Fermentation is a metabolic process that produces chemical changes in organic substrates through the action of enzymes. In biochemistry, it is narrowly defined as the extraction of energy from carbohydrates in the absence of oxygen. In the context of food production, it may more broadly refer to any process in which the activity of microorganisms brings about a desirable change to a foodstuff or beverage; the science of fermentation is known as zymology. In microorganisms, fermentation is the primary means of producing ATP by the degradation of organic nutrients anaerobically. Humans have used fermentation to produce beverages since the Neolithic age. For example, fermentation is used for preservation in a process that produces lactic acid found in such sour foods as pickled cucumbers and yogurt, as well as for producing alcoholic beverages such as wine and beer. Fermentation occurs within the gastrointestinal tracts including humans. Below are some definitions of fermentation, they range from general usages to more scientific definitions.
Preservation methods for food via microorganisms. Any process that produces alcoholic beverages or acidic dairy products. Any large-scale microbial process occurring with or without air. Any energy-releasing metabolic process that takes place only under anaerobic conditions. Any metabolic process that releases energy from a sugar or other organic molecule, does not require oxygen or an electron transport system, uses an organic molecule as the final electron acceptor. Along with photosynthesis and aerobic respiration, fermentation is a way of extracting energy from molecules, but it is the only one common to all bacteria and eukaryotes, it is therefore considered the oldest metabolic pathway, suitable for an environment that does not yet have oxygen. Yeast, a form of fungus, occurs in any environment capable of supporting microbes, from the skins of fruits to the guts of insects and mammals and the deep ocean, they harvest sugar-rich materials to produce ethanol and carbon dioxide; the basic mechanism for fermentation remains present in all cells of higher organisms.
Mammalian muscle carries out the fermentation that occurs during periods of intense exercise where oxygen supply becomes limited, resulting in the creation of lactic acid. In invertebrates, fermentation produces succinate and alanine. Fermentative bacteria play an essential role in the production of methane in habitats ranging from the rumens of cattle to sewage digesters and freshwater sediments, they produce hydrogen, carbon dioxide and acetate and carboxylic acids. Acetogenic bacteria oxidize the acids, obtaining more acetate and either formate. Methanogens convert acetate to methane. Fermentation reacts NADH with an organic electron acceptor; this is pyruvate formed from sugar through glycolysis. The reaction produces NAD+ and an organic product, typical examples being ethanol, lactic acid, carbon dioxide, hydrogen gas. However, more exotic compounds can be produced by fermentation, such as butyric acetone. Fermentation products contain chemical energy, but are considered waste products, since they cannot be metabolized further without the use of oxygen.
Fermentation occurs in an anaerobic environment. In the presence of O2, NADH, pyruvate are used to generate ATP in respiration; this is called oxidative phosphorylation, it generates much more ATP than glycolysis alone. For that reason, fermentation is utilized when oxygen is available; however in the presence of abundant oxygen, some strains of yeast such as Saccharomyces cerevisiae prefer fermentation to aerobic respiration as long as there is an adequate supply of sugars. Some fermentation processes involve obligate anaerobes. Although yeast carries out the fermentation in the production of ethanol in beers and other alcoholic drinks, this is not the only possible agent: bacteria carry out the fermentation in the production of xanthan gum. In ethanol fermentation, one glucose molecule is converted into two ethanol molecules and two carbon dioxide molecules, it is used to make bread dough rise: the carbon dioxide forms bubbles, expanding the dough into a foam. The ethanol is the intoxicating agent in alcoholic beverages such as wine and liquor.
