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Number of Bacteria

Number of Bacteria


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I am creating a mathematical model for the growth of Synechocystis. sp PCC 6803 and Methanosarcina barkeri Fusaro in photobioreactors and anaerobic membrane bioreactors respectively. I have a couple of questions regarding this:

  1. When you buy these strains, or bacteria in general, from a supplier, how many bacteria will you receive? (I need this for the initial number of bacteria)
  2. How do you find/calculate the half-saturation constant? (Used in Monod's equation)
  3. How do you find/calculate the growth limiting substrate? (Used in Monod's equation)

Any help would be appreciated!


  1. When you buy these strains, or bacteria in general, from a supplier, how many bacteria will you receive? (I need this for the initial number of bacteria)

You don't know how many cells you'll get. Depending on the strain and on how it was preserved (frozen, freeze-dried, liquid culture), the percentage of viable cells in the sample you get can vary a lot. Anyway, it is not like this that you will find the initial number of bacteria for your model. Before inoculating your bioreactors, pre-cultures have to be prepared. You won't be directly using the supplier's sample as inoculum.

As for how to determine the cell count in your pre-culture, it really depends on what kind of equipment you have access to. If you have access to a flow cytometer, then you can get the cell count directly. Otherwise, you can use more "traditional" microbiological techniques (Optical density, Petri dishes, Dry weight… ).

You might even consider using another variable than cell number for your growth model. It is often the optical density or the dry wheight that is modelled, rather than the number of cells.


What Is a CFU in Microbiology?

When scientists want to know how many microorganisms there are in a solution of bacteria or fungi, it's usually too time-consuming to count every cell individually under the microscope. By diluting a sample of microbes and spreading it across a petri plate, microbiologists can instead count groups of microbes, called colonies, with the naked eye. Each colony is assumed to have grown from a single colony-forming unit, or CFU.


Introduction

How many cells are there in the human body? Beyond order of magnitude statements that give no primary reference or uncertainty estimates, very few detailed estimates have been performed (the one exception [1] is discussed below). Similarly, the ubiquitous statements regarding 10 14 –10 15 bacteria residing in our body trace back to an old back-of-the-envelope calculation [2–4].

The aim of this study is to critically revisit former estimates for the number of human and bacterial cells in the human body. We give up-to-date detailed estimates where the calculation logic and sources are fully documented and uncertainty ranges are derived. By updating the cell counts in the body, we also revisit the 10:1 value that has been so thoroughly repeated as to achieve the status of an established common knowledge fact [4]. This ratio was criticized recently in a letter to the journal Microbe [5], but an alternative detailed estimate that will give concrete values and estimate the uncertainty range is needed. Here, we provide an account of the methodologies employed hitherto for cell count and revise past estimates. Doing so, we repeat and reflect on the assumptions in previous back-of-the-envelope calculations, also known as Fermi problems. We find such estimates as effective sanity checks and a way to improve our quantitative understanding in biology.

A major part of the available literature used in the derivation of human cell numbers was based on cohorts of exclusively or mostly men, and as we use these sources, our analysis starts with adult men. As discussed below, relatively modest quantitative differences apply for women due to changes in characteristic body mass, blood volume, and the genital microbiota. For our analysis, we used the definition of the standard reference man as given in the literature [6] as: "Reference Man is defined as being between 20–30 years of age, weighing 70 kg, is 170 cm in height.” Our analysis revisits the estimates for the number of microbial cells, human cells, and their ratio in the body of such a standard man.

We begin our analysis by revisiting the number of bacteria through surveying earlier sources, comparing counts in different body organs and finally focusing on the content of the colon. We then estimate the total number of human cells in the body, comparing calculations using a "representative" cell size to aggregation by cell type. We then contrast the cell number distribution by tissue type to the mass distribution. In closing, we revisit the ratio of bacterial to human cells and evaluate the effect of gender, age, and obesity.


Number of Bacteria - Biology

Bacteria are tiny, one-celled organisms – generally 4/100,000 of an inch wide (1 µm) and somewhat longer in length. What bacteria lack in size, they make up in numbers. A teaspoon of productive soil generally contains between 100 million and 1 billion bacteria. That is as much mass as two cows per acre.

Bacteria fall into four functional groups. Most are decomposers that consume simple carbon compounds, such as root exudates and fresh plant litter. By this process, bacteria convert energy in soil organic matter into forms useful to the rest of the organisms in the soil food web. A number of decomposers can break down pesticides and pollutants in soil. Decomposers are especially important in immobilizing, or retaining, nutrients in their cells, thus preventing the loss of nutrients, such as nitrogen, from the rooting zone.

A second group of bacteria are the mutualists that form partnerships with plants. The most well-known of these are the nitrogen-fixing bacteria. The third group of bacteria is the pathogens. Bacterial pathogens include Xymomonas and Erwinia species, and species of Agrobacterium that cause gall formation in plants. A fourth group, called lithotrophs or chemoautotrophs, obtains its energy from compounds of nitrogen, sulfur, iron or hydrogen instead of from carbon compounds. Some of these species are important to nitrogen cycling and degradation of pollutants.

WHAT DO BACTERIA DO?

Bacteria from all four groups perform important services related to water dynamics, nutrient cycling, and disease suppression. Some bacteria affect water movement by producing substances that help bind soil particles into small aggregates (those with diameters of 1/10,000-1/100 of an inch or 2-200µm). Stable aggregates improve water infiltration and the soil’s water-holding ability. In a diverse bacterial community, many organisms will compete with disease-causing organisms in roots and on aboveground surfaces of plants.

A FEW IMPORTANT BACTERIA

Nitrogen-fixing bacteria form symbiotic associations with the roots of legumes like clover and lupine, and trees such as alder and locust. Visible nodules are created where bacteria infect a growing root hair (Figure 4). The plant supplies simple carbon compounds to the bacteria, and the bacteria convert nitrogen (N2) from air into a form the plant host can use. When leaves or roots from the host plant decompose, soil nitrogen increases in the surrounding area.

Nitrifying bacteria change ammonium (NH4+) to nitrite (NO2-) then to nitrate (NO3-) – a preferred form of nitrogen for grasses and most row crops. Nitrate is leached more easily from the soil, so some farmers use nitrification inhibitors to reduce the activity of one type of nitrifying bacteria. Nitrifying bacteria are suppressed in forest soils, so that most of the nitrogen remains as ammonium.

Denitrifying bacteria convert nitrate to nitrogen (N2) or nitrous oxide (N2O) gas. Denitrifiers are anaerobic, meaning they are active where oxygen is absent, such as in saturated soils or inside soil aggregates.

Actinomycetes are a large group of bacteria that grow as hyphae like fungi (Figure 3). They are responsible for the characteristically “earthy” smell of freshly turned, healthy soil. Actinomycetes decompose a wide array of substrates, but are especially important in degrading recalcitrant (hard-to-decompose) compounds, such as chitin and cellulose, and are active at high pH levels. Fungi are more important in degrading these compounds at low pH. A number of antibiotics are produced by actinomycetes such as Streptomyces.

WHERE ARE BACTERIA?

Various species of bacteria thrive on different food sources and in different microenvironments. In general, bacteria are more competitive when labile (easy-to-metabolize) substrates are present. This includes fresh, young plant residue and the compounds found near living roots. Bacteria are especially concentrated in the rhizosphere, the narrow region next to and in the root. There is evidence that plants produce certain types of root exudates to encourage the growth of protective bacteria.

Bacteria alter the soil environment to the extent that the soil environment will favor certain plant communities over others. Before plants can become established on fresh sediments, the bacterial community must establish first, starting with photosynthetic bacteria. These fix atmospheric nitrogen and carbon, produce organic matter, and immobilize enough nitrogen and other nutrients to initiate nitrogen cycling processes in the young soil. Then, early successional plant species can grow. As the plant community is established, different types of organic matter enter the soil and change the type of food available to bacteria. In turn, the altered bacterial community changes soil structure and the environment for plants. Some researchers think it may be possible to control the plant species in a place by managing the soil bacteria community.

