ETH Zurich

From Wikipedia, the free encyclopedia

Other name	Swiss Federal Institute of Technology in Zurich, German: Polytechnikum (colloquially)
Former name	eidgenössische polytechnische Schule
Type	Public
Established	1855
Budget	CHF 1.885 billion (2017)
President	Joël Mesot
Rector	Sarah M. Springman
Academic staff	6,455 (full-time equivalents 2017, 29.5% female, 70.2% foreign nationals)
Administrative staff	2,658 (full-time equivalents 2017, 42.5% female, 24.4% foreign nationals)
Students	20,607 (headcount 2017, 31.8% female, 38.7% foreign nationals)
Undergraduates	9,262
Postgraduates	6,158
Doctoral students	4,092
Other students	1,095
Address	Rämistrasse 101 CH-8092 Zürich Switzerland , Zurich 47°22′35″N 8°32′53″ECoordinates: 47°22′35″N 8°32′53″E
Campus	Urban
Language	German, English (Masters and upwards, sometimes Bachelor)
Colors	Blue and White
Affiliations	CESAER, EUA, GlobalTech, IARU, IDEA League
Website	www.ethz.ch

Location: ETH Zurich, Switzerland

 

ETH Zurich (Swiss Federal Institute of Technology in Zurich; German: Eidgenössische Technische Hochschule Zürich) is a science, technology, engineering and mathematics university in the city of Zürich, Switzerland. Like its sister institution EPFL, it is an integral part of the Swiss Federal Institutes of Technology Domain (ETH Domain) that is directly subordinate to Switzerland's Federal Department of Economic Affairs, Education and Research. The school was founded by the Swiss Federal Government in 1854 with the stated mission to educate engineers and scientists, serve as a national center of excellence in science and technology and provide a hub for interaction between the scientific community and industry.

In the 2019 edition of the QS World University Rankings ETH Zurich is ranked 7th in the world (3rd in Europe after Oxbridge), and is also ranked 10th in the world by the Times Higher Education World Rankings 2018 (4th in Europe after Oxbridge and Imperial College London). In the 2019 QS World University Rankings by subject it is ranked 3rd in the world for engineering and technology (1st in Europe), and 1st for Earth & Marine Science.

As of August 2018, 32 Nobel laureates, 4 Fields Medalists, and 1 Turing Award winner have been affiliated with the Institute, including Albert Einstein. 

It is a founding member of the IDEA League and the International Alliance of Research Universities (IARU) and a member of the CESAER network.

History

Polytechnikum in 1865

 

ETH Zürich Zentrum

 

ETH was founded on 7 February 1854 by the Swiss Confederation and began giving its first lectures on 16 October 1855 as a polytechnic institute (eidgenössische polytechnische Schule) at various sites throughout the city of Zurich. It was initially composed of six faculties: architecture, civil engineering, mechanical engineering, chemistry, forestry, and an integrated department for the fields of mathematics, natural sciences, literature, and social and political sciences.

It is locally still known as Polytechnikum, or simply as Poly, derived from the original name eidgenössische polytechnische Schule, which translates to "federal polytechnic school". 

ETH is a federal institute (i.e., under direct administration by the Swiss government), whereas the University of Zürich is a cantonal institution. The decision for a new federal university was heavily disputed at the time; the liberals pressed for a "federal university", while the conservative forces wanted all universities to remain under cantonal control, worried that the liberals would gain more political power than they already had. In the beginning, both universities were co-located in the buildings of the University of Zürich. 

From 1905 to 1908, under the presidency of Jérôme Franel, the course program of ETH was restructured to that of a real university and ETH was granted the right to award doctorates. In 1909 the first doctorates were awarded. In 1911, it was given its current name, Eidgenössische Technische Hochschule. In 1924, another reorganization structured the university in 12 departments. However, it now has 16 departments. 

Interior skylights in the main building

 

ETH Zurich, the EPFL, and four associated research institutes form the "ETH Domain" with the aim of collaborating on scientific projects.

Reputation and ranking

University rankings
Global
ARWU World	19
THE World	10
QS World	7

ETH Zurich is ranked among the top universities in the world. Typically, popular rankings place the institution as the best university in continental Europe and ETH Zurich is consistently ranked among the top 1-5 universities in Europe, and among the top 3-10 best universities of the world. 

Historically, ETH Zurich has achieved its reputation particularly in the fields of chemistry, mathematics and physics. There are 32 Nobel Laureates who are associated with ETH. The most recent Nobel Laureate is Richard F. Heck who was awarded the Nobel Prize in chemistry in 2010. Albert Einstein is perhaps its most famous alumnus.

In 2018, the QS World University Rankings placed ETH Zurich at 7th overall in the world. In 2015, ETH was ranked 5th in the world in Engineering, Science and Technology, just behind the Massachusetts Institute of Technology, Stanford University, Cambridge University and National University of Singapore. In 2015, ETH also ranked 6th in the world in Natural Sciences, and in 2016 ranked 1st in the world for Earth & Marine Sciences for the second consecutive year.

In 2016, Times Higher Education World University Rankings ranked ETH Zurich 9th overall in the world and 8th in the world in the field of Engineering & Technology, just behind the Massachusetts Institute of Technology, Stanford University, California Institute of Technology, Princeton University, Cambridge University, Imperial College London and Oxford University.

In a comparison of Swiss universities by swissUP Ranking and in rankings published by CHE comparing the universities of German-speaking countries, ETH Zurich traditionally is ranked first in natural sciences, computer science and engineering sciences. 

