sunlight as an energy source. The role of

5311-437: The sediment or rock at the bottom, between air and rock or sediment, between soil and bed-rock, etc. Such interfaces form vertical chemical gradients , i.e. vertical variations in chemical composition, which make different levels suitable for different types of bacteria and thus divide microbial mats into layers, which may be sharply defined or may merge more gradually into each other. A variety of microbes are able to transcend

5424-424: The "elephant skin" texture characteristic of microbial mats contain fossils, and Ediacaran fossils are hardly ever found in beds that do not contain these microbial mats. Adolf Seilacher categorized the animals as: "mat encrusters", which were permanently attached to the mat; "mat scratchers", which grazed the surface of the mat without destroying it; "mat stickers", suspension feeders that were partially embedded in

5537-645: The ability of bacteria to form biofilms. Bacteria with increased hydrophobicity have reduced repulsion between the substratum and the bacterium. Some bacteria species are not able to attach to a surface on their own successfully due to their limited motility but are instead able to anchor themselves to the matrix or directly to other, earlier bacteria colonists. Non-motile bacteria cannot recognize surfaces or aggregate together as easily as motile bacteria. During surface colonization bacteria cells are able to communicate using quorum sensing (QS) products such as N-acyl homoserine lactone (AHL). Once colonization has begun,

5650-566: The aquatic invertebrates upon which many fish feed. Biofilms are found on the surface of and inside plants. They can either contribute to crop disease or, as in the case of nitrogen-fixing rhizobia on root nodules , exist symbiotically with the plant . Examples of crop diseases related to biofilms include citrus canker, Pierce's disease of grapes, and bacterial spot of plants such as peppers and tomatoes. Percolating filters in sewage treatment works are highly effective removers of pollutants from settled sewage liquor. They work by trickling

5763-502: The bacteria form filaments (threads), which tangle and thus increase the colonies' structural strength, especially if the filaments have sheaths (tough outer coverings). This combination of slime and tangled threads attracts other microorganisms which become part of the mat community, for example protozoa , some of which feed on the mat-forming bacteria, and diatoms , which often seal the surfaces of submerged microbial mats with thin, parchment -like coverings. Marine mats may grow to

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5876-551: The bacteria species in the biofilm on the respective patient's tissue. In other words, the cultures were negative though the bacteria were present. New staining techniques are being developed to differentiate bacterial cells growing in living animals, e.g. from tissues with allergy-inflammations. Research has shown that sub-therapeutic levels of β-lactam antibiotics induce biofilm formation in Staphylococcus aureus . This sub-therapeutic level of antibiotic may result from

5989-516: The bedside to permit timely initiation of treatment. It has been shown that biofilms are present on the removed tissue of 80% of patients undergoing surgery for chronic sinusitis . The patients with biofilms were shown to have been denuded of cilia and goblet cells , unlike the controls without biofilms who had normal cilia and goblet cell morphology. Biofilms were also found on samples from two of 10 healthy controls mentioned. The species of bacteria from intraoperative cultures did not correspond to

6102-444: The behavioral step of reducing the supply of fermentable carbohydrates (i.e. sugar intake) and frequent removal of the biofilm (i.e., toothbrushing ). A peptide pheromone quorum sensing signaling system in S. mutans includes the competence stimulating peptide (CSP) that controls genetic competence. Genetic competence is the ability of a cell to take up DNA released by another cell. Competence can lead to genetic transformation,

6215-676: The biofilm form of Pseudomonas aeruginosa has no greater resistance to antimicrobials than do stationary-phase planktonic cells, although when the biofilm is compared to logarithmic-phase planktonic cells, the biofilm does have greater resistance to antimicrobials. This resistance to antibiotics in both stationary-phase cells and biofilms may be due to the presence of persister cells . Biofilms are ubiquitous in organic life. Nearly every species of microorganism have mechanisms by which they can adhere to surfaces and to each other. Biofilms will form on virtually every non-shedding surface in non-sterile aqueous or humid environments. Biofilms can grow in