BUG BIOGRAPHY
By Ann Kennedy, USDA Agricultural Research Service, Pullman, WA

Bacteria That Promote Plant Growth: Certain strains of the soil bacteria Pseudomonas fluorescens have anti-fungal activity that inhibits some plant pathogens. P. fluorescens and other Pseudomonas and Xanthomonas species can increase plant growth in several ways. They may produce a compound that inhibits the growth of pathogens or reduces invasion of the plant by a pathogen. They may also produce compounds (growth factors) that directly increase plant growth.

These plant growth-enhancing bacteria occur naturally in soils, but not always in high enough numbers to have a dramatic effect. In the future, farmers may be able to inoculate seeds with anti-fungal bacteria, such as P. fluorescens, to ensure that the bacteria reduce pathogens around the seed and root of the crop.


A microbe is any organism that is not visible with the naked eye. The unaided resolution of the eye is about 0.1mm

Bacteria are classified according to their shape:

1) Cocci: spherical bacteria

  • Cocci – smallest bacteria, occur as single spheres
  • Diplococci – pairs of spheres, e.g. pneumonia
  • Staphylococci – clusters of spheres, e.g. food poisoning
  • Streptococci – chains of spheres, e.g. sore throat

2) Bacilli: rod-shaped bacteria:

3) Spirilla – large, spiral-shaped bacteria - e.g. syphilis

4) Vibrio – crescent-shaped bacteria - e.g. cholera

Cell elongation results in the synthesis of additional cytoplasm & nuclear material

DNA replication takes place (there is no mitotic spindle), & the nuclear material attaches to the plasma membrane or mesosome

A septum begins to develop, & the nuclear material is distributed to both sides

The septum is completed, & a cell wall develops to divide the cell into two

The two daughter cells grow to a critical size, & then repeat this process

New genetic material can be inserted into a bacterium in three main ways:

1) Conjugation: bacteria link together by their pili.

  • Donor passes a plasmid called the F-factor (fertility) to the recipient cell.
  • The F-factor may be in a plasmid (replicating independently), or incorporated into the main bacterial chromosome

2) Transformation: one bacterium releases DNA which is absorbed by a second bacterium, allowing it to acquire new characteristics

3) Transduction: new genes can be inserted into the bacterial chromosome by a bacteria phage (a virus acting as a vector)

The bacterial population growth curve occurs in four main phases:

1) Lag phase: cells are active, but there is little increase in number.

2) Log phase: Nutrients & space are in plentiful supply, so there is little competition, & the bacteria multiply at their maximum rate

3) Stationary phase: carrying capacity (maximum number of bacteria that the environment can support) is reached, so intraspecific competition takes place between bacteria.

Hence the death rate balances the population growth rate, & the number of bacteria remains roughly constant

4) Death phase: nutrient supply is running out & waste products accumulate resulting in increased toxicity of environment.

Organisms are killed & population size eventually falls to zero.

Spores may be produced during stationary phase that are resistant to the adverse conditions

Bacterial growth can be controlled using physical methods (gamma irradiation or in an Autoclave using high temperatures) or by chemical means:


Ecology of bacteria

Prokaryotes are ubiquitous on Earth’s surface. They are found in every accessible environment, from polar ice to bubbling hot springs, from mountaintops to the ocean floor, and from plant and animal bodies to forest soils. Some bacteria can grow in soil or water at temperatures near freezing (0 °C [32 °F]), whereas others thrive in water at temperatures near boiling (100 °C [212 °F]). Each bacterium is adapted to live in a particular environmental niche, be it oceanic surfaces, mud sediments, soil, or the surfaces of another organism. The level of bacteria in the air is low but significant, especially when dust has been suspended. In uncontaminated natural bodies of water, bacterial counts can be in the thousands per millilitre in fertile soil, bacterial counts can be in the millions per gram and in feces, bacterial counts can exceed billions per gram.

Prokaryotes are important members of their habitats. Although they are small in size, their sheer numbers mean that their metabolism plays an enormous role—sometimes beneficial, sometimes harmful—in the conversion of elements in their external environment. Probably every naturally occurring substance, and many synthetic ones, can be degraded (metabolized) by some species of bacteria. The largest stomach of the cow, the rumen, is a fermentation chamber in which bacteria digest the cellulose in grasses and feeds, converting them to fatty acids and amino acids, which are the fundamental nutrients used by the cow and the basis for the cow’s production of milk. Organic wastes in sewage or compost piles are converted by bacteria either into suitable nutrients for plant metabolism or into gaseous methane (CH4) and carbon dioxide. The remains of all organic materials, including plants and animals, are eventually converted to soil and gases through the activities of bacteria and other microorganisms and are thereby made available for further growth.

Many bacteria live in streams and other sources of water, and their presence at low population densities in a sample of water does not necessarily indicate that the water is unfit for consumption. However, water that contains bacteria such as E. coli, which are normal inhabitants of the intestinal tract of humans and animals, indicates that sewage or fecal material has recently polluted that water source. Such coliform bacteria may be pathogens (disease-causing organisms) themselves, and their presence signals that other, less easily detected bacterial and viral pathogens may also be present. Procedures used in water purification plants—settling, filtration, and chlorination—are designed to remove these and any other microorganisms and infectious agents that may be present in water that is intended for human consumption. Also, sewage treatment is necessary to prevent the release of pathogenic bacteria and viruses from wastewater into water supplies. Sewage treatment plants also initiate the decay of organic materials (proteins, fats, and carbohydrates) in the wastewater. The breakdown of organic material by microorganisms in the water consumes oxygen (biochemical oxygen demand), causing a decrease in the oxygen level, which can be very harmful to aquatic life in streams and lakes that receive the wastewater. One objective of sewage treatment is to oxidize as much organic material as possible before its discharge into the water system, thereby reducing the biochemical oxygen demand of the wastewater. Sewage digestion tanks and aeration devices specifically exploit the metabolic capacity of bacteria for this purpose. (For more information about the treatment of wastewater, see environmental works: Water-pollution control.)

Soil bacteria are extremely active in effecting biochemical changes by transforming the various substances, humus and minerals, that characterize soil. Elements that are central to life, such as carbon, nitrogen, and sulfur, are converted by bacteria from inorganic gaseous compounds into forms that can be used by plants and animals. Bacteria also convert the end products of plant and animal metabolism into forms that can be used by bacteria and other microorganisms. The nitrogen cycle can illustrate the role of bacteria in effecting various chemical changes. Nitrogen exists in nature in several oxidation states, as nitrate, nitrite, dinitrogen gas, several nitrogen oxides, ammonia, and organic amines (ammonia compounds containing one or more substituted hydrocarbons). Nitrogen fixation is the conversion of dinitrogen gas from the atmosphere into a form that can be used by living organisms. Some nitrogen-fixing bacteria, such as Azotobacter, Clostridium pasteurianum, and Klebsiella pneumoniae, are free-living, whereas species of Rhizobium live in an intimate association with leguminous plants. Rhizobium organisms in the soil recognize and invade the root hairs of their specific plant host, enter the plant tissues, and form a root nodule. This process causes the bacteria to lose many of their free-living characteristics. They become dependent upon the carbon supplied by the plant, and, in exchange for carbon, they convert nitrogen gas to ammonia, which is used by the plant for its protein synthesis and growth. In addition, many bacteria can convert nitrate to amines for purposes of synthesizing cellular materials or to ammonia when nitrate is used as electron acceptor. Denitrifying bacteria convert nitrate to dinitrogen gas. The conversion of ammonia or organic amines to nitrate is accomplished by the combined activities of the aerobic organisms Nitrosomonas and Nitrobacter, which use ammonia as an electron donor.

In the carbon cycle, carbon dioxide is converted into cellular materials by plants and autotrophic prokaryotes, and organic carbon is returned to the atmosphere by heterotrophic life-forms. The major breakdown product of microbial decomposition is carbon dioxide, which is formed by respiring aerobic organisms.