Fermentation of feedstocks, including sugarcane and sugar beets, produces ethanol, added to gasoline. In some species of fish, including goldfish and carp, it provides energy; the figure illustrates the process. Before fermentation, a glucose molecule breaks down into two pyruvate molecules; the energy from this exothermic reaction is used to bind inorganic phosphates to ATP and convert NAD+ to NADH. The pyruvates break down into two acetaldehyde molecules and give off two carbon dioxide molecules as a waste product; the acetaldehyde is reduced into ethanol using the energy and hydrogen from NADH, the NADH is oxidized into NAD+ so that the cycle may repeat. The reaction is catalysed by the enzymes pyruvate alcohol dehydrogenase. Homolactic fermentation is the simplest type of fermentation; the pyruvate from glycolysis undergoes a simple redox reaction. It is unique because it is one of the only respiration processes to not produce a gas as a byproduct. Overall, one molecule of glucose is converted to two molecules of lactic ac
Phototrophs are the organisms that carry out photon capture to acquire energy. They use the energy from light to carry out various cellular metabolic processes, it is a common misconception. Many, but not all, phototrophs photosynthesize: they anabolically convert carbon dioxide into organic material to be utilized structurally, functionally, or as a source for catabolic processes. All phototrophs either use electron transport chains or direct proton pumping to establish an electro-chemical gradient, utilized by ATP synthase, to provide the molecular energy currency for the cell. Phototrophs can be either heterotrophs; as their electron and hydrogen donors are inorganic compounds they can be called as lithotrophs, so, some photoautotrophs are called photolithoautotrophs. Examples of phototroph organisms: Rhodobacter capsulatus, Chlorobium etc. Used with a different meaning, the term took its current definition after Lwoff and collaborators. Most of the well-recognized phototrophs are autotrophic known as photoautotrophs, can fix carbon.
They can be contrasted with chemotrophs that obtain their energy by the oxidation of electron donors in their environments. Photoautotrophs are capable of synthesizing their own food from inorganic substances using light as an energy source. Green plants and photosynthetic bacteria are photoautotrophs. Photoautotrophic organisms are sometimes referred to as holophytic; such organisms derive their energy for food synthesis from light and are capable of using carbon dioxide as their principal source of carbon. Oxygenic photosynthetic organisms use chlorophyll for light-energy capture and oxidize water, "splitting" it into molecular oxygen. In contrast, anoxygenic photosynthetic bacteria have a substance called bacteriochlorophyll - which absorbs predominantly at non-optical wavelengths - for light-energy capture, live in aquatic environments, will, using light, oxidize chemical substances such as hydrogen sulfide rather than water. In an ecological context, phototrophs are the food source for neighboring heterotrophic life.
In terrestrial environments, plants are the predominant variety, while aquatic environments include a range of phototrophic organisms such as algae, other protists and bacteria. The depth to which sunlight or artificial light can penetrate into water, so that photosynthesis may occur, is known as the photic zone. Cyanobacteria, which are prokaryotic organisms which carry out oxygenic photosynthesis, occupy many environmental conditions, including fresh water, seas and lichen. Cyanobacteria carry out plant-like photosynthesis because the organelle in plants that carries out photosynthesis is derived from an endosymbiotic cyanobacterium; this bacterium can use water as a source of electrons. Evolutionarily, cyanobacteria's ability to survive in oxygenic conditions, which are considered toxic to most anaerobic bacteria, might have given the bacteria an adaptive advantage which could have allowed the cyanobacteria to populate more efficiently. A photolithoautotroph is an autotrophic organism that uses light energy, an inorganic electron donor, CO2 as its carbon source.
Examples include plants. In contrast to photoautotrophs, photoheterotrophs are organisms that depend on light for their energy and principally on organic compounds for their carbon. Photoheterotrophs produce ATP through photophosphorylation but use environmentally obtained organic compounds to build structures and other bio-molecules. Autotroph Chemoautotroph Photoautotroph Retinalophototroph Heterotroph Chemoheterotroph Photoheterotroph Primary nutritional groups Prototroph
Metabolism is the set of life-sustaining chemical reactions in organisms. The three main purposes of metabolism are: the conversion of food to energy to run cellular processes; these enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, respond to their environments.. Metabolic reactions may be categorized as catabolic - the breaking down of compounds. Catabolism releases energy, anabolism consumes energy; the chemical reactions of metabolism are organized into metabolic pathways, in which one chemical is transformed through a series of steps into another chemical, each step being facilitated by a specific enzyme. Enzymes are crucial to metabolism because they allow organisms to drive desirable reactions that require energy that will not occur by themselves, by coupling them to spontaneous reactions that release energy. Enzymes act as catalysts - they allow a reaction to proceed more - and they allow the regulation of the rate of a metabolic reaction, for example in response to changes in the cell's environment or to signals from other cells.
