57-412: See text The Rhodobacteraceae are a family of Pseudomonadota in the order Rhodobacterales within the alpha subgroup. Like all Pseudomonadota , they are gram-negative . It contains chemoorganotrophs and photoheterotrophs . Many occur in aquatic habitats. The following genera have been effectively and validly published: The following genera have been published, but not validated according to
114-654: A PhD in biophysics at Yale University , where his doctoral research focused on the inactivation of viruses by heat and ionizing radiation . He studied medicine at the University of Rochester for two years. Then he became a postdoctoral researcher in biophysics at Yale University investigating bacterial spores. From 1960 to 1963, he worked as a biophysicist at the General Electric Research Laboratory in Schenectady, New York . In 1964, Woese joined
171-410: A broader purpose than the pursuit of "an engineered environment": What was formally recognized in physics needs now to be recognized in biology: science serves a dual function. On the one hand it is society's servant, attacking the applied problems posed by society. On the other hand, it functions as society's teacher, helping the latter to understand its world and itself. It is the latter function that
228-415: A correlation of microbial composition in children with and without nonalcoholic fatty liver disease (NAFLD), wherein patients with NAFLD have a higher abundance of Gammaproteobacteria than patients without the disease. Classes Betaproteobacteria and Gammaproteobacteria are prevalent within the human oral cavity, and are markers for good oral health. The oral microbiome consists of 11 habitats, including
285-496: A diverse group. Though some species may stain Gram-positive or Gram-variable in the laboratory, they are nominally Gram-negative . Their unique outer membrane is mainly composed of lipopolysaccharides , which helps differentiate them from the Gram-positive species. Most Pseudomonadota are motile and move using flagella. Many move about using flagella , but some are nonmotile, or rely on bacterial gliding . Pseudomonadota have
342-408: A level of complexity and connectedness that made genes from other organisms much less able to displace an individual's own genes. In later years, Woese's work concentrated on genomic analysis to elucidate the significance of horizontal gene transfer (HGT) for evolution. He worked on detailed analyses of the phylogenies of the aminoacyl-tRNA synthetases and on the effect of horizontal gene transfer on
399-492: A news article printed in the journal Science . The growing body of supporting data led the scientific community to accept the Archaea by the mid-1980s. Today, few scientists cling to the idea of a unified Prokarya. Woese's work on Archaea is also significant in its implications for the search for life on other planets. Before the discovery by Woese and Fox, scientists thought that Archaea were extreme organisms that evolved from
456-683: A proposal for its reclassification into distinct phyla: Desulfobacterota (encompassing Thermodesulfobacteria ), Myxococcota , and Bdellovibrionota (comprising Oligoflexia ). The class Epsilonproteobacteria was additionally identified within the Pseudomonadota phylum. This class is characterized by its significance as chemolithotrophic primary producers and its metabolic prowess in deep-sea hydrothermal vent ecosystems. Noteworthy pathogenic genera within this class include Campylobacter , Helicobacter , and Arcobacter . Analysis of phylogenetic tree topology and genetic markers revealed
513-426: A relevant signature of disease in the human gastrointestinal (GI) tract, by operating as a marker for microbiota instability. The human gut microbiome consists mainly of four phyla: Firmicutes , Bacteroidetes , Actinobacteria , and Pseudomonadota. Microorganism gut colonization is dynamic from birth to death, with stabilization at the first few years of life, to higher diversity in adults, to reduced diversity in
570-520: A single ancestral cellular organization? The second major direction involves the nature of the global ecosystem. . . . Bacteria are the major organisms on this planet—in numbers, in total mass, in importance to the global balances. Thus, it is microbial ecology that . . . is most in need of development, both in terms of facts needed to understand it, and in terms of the framework in which to interpret them. Woese considered biology to have an "all-important" role in society. In his view, biology should serve