Methane, another gaseous end product of carbon metabolism, is a relatively minor component of the global carbon cycle but of importance in local situations and as a renewable energy source for human use. Methane production is carried out by the highly specialized and obligately anaerobic methanogenic prokaryotes, all of which are archaea. Methanogens use carbon dioxide as their terminal electron acceptor and receive electrons from hydrogen gas (H2). A few other substances can be converted to methane by these organisms, including methanol, formic acid, acetic acid, and methylamines. Despite the extremely narrow range of substances that can be used by methanogens, methane production is very common during the anaerobic decomposition of many organic materials, including cellulose, starch, proteins, amino acids, fats, alcohols, and most other substrates. Methane formation from these materials requires that other anaerobic bacteria degrade these substances either to acetate or to carbon dioxide and hydrogen gas, which are then used by the methanogens. The methanogens support the growth of the other anaerobic bacteria in the mixture by removing hydrogen gas formed during their metabolic activities for methane production. Consumption of the hydrogen gas stimulates the metabolism of other bacteria.

Despite the fact that methanogens have such a restricted metabolic capability and are quite sensitive to oxygen, they are widespread on Earth. Large amounts of methane are produced in anaerobic environments, such as swamps and marshes, but significant amounts also are produced in soil and by ruminant animals. At least 80 percent of the methane in the atmosphere has been produced by the action of methanogens, the remainder being released from coal deposits or natural gas wells.


Contents

The word bacteria is the plural of the New Latin bacterium, which is the latinisation of the Greek βακτήριον (bakterion), [17] the diminutive of βακτηρία (bakteria), meaning "staff, cane", [18] because the first ones to be discovered were rod-shaped. [19] [20]

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, and bacteria and archaea were the dominant forms of life. [21] [22] 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, and these studies indicate that bacteria diverged first from the archaeal/eukaryotic lineage. [23] The most recent common ancestor of bacteria and archaea was probably a hyperthermophile that lived about 2.5 billion–3.2 billion years ago. [24] [25] The earliest life on land may have been bacteria some 3.22 billion years ago. [26]

Bacteria were also 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 possibly related to the Archaea. [27] [28] 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 (sometimes in highly reduced form, e.g. in ancient "amitochondrial" protozoa). Later, some eukaryotes that already contained mitochondria also engulfed cyanobacteria-like organisms, leading to the formation of chloroplasts in algae and plants. This is known as primary endosymbiosis. [29] [30]

Bacteria display a wide diversity of shapes and sizes, called morphologies. Bacterial cells are about one-tenth the size of eukaryotic cells and are typically 0.5–5.0 micrometres in length. However, a few species are visible to the unaided eye—for example, Thiomargarita namibiensis is up to half a millimetre long [31] and Epulopiscium fishelsoni reaches 0.7 mm. [32] Among the smallest bacteria are members of the genus Mycoplasma, which measure only 0.3 micrometres, as small as the largest viruses. [33] Some bacteria may be even smaller, but these ultramicrobacteria are not well-studied. [34]

Most bacterial species are either spherical, called cocci (singular coccus, from Greek kókkos, grain, seed), or rod-shaped, called bacilli (sing. bacillus, from Latin baculus, stick). [35] Some bacteria, called vibrio, are shaped like slightly curved rods or comma-shaped others can be spiral-shaped, called spirilla, or tightly coiled, called spirochaetes. A small number of other unusual shapes have been described, such as star-shaped bacteria. [36] This wide variety of shapes is determined by the bacterial cell wall and cytoskeleton, and is important because it can influence the ability of bacteria to acquire nutrients, attach to surfaces, swim through liquids and escape predators. [37] [38]

Many bacterial species exist simply as single cells, others associate in characteristic patterns: Neisseria form diploids (pairs), Streptococcus form chains, and Staphylococcus group together in "bunch of grapes" clusters. Bacteria can also group to form larger multicellular structures, such as the elongated filaments of Actinobacteria, the aggregates of Myxobacteria, and the complex hyphae of Streptomyces. [39] These multicellular structures are often only seen in certain conditions. For example, when starved of amino acids, Myxobacteria detect surrounding cells in a process known as quorum sensing, migrate towards each other, and aggregate to form fruiting bodies up to 500 micrometres long and containing approximately 100,000 bacterial cells. [40] In these fruiting bodies, the bacteria perform separate tasks for example, about one in ten cells migrate to the top of a fruiting body and differentiate into a specialised dormant state called a myxospore, which is more resistant to drying and other adverse environmental conditions. [41]

Bacteria often attach to surfaces and form dense aggregations called biofilms, and larger formations known as microbial mats. These biofilms and mats can range from a few micrometres in thickness to up to half a metre in depth, and may contain multiple species of bacteria, protists and archaea. Bacteria living in biofilms display a complex arrangement of cells and extracellular components, forming secondary structures, such as microcolonies, through which there are networks of channels to enable better diffusion of nutrients. [42] [43] In natural environments, such as soil or the surfaces of plants, the majority of bacteria are bound to surfaces in biofilms. [44] Biofilms are also important in medicine, as these structures are often present during chronic bacterial infections or in infections of implanted medical devices, and bacteria protected within biofilms are much harder to kill than individual isolated bacteria. [45]

Intracellular structures

The bacterial cell is surrounded by a cell membrane, which is made primarily of phospholipids. This membrane encloses the contents of the cell and acts as a barrier to hold nutrients, proteins and other essential components of the cytoplasm within the cell. [46] Unlike eukaryotic cells, bacteria usually lack large membrane-bound structures in their cytoplasm such as a nucleus, mitochondria, chloroplasts and the other organelles present in eukaryotic cells. [47] However, some bacteria have protein-bound organelles in the cytoplasm which compartmentalize aspects of bacterial metabolism, [48] [49] such as the carboxysome. [50] Additionally, bacteria have a multi-component cytoskeleton to control the localisation of proteins and nucleic acids within the cell, and to manage the process of cell division. [51] [52] [53]

Many important biochemical reactions, such as energy generation, occur due to concentration gradients across membranes, creating a potential difference analogous to a battery. The general lack of internal membranes in bacteria means these reactions, such as electron transport, occur across the cell membrane between the cytoplasm and the outside of the cell or periplasm. [54] However, in many photosynthetic bacteria the plasma membrane is highly folded and fills most of the cell with layers of light-gathering membrane. [55] These light-gathering complexes may even form lipid-enclosed structures called chlorosomes in green sulfur bacteria. [56]

Bacteria do not have a membrane-bound nucleus, and their genetic material is typically a single circular bacterial chromosome of DNA located in the cytoplasm in an irregularly shaped body called the nucleoid. [57] The nucleoid contains the chromosome with its associated proteins and RNA. Like all other organisms, bacteria contain ribosomes for the production of proteins, but the structure of the bacterial ribosome is different from that of eukaryotes and Archaea. [58]

Some bacteria produce intracellular nutrient storage granules, such as glycogen, [59] polyphosphate, [60] sulfur [61] or polyhydroxyalkanoates. [62] Bacteria such as the photosynthetic cyanobacteria, produce internal gas vacuoles, which they use to regulate their buoyancy, allowing them to move up or down into water layers with different light intensities and nutrient levels. [63]

Extracellular structures

Around the outside of the cell membrane is the cell wall. Bacterial cell walls are made of peptidoglycan (also called murein), which is made from polysaccharide chains cross-linked by peptides containing D-amino acids. [64] Bacterial cell walls are different from the cell walls of plants and fungi, which are made of cellulose and chitin, respectively. [65] The cell wall of bacteria is also distinct from that of Archaea, which do not contain peptidoglycan. The cell wall is essential to the survival of many bacteria, and the antibiotic penicillin (produced by a fungus called Penicillium) is able to kill bacteria by inhibiting a step in the synthesis of peptidoglycan. [65]

There are broadly speaking two different types of cell wall in bacteria, that classify bacteria into Gram-positive bacteria and Gram-negative bacteria. The names originate from the reaction of cells to the Gram stain, a long-standing test for the classification of bacterial species. [66]

Gram-positive bacteria possess a thick cell wall containing many layers of peptidoglycan and teichoic acids. In contrast, Gram-negative bacteria have a relatively thin cell wall consisting of a few layers of peptidoglycan surrounded by a second lipid membrane containing lipopolysaccharides and lipoproteins. Most bacteria have the Gram-negative cell wall, and only the Firmicutes and Actinobacteria (previously known as the low G+C and high G+C Gram-positive bacteria, respectively) have the alternative Gram-positive arrangement. [67] These differences in structure can produce differences in antibiotic susceptibility for instance, vancomycin can kill only Gram-positive bacteria and is ineffective against Gram-negative pathogens, such as Haemophilus influenzae or Pseudomonas aeruginosa. [68] Some bacteria have cell wall structures that are neither classically Gram-positive or Gram-negative. This includes clinically important bacteria such as Mycobacteria which have a thick peptidoglycan cell wall like a Gram-positive bacterium, but also a second outer layer of lipids. [69]