6328-527: The biofilm grows by a combination of cell division and recruitment. Polysaccharide matrices typically enclose bacterial biofilms. The matrix exopolysaccharides can trap QS autoinducers within the biofilm to prevent predator detection and ensure bacterial survival. In addition to the polysaccharides, these matrices may also contain material from the surrounding environment, including but not limited to minerals, soil particles, and blood components, such as erythrocytes and fibrin. The final stage of biofilm formation

6441-452: The biofilm helps plants build stronger resistance to pathogens. Plants that have been colonized by PGPR forming a biofilm have gained systemic resistances and are primed for defense against pathogens. This means that the genes necessary for the production of proteins that work towards defending the plant against pathogens have been expressed, and the plant has a "stockpile" of compounds to release to fight off pathogens. A primed defense system

6554-408: The biofilm matrix may be useful as anti-biofilm agents. Evidence has shown that a fatty acid messenger, cis -2-decenoic acid , is capable of inducing dispersion and inhibiting growth of biofilm colonies. Secreted by Pseudomonas aeruginosa , this compound induces cyclo heteromorphic cells in several species of bacteria and the yeast Candida albicans . Nitric oxide has also been shown to trigger

6667-425: The biofilm mode of growth undergoes a phenotypic shift in behavior in which large suites of genes are differentially regulated . A biofilm may also be considered a hydrogel , which is a complex polymer that contains many times its dry weight in water. Biofilms are not just bacterial slime layers but biological systems; the bacteria organize themselves into a coordinated functional community. Biofilms can attach to

6780-433: The biofilm, containing S. mutans and related oral streptococci, is subjected to acid stress, the competence regulon is induced, leading to resistance to being killed by acid. As pointed out by Michod et al., transformation in bacterial pathogens likely provides for effective and efficient recombinational repair of DNA damages. It appears that S. mutans can survive the frequent acid stress in oral biofilms, in part, through

6893-450: The biofilms developed in the gut. This is especially important because the appendix holds a mass amount of these bacterial biofilms. This discovery helps to distinguish the possible function of the appendix and the idea that the appendix can help reinoculate the gut with good gut flora. However, modified or disrupted states of biofilms in the gut have been connected to diseases such as inflammatory bowel disease and colorectal cancer . In

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7006-477: The cells. Thus, the matrix represents an external digestion system and allows for stable synergistic microconsortia of different species. Some biofilms have been found to contain water channels that help distribute nutrients and signalling molecules. This matrix is strong enough that under certain conditions, biofilms can become fossilized ( stromatolites ). Bacteria living in a biofilm usually have significantly different properties from free-floating bacteria of

7119-406: The dental biofilm is driven by certain (cariogenic) microbiological populations beginning to dominate when the environment favors them. The shift to an acidogenic , aciduric, and cariogenic microbiological population develops and is maintained by frequent consumption of fermentable dietary carbohydrate . The resulting activity shift in the biofilm (and resulting acid production within the biofilm, at

7232-479: The depth drops below the chemocline . The black color is due to the high amounts of iron sulfide generated by the green sulfur-reducing bacteria. The layer consists mostly of green sulfur bacteria belonging to the Prosthecochloris , which are a small group of prosthecate bacteria containing many knobby projections. Organisms in this layer decompose organic matter formed by the upper layers, thus recycling

7345-585: The development of complex interactions between the cells in the biofilm. The formation of a biofilm begins with the attachment of free-floating microorganisms to a surface. The first colonist bacteria of a biofilm may adhere to the surface initially by the weak van der Waals forces and hydrophobic effects. If the colonists are not immediately separated from the surface, they can anchor themselves more permanently using cell adhesion structures such as pili . A unique group of Archaea that inhabit anoxic groundwater have similar structures called hami . Each hamus