627-460: A son and daughter. Woese turned his attention to the genetic code while setting up his lab at General Electric 's Knolls Laboratory in the fall of 1960. Interest among physicists and molecular biologists had begun to coalesce around deciphering the correspondence between the twenty amino acids and the four letter alphabet of nucleic acid bases in the decade following James D. Watson , Francis Crick , and Rosalind Franklin 's discovery of
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#1732905927058684-407: A symbiotic relationship with plant roots, incorporating Pseudomonadota into agricultural practices aligns with principles of sustainable farming . These bacteria contribute to soil health and fertility, promote natural pest management, and enhance the resilience of crops to environmental stressors. Carl Woese Carl Richard Woese ( / ˈ w oʊ z / ; July 15, 1928 – December 30, 2012)
741-427: A variety of compounds. Bioleaching , done by various Thiobacillus species, are a primary example of this. Any iron and sulfur oxidizing species has the potential to uncover metals and low-grade ores that conventional mining techniques were unable to extract. At present, they are most often used for recovering copper and uranium, but researchers are looking to expand this field in the future. The downside of this method
798-475: A well-known pathogenic genus, Pseudomonas is also capable of biodegradation of certain materials, like cellulose. The Hydrogenophilalia are thermophilic chemoheterotrophs and autotrophs. The bacteria typically use hydrogen gas as an electron donor, but can also use reduced sulfuric compounds. Because of this ability, scientists have begun to use certain species of Hydrogenophilalia to remove sulfides that contaminate industrial wastewater systems. The type order
855-431: A wide variety of metabolism types. Most are facultative or obligate anaerobes , chemolithoautotrophs , and heterotrophs , though numerous exceptions exist. A variety of distantly related genera within the Pseudomonadota obtain their energy from light through conventional photosynthesis or anoxygenic photosynthesis . The Acidithiobacillia contain only sulfur, iron, and uranium-oxidizing autotrophs . The type order
912-632: Is a major phylum of Gram-negative bacteria . Currently, they are considered the predominant phylum within the realm of bacteria. They are naturally found as pathogenic and free-living (non- parasitic ) genera. The phylum comprises six classes Acidithiobacillia , Alphaproteobacteria , Betaproteobacteria , Gammaproteobacteria , Hydrogenophilia , and Zetaproteobacteria . The Pseudomonadota are widely diverse, with differences in morphology , metabolic processes, relevance to humans, and ecological influence. American microbiologist Carl Woese established this grouping in 1987, calling it informally
969-685: Is effectively missing today. Woese was a MacArthur Fellow in 1984, was made a member of the National Academy of Sciences in 1988, received the Leeuwenhoek Medal (microbiology's highest honor) in 1992, the Selman A. Waksman Award in Microbiology in 1995 from the National Academy of Sciences , and was a National Medal of Science recipient in 2000. In 2003, he received the Crafoord Prize from
1026-511: Is one of the most influential in microbiology and arguably, all of biology. It ranks with the works of Watson and Crick and Darwin, providing an evolutionary framework for the incredible diversity of the microbial world". With regard to Woese's work on horizontal gene transfer as a primary evolutionary process, Professor Norman R. Pace of the University of Colorado at Boulder said, "I think Woese has done more for biology writ large than any biologist in history, including Darwin ... There's
1083-490: Is present in the atmosphere, they are able to compete with the abiotic iron(II) oxidation that is already occurring in the environment. The only confirmed type order for this class is the Mariprofundaceae , which does not contain any known pathogenic species. Transformation , a process in which genetic material passes from one bacterium to another, has been reported in at least 30 species of Pseudomonadota distributed in
1140-730: Is that the bacteria produce acidic byproducts that end up in acid mine drainage . Bioleaching has significant economic promise if it can be controlled and not cause any further harm to the environment. Pseudomonadota are microbes commonly found within soil systems. Microbes play a crucial role in the surrounding ecosystem by performing functions such as nutrient cycling , carbon dioxide fixation, decomposition , and nitrogen fixation. Pseudomonadota can be described as phototrophs , heterotrophs , and lithotrophs . As heterotrophs (examples Pseudomonas and Xanthomonas ) these bacteria are effective in breaking down organic matter, contributing to nutrient cycling. Additionally, photolithotrophs within
