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In bacteriology, gram-positive bacteria are bacteria that give a positive result in the Gram stain test, which is traditionally used to quickly classify bacteria into two broad categories according to their type of cell wall.
A halophile is an extremophile that thrives in high salt concentrations. In chemical terms, halophile refers to a Lewis acidic species that has some ability to extract halides from other chemical species.
Escherichia coli ( ESH-ə-RIK-ee-ə KOH-ly) is a gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus Escherichia that is commonly found in the lower intestine of warm-blooded organisms. Most E. coli strains are harmless, but some serotypes such as EPEC, and ETEC are pathogenic and can cause serious food poisoning in their hosts, and are occasionally responsible for food contamination incidents that prompt product recalls. Most strains are part of the normal microbiota of the gut and are harmless or even beneficial to humans (although these strains tend to be less studied than the pathogenic ones). For example, some strains of E. coli benefit their hosts by producing vitamin K2 or by preventing the colonization of the intestine by pathogenic bacteria. These mutually beneficial relationships between E. coli and humans are a type of mutualistic biological relationship — where both the humans and the E. coli are benefitting each other. E. coli is expelled into the environment within fecal matter. The bacterium grows massively in fresh fecal matter under aerobic conditions for three days, but its numbers decline slowly afterwards.
Listeria monocytogenes is the species of pathogenic bacteria that causes the infection listeriosis. It is a facultative anaerobic bacterium, capable of surviving in the presence or absence of oxygen. It can grow and reproduce inside the host's cells and is one of the most virulent foodborne pathogens: 20 to 30% of foodborne listeriosis infections in high-risk individuals may be fatal. In the European Union, listeriosis follows an upward trend that began in 2008, causing 2,161 confirmed cases and 210 reported deaths in 2014, 16% more than in 2013. Listeriosis mortality rates are also higher in the EU than for other foodborne pathogens. Responsible for an estimated 1,600 illnesses and 260 deaths in the United States annually, listeriosis ranks third in total number of deaths among foodborne bacterial pathogens, with fatality rates exceeding even Salmonella spp. and Clostridium botulinum.
Mycoplasma pneumoniae is a very small bacterium in the class Mollicutes. It is a human pathogen that causes the disease mycoplasma pneumonia, a form of atypical bacterial pneumonia related to cold agglutinin disease. M. pneumoniae is characterized by the absence of a peptidoglycan cell wall and resulting resistance to many antibacterial agents. The persistence of M. pneumoniae infections even after treatment is associated with its ability to mimic host cell surface composition.
Aliivibrio fischeri is a Gram-negative, rod-shaped bacterium found globally in marine environments. This species has bioluminescent properties, and is found predominantly in symbiosis with various marine animals, such as the Hawaiian bobtail squid. It is heterotrophic, oxidase-positive, and motile by means of a single polar flagella. Free-living A. fischeri cells survive on decaying organic matter. The bacterium is a key research organism for examination of microbial bioluminescence, quorum sensing, and bacterial-animal symbiosis. It is named after Bernhard Fischer, a German microbiologist.
Proteus mirabilis is a Gram-negative, facultatively anaerobic, rod-shaped bacterium. It shows swarming motility and urease activity. P. mirabilis causes 90% of all Proteus infections in humans. It is widely distributed in soil and water. Proteus mirabilis can migrate across the surface of solid media or devices using a type of cooperative group motility called swarming. Proteus mirabilis is most frequently associated with infections of the urinary tract, especially in complicated or catheter-associated urinary tract infections.
Thermus thermophilus is a Gram-negative bacterium used in a range of biotechnological applications, including as a model organism for genetic manipulation, structural genomics, and systems biology. The bacterium is extremely thermophilic, with an optimal growth temperature of about 65 °C (149 °F). Thermus thermophilus was originally isolated from a thermal vent within a hot spring in Izu, Japan by Tairo Oshima and Kazutomo Imahori. The organism has also been found to be important in the degradation of organic materials in the thermogenic phase of composting. T. thermophilus is classified into several strains, of which HB8 and HB27 are the most commonly used in laboratory environments. Genome analyses of these strains were independently completed in 2004. Thermus also displays the highest frequencies of natural transformation known to date.
A brine pool, sometimes called an underwater lake, deepwater or brine lake, is a volume of brine collected in a seafloor depression. The pools are dense bodies of water that have a salinity that is three to eight times greater than the surrounding ocean. Brine pools are commonly found below polar sea ice and in the deep ocean. Those below sea ice form through a process called brine rejection. For deep-sea brine pools, salt is necessary to increase the salinity gradient. The salt can come from one of two processes: the dissolution of large salt deposits through salt tectonics or geothermally heated brine issued from tectonic spreading centers.
Bacteria are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste, and the deep biosphere of Earth's crust. Bacteria play a vital role in many stages of the nutrient cycle by recycling nutrients and the fixation of nitrogen from the atmosphere. The nutrient cycle includes the decomposition of dead bodies; bacteria are responsible for the putrefaction stage in this process. 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. Bacteria also live in mutualistic, commensal and parasitic relationships with plants and animals. Most bacteria have not been characterised and there are many species that cannot be grown in the laboratory. The study of bacteria is known as bacteriology, a branch of microbiology.
Archaea is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria, but this term has fallen out of use.
Nitratidesulfovibrio vulgaris is a species of Gram-negative sulfate-reducing bacteria in the Desulfovibrionaceae family. It is also an anaerobic sulfate-reducing bacterium that is an important organism involved in the bioremediation of heavy metals in the environment. Nitratidesulfovibrio vulgaris is often used as a model organism for sulfur-reducing bacteria and was the first of such bacteria to have its genome sequenced. It is ubiquitous in nature and has also been implicated in a variety of human bacterial infections, although it may only be an opportunistic pathogen. This microbe also has the ability to endure high salinity environments, which is done through the utilization of osmoprotectants and efflux systems.