7458-708: The diffusion of quorum sensing molecules into the environment and prevented the detection of C. elegans . Many different bacteria form biofilms, including gram-positive (e.g. Bacillus spp, Listeria monocytogenes , Staphylococcus spp, and lactic acid bacteria , including Lactobacillus plantarum and Lactococcus lactis ) and gram-negative species (e.g. Escherichia coli , or Pseudomonas aeruginosa ). Cyanobacteria also form biofilms in aquatic environments. Biofilms are formed by bacteria that colonize plants, e.g. Pseudomonas putida , Pseudomonas fluorescens , and related pseudomonads which are common plant-associated bacteria found on leaves, roots, and in

7571-408: The dispersal of biofilms of several bacteria species at sub-toxic concentrations. Nitric oxide has potential as a treatment for patients that have chronic infections caused by biofilms. It was generally assumed that cells dispersed from biofilms immediately go into the planktonic growth phase. However, studies have shown that the physiology of dispersed cells from Pseudomonas aeruginosa biofilms

7684-684: The effects they have on geochemical cycling and nutrient cycling for other organisms. The Sippewissett salt marsh is of particular importance for research, as it is one of the few generally undisturbed salt marshes in New England. 41°35′17″N 70°38′27″W  /  41.588099°N 70.640961°W  / 41.588099; -70.640961 Microbial mat A microbial mat is a multi-layered sheet or biofilm of microbial colonies , composed of mainly bacteria and/or archaea . Microbial mats grow at interfaces between different types of material, mostly on submerged or moist surfaces , but

7797-591: The environment, as a general rule the by-products of each group of microorganisms serve as "food" for other groups. In effect each mat forms its own food chain , with one or a few groups at the top of the food chain as their by-products are not consumed by other groups. Different types of microorganism dominate different layers based on their comparative advantage for living in that layer. In other words, they live in positions where they can out-perform other groups rather than where they would absolutely be most comfortable — ecological relationships between different groups are

7910-459: The evolution of the more complex eukaryote type of cell, from which all multicellular organisms are built. Cyanobacteria have the most complete biochemical "toolkits" of all the mat-forming organisms: the photosynthesis mechanisms of both green bacteria and purple bacteria; oxygen production; and the Calvin cycle , which converts carbon dioxide and water into carbohydrates and sugars . It

8023-420: The free oxygen content of the Earth's atmosphere, both directly by emitting oxygen and because the mats emitted molecular hydrogen (H 2 ), some of which would have escaped from the Earth's atmosphere before it could re-combine with free oxygen to form more water. Microbial mats thus played a major role in the evolution of organisms which could first tolerate free oxygen and then use it as an energy source. Oxygen

8136-409: The growth of pathogens. These functions of disease suppression and pathogen resistance ultimately lead to an increase in agricultural production and a decrease in the use of chemical pesticides, herbicides, and fungicides because there is a reduced amount of crop loss due to disease. Induced systemic resistance and pathogen-induced systemic acquired resistance are both potential functions of biofilms in

8249-641: The hindguts of some echinoids . Microbial mats use all of the types of metabolism and feeding strategy that have evolved on Earth—anoxygenic and oxygenic photosynthesis ; anaerobic and aerobic chemotrophy (using chemicals rather than sunshine as a source of energy); organic and inorganic respiration and fermentation (i..e converting food into energy with and without using oxygen in the process); autotrophy (producing food from inorganic compounds) and heterotrophy (producing food only from organic compounds, by some combination of predation and detritivory ). Most sedimentary rocks and ore deposits have grown by

8362-535: The human environment, biofilms can grow in showers very easily since they provide a moist and warm environment for them to thrive. Mold biofilms on ceilings may form due to roof leaks. They can form inside water and sewage pipes and cause clogging and corrosion . On floors and counters, they can make sanitation difficult in food preparation areas. In soil, they can cause bioclogging . In cooling- or heating-water systems, they are known to reduce heat transfer. Biofilms in marine engineering systems, such as pipelines of

8475-475: The hydrothermal vents was now limited to supplying reduced metals into the oceans as a whole rather than being the main supporters of life in specific locations. Heterotrophic scavengers would have accompanied the photosynthesizers in their migration out of the "hydrothermal ghetto". The evolution of purple bacteria, which do not produce or use oxygen but can tolerate it, enabled mats to colonize areas that locally had relatively high concentrations of oxygen, which