In many bacteria, an S-layer of rigidly arrayed protein molecules covers the outside of the cell. [70] This layer provides chemical and physical protection for the cell surface and can act as a macromolecular diffusion barrier. S-layers have diverse but mostly poorly understood functions, but are known to act as virulence factors in Campylobacter and contain surface enzymes in Bacillus stearothermophilus. [71]

Flagella are rigid protein structures, about 20 nanometres in diameter and up to 20 micrometres in length, that are used for motility. Flagella are driven by the energy released by the transfer of ions down an electrochemical gradient across the cell membrane. [72]

Fimbriae (sometimes called "attachment pili") are fine filaments of protein, usually 2–10 nanometres in diameter and up to several micrometres in length. They are distributed over the surface of the cell, and resemble fine hairs when seen under the electron microscope. Fimbriae are believed to be involved in attachment to solid surfaces or to other cells, and are essential for the virulence of some bacterial pathogens. [73] Pili (sing. pilus) are cellular appendages, slightly larger than fimbriae, that can transfer genetic material between bacterial cells in a process called conjugation where they are called conjugation pili or sex pili (see bacterial genetics, below). [74] They can also generate movement where they are called type IV pili. [75]

Glycocalyx is produced by many bacteria to surround their cells, and varies in structural complexity: ranging from a disorganised slime layer of extracellular polymeric substances to a highly structured capsule. These structures can protect cells from engulfment by eukaryotic cells such as macrophages (part of the human immune system). [76] They can also act as antigens and be involved in cell recognition, as well as aiding attachment to surfaces and the formation of biofilms. [77]

The assembly of these extracellular structures is dependent on bacterial secretion systems. These transfer proteins from the cytoplasm into the periplasm or into the environment around the cell. Many types of secretion systems are known and these structures are often essential for the virulence of pathogens, so are intensively studied. [78]

Endospores

Certain genera of Gram-positive bacteria, such as Bacillus, Clostridium, Sporohalobacter, Anaerobacter, and Heliobacterium, can form highly resistant, dormant structures called endospores. [79] Endospores develop within the cytoplasm of the cell generally a single endospore develops in each cell. [80] Each endospore contains a core of DNA and ribosomes surrounded by a cortex layer and protected by a multilayer rigid coat composed of peptidoglycan and a variety of proteins. [80]

Endospores show no detectable metabolism and can survive extreme physical and chemical stresses, such as high levels of UV light, gamma radiation, detergents, disinfectants, heat, freezing, pressure, and desiccation. [81] In this dormant state, these organisms may remain viable for millions of years, [82] [83] [84] and endospores even allow bacteria to survive exposure to the vacuum and radiation in space, possibly bacteria could be distributed throughout the Universe by space dust, meteoroids, asteroids, comets, planetoids or via directed panspermia. [85] [86] Endospore-forming bacteria can also cause disease: for example, anthrax can be contracted by the inhalation of Bacillus anthracis endospores, and contamination of deep puncture wounds with Clostridium tetani endospores causes tetanus. [87]

Bacteria exhibit an extremely wide variety of metabolic types. [88] The distribution of metabolic traits within a group of bacteria has traditionally been used to define their taxonomy, but these traits often do not correspond with modern genetic classifications. [89] Bacterial metabolism is classified into nutritional groups on the basis of three major criteria: the source of energy, the electron donors used, and the source of carbon used for growth. [90]

Bacteria either derive energy from light using photosynthesis (called phototrophy), or by breaking down chemical compounds using oxidation (called chemotrophy). [91] Chemotrophs use chemical compounds as a source of energy by transferring electrons from a given electron donor to a terminal electron acceptor in a redox reaction. This reaction releases energy that can be used to drive metabolism. Chemotrophs are further divided by the types of compounds they use to transfer electrons. Bacteria that use inorganic compounds such as hydrogen, carbon monoxide, or ammonia as sources of electrons are called lithotrophs, while those that use organic compounds are called organotrophs. [91] The compounds used to receive electrons are also used to classify bacteria: aerobic organisms use oxygen as the terminal electron acceptor, while anaerobic organisms use other compounds such as nitrate, sulfate, or carbon dioxide. [91]

Many bacteria get their carbon from other organic carbon, called heterotrophy. Others such as cyanobacteria and some purple bacteria are autotrophic, meaning that they obtain cellular carbon by fixing carbon dioxide. [92] In unusual circumstances, the gas methane can be used by methanotrophic bacteria as both a source of electrons and a substrate for carbon anabolism. [93]

Nutritional types in bacterial metabolism
Nutritional type Source of energy Source of carbon Examples
Phototrophs Sunlight Organic compounds (photoheterotrophs) or carbon fixation (photoautotrophs) Cyanobacteria, Green sulfur bacteria, Chloroflexi, or Purple bacteria
Lithotrophs Inorganic compounds Organic compounds (lithoheterotrophs) or carbon fixation (lithoautotrophs) Thermodesulfobacteria, Hydrogenophilaceae, or Nitrospirae
Organotrophs Organic compounds Organic compounds (chemoheterotrophs) or carbon fixation (chemoautotrophs) Bacillus, Clostridium or Enterobacteriaceae

In many ways, bacterial metabolism provides traits that are useful for ecological stability and for human society. One example is that some bacteria have the ability to fix nitrogen gas using the enzyme nitrogenase. This environmentally important trait can be found in bacteria of most metabolic types listed above. [94] This leads to the ecologically important processes of denitrification, sulfate reduction, and acetogenesis, respectively. [95] [96] Bacterial metabolic processes are also important in biological responses to pollution for example, sulfate-reducing bacteria are largely responsible for the production of the highly toxic forms of mercury (methyl- and dimethylmercury) in the environment. [97] Non-respiratory anaerobes use fermentation to generate energy and reducing power, secreting metabolic by-products (such as ethanol in brewing) as waste. Facultative anaerobes can switch between fermentation and different terminal electron acceptors depending on the environmental conditions in which they find themselves. [98]

Unlike in multicellular organisms, increases in cell size (cell growth) and reproduction by cell division are tightly linked in unicellular organisms. Bacteria grow to a fixed size and then reproduce through binary fission, a form of asexual reproduction. [99] Under optimal conditions, bacteria can grow and divide extremely rapidly, and bacterial populations can double as quickly as every 9.8 minutes. [100] In cell division, two identical clone daughter cells are produced. Some bacteria, while still reproducing asexually, form more complex reproductive structures that help disperse the newly formed daughter cells. Examples include fruiting body formation by Myxobacteria and aerial hyphae formation by Streptomyces, or budding. Budding involves a cell forming a protrusion that breaks away and produces a daughter cell. [101]

In the laboratory, bacteria are usually grown using solid or liquid media. Solid growth media, such as agar plates, are used to isolate pure cultures of a bacterial strain. However, liquid growth media are used when the measurement of growth or large volumes of cells are required. Growth in stirred liquid media occurs as an even cell suspension, making the cultures easy to divide and transfer, although isolating single bacteria from liquid media is difficult. The use of selective media (media with specific nutrients added or deficient, or with antibiotics added) can help identify specific organisms. [103]

Most laboratory techniques for growing bacteria use high levels of nutrients to produce large amounts of cells cheaply and quickly. However, in natural environments, nutrients are limited, meaning that bacteria cannot continue to reproduce indefinitely. This nutrient limitation has led the evolution of different growth strategies (see r/K selection theory). Some organisms can grow extremely rapidly when nutrients become available, such as the formation of algal (and cyanobacterial) blooms that often occur in lakes during the summer. [104] Other organisms have adaptations to harsh environments, such as the production of multiple antibiotics by Streptomyces that inhibit the growth of competing microorganisms. [105] In nature, many organisms live in communities (e.g., biofilms) that may allow for increased supply of nutrients and protection from environmental stresses. [44] These relationships can be essential for growth of a particular organism or group of organisms (syntrophy). [106]