1197-705: Is the Acidithiobacillaceae , which includes five different Acidithiobacillus species used in the mining industry. In particular, these microbes assist with the process of bioleaching , which involves microbes assisting in metal extraction from mining waste that typically extraction methods cannot remove. Some Alphaproteobacteria can grow at very low levels of nutrients and have unusual morphology within their life cycles. Some form stalks to help with colonization, and form buds during cell division. Others include agriculturally important bacteria capable of inducing nitrogen fixation in symbiosis with plants. The type order
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#17329059270581254-633: Is the Caulobacterales , comprising stalk-forming bacteria such as Caulobacter . The mitochondria of eukaryotes are thought to be descendants of an alphaproteobacterium. The Betaproteobacteria are highly metabolically diverse and contain chemolithoautotrophs , photoautotrophs , and generalist heterotrophs . The type order is the Burkholderiales , comprising an enormous range of metabolic diversity, including opportunistic pathogens . These pathogens are primary for both humans and animals, such as
1311-542: Is the Hydrogenophilaceae which contains the genera Thiobacillus, Petrobacter, Sulfuricella, Hydrogenophilus and Tepidiphilus . Currently, no members of this class have been identified as pathogenic. The Zetaproteobacteria are the iron-oxidizing neutrophilic chemolithoautotrophs , distributed worldwide in estuaries and marine habitats. This group is so successful in its environment due to their microaerophilic nature. Because they require less oxygen than what
1368-446: Is the evolution of (proteinaceous) cellular organization, which includes sub-questions such as the evolution of the translation apparatus and the genetic code, and the origin and nature of the hierarchies of control that fine-tune and precisely interrelate the panoply of cellular processes that constitute cells. It also includes the question of the number of different basic cell types that exist on earth today: did all modern cells come from
1425-1299: The Bacteriological Code : The following candidatus genera have been published: The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature and the phylogeny is based on whole-genome sequences. Rubrimonas Albimonas Oceanicella Pontivivens Monaibacterium Amylibacter Neptunicoccus Hasllibacter Jannaschia Dinoroseobacter Jannaschia Planktomarina Nereida Litoreibacter Brevirhabdus Kandeliimicrobium Oceaniglobus Tranquillimonas Palleronia Hwanghaeicola Maribius Meinhardsimonia Silicimonas Boseongicola Pararhodobacter Roseicitreum Roseinatronobacter Rhodobaca Defluviimonas Albidovulum Wagnerdoeblera Cereibacter Pseudorhodobacter Gemmobacter Cypionkella Tabrizicola Frigidibacter Bieblia Thioclava Paenirhodobacter Rhodobacter Haematobacter Paracoccus Pseudomonadota Pseudomonadota (synonym Proteobacteria )
1482-684: The Royal Swedish Academy of Sciences "for his discovery of a third domain of life". He was elected to the American Philosophical Society in 2004. In 2006, he was made a foreign member of the Royal Society . Many microbial species, such as Pyrococcus woesei , Methanobrevibacter woesei , and Conexibacter woesei , are named in his honor. Microbiologist Justin Sonnenburg of Stanford University said "The 1977 paper
1539-471: The University of Illinois after hearing his research goals; at this visit Spiegelman offered Woese a position with immediate tenure beginning in the fall of 1964. With the freedom to patiently pursue more speculative threads of inquiry outside the mainstream of biological research, Woese began to consider the genetic code in evolutionary terms, asking how the codon assignments and their translation into an amino acid sequence might have evolved. For much of
1596-701: The University of Illinois Urbana–Champaign . Woese was born in Syracuse, New York on July 15, 1928. His family was German American . Woese attended Deerfield Academy in Massachusetts . He received a bachelor's degree in mathematics and physics from Amherst College in 1950. During his time at Amherst, Woese took only one biology course ( Biochemistry , in his senior year) and had "no scientific interest in plants and animals" until advised by William M. Fairbank , then an assistant professor of physics at Amherst, to pursue biophysics at Yale . In 1953, he completed