8588-452: The hypogeal layer, particles of foreign matter are trapped in the mucilaginous matrix and soluble organic material is adsorbed . The contaminants are metabolised by the bacteria, fungi and protozoa. The water produced from an exemplary slow sand filter is of excellent quality with 90–99% bacterial cell count reduction. Plant-beneficial microbes can be categorized as plant growth-promoting rhizobacteria . These plant growth-promoters colonize

8701-408: The inhibition of efflux pump activity and interactions with extracellular and intracellular nucleic acids. Escherichia coli biofilms are responsible for many intestinal infectious diseases. The Extraintestinal group of E. coli (ExPEC) is the dominant bacterial group that attacks the urinary system , which leads to urinary tract infections . The biofilm formation of these pathogenic E. coli

8814-452: The invading bacteria, and this response can kill bacteria by damaging their DNA. Competent S. pneumoniae in a biofilm have the survival advantage that they can more easily take up transforming DNA from nearby cells in the biofilm to use for recombinational repair of oxidative damages in their DNA. Competent S. pneumoniae can also secrete an enzyme (murein hydrolase) that destroys non-competent cells (fratricide) causing DNA to be released into

8927-489: The layers. The mats are often coated by green macro- and microalgae that adhere to the surface. The top, green-brown layer is composed of cyanobacteria and diatom species. A blue-green intermediate layer is formed by Oscillatoria species. Purple sulfur bacteria are found in the pink central layer. Below the pink layer, an orange-black layer is formed predominately by a single species of purple sulfur bacteria, Thiocapsa pfennigii, and spirochetes . The thin, bottom layer

9040-475: The limits of diffusion by using "nanowires" to shuttle electrons from their metabolic reactions up to two centimetres deep in the sediment – for example, electrons can be transferred from reactions involving hydrogen sulfide deeper within the sediment to oxygen in the water, which acts as an electron acceptor. The best-known types of microbial mat may be flat laminated mats, which form on approximately horizontal surfaces, and stromatolites , stubby pillars built as

9153-423: The liquid over a bed of hard material which is designed to have a very large surface area. A complex biofilm develops on the surface of the medium which absorbs, adsorbs and metabolises the pollutants. The biofilm grows rapidly and when it becomes too thick to retain its grip on the media it washes off and is replaced by newly grown film. The washed off ("sloughed" off) film is settled out of the liquid stream to leave

9266-432: The lower layers and which fed respectively on the by-products of the photosynthesizers and on the corpses and / or living bodies of the other mat organisms. These increases would have made microbial mats the planet's dominant ecosystems. From this point onwards life itself produced significantly more of the resources it needed than did geochemical processes. Oxygenic photosynthesis in microbial mats would also have increased

9379-859: The main progenitors of biofilms are diatoms , which colonise both fresh and marine environments worldwide. For other species in disease-associated biofilms and biofilms arising from eukaryotes , see below. Biofilms have been found to be involved in a wide variety of microbial infections in the body, by one estimate 80% of all infections. Infectious processes in which biofilms have been implicated include common problems such as bacterial vaginosis , urinary tract infections , catheter infections, middle-ear infections , formation of dental plaque , gingivitis , coating contact lenses , and less common but more lethal processes such as endocarditis , infections in cystic fibrosis , and infections of permanent indwelling devices such as joint prostheses , heart valves , and intervertebral disc. The first visual evidence of

9492-576: The mat; and "undermat miners", which burrowed underneath the mat and fed on decomposing mat material. In the Early Cambrian, however, organisms began to burrow vertically for protection or food, breaking down the microbial mats, and thus allowing water and oxygen to penetrate a considerable distance below the surface and kill the oxygen-intolerant microorganisms in the lower layers. As a result of this Cambrian substrate revolution , marine microbial mats are confined to environments in which burrowing