Bacterial growth follows four phases. When a population of bacteria first enter a high-nutrient environment that allows growth, the cells need to adapt to their new environment. The first phase of growth is the lag phase, a period of slow growth when the cells are adapting to the high-nutrient environment and preparing for fast growth. The lag phase has high biosynthesis rates, as proteins necessary for rapid growth are produced. [107] [108] The second phase of growth is the logarithmic phase, also known as the exponential phase. The log phase is marked by rapid exponential growth. The rate at which cells grow during this phase is known as the growth rate (k), and the time it takes the cells to double is known as the generation time (g). During log phase, nutrients are metabolised at maximum speed until one of the nutrients is depleted and starts limiting growth. The third phase of growth is the stationary phase and is caused by depleted nutrients. The cells reduce their metabolic activity and consume non-essential cellular proteins. The stationary phase is a transition from rapid growth to a stress response state and there is increased expression of genes involved in DNA repair, antioxidant metabolism and nutrient transport. [109] The final phase is the death phase where the bacteria run out of nutrients and die. [110]

Most bacteria have a single circular chromosome that can range in size from only 160,000 base pairs in the endosymbiotic bacteria Carsonella ruddii, [111] to 12,200,000 base pairs (12.2 Mbp) in the soil-dwelling bacteria Sorangium cellulosum. [112] There are many exceptions to this, for example some Streptomyces and Borrelia species contain a single linear chromosome, [113] [114] while some Vibrio species contain more than one chromosome. [115] Bacteria can also contain plasmids, small extra-chromosomal molecules of DNA that may contain genes for various useful functions such as antibiotic resistance, metabolic capabilities, or various virulence factors. [116]

Bacteria genomes usually encode a few hundred to a few thousand genes. The genes in bacterial genomes are usually a single continuous stretch of DNA and although several different types of introns do exist in bacteria, these are much rarer than in eukaryotes. [117]

Bacteria, as asexual organisms, inherit an identical copy of the parent's genomes and are clonal. However, all bacteria can evolve by selection on changes to their genetic material DNA caused by genetic recombination or mutations. Mutations come from errors made during the replication of DNA or from exposure to mutagens. Mutation rates vary widely among different species of bacteria and even among different clones of a single species of bacteria. [118] Genetic changes in bacterial genomes come from either random mutation during replication or "stress-directed mutation", where genes involved in a particular growth-limiting process have an increased mutation rate. [119]

Some bacteria also transfer genetic material between cells. This can occur in three main ways. First, bacteria can take up exogenous DNA from their environment, in a process called transformation. [120] Many bacteria can naturally take up DNA from the environment, while others must be chemically altered in order to induce them to take up DNA. [121] The development of competence in nature is usually associated with stressful environmental conditions, and seems to be an adaptation for facilitating repair of DNA damage in recipient cells. [122] The second way bacteria transfer genetic material is by transduction, when the integration of a bacteriophage introduces foreign DNA into the chromosome. Many types of bacteriophage exist, some simply infect and lyse their host bacteria, while others insert into the bacterial chromosome. [123] Bacteria resist phage infection through restriction modification systems that degrade foreign DNA, [124] and a system that uses CRISPR sequences to retain fragments of the genomes of phage that the bacteria have come into contact with in the past, which allows them to block virus replication through a form of RNA interference. [125] [126] The third method of gene transfer is conjugation, whereby DNA is transferred through direct cell contact. In ordinary circumstances, transduction, conjugation, and transformation involve transfer of DNA between individual bacteria of the same species, but occasionally transfer may occur between individuals of different bacterial species and this may have significant consequences, such as the transfer of antibiotic resistance. [127] [128] In such cases, gene acquisition from other bacteria or the environment is called horizontal gene transfer and may be common under natural conditions. [129]

Movement

Many bacteria are motile (able to move themselves) and do so using a variety of mechanisms. The best studied of these are flagella, long filaments that are turned by a motor at the base to generate propeller-like movement. [130] The bacterial flagellum is made of about 20 proteins, with approximately another 30 proteins required for its regulation and assembly. [130] The flagellum is a rotating structure driven by a reversible motor at the base that uses the electrochemical gradient across the membrane for power. [131]

Bacteria can use flagella in different ways to generate different kinds of movement. Many bacteria (such as E. coli) have two distinct modes of movement: forward movement (swimming) and tumbling. The tumbling allows them to reorient and makes their movement a three-dimensional random walk. [132] Bacterial species differ in the number and arrangement of flagella on their surface some have a single flagellum (monotrichous), a flagellum at each end (amphitrichous), clusters of flagella at the poles of the cell (lophotrichous), while others have flagella distributed over the entire surface of the cell (peritrichous). The flagella of a unique group of bacteria, the spirochaetes, are found between two membranes in the periplasmic space. They have a distinctive helical body that twists about as it moves. [130]

Two other types of bacterial motion are called twitching motility that relies on a structure called the type IV pilus, [133] and gliding motility, that uses other mechanisms. In twitching motility, the rod-like pilus extends out from the cell, binds some substrate, and then retracts, pulling the cell forward. [134]

Motile bacteria are attracted or repelled by certain stimuli in behaviours called taxes: these include chemotaxis, phototaxis, energy taxis, and magnetotaxis. [135] [136] [137] In one peculiar group, the myxobacteria, individual bacteria move together to form waves of cells that then differentiate to form fruiting bodies containing spores. [41] The myxobacteria move only when on solid surfaces, unlike E. coli, which is motile in liquid or solid media. [138]

Several Listeria and Shigella species move inside host cells by usurping the cytoskeleton, which is normally used to move organelles inside the cell. By promoting actin polymerisation at one pole of their cells, they can form a kind of tail that pushes them through the host cell's cytoplasm. [139]

Communication

A few bacteria have chemical systems that generate light. This bioluminescence often occurs in bacteria that live in association with fish, and the light probably serves to attract fish or other large animals. [140]

Bacteria often function as multicellular aggregates known as biofilms, exchanging a variety of molecular signals for inter-cell communication, and engaging in coordinated multicellular behaviour. [141] [142]

The communal benefits of multicellular cooperation include a cellular division of labour, accessing resources that cannot effectively be used by single cells, collectively defending against antagonists, and optimising population survival by differentiating into distinct cell types. [141] For example, bacteria in biofilms can have more than 500 times increased resistance to antibacterial agents than individual "planktonic" bacteria of the same species. [142]

One type of inter-cellular communication by a molecular signal is called quorum sensing, which serves the purpose of determining whether there is a local population density that is sufficiently high that it is productive to invest in processes that are only successful if large numbers of similar organisms behave similarly, as in excreting digestive enzymes or emitting light. [143] [144]

Quorum sensing allows bacteria to coordinate gene expression, and enables them to produce, release and detect autoinducers or pheromones which accumulate with the growth in cell population. [145]

Classification seeks to describe the diversity of bacterial species by naming and grouping organisms based on similarities. Bacteria can be classified on the basis of cell structure, cellular metabolism or on differences in cell components, such as DNA, fatty acids, pigments, antigens and quinones. [103] While these schemes allowed the identification and classification of bacterial strains, it was unclear whether these differences represented variation between distinct species or between strains of the same species. This uncertainty was due to the lack of distinctive structures in most bacteria, as well as lateral gene transfer between unrelated species. [147] Due to lateral gene transfer, some closely related bacteria can have very different morphologies and metabolisms. To overcome this uncertainty, modern bacterial classification emphasises molecular systematics, using genetic techniques such as guanine cytosine ratio determination, genome-genome hybridisation, as well as sequencing genes that have not undergone extensive lateral gene transfer, such as the rRNA gene. [148] Classification of bacteria is determined by publication in the International Journal of Systematic Bacteriology, [149] and Bergey's Manual of Systematic Bacteriology. [150] The International Committee on Systematic Bacteriology (ICSB) maintains international rules for the naming of bacteria and taxonomic categories and for the ranking of them in the International Code of Nomenclature of Bacteria. [151]