1653-420: The bacteria responsible for nitrogen fixation . Previously, the Pseudomonadota phylum included two additional classes, namely Deltaproteobacteria and Oligoflexia . However, further investigation into the phylogeny of these taxa through genomic marker analysis demonstrated their separation from the Pseudomonadota phylum. Deltaproteobacteria has been identified as a diverse taxonomic unit, leading to
1710-589: The "purple bacteria and their relatives". The group was later formally named the 'Proteobacteria' after the Greek god Proteus, who was known to assume many forms. In 2021 the International Committee on Systematics of Prokaryotes designated the synonym Pseudomonadota, and renamed many other prokaryotic phyla as well. This renaming of several prokaryote phyla in 2021, including Pseudomonadota, remains controversial among microbiologists, many of whom continue to use
1767-465: The 20th century, prokaryotes were regarded as a single group of organisms and classified based on their biochemistry , morphology and metabolism . In a highly influential 1962 paper, Roger Stanier and C. B. van Niel first established the division of cellular organization into prokaryotes and eukaryotes , defining prokaryotes as those organisms lacking a cell nucleus . Adapted from Édouard Chatton 's generalization, Stanier and Van Niel's concept
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1824-648: The basic structure of the tree of life . Woese and Fox discovered a kind of microbial life which they called the “archaebacteria” ( Archaea ). They reported that the archaebacteria comprised "a third kingdom" of life as distinct from bacteria as plants and animals. Having defined Archaea as a new "urkingdom" (later domain ) which were neither bacteria nor eukaryotes, Woese redrew the taxonomic tree. His three-domain system , based on phylogenetic relationships rather than obvious morphological similarities, divided life into 23 main divisions, incorporated within three domains: Bacteria , Archaea , and Eucarya . Acceptance of
1881-410: The classes alpha, beta, and gamma. The best-studied Pseudomonadota with respect to natural genetic transformation are the medically important human pathogens Neisseria gonorrhoeae (class beta), and Haemophilus influenzae (class gamma). Natural genetic transformation is a sexual process involving DNA transfer from one bacterial cell to another through the intervening medium and the integration of
1938-471: The direct divergence of Epsilonproteobacteria from the Pseudomonadota phylum. Limited outgroup data and low bootstrap values support these discoveries. Despite further investigations, consensus has not been reached regarding the monophyletic nature of Epsilonproteobacteria within Proteobacteria, prompting researchers to propose its taxonomic separation from the phylum. The proposed reclassification of
1995-510: The distribution of those key enzymes among organisms. The goal of the research was to explain how the primary cell types (the archaeal, eubacterial, and eukaryotic) evolved from an ancestral state in the RNA world . Woese shared his thoughts on the past, present, and future of biology in Current Biology : The "important questions" that 21st century biology faces all stem from a single question,
2052-436: The donor sequence into the recipient genome. In pathogenic Pseudomonadota, transformation appears to serve as a DNA repair process that protects the pathogen's DNA from attack by their host's phagocytic defenses that employ oxidative free radicals . Due to the distinctive nature of each of the six classes of Pseudomonadota, this phylum occupies a multitude of habitats. These include: Studies have suggested Pseudomonadota as
2109-463: The earlier name Proteobacteria, of long standing in the literature. The phylum Pseudomonadota encompasses classes Acidithiobacillia, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Hydrogenophilia , and Zetaproteobacteria. The phylum includes a wide variety of pathogenic genera, such as Escherichia , Salmonella , Vibrio , Yersinia , Legionella , and many others. Others are free-living (non- parasitic ) and include many of
2166-535: The elderly. The gut microbiome conducts processes like nutrient synthesis, chemical metabolism , and the formation of the gut barrier. Additionally, the gut microbiome facilitates host interactions with its surrounding environment through regulation of nutrient absorption and bacterial intake. In 16s rRNA and metagenome sequencing studies, Proteobacteria have been identified as bacteria that prompts endotoxemia (an inflammatory gut response) and metabolic disorders in human GI tracts. Another study by Michail et al. showed