9605-626: The mats' structure may already have been similar to that of modern mats that do not include photosynthesizing bacteria. It is even possible that non-photosynthesizing mats were present as early as 4,000  million years ago . If so, their energy source would have been hydrothermal vents (high-pressure hot springs around submerged volcanoes ), and the evolutionary split between bacteria and archea may also have occurred around this time. The earliest mats may have been small, single-species biofilms of chemotrophs that relied on hydrothermal vents to supply both energy and chemical "food". Within

9718-427: The matter. The thin, bottommost layer lies below the chemocline and contains fewer organisms than the slightly thicker black layer. The gray color is due to the presence of pyrite. Here, the empty shells of diatoms can be found. Microbial species here are dominated by methylotrophic methanogens which generate the methane observed in the salt marsh. This layer is not active year-round; the organisms are largely dormant in

9831-435: The microbes slowly move upwards to avoid being smothered by sediment deposited on them by water. However, there are also spherical mats, some on the outside of pellets of rock or other firm material and others inside spheres of sediment. A microbial mat consists of several layers, each of which is dominated by specific types of microorganism , mainly bacteria . Although the composition of individual mats varies depending on

9944-436: The microorganisms. In many cases some of the bacteria form tangled webs of filaments which make the mat tougher. The best known physical forms are flat mats and stubby pillars called stromatolites , but there are also spherical forms. Microbial mats are the earliest form of life on Earth for which there is good fossil evidence, from 3,500  million years ago , and have been the most important members and maintainers of

10057-401: The most extreme environments: from, for example, the extremely hot, briny waters of hot springs ranging from very acidic to very alkaline, to frozen glaciers . Biofilms can be found on rocks and pebbles at the bottoms of most streams or rivers and often form on the surfaces of stagnant pools of water. Biofilms are important components of food chains in rivers and streams and are grazed by

10170-404: The offshore oil and gas industry, can lead to substantial corrosion problems. Corrosion is mainly due to abiotic factors; however, at least 20% of corrosion is caused by microorganisms that are attached to the metal subsurface (i.e., microbially influenced corrosion ). Bacterial adhesion to boat hulls serves as the foundation for biofouling of seagoing vessels. Once a film of bacteria forms, it

10283-707: The orange-black layer are chemoheterotrophic and use iron as an electron donor. The Sippewissett Salt Marsh has served as a hallmark for studies done on estuarine environments. Scientists at the Woods Hole Oceanographic Institution , the Boston University Marine Program, and the Marine Biological Laboratory have been studying Great Sippewissett Salt Marsh extensively since 1970 to gain a better understanding of microbial diversity and

10396-456: The planet's ecosystems . Originally they depended on hydrothermal vents for energy and chemical "food", but the development of photosynthesis allowed mats to proliferate outside of these environments by utilizing a more widely available energy source, sunlight. The final and most significant stage of this liberation was the development of oxygen-producing photosynthesis, since the main chemical inputs for this are carbon dioxide and water. As

10509-477: The product of a microbial developmental process. The process is summarized by five major stages of biofilm development, as shown in the diagram below: Dispersal of cells from the biofilm colony is an essential stage of the biofilm life cycle. Dispersal enables biofilms to spread and colonize new surfaces. Enzymes that degrade the biofilm extracellular matrix , such as dispersin B and deoxyribonuclease , may contribute to biofilm dispersal. Enzymes that degrade

10622-475: The recombinational repair provided by competence and transformation. Predator-prey interactions Predator - prey interactions between biofilms and bacterivores, such as the soil-dwelling nematode Caenorhabditis elegans , had been extensively studied. Via the production of sticky matrix and formation of aggregates, Yersinia pestis biofilms can prevent feeding by obstructing the mouth of C. elegans . Moreover, Pseudomonas aeruginosa biofilms can impede