The metabolic system of a particular organism determines which substances it will find nutritious and which poisonous. For example, some prokaryotes use hydrogen sulfide as a nutrient, yet this gas is poisonous to animals; the basal metabolic rate of an organism is the measure of the amount of energy consumed by all of these chemical reactions. A striking feature of metabolism is the similarity of the basic metabolic pathways among vastly different species. For example, the set of carboxylic acids that are best known as the intermediates in the citric acid cycle are present in all known organisms, being found in species as diverse as the unicellular bacterium Escherichia coli and huge multicellular organisms like elephants; these similarities in metabolic pathways are due to their early appearance in evolutionary history, their retention because of their efficacy. Most of the structures that make up animals and microbes are made from three basic classes of molecule: amino acids and lipids; as these molecules are vital for life, metabolic reactions either focus on making these molecules during the construction of cells and tissues, or by breaking them down and using them as a source of energy, by their digestion.
These biochemicals can be joined together to make polymers such as DNA and proteins, essential macromolecules of life. Proteins are made of amino acids arranged in a linear chain joined together by peptide bonds. Many proteins are enzymes. Other proteins have structural or mechanical functions, such as those that form the cytoskeleton, a system of scaffolding that maintains the cell shape. Proteins are important in cell signaling, immune responses, cell adhesion, active transport across membranes, the cell cycle. Amino acids contribute to cellular energy metabolism by providing a carbon source for entry into the citric acid cycle when a primary source of energy, such as glucose, is scarce, or when cells undergo metabolic stress. Lipids are the most diverse group of biochemicals, their main structural uses are as part of biological membranes both internal and external, such as the cell membrane, or as a source of energy. Lipids are defined as hydrophobic or amphipathic biological molecules but will dissolve in organic solvents such as benzene or chloroform.
The fats are a large group of compounds that contain fatty glycerol. Several variations on this basic structure exist, including alternate backbones such as sphingosine in the sphingolipids, hydrophilic groups such as phosphate as in phospholipids. Steroids such as cholesterol are another major class of lipids. Carbohydrates are aldehydes or ketones, with many hydroxyl groups attached, that can exist as straight chains or rings. Carbohydrates are the most abundant biological molecules, fill numerous roles, such as the storage and transport of energy and structural components; the basic carbohydrate units are called monosaccharides and include galactose and most glucose. Monosaccharides can be linked together to form polysaccharides in limitless ways; the two nucleic acids, DNA and RNA, are polymers of nucleotides. Each nucleotide is composed of a phosphate attached to a ribose or deoxyribose sugar group, attached to a nitrogenous base. Nucleic acids are critical for the storage and use of genetic information, its interpretation through the processes of transcription and protein biosynthesis.
This information is propagated through DNA replication. Many viruses have an RNA genome, such as HIV, which uses reverse transcription to create a DNA template from its viral RNA genome. RNA in ribozymes such as spliceosomes and ribosomes is similar to enzymes as it can catalyze chemical reactions. Individual nucleosides are made
Chemotrophs are organisms that obtain energy by the oxidation of electron donors in their environments. These molecules can be inorganic; the chemotroph designation is in contrast to phototrophs. Chemotrophs can be either heterotrophic. Chemotrophs are found in ocean floors where sunlight cannot reach them because they are not dependent on solar energy. Ocean floors contain underwater volcanos that can provide heat as a substitute for sunlight's warmth. Chemoautotrophs, in addition to deriving energy from chemical reactions, synthesize all necessary organic compounds from carbon dioxide. Chemoautotrophs use inorganic energy sources such as hydrogen sulfide, elemental sulfur, ferrous iron, molecular hydrogen, ammonia. Most chemoautotrophs are extremophiles, bacteria or archaea that live in hostile environments and are the primary producers in such ecosystems. Chemoautotrophs fall into several groups: methanogens, sulfur oxidizers and reducers, anammox bacteria, thermoacidophiles. An example of one of these prokaryotes would be Sulfolobus.