The term "bacteria" was traditionally applied to all microscopic, single-cell prokaryotes. However, molecular systematics showed prokaryotic life to consist of two separate domains, originally called Eubacteria and Archaebacteria, but now called Bacteria and Archaea that evolved independently from an ancient common ancestor. [1] The archaea and eukaryotes are more closely related to each other than either is to the bacteria. These two domains, along with Eukarya, are the basis of the three-domain system, which is currently the most widely used classification system in microbiology. [152] However, due to the relatively recent introduction of molecular systematics and a rapid increase in the number of genome sequences that are available, bacterial classification remains a changing and expanding field. [153] [154] For example, Cavalier-Smith argued that the Archaea and Eukaryotes evolved from Gram-positive bacteria. [155]

The identification of bacteria in the laboratory is particularly relevant in medicine, where the correct treatment is determined by the bacterial species causing an infection. Consequently, the need to identify human pathogens was a major impetus for the development of techniques to identify bacteria. [156]

The Gram stain, developed in 1884 by Hans Christian Gram, characterises bacteria based on the structural characteristics of their cell walls. [66] The thick layers of peptidoglycan in the "Gram-positive" cell wall stain purple, while the thin "Gram-negative" cell wall appears pink. By combining morphology and Gram-staining, most bacteria can be classified as belonging to one of four groups (Gram-positive cocci, Gram-positive bacilli, Gram-negative cocci and Gram-negative bacilli). Some organisms are best identified by stains other than the Gram stain, particularly mycobacteria or Nocardia, which show acid-fastness on Ziehl–Neelsen or similar stains. [157] Other organisms may need to be identified by their growth in special media, or by other techniques, such as serology. [158]

Culture techniques are designed to promote the growth and identify particular bacteria, while restricting the growth of the other bacteria in the sample. Often these techniques are designed for specific specimens for example, a sputum sample will be treated to identify organisms that cause pneumonia, while stool specimens are cultured on selective media to identify organisms that cause diarrhea, while preventing growth of non-pathogenic bacteria. Specimens that are normally sterile, such as blood, urine or spinal fluid, are cultured under conditions designed to grow all possible organisms. [103] [159] Once a pathogenic organism has been isolated, it can be further characterised by its morphology, growth patterns (such as aerobic or anaerobic growth), patterns of hemolysis, and staining. [160]

As with bacterial classification, identification of bacteria is increasingly using molecular methods. Diagnostics using DNA-based tools, such as polymerase chain reaction, are increasingly popular due to their specificity and speed, compared to culture-based methods. [161] These methods also allow the detection and identification of "viable but nonculturable" cells that are metabolically active but non-dividing. [162] However, even using these improved methods, the total number of bacterial species is not known and cannot even be estimated with any certainty. Following present classification, there are a little less than 9,300 known species of prokaryotes, which includes bacteria and archaea [163] but attempts to estimate the true number of bacterial diversity have ranged from 10 7 to 10 9 total species—and even these diverse estimates may be off by many orders of magnitude. [164] [165]

Phylogenetic tree

According to the phylogenetic analysis of Zhu (2019), the relationships could be the following: [166]

Despite their apparent simplicity, bacteria can form complex associations with other organisms. These symbiotic associations can be divided into parasitism, mutualism and commensalism. Due to their small size, commensal bacteria are ubiquitous and grow on animals and plants exactly as they will grow on any other surface. However, their growth can be increased by warmth and sweat, and large populations of these organisms in humans are the cause of body odour. [168]

Predators

Some species of bacteria kill and then consume other microorganisms, these species are called predatory bacteria. [169] These include organisms such as Myxococcus xanthus, which forms swarms of cells that kill and digest any bacteria they encounter. [170] Other bacterial predators either attach to their prey in order to digest them and absorb nutrients, such as Vampirovibrio chlorellavorus, [171] or invade another cell and multiply inside the cytosol, such as Daptobacter. [172] These predatory bacteria are thought to have evolved from saprophages that consumed dead microorganisms, through adaptations that allowed them to entrap and kill other organisms. [173]

Mutualists

Certain bacteria form close spatial associations that are essential for their survival. One such mutualistic association, called interspecies hydrogen transfer, occurs between clusters of anaerobic bacteria that consume organic acids, such as butyric acid or propionic acid, and produce hydrogen, and methanogenic Archaea that consume hydrogen. [174] The bacteria in this association are unable to consume the organic acids as this reaction produces hydrogen that accumulates in their surroundings. Only the intimate association with the hydrogen-consuming Archaea keeps the hydrogen concentration low enough to allow the bacteria to grow. [175]

In soil, microorganisms that reside in the rhizosphere (a zone that includes the root surface and the soil that adheres to the root after gentle shaking) carry out nitrogen fixation, converting nitrogen gas to nitrogenous compounds. [176] This serves to provide an easily absorbable form of nitrogen for many plants, which cannot fix nitrogen themselves. Many other bacteria are found as symbionts in humans and other organisms. For example, the presence of over 1,000 bacterial species in the normal human gut flora of the intestines can contribute to gut immunity, synthesise vitamins, such as folic acid, vitamin K and biotin, convert sugars to lactic acid (see Lactobacillus), as well as fermenting complex undigestible carbohydrates. [177] [178] [179] The presence of this gut flora also inhibits the growth of potentially pathogenic bacteria (usually through competitive exclusion) and these beneficial bacteria are consequently sold as probiotic dietary supplements. [180]

Pathogens

If bacteria form a parasitic association with other organisms, they are classed as pathogens. Pathogenic bacteria are a major cause of human death and disease and cause infections such as tetanus (caused by Clostridium tetani), typhoid fever, diphtheria, syphilis, cholera, foodborne illness, leprosy (caused by Micobacterium leprae) and tuberculosis (caused by Mycobacterium tuberculosis). A pathogenic cause for a known medical disease may only be discovered many years later, as was the case with Helicobacter pylori and peptic ulcer disease. Bacterial diseases are also important in agriculture, with bacteria causing leaf spot, fire blight and wilts in plants, as well as Johne's disease, mastitis, salmonella and anthrax in farm animals. [181]

Each species of pathogen has a characteristic spectrum of interactions with its human hosts. Some organisms, such as Staphylococcus or Streptococcus, can cause skin infections, pneumonia, meningitis and sepsis, a systemic inflammatory response producing shock, massive vasodilation and death. [182] Yet these organisms are also part of the normal human flora and usually exist on the skin or in the nose without causing any disease at all. Other organisms invariably cause disease in humans, such as the Rickettsia, which are obligate intracellular parasites able to grow and reproduce only within the cells of other organisms. One species of Rickettsia causes typhus, while another causes Rocky Mountain spotted fever. Chlamydia, another phylum of obligate intracellular parasites, contains species that can cause pneumonia or urinary tract infection and may be involved in coronary heart disease. [183] Finally, some species, such as Pseudomonas aeruginosa, Burkholderia cenocepacia, and Mycobacterium avium, are opportunistic pathogens and cause disease mainly in people suffering from immunosuppression or cystic fibrosis. [184] [185]

Bacterial infections may be treated with antibiotics, which are classified as bacteriocidal if they kill bacteria or bacteriostatic if they just prevent bacterial growth. There are many types of antibiotics, and each class inhibits a process that is different in the pathogen from that found in the host. An example of how antibiotics produce selective toxicity are chloramphenicol and puromycin, which inhibit the bacterial ribosome, but not the structurally different eukaryotic ribosome. [186] Antibiotics are used both in treating human disease and in intensive farming to promote animal growth, where they may be contributing to the rapid development of antibiotic resistance in bacterial populations. [187] Infections can be prevented by antiseptic measures such as sterilising the skin prior to piercing it with the needle of a syringe, and by proper care of indwelling catheters. Surgical and dental instruments are also sterilised to prevent contamination by bacteria. Disinfectants such as bleach are used to kill bacteria or other pathogens on surfaces to prevent contamination and further reduce the risk of infection. [188]

Bacteria, often lactic acid bacteria, such as Lactobacillus and Lactococcus, in combination with yeasts and moulds, have been used for thousands of years in the preparation of fermented foods, such as cheese, pickles, soy sauce, sauerkraut, vinegar, wine and yogurt. [189] [190]