10735-812: The rhizosphere often result in pathogen or plant induced systemic resistances. Molecular properties on the surface of the bacterium cause an immune response in the plant host. These microbe associated molecules interact with receptors on the surface of plant cells, and activate a biochemical response that is thought to include several different genes at a number of loci. Several other signaling molecules have been linked to both induced systemic responses and pathogen-induced systemic responses, such as jasmonic acid and ethylene. Cell envelope components such as bacterial flagella and lipopolysaccharides, which are recognized by plant cells as components of pathogens. Certain iron metabolites produced by Pseudomonas have also been shown to create an induced systemic response. This function of

10848-459: The rhizosphere, and should be taken into consideration when applied to new age agricultural practices because of their effect on disease suppression without the use of dangerous chemicals. Studies in 2003 discovered that the immune system supports biofilm development in the large intestine. This was supported mainly with the fact that the two most abundantly produced molecules by the immune system also support biofilm production and are associated with

10961-769: The roots of plants, and provide a wide range of beneficial functions for their host including nitrogen fixation, pathogen suppression, anti-fungal properties, and the breakdown of organic materials. One of these functions is the defense against pathogenic, soil-borne bacteria and fungi by way of induced systemic resistance (ISR) or induced systemic responses triggered by pathogenic microbes (pathogen-induced systemic acquired resistance). Plant exudates act as chemical signals for host specific bacteria to colonize. Rhizobacteria colonization steps include attractions, recognition, adherence, colonization, and growth. Bacteria that have been shown to be beneficial and form biofilms include Bacillus , Pseudomonas , and Azospirillum . Biofilms in

11074-540: The same organism, which, by contrast, are single cells that may float or swim in a liquid medium. Biofilms can form on the teeth of most animals as dental plaque , where they may cause tooth decay and gum disease . Microbes form a biofilm in response to a number of different factors, which may include cellular recognition of specific or non-specific attachment sites on a surface, nutritional cues, or in some cases, by exposure of planktonic cells to sub-inhibitory concentrations of antibiotics . A cell that switches to

11187-417: The same species, as the dense and protected environment of the film allows them to cooperate and interact in various ways. One benefit of this environment is increased resistance to detergents and antibiotics , as the dense extracellular matrix and the outer layer of cells protect the interior of the community. In some cases antibiotic resistance can be increased up to 5,000 times. Lateral gene transfer

11300-450: The significance of oxygenic photosynthesis is that it uses water as a reducing agent, and water is much more plentiful than the geologically produced reducing agents on which photosynthesis previously depended. The resulting increases in the populations of photosynthesizing bacteria in the top layers of microbial mats would have caused corresponding population increases among the chemotrophic and heterotrophic microorganisms that inhabited

11413-420: The slithering motility of C. elegans , termed as 'quagmire phenotype', resulting in trapping of C. elegans within the biofilms and preventing the exploration of nematodes to feed on susceptible biofilms. This significantly reduced the ability of predator to feed and reproduce, thereby promoting the survival of biofilms. Pseudomonas aeruginosa biofilms can also mask their chemical signatures, where they reduced

11526-434: The soil, and the majority of their natural isolates form biofilms. Several nitrogen-fixing symbionts of legumes such as Rhizobium leguminosarum and Sinorhizobium meliloti form biofilms on legume roots and other inert surfaces. Along with bacteria, biofilms are also generated by archaea and by a range of eukaryotic organisms, including fungi e.g. Cryptococcus laurentii and microalgae . Among microalgae, one of

11639-401: The species of purple sulfur bacteria identified. Purple sulfur bacteria can use a number of different electron donors for their anaerobic phototrophic growth, including: hydrogen sulfide, sulfur, thiosulfate, and molecular hydrogen. Their diverse use of many electron donors makes this layer stand out in the microbial mat community. The bottom layer makes up the lower 2 mm of the mat before

11752-484: The surface of leaves, particularly in high humidity climates. Given sufficient resources for growth, a biofilm will quickly grow to be macroscopic (visible to the naked eye). Biofilms can contain many different types of microorganism, e.g. bacteria, archaea , protozoa , fungi and algae ; each group performs specialized metabolic functions. However, some organisms will form single-species films under certain conditions. The social structure (cooperation/competition) within