Chemolithotrophic growth can be fast, such as Hydrogenovibrio crunogenus with a doubling time around one hour. The term "chemosynthesis", coined in 1897 by Wilhelm Pfeffer was defined as the energy production by oxidation of inorganic substances in association with autotrophy - what would be named today as chemolithoautotrophy; the term would include the chemoorganoautotrophy, that is, it can be seen as a synonym of chemoautotrophy. Chemoheterotrophs are unable to fix carbon to form their own organic compounds. Chemoheterotrophs can be chemolithoheterotrophs, utilizing inorganic energy sources such as sulfur or chemoorganoheterotrophs, utilizing organic energy sources such as carbohydrates and proteins. Most animals and fungi are examples of chemoheterotrophs. In the deep oceans, iron-oxidizing bacteria derive their energy needs by oxidizing ferrous iron to ferric iron; the electron conserved from this reaction reduces the respiratory chain and can be thus used in the synthesis of ATP by forward electron transport or NADH by reverse electron transport, replacing or augmenting traditional phototrophism.
In general, iron-oxidizing bacteria can exist only in areas with high ferrous iron concentrations, such as new lava beds or areas of hydrothermal activity. Most of the ocean is devoid of ferrous iron, due to both the oxidative effect of dissolved oxygen in the water and the tendency of bacteria to take up the iron. Lava beds supply bacteria with ferrous iron straight from the Earth's mantle, but only newly formed igneous rocks have high enough levels of ferrous iron. In addition, because oxygen is necessary for the reaction, these bacteria are much more common in the upper ocean, where oxygen is more abundant. What is still unknown is how iron bacteria extract iron from rock, it is accepted that some mechanism exists that eats away at the rock through specialized enzymes or compounds that bring more FeO to the surface. It has been long debated about how much of the weathering of the rock is due to biotic components and how much can be attributed to abiotic components. Hydrothermal vents release large quantities of dissolved iron into the deep ocean, allowing bacteria to survive.
In addition, the high thermal gradient around vent systems means a wide variety of bacteria can coexist, each with its own specialized temperature niche. Regardless of the catalytic method used, chemoautotrophic bacteria provide a significant but overlooked food source for deep sea ecosystems - which otherwise receive limited sunlight and organic nutrients. Manganese-oxidizing bacteria make use of igneous lava rocks in much the same way. Manganese is more scarce than iron oceanic crust, but is much easier for bacteria to extract from igneous glass. In addition, each manganese oxidation donates two electrons to the cell versus one for each iron oxidation, though the amount of ATP or NADH that can be synthesised in couple to these reactions varies with pH and specific reaction thermodynamics in terms of how much of a Gibbs free energy change there is during the oxidation reactions versus the energy change required for the formation of ATP or NADH, all of which vary with concentration, pH etc.