2223-408: The history of life. Woese wrote, "My evolutionary concerns center on the bacteria and the archaea, whose evolutions cover most of the planet's 4.5-billion-year history. Using ribosomal RNA sequence as an evolutionary measure, my laboratory has reconstructed the phylogeny of both groups, and thereby provided a phylogenetically valid system of classification for prokaryotes. The discovery of the archaea
2280-495: The horse pathogen Burkholderia mallei , and Burkholderia cepacia which causes respiratory tract infections in people with cystic fibrosis. The Gammaproteobacteria are one of the largest classes in terms of genera, containing approximately 250 validly published names. The type order is the Pseudomonadales , which include the genera Pseudomonas and the nitrogen-fixing Azotobacter , along with many others. Besides being
2337-612: The mechanistic basis of protein translation, but in Woese's view, largely overlooked the genetic code's evolutionary origins as an afterthought. In 1962, Woese spent several months as a visiting researcher at the Pasteur Institute in Paris , a locus of intense activity on the molecular biology of gene expression and gene regulation. While in Paris, he met Sol Spiegelman , who invited Woese to visit
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2394-525: The microbiology faculty of the University of Illinois Urbana–Champaign, where he focused on Archaea, genomics, and molecular evolution as his areas of expertise. He became a professor at the University of Illinois Urbana–Champaign's Carl R. Woese Institute for Genomic Biology , which was renamed in his honor in 2015, after his death. Woese died on December 30, 2012, following complications from pancreatic cancer , leaving as survivors his wife Gabriella and
2451-471: The microorganisms more familiar to us. Now, most believe they are ancient, and may have robust evolutionary connections to the first organisms on Earth. Organisms similar to those archaea that exist in extreme environments may have developed on other planets, some of which harbor conditions conducive to extremophile life. Notably, Woese's elucidation of the tree of life shows the overwhelming diversity of microbial lineages: single-celled organisms represent
2508-564: The name Epsilonproteobacteria is Epsilonbacteraeota , later revised to Campylobacterota in 2018. The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN) and the National Center for Biotechnology Information (NCBI). The group Pseudomonadota is defined based on ribosomal RNA (rRNA) sequencing, and are divided into several subclasses. These subclasses were regarded as such for many years, but are now treated as various classes of
2565-460: The nature and generation of biological organization . . . . Yes, Darwin is back, but in the company of . . . scientists who can see much further into the depths of biology than was possible heretofore. It is no longer a "10,000 species of birds" view of evolution—evolution seen as a procession of forms. The concern is now with the process of evolution itself. I see the question of biological organization taking two prominent directions today. The first
2622-704: The oral cavity. Pseudomonadota bacteria have a symbiotic or mutualistic association with plant roots, an example being in the rhizomes of potato plants. Because of this symbiotic relationship, farmers have the ability to increase their crop yields. Healthier root systems can lead to better nutrient uptake, improved water retention, increased resistance to diseases and pests, and ultimately higher crop yields per acre. Increased agricultural output can spark economic growth, contribute to food security, and lead to job creation in rural areas. As briefly mentioned in previous sections, members of Pseudomonadota have vast metabolic abilities that allow them to utilize and produce
2679-857: The order Hydrogenophilales Pseudomonadota classes with validly published names include some prominent genera: e.g.: Alphaproteobacteria Zetaproteobacteria Gammaproteobacteria Betaproteobacteria Hydrogenophilalia Alphaproteobacteria " Mariprofundia " ( Zetaproteobacteria ) " Thiohalorhabdales " Methylothermaceae 2 Algiphilaceae Methylothermaceae Acidithiobacillia Gammaproteobacteria (nested Betaproteobacteria & Hydrogenophilalia ) " Caulobacteria " ( Alphaproteobacteria ) " Mariprofundia " ( Zetaproteobacteria ) " Magnetococcia " clade 1 "Foliamicales" clade 3 Immundisolibacterales clade 5 "Acidithiobacillidae" ( Acidithiobacillia ) "Neisseriidae" ( Betaproteobacteria & nested Hydrogenophilalia ) "Pseudomonadidae" ( Gammaproteobacteria ) Pseudomonadota are