The ability of bacteria to degrade a variety of organic compounds is remarkable and has been used in waste processing and bioremediation. Bacteria capable of digesting the hydrocarbons in petroleum are often used to clean up oil spills. [191] Fertiliser was added to some of the beaches in Prince William Sound in an attempt to promote the growth of these naturally occurring bacteria after the 1989 Exxon Valdez oil spill. These efforts were effective on beaches that were not too thickly covered in oil. Bacteria are also used for the bioremediation of industrial toxic wastes. [192] In the chemical industry, bacteria are most important in the production of enantiomerically pure chemicals for use as pharmaceuticals or agrichemicals. [193]

Bacteria can also be used in the place of pesticides in the biological pest control. This commonly involves Bacillus thuringiensis (also called BT), a Gram-positive, soil dwelling bacterium. Subspecies of this bacteria are used as a Lepidopteran-specific insecticides under trade names such as Dipel and Thuricide. [194] Because of their specificity, these pesticides are regarded as environmentally friendly, with little or no effect on humans, wildlife, pollinators and most other beneficial insects. [195] [196]

Because of their ability to quickly grow and the relative ease with which they can be manipulated, bacteria are the workhorses for the fields of molecular biology, genetics and biochemistry. By making mutations in bacterial DNA and examining the resulting phenotypes, scientists can determine the function of genes, enzymes and metabolic pathways in bacteria, then apply this knowledge to more complex organisms. [197] This aim of understanding the biochemistry of a cell reaches its most complex expression in the synthesis of huge amounts of enzyme kinetic and gene expression data into mathematical models of entire organisms. This is achievable in some well-studied bacteria, with models of Escherichia coli metabolism now being produced and tested. [198] [199] This understanding of bacterial metabolism and genetics allows the use of biotechnology to bioengineer bacteria for the production of therapeutic proteins, such as insulin, growth factors, or antibodies. [200] [201]

Because of their importance for research in general, samples of bacterial strains are isolated and preserved in Biological Resource Centers. This ensures the availability of the strain to scientists worldwide. [202]

Bacteria were first observed by the Dutch microscopist Antonie van Leeuwenhoek in 1676, using a single-lens microscope of his own design. [203] He then published his observations in a series of letters to the Royal Society of London. [204] [205] [206] Bacteria were Leeuwenhoek's most remarkable microscopic discovery. They were just at the limit of what his simple lenses could make out and, in one of the most striking hiatuses in the history of science, no one else would see them again for over a century. [207] His observations had also included protozoans which he called animalcules, and his findings were looked at again in the light of the more recent findings of cell theory. [208]

Christian Gottfried Ehrenberg introduced the word "bacterium" in 1828. [209] In fact, his Bacterium was a genus that contained non-spore-forming rod-shaped bacteria, [210] as opposed to Bacillus, a genus of spore-forming rod-shaped bacteria defined by Ehrenberg in 1835. [211]

Louis Pasteur demonstrated in 1859 that the growth of microorganisms causes the fermentation process, and that this growth is not due to spontaneous generation (yeasts and molds, commonly associated with fermentation, are not bacteria, but rather fungi). Along with his contemporary Robert Koch, Pasteur was an early advocate of the germ theory of disease. [212] Before them, Ignaz Semmelweis and Joseph Lister had realised the importance of sanitized hands in medical work. Semmelweis ideas was rejected and his book on the topic condemned by the medical community, but after Lister doctors started sanitizing their hands in the 1870s. While Semmelweis who started with rules about handwashing in his hospital in the 1840s predated the spread of the ideas about germs themselves and attributed diseases to "decomposing animal organic matter", Lister was active later. [213]

Robert Koch, a pioneer in medical microbiology, worked on cholera, anthrax and tuberculosis. In his research into tuberculosis Koch finally proved the germ theory, for which he received a Nobel Prize in 1905. [214] In Koch's postulates, he set out criteria to test if an organism is the cause of a disease, and these postulates are still used today. [215]

Ferdinand Cohn is said to be a founder of bacteriology, studying bacteria from 1870. Cohn was the first to classify bacteria based on their morphology. [216] [217]

Though it was known in the nineteenth century that bacteria are the cause of many diseases, no effective antibacterial treatments were available. [218] In 1910, Paul Ehrlich developed the first antibiotic, by changing dyes that selectively stained Treponema pallidum—the spirochaete that causes syphilis—into compounds that selectively killed the pathogen. [219] Ehrlich had been awarded a 1908 Nobel Prize for his work on immunology, and pioneered the use of stains to detect and identify bacteria, with his work being the basis of the Gram stain and the Ziehl–Neelsen stain. [220]

A major step forward in the study of bacteria came in 1977 when Carl Woese recognised that archaea have a separate line of evolutionary descent from bacteria. [3] This new phylogenetic taxonomy depended on the sequencing of 16S ribosomal RNA, and divided prokaryotes into two evolutionary domains, as part of the three-domain system. [1]

Adams, Casey J. Meade, Thomas J. (2021). "Chapter 15. Imaging Bacteria with Contrast-Enhanced Magnetic Resonance". Metal Ions in Bio-Imaging Techniques. Springer. pp. 425–435. doi:10.1515/9783110685701-021.


Different Types of Bacteria

Bacterial classification is more complex than the one based on basic factors like whether they are harmful or helpful to humans or the environment in which they exist. This article will give you a detailed classification of bacteria.

Bacterial classification is more complex than the one based on basic factors like whether they are harmful or helpful to humans or the environment in which they exist. This article will give you a detailed classification of bacteria.

What are bacteria?

Bacteria (singular: bacterium) are single-celled organisms which can only be seen through a microscope. They come in different shapes and sizes, and their sizes are measured in micrometer – which is a millionth part of a meter. There are several different types of bacteria, and they are found everywhere and in all types of environment.

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There are various groups of bacteria, which belong to the same family and have evolved from the same bacteria (ancestoral). However, each of these types possess their own peculiar characteristics – which have evolved after separation from the original species. The classification of bacteria is based on many factors like morphology, DNA sequencing, requirement of oxygen and carbon-dioxide, staining methods, presence of flagellae, cell structure, etc. This article will give you the classification of these micro-organisms based on all these factors, as well as a few other factors.

Classification of Bacteria

Before the invention of the DNA sequencing technique, bacteria were mainly classified based on their shapes – also known as morphology, biochemistry and staining – i.e. either Gram positive or Gram negative staining. Nowadays, along with the morphology, DNA sequencing is also used in order to classify bacteria. DNA sequencing helps in understanding the relationship between two types of bacteria i.e. if they are related to each other despite their different shapes. Along with the shape and DNA sequence, other things such as their metabolic activities, conditions required for their growth, biochemical reactions (i.e., biochemistry as mentioned above), antigenic properties etc. are also helpful in classifying the bacteria.

Based on Morphology, DNA Sequencing, and Biochemistry

Based on the morphology, DNA sequencing, conditions required and biochemistry, scientists have come up with the following classification with 28 different bacterial phyla:

  1. Acidobacteria
  2. Actinobacteria
  3. Aquificae
  4. Bacteroidetes
  5. Caldiserica
  6. Chlamydiae
  7. Chlorobi
  8. Chloroflexi
  9. Chrysiogenetes
  10. Cyanobacteria
  11. Deferribacteres
  12. Deinococcus-Thermus
  13. Dictyoglomi
  14. Elusimicrobia
  15. Fibrobacteres
  16. Firmicutes
  17. Fusobacteria
  18. Gemmatimonadetes
  19. Lentisphaerae
  20. Nitrospira
  21. Planctomycetes
  22. Proteobacteria
  23. Spirochaetes
  24. Synergistetes
  25. Tenericutes
  26. Thermodesulfobacteria
  27. Thermotogae
  28. Verrucomicrobia

Each phylum further corresponds to the number of species and genera of bacteria. In a broad sense, this bacterial classification includes bacteria which are found in various types of environment such as fresh-water bacteria, saline-water bacteria, bacteria that can survive extreme temperatures (as in sulfur-water-spring bacteria and bacteria found in Antarctica ice), bacteria that can survive in highly acidic environment, bacteria that can survive in highly alkaline environment, bacteria that can withstand high radiations, aerobic bacteria, anaerobic bacteria, autotrophic bacteria, heterotrophic bacteria, and so on…


Number of Bacteria - Biology

  1. How many bacteria are present after 51 hours if a culture is inoculated with 1 bacterium?

  2. With how many bacteria should a culture be inoculated if there are to be 81,920 bacteria present on hour 42?

  3. How long would it take for an initial population of 6 to reach a size of 12,288 bacteria?

Why are we using exponential functions to answer these questions?