11865-484: The surface of teeth is frequently subject to oxidative stress and acid stress. Dietary carbohydrates can cause a dramatic decrease in pH in oral biofilms to values of 4 and below (acid stress). A pH of 4 at body temperature of 37 °C causes depurination of DNA, leaving apurinic (AP) sites in DNA, especially loss of guanine. Dental plaque biofilm can result in dental caries if it is allowed to develop over time. An ecologic shift away from balanced populations within

11978-492: The surfaces of mats and let oxygenated water into the deeper layers, poisoning the oxygen-intolerant microorganisms that lived there. Although this revolution drove mats off soft floors of shallow seas, they still flourish in many environments where burrowing is limited or impossible, including rocky seabeds and shores, and hyper-saline and brackish lagoons. They are found also on the floors of the deep oceans. Because of microbial mats' ability to use almost anything as "food", there

12091-508: The surrounding medium for potential use by the competent cells. The insect antimicrobial peptide cecropin A can destroy planktonic and sessile biofilm-forming uropathogenic E. coli cells, either alone or when combined with the antibiotic nalidixic acid , synergistically clearing infection in vivo (in the insect host Galleria mellonella ) without off-target cytotoxicity. The multi-target mechanism of action involves outer membrane permeabilization followed by biofilm disruption triggered by

12204-408: The tooth surface) is associated with an imbalance of demineralization over remineralization, leading to net mineral loss within dental hard tissues ( enamel and then dentin ), the symptom being a carious lesion , or cavity. By preventing the dental plaque biofilm from maturing or by returning it back to a non-cariogenic state, dental caries can be prevented and arrested. This can be achieved through

12317-449: The trapping, binding and cementation of sedimentary grains by microbial biofilms, especially of cyanobacteria . Stromatolites include some of the most ancient records of life on Earth, and are still forming today. Within the human body, biofilms are present on the teeth as dental plaque , where they may cause tooth decay and gum disease . These biofilms can either be in an uncalcified state that can be removed by dental instruments, or

12430-733: The use of antibiotics as growth promoters in agriculture, or during the normal course of antibiotic therapy. The biofilm formation induced by low-level methicillin was inhibited by DNase, suggesting that the sub-therapeutic levels of antibiotic also induce extracellular DNA release. Moreover, from an evolutionary point of view, the creation of the tragedy of the commons in pathogenic microbes may provide advanced therapeutic ways for chronic infections caused by biofilms via genetically engineered invasive cheaters who can invade wild-types 'cooperators' of pathogenic bacteria until cooperator populations go to extinction or overall population 'cooperators and cheaters ' go to extinction. P. aeruginosa represents

12543-625: The winter. The metabolism of the organisms throughout each layer of the microbial mats are tightly coupled to each other and play important roles in providing nutrients for the plants and animals that live in the marsh. The cyanobacteria and diatom algae present in the mat are aerobic photoautotrophs whose energy is derived from the light with oxygen as the electron acceptor and use hydrogen gas and iron as electron donors . Purple sulfur bacteria are anaerobic or microaerophilic photoautotrophs, and use hydrogen sulfide, sulfur, thiosulfate, and molecular hydrogen as electron donors. Spirochaetes in

12656-529: Was many years before these textures were recognized as trace fossils of mats. Microbial mats have increased the concentration of metal in many ore deposits, and without this it would not be feasible to mine them—examples include iron (both sulfide and oxide ores), uranium, copper, silver and gold deposits. Microbial mats are among the oldest clear signs of life, as microbially induced sedimentary structures (MISS) formed 3,480  million years ago have been found in western Australia . At that early stage

12769-479: Was not catastrophic for microbial mats, but it did greatly reduce their extent. Most fossils preserve only the hard parts of organisms, e.g. shells. The rare cases where soft-bodied fossils are preserved (the remains of soft-bodied organisms and also of the soft parts of organisms for which only hard parts such as shells are usually found) are extremely valuable because they provide information about organisms that are hardly ever fossilized and much more information than

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