2736-640: The phylum are able to perform photosynthesis using sulfide or elemental sulfur as electron donors , which enables them to participate in carbon fixation and oxygen production even in anaerobic conditions. These Pseudomonadota bacteria are also considered copiotrophic organisms, meaning they can be found in environments with high nutrient availability. These environments have ample sources of carbon and other nutrients, environments like fertile soils, compost, and sewage. These copiotrophic bacteria are able to enhance soil health by performing nutrient cycling and waste decomposition. Because this phylum are able to form
2793-536: The phylum. These classes are monophyletic . The genus Acidithiobacillus , part of the Gammaproteobacteria until it was transferred to class Acidithiobacillia in 2013, was previously regarded as paraphyletic to the Betaproteobacteria according to multigenome alignment studies . In 2017, the Betaproteobacteria was subject to major revisions and the class Hydrogenophilalia was created to contain
2850-612: The specificity of cellular interaction and the size of the genome. This early translation apparatus would have produced a group of structurally similar, functionally equivalent proteins, rather than a single protein. Furthermore, because of this reduced specificity, all cellular components were susceptible to horizontal gene transfer, and rapid evolution occurred at the level of the ecosystem. The transition to modern cells (the " Darwinian Threshold ") occurred when organisms evolved translation mechanisms with modern levels of fidelity: improved performance allowed cellular organization to reach
2907-461: The structure of DNA in 1953. Woese published a series of papers on the topic. In one, he deduced a correspondence table between what was then known as "soluble RNA" and DNA based upon their respective base pair ratios. He then re-evaluated experimental data associated with the hypothesis that viruses used one base, rather than a triplet, to encode each amino acid, and suggested 18 codons, correctly predicting one for proline . Other work established
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#17329059270582964-407: The tongue dorsum, hard palate , tonsils, throat, saliva, and more. Changes in the oral microbiome are due to endogenous and exogenous factors like host lifestyle, genotype , environment, immune system, and socioeconomic status. Considering diet as a factor, high saturated fatty acid (SAF) content, achieved through poor diet, has been correlated to increased abundance of Betaproteobacteria in
3021-436: The validity of Woese's phylogenetically valid classification was a slow process. Prominent biologists including Salvador Luria and Ernst Mayr objected to his division of the prokaryotes. Not all criticism of him was restricted to the scientific level. A decade of labor-intensive oligonucleotide cataloging left him with a reputation as "a crank," and Woese would go on to be dubbed as "Microbiology's Scarred Revolutionary" by
3078-411: The vast majority of the biosphere's genetic, metabolic, and ecologic niche diversity. As microbes are crucial for many biogeochemical cycles and to the continued function of the biosphere, Woese's efforts to clarify the evolution and diversity of microbes provided an invaluable service to ecologists and conservationists . It was a major contribution to the theory of evolution and to our knowledge of
3135-515: Was an American microbiologist and biophysicist . Woese is famous for defining the Archaea (a new domain of life) in 1977 through a pioneering phylogenetic taxonomy of 16S ribosomal RNA , a technique that has revolutionized microbiology. He also originated the RNA world hypothesis in 1967, although not by that name. Woese held the Stanley O. Ikenberry Chair and was professor of microbiology at
3192-521: Was in fact a product of these studies". Woese also speculated about an era of rapid evolution in which considerable horizontal gene transfer occurred between organisms. First described by Woese and Fox in a 1977 paper and explored further with microbiologist Jane Gibson in a 1980 paper, these organisms, or progenotes , were imagined as protocells with very low complexity due to their error-prone translation apparatus ("noisy genetic transmission channel"), which produced high mutation rates that limited
3249-505: Was quickly accepted as the most important distinction among organisms; yet they were nevertheless skeptical of microbiologists' attempts to construct a natural phylogenetic classification of bacteria. However, it became generally assumed that all life shared a common prokaryotic (implied by the Greek root πρό (pro-), before, in front of) ancestor. In 1977, Woese and George E. Fox experimentally disproved this universally held hypothesis about
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