Much still remains unknown about manganese-oxidizing bacteria because they have not been cultured and documented to any great extent. Autotroph Chemoautotroph Photoautotroph Heterotroph Chemoheterotroph Photoheterotroph Chemosynthesis Lithotroph 1. Katrina Edwards. Microbiology of a Sediment Pond and the Underlying Young, Hydrologically Active Ridge Flank. Woods Hole Oceanographic Institution. 2. Coupled Photochemical and Enzymatic Mn Oxidation Pathways of a Planktonic Roseobacter-Like Bacterium Colleen M. Hansel and Chris A. Francis* Department of Geological and Environmental Sciences, Stanford University, California 94305-2115 Received 28 September 2005/ Accepted 17 February 2006
Purple bacteria or purple photosynthetic bacteria are proteobacteria that are phototrophic, that is, capable of producing their own food via photosynthesis. They are pigmented with bacteriochlorophyll a or b, together with various carotenoids, which give them colours ranging between purple, red and orange, they may be divided into two groups -- purple non-sulfur bacteria. In a 2018 Frontiers in Energy Research paper, it has been suggested purple bacteria be used as a biorefinery. Purple bacteria are photoautotrophic, but are known to be chemoautotrophic and photoheterotrophic, they can be capable of aerobic respiration and fermentation. Photosynthesis occurs at reaction centers on the cell membrane, where the photosynthetic pigments and pigment-binding proteins are invaginated to form vesicle sacs, tubules, or single-paired or stacked lamellar sheets; this is called the intracytoplasmic membrane which has increased surface area to maximize light absorption. Purple bacteria use cyclic electron transport driven by a series of redox reactions.
Light-harvesting complexes surrounding a reaction centre harvest photons in the form of resonance energy, exciting chlorophyll pigments P870 or P960 located in the RC. Excited electrons are cycled from P870 to quinones QA and QB passed to cytochrome bc1, cytochrome c2, back to P870; the reduced quinone QB attracts two cytoplasmic protons and becomes QH2 being oxidized and releasing the protons to be pumped into the periplasm by the cytochrome bc1 complex. The resulting charge separation between the cytoplasm and periplasm generates a proton motive force used by ATP synthase to produce ATP energy. Purple bacteria transfer electrons from external electron donors directly to cytochrome bc1 to generate NADH or NADPH used for anabolism, they are anoxygenic. One type of purple bacteria, called purple sulfur bacteria, use sulfide or sulfur as electron donors. Another type, called purple non-sulfur bacteria use hydrogen as an electron donor but can use sulfide or organic compounds at lower concentrations compared to PSB.
Purple bacteria lack external electron carriers to spontaneously reduce NAD+ to NADH, so they must use their reduced quinones to endergonically reduce NAD+. This process is called reverse electron flow. Purple bacteria were the first bacteria discovered to photosynthesize without having an oxygen byproduct. Instead, their byproduct is sulfur; this was demonstrated by first establishing the bacteria's reactions to different concentrations of oxygen. What was found was that the bacteria moved away from the slightest trace of oxygen. A dish of the bacteria was taken, a light was focused on one part of the dish leaving the rest dark; as the bacteria cannot survive without light, all the bacteria moved into the circle of light, becoming crowded. If the bacteria's byproduct was oxygen, the distances between individuals would become larger and larger as more oxygen was produced, but because of the bacteria's behavior in the focused light, it was concluded that the bacteria's photosynthetic byproduct could not be oxygen.
Researchers have theorized that some purple bacteria are related to the mitochondria, symbiotic bacteria in plant and animal cells today that act as organelles. Comparisons of their protein structure suggests. Purple non-sulfur bacteria are found among the alpha and beta subgroups, including: Purple sulfur bacteria are included among the gamma subgroup, make up the order Chromatiales; the similarity between the photosynthetic machinery in these different lines indicates it had a common origin, either from some common ancestor or passed by lateral transfer
Bacteria are a type of biological cell. They constitute a large domain of prokaryotic microorganisms. A few micrometres in length, bacteria have a number of shapes, ranging from spheres to rods and spirals. Bacteria were among the first life forms to appear on Earth, are present in most of its habitats. Bacteria inhabit soil, acidic hot springs, radioactive waste, the deep portions of Earth's crust. Bacteria live in symbiotic and parasitic relationships with plants and animals. Most bacteria have not been characterised, only about half of the bacterial phyla have species that can be grown in the laboratory; the study of bacteria is known as a branch of microbiology. There are 40 million bacterial cells in a gram of soil and a million bacterial cells in a millilitre of fresh water. There are 5×1030 bacteria on Earth, forming a biomass which exceeds that of all plants and animals. Bacteria are vital in many stages of the nutrient cycle by recycling nutrients such as the fixation of nitrogen from the atmosphere.