Alcanivorax pacificus is a pyrene-degrading marine gammaproteobacterium. It is of the genus Alcanivorax, a group of marine bacteria known for degrading hydrocarbons. When originally proposed, the genus Alcanivorax comprised six distinguishable species. However, A. pacificus, a seventh strain, was isolated from deep sea sediments in the West Pacific Ocean by Shanghai Majorbio Bio-pharm Technology Co., Ltd. in 2011. A. pacificus’s ability to degrade hydrocarbons can be employed for cleaning up oil-contaminated oceans through bioremediation. The genomic differences present in this strain of Alcanivorax that distinguish it from the original consortium are important to understand to better utilize this bacteria for bioremediation.
Haloquadratum walsbyi is a species of the genus Haloquadratum, within the archaea domain known for its square halophilic nature. First discovered in a brine pool in the Sinai peninsula of Egypt, H. walsbyi is noted for its flat, square-shaped cells, and its unusual ability to survive in aqueous environments with high concentrations of sodium chloride and magnesium chloride. The species' genus name Haloquadratum translates from Greek and Latin as "salt square". This archaean is also commonly referred to as "Walsby's Square Bacterium" because of its identifying square shape which makes it unique. In accordance with its name, Haloquadratum walsbyi are most abundantly observed in salty environments.
Persephonella marina is a Gram-negative, rod shaped bacteria that is a member of the Aquificota phylum. Stemming from Greek, the name Persephonella is based upon the mythological goddess Persephone. Marina stems from a Latin origin, meaning "belonging to the sea". It is a thermophile with an obligate chemolithoautotrophic metabolism. Growth of P. marina can occur in pairs or individually, but is rarely seen aggregating in large groups. The organism resides on sulfidic chimneys in the deep ocean and has never been documented as a pathogen.
Arhodomonas aquaeolei is a species of the bacterial genus Arhodomonas noted for its ability to grow in an environment of high salinity. It is an aerobic, oval rod-shaped, gram-negative bacterium. It is motile by means a single polar flagellum.
Gemmata obscuriglobus is a species of Gram-negative, aerobic, heterotrophic bacteria of the phylum Planctomycetota. G. obscuriglobus occur in freshwater habitats and was first described in 1984, and is the only described species in its genus.
Rhodobacter capsulatus is a species of purple bacteria, a group of bacteria that can obtain energy through photosynthesis. Its name is derived from the Latin adjective "capsulatus", itself derived Latin noun "capsula", and the associated Latin suffix for masculine nouns, "-atus".
Chromids, formerly secondary chromosomes, are a class of bacterial replicons. These replicons are called "chromids" because they have characteristic features of both chromosomes and plasmids. Early on, it was thought that all core genes could be found on the main chromosome of the bacteria. However, in 1989 a replicon was discovered containing core genes outside of the main chromosome. These core genes make the chromid indispensable to the organism. Chromids are large replicons, although not as large as the main chromosome. However, chromids are almost always larger than a plasmid. Chromids also share many genomic signatures of the chromosome, including their GC-content and their codon usage bias. On the other hand, chromids do not share the replication systems of chromosomes. Instead, they use the replication system of plasmids. Chromids are present in 10% of bacteria species sequenced by 2009.
The Red Sea and its extensions of the Gulf of Suez and the Gulf of Aqaba contain the largest recorded concentration of deep sea brine pools on the planet. These pools have many features that make them un-inhabitable to almost all organisms on the planet, yet, certain communities of microbes thrive within these extreme environments that have temperature ranging from 2.0 °C all the way up to the high of 75 °C. The Red Sea brine pools have extreme salinity concentrations and varying compositions of nutrients, chemicals properties and molecules that directly affect the microbiome between the estimated 25 individual pools in the region, some of which are closely clustered together in groups leading to their undetermined classification of names. The brine pools in the region originate from hydrothermal vents and shifting of tectonic plates and the accumulation of water with properties that make it unsuitable for mixing leading to its accumulation within faults and divots in the sea floor. Atlantis Deep II, Discovery Deep and the Kebrit are the most investigated and researched brine pools among the many located within the Red Sea Additionally, many microbial species form beneficial symbiotic relationships with organisms living and feeding in proximity to the pools. These relationships allow for the study of specialised adaptations of microbes to brine pool environments.
References
- 1 2 André Antunes; Fred A. Rainey; Gerhard Wanner; Marco Taborda; Jürgen Pätzold; M. Fernanda Nobre; Milton S. da Costa; Robert Huber (2008). "A new lineage of halophilic, wall-less, contractile bacteria from a brine-filled deep of the Red Sea". Journal of Bacteriology . 190 (10): 3580–3587. doi:10.1128/JB.01860-07. PMC 2394993 . PMID 18326567.
- ↑ J. P. Euzéby. "Order Haloplasmatales". List of Prokaryotic names with Standing in Nomenclature.
3. Antunes, A., et al. “A New Lineage of Halophilic, Wall-Less, Contractile Bacteria from a Brine-Filled Deep of the Red Sea.” Journal of Bacteriology, vol. 190, no. 10, July 2008, pp. 3580–3587., doi:10.1128/jb.01860-07.
4. Antunes, A., et al. “Genome Sequence of Haloplasma Contractile, an Unusual Contractile Bacterium from a Deep-Sea Anoxic Brine Lake.” Journal of Bacteriology, vol. 193, no. 17, 2011, pp. 4551–4552., doi:10.1128/jb.05461-11.