The population of bacteria in our example doubles every 3 hours. What exactly does that mean? Imagine you inoculate a fresh culture with N bacteria at 12:00 pm. At 3 pm, you will have 2N bacteria, at 6 pm you will have 4N bacteria, at 9 pm you will have 8N bacteria, and so on. If these cell divisions occur at EXACTLY each of these time points the cells are said to be growing synchronously. If this were the case, the growth process would be geometric. A geometric growth model predicts that the population increases at discrete time points (in this example hours 3, 6, and 9). In other words, there is not a continuous increase in the population.

However, this is not what actually happens. Returning to our example above, imagine you take a small sample of the culture every hour and count the number of bacteria cells present. If bacterial growth were geometric, you would expect to have N bacteria between 12 pm and 3pm, 2N bacteria between 3 pm and 6 pm, etc. However, if you perform this experiment in the laboratory, even under the best experimental conditions, this will not be the case. If you go a step further and make a graph with the number of bacteria on the y-axis and time on the x-axis, you will get a plot that looks much more like exponential growth than geometric growth.

Why does bacterial growth look like exponential growth in practice?

The answer is because bacterial growth is not completely synchronized. Some cells divide in fewer than 3 hours while others will take a little longer to divide. Even if you start a culture with a single cell, synchronicity will be maintained only through a few cell divisions. A single cell will divide at a discrete point in time, and the resulting 2 cells will divide at ABOUT the same time, and the resulting 4 will again divide at ABOUT the same time. As the population grows, the individual nature of cells will result in a smoothing of the division process. This smoothing yields an exponential growth curve, and allows us to use exponential functions to make calculations that predict bacterial growth. So, while exponential growth might not be the perfect model of bacterial growth by binary fission, it is the appropriate model to use given experimental reality.

Now try solving the 3 problems posed at the beginning of this section

Next Application: Carbon Dating

The Biology Project > Biomath > Applications > Exponential Population Growth


THE LIVING SOIL: BACTERIA

Bacteria are tiny, one-celled organisms &ndash generally 4/100,000 of an inch wide (1 µm) and somewhat longer in length. What bacteria lack in size, they make up in numbers. A teaspoon of productive soil generally contains between 100 million and 1 billion bacteria. That is as much mass as two cows per acre.

A ton of microscopic bacteria may be active in each acre of soil.

Credit: Michael T. Holmes, Oregon State University, Corvallis. Please contact the Soil and Water Conservation Society at [email protected] for assistance with copyrighted (credited) images.

Bacteria dot the surface of strands of fungal hyphae.

Credit: R. Campbell. In R. Campbell. 1985. Plant Microbiology. Edward Arnold London. P. 149. Reprinted with the permission of Cambridge University Press. P lease contact the Soil and Water Conservation Society at [email protected] for assistance with copyrighted (credited) images.

Bacteria fall into four functional groups. Most are decomposers that consume simple carbon compounds, such as root exudates and fresh plant litter. By this process, bacteria convert energy in soil organic matter into forms useful to the rest of the organisms in the soil food web. A number of decomposers can break down pesticides and pollutants in soil. Decomposers are especially important in immobilizing, or retaining, nutrients in their cells, thus preventing the loss of nutrients, such as nitrogen, from the rooting zone.

A second group of bacteria are the mutualists that form partnerships with plants. The most well-known of these are the nitrogen-fixing bacteria. The third group of bacteria is the pathogens. Bacterial pathogens include Xymomonas and Erwinia species, and species of Agrobacterium that cause gall formation in plants. A fourth group, called lithotrophs or chemoautotrophs, obtains its energy from compounds of nitrogen, sulfur, iron or hydrogen instead of from carbon compounds. Some of these species are important to nitrogen cycling and degradation of pollutants.

What Do Bacteria Do?

Bacteria from all four groups perform important services related to water dynamics, nutrient cycling, and disease suppression. Some bacteria affect water movement by producing substances that help bind soil particles into small aggregates (those with diameters of 1/10,000-1/100 of an inch or 2-200µm). Stable aggregates improve water infiltration and the soil&rsquos water-holding ability. In a diverse bacterial community, many organisms will compete with disease-causing organisms in roots and on aboveground surfaces of plants.

A Few Important Bacteria

Nitrogen-fixing bacteria form symbiotic associations with the roots of legumes like clover and lupine, and trees such as alder and locust. Visible nodules are created where bacteria infect a growing root hair. The plant supplies simple carbon compounds to the bacteria, and the bacteria convert nitrogen (N2) from air into a form the plant host can use. When leaves or roots from the host plant decompose, soil nitrogen increases in the surrounding area.

Nitrifying bacteria change ammonium (NH4+) to nitrite (NO2-) then to nitrate (NO3-) &ndash a preferred form of nitrogen for grasses and most row crops. Nitrate is leached more easily from the soil, so some farmers use nitrification inhibitors to reduce the activity of one type of nitrifying bacteria. Nitrifying bacteria are suppressed in forest soils, so that most of the nitrogen remains as ammonium.

Denitrifying bacteria convert nitrate to nitrogen (N2) or nitrous oxide (N2O) gas. Denitrifiers are anaerobic, meaning they are active where oxygen is absent, such as in saturated soils or inside soil aggregates.

Actinomycetes are a large group of bacteria that grow as hyphae like fungi. They are responsible for the characteristically &ldquoearthy&rdquo smell of freshly turned, healthy soil. Actinomycetes decompose a wide array of substrates, but are especially important in degrading recalcitrant (hard-to-decompose) compounds, such as chitin and cellulose, and are active at high pH levels. Fungi are more important in degrading these compounds at low pH. A number of antibiotics are produced by actinomycetes such as Streptomyces.

Nodules formed where Rhizobium bacteria infected soybean roots.

Credit: Stephen Temple, New Mexico State University. P lease contact the Soil and Water Conservation Society at [email protected] for assistance with copyrighted (credited) images.

Actinomycetes, such as this Streptomyces, give soil its "earthy" smell.

Credit: No. 14 from Soil Microbiology and Biochemistry Slide Set. 1976. J.P. Martin, et al., eds. SSSA, Madison, WI. P lease contact the Soil and Water Conservation Society at [email protected] for assistance with copyrighted (credited) images.

Where Are Bacteria?

Various species of bacteria thrive on different food sources and in different microenvironments. In general, bacteria are more competitive when labile (easy-to-metabolize) substrates are present. This includes fresh, young plant residue and the compounds found near living roots. Bacteria are especially concentrated in the rhizosphere, the narrow region next to and in the root. There is evidence that plants produce certain types of root exudates to encourage the growth of protective bacteria.

Bacteria alter the soil environment to the extent that the soil environment will favor certain plant communities over others. Before plants can become established on fresh sediments, the bacterial community must establish first, starting with photosynthetic bacteria. These fix atmospheric nitrogen and carbon, produce organic matter, and immobilize enough nitrogen and other nutrients to initiate nitrogen cycling processes in the young soil. Then, early successional plant species can grow. As the plant community is established, different types of organic matter enter the soil and change the type of food available to bacteria. In turn, the altered bacterial community changes soil structure and the environment for plants. Some researchers think it may be possible to control the plant species in a place by managing the soil bacteria community.

Bug Biography: Bacteria That Promote Plant Growth

By Ann Kennedy, USDA Agricultural Research Service, Pullman, WA

Certain strains of the soil bacteria Pseudomonas fluorescens have anti-fungal activity that inhibits some plant pathogens. P. fluorescens and other Pseudomonas and Xanthomonas species can increase plant growth in several ways. They may produce a compound that inhibits the growth of pathogens or reduces invasion of the plant by a pathogen. They may also produce compounds (growth factors) that directly increase plant growth.

These plant growth-enhancing bacteria occur naturally in soils, but not always in high enough numbers to have a dramatic effect. In the future, farmers may be able to inoculate seeds with anti-fungal bacteria, such as P. fluorescens, to ensure that the bacteria reduce pathogens around the seed and root of the crop.


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