The nutrient cycle includes the decomposition of dead bodies. In the biological communities surrounding hydrothermal vents and cold seeps, extremophile bacteria provide the nutrients needed to sustain life by converting dissolved compounds, such as hydrogen sulphide and methane, to energy. Data reported by researchers in October 2012 and published in March 2013 suggested that bacteria thrive in the Mariana Trench, with a depth of up to 11 kilometres, is the deepest known part of the oceans. Other researchers reported related studies that microbes thrive inside rocks up to 580 metres below the sea floor under 2.6 kilometres of ocean off the coast of the northwestern United States. According to one of the researchers, "You can find microbes everywhere—they're adaptable to conditions, survive wherever they are."The famous notion that bacterial cells in the human body outnumber human cells by a factor of 10:1 has been debunked. There are 39 trillion bacterial cells in the human microbiota as personified by a "reference" 70 kg male 170 cm tall, whereas there are 30 trillion human cells in the body.
This means that although they do have the upper hand in actual numbers, it is only by 30%, not 900%. The largest number exist in the gut flora, a large number on the skin; the vast majority of the bacteria in the body are rendered harmless by the protective effects of the immune system, though many are beneficial in the gut flora. However several species of bacteria are pathogenic and cause infectious diseases, including cholera, anthrax and bubonic plague; the most common fatal bacterial diseases are respiratory infections, with tuberculosis alone killing about 2 million people per year in sub-Saharan Africa. In developed countries, antibiotics are used to treat bacterial infections and are used in farming, making antibiotic resistance a growing problem. In industry, bacteria are important in sewage treatment and the breakdown of oil spills, the production of cheese and yogurt through fermentation, the recovery of gold, palladium and other metals in the mining sector, as well as in biotechnology, the manufacture of antibiotics and other chemicals.
Once regarded as plants constituting the class Schizomycetes, bacteria are now classified as prokaryotes. Unlike cells of animals and other eukaryotes, bacterial cells do not contain a nucleus and harbour membrane-bound organelles. Although the term bacteria traditionally included all prokaryotes, the scientific classification changed after the discovery in the 1990s that prokaryotes consist of two different groups of organisms that evolved from an ancient common ancestor; these evolutionary domains are called Archaea. The word bacteria is the plural of the New Latin bacterium, the latinisation of the Greek βακτήριον, the diminutive of βακτηρία, meaning "staff, cane", because the first ones to be discovered were rod-shaped; the ancestors of modern bacteria were unicellular microorganisms that were the first forms of life to appear on Earth, about 4 billion years ago. For about 3 billion years, most organisms were microscopic, bacteria and archaea were the dominant forms of life. Although bacterial fossils exist, such as stromatolites, their lack of distinctive morphology prevents them from being used to examine the history of bacterial evolution, or to date the time of origin of a particular bacterial species.
However, gene sequences can be used to reconstruct the bacterial phylogeny, these studies indicate that bacteria diverged first from the archaeal/eukaryotic lineage. The most recent common ancestor of bacteria and archaea was a hyperthermophile that lived about 2.5 billion–3.2 billion years ago. Bacteria were involved in the second great evolutionary divergence, that of the archaea and eukaryotes. Here, eukaryotes resulted from the entering of ancient bacteria into endosymbiotic associations with the ancestors of eukaryotic cells, which were themselves related to the Archaea; this involved the engulfment by proto-eukaryotic cells of alphaproteobacterial symbionts to form either mitochondria or hydrogenosomes, which are still found in all known Eukarya. Some eukaryotes that contained mitochondria engulfed cyanobacteria-like organisms, leading to the formation of chloroplasts in algae and plants; this is known as primary endosymbiosis. Bacteria display a wide diversity of sizes, called morphologies.
Bacterial cells are about one-tenth the size of eukaryotic cells