In the survey CHE ExcellenceRanking on the quality of Western European graduate school programmes in the fields biology, chemistry, physics and mathematics, ETH was assessed as one of the three institutions to have excellent graduate programmes in all considered fields, the other two being the Imperial College London and the University of Cambridge. ETH Zurich had a total budget of 1.885 billion CHF in the year 2017.

Admission and education

Students and locals in ETH front courtyard

 

For Swiss students, ETH is not selective in its undergraduate admission procedures. Like every public university in Switzerland, ETH is obliged to grant admission to every Swiss resident who took the Matura. Applicants from foreign countries are required to take either the reduced entrance exam or the comprehensive entrance exam although some applicants from several European countries are exempted from this rule. An applicant can be admitted to ETH even without any verifiable educational records by passing the comprehensive entrance exam.

As at all universities in Switzerland, the academic year is divided into two semesters. Examinations are often held during examination sessions which are immediately before the beginning of the next semester (only a few select courses offer an exam immediately after the semester ends). After the first year of study, bachelor students must pass a block examination of all courses taken in the first year, called the Basisprüfung. If the weighted average score is not sufficient, a student is required to retake the entire Basisprüfung which usually means having to re-sit the whole first year. About 50% of the students fail the Basisprüfung on the first try and many of them choose to drop out of the course instead of repeating the Basisprüfung. The structure of examinations in higher academic years is similar to the Basisprüfung (Basis examination), but with a higher success rate. The regular time to reach graduation is six semesters for the Bachelor of Science degree and three or four further semesters for the Master of Science degree. The final semester is dedicated to writing a thesis. 

Education at ETH Zurich generally focuses more on theoretical aspects than application and most degree programs contain a high amount of mathematical training. The main language of instruction in undergraduate (Bachelor) studies is German and for admission a proof of sufficient knowledge of the German language is required for Bachelor students. Most Master's programmes and doctoral studies are in English.

Campus

ETH Hönggerberg with the new HIT building

 

ETH Zurich has two campuses. The main building was constructed 1858–1864 outside and right above the eastern border of the town, but nowadays it is located right in the heart of the city. As the town and university grew, the ETH spread into the surrounding vineyards and later quarters. As a result, the Zentrum campus consists of various buildings and institutions throughout Zürich and firmly integrates the ETH in the city. The main building stands directly across the street from the University Hospital of Zurich and the University of Zurich. 

Because this geographic situation substantially hindered the expansion of ETH, a new campus was built from 1964 to 1976 on the Hönggerberg on a northern hill in the outskirts of the city. The last major expansion project of this new campus was completed in 2003; since then, the Hönggerberg location houses the departments of architecture, civil engineering, biology, chemistry, materials science and physics.

Main building

Main building as seen from Polyterrasse

 

ETH Zurich at night.

 

The main building of ETH was built from 1858 to 1864 under Gustav Zeuner; the architect, however, was Gottfried Semper, who was a professor of architecture at ETH at the time and one of the most important architectural writers and theorists of the age. Semper worked in a neoclassical style that was unique to him; and the namesake and architect of the Semperoper in Dresden. It emphasized bold and clear massings with a detailing, such as the rusticated ground level and giant order above, that derived in part from the work of Andrea Palladio and Donato Bramante. During the construction of the University of Zürich, the south wing of the building was allocated to the University until its own new main building was constructed (1912–1914). At about the same time, Semper's ETH building was enlarged and received its impressive cupola.

Science City

In the year of ETH Zurich's 150th anniversary, an extensive project called "Science City" for the Hönggerberg Campus was started with the goal to transform the campus into an attractive district based on the principle of sustainability. 

ETH Hönggerberg from the south, looking at the five "fingers" of the HCI and behind the high HPP building.

 

In September 2014 a new project to connect Science City by train was published.

ETH Laboratory of Ion Beam Physics

The ETH Laboratory of Ion Beam Physics (LIB) is a physics laboratory located in Science City. It specializes in accelerator mass spectrometry (AMS) and the use of ion beam based techniques with applications in archeology, earth sciences, life sciences, material sciences and fundamental physics. An example of such application is the tracing of isotopes and the detection of rare radionuclides with radiocarbon dating and the use of techniques such as Rutherford backscattering spectrometry or elastic recoil detection. The LIB is developing the next generation of AMS machines. It is also a laboratory available for users interested in applying the techniques of ion beam analysis.

Student life

ETH students were found to be the busiest students of all institutions of higher education in Switzerland. The undergraduates' tight curriculum consists of as much as twice the number of lectures as comparable courses of other Swiss universities.

ETH has well over 100 student associations. Most notable is the VSETH (Verband der Studierenden an der ETH) which comprises all department associations. The associations regularly organize events with varying size and popularity. Events of the neighboring University of Zürich are well-attended by ETH students and vice versa. The VSETH organizes events of greater public attention, such as the Polyball, the Polyparty (does not exist any more) and the Erstsemestrigenfest, the first two housed in the main building of ETH. Sometimes, the annual Erstsemestrigenfest takes place at extraordinary locations, for example the Zürich Airport. All freshmen enjoy special treatment at that event. 

Some of the notable associations that are not affiliated with a specific department are the ETH Entrepreneur Club and ETH Model United Nations. Both organisations enjoy high international standings and are regularly awarded for excellence in their field. ETH Juniors is another student run organisation. It forms a bridge between the industry and ETH and offers many services for students and companies alike.

The Academic Sports Association of Zürich (ASVZ) offers more than 120 sports. The biggest annual sports event is the SOLA-Stafette (SOLA relay race) which consists of 14 sections over a total distance of 140 kilometers. More than 760 teams participated in the 2009 edition. The 40th edition of the SOLA, held on May 4, 2013, had 900 enrolled teams, of which 893 started and 876 were classified. In 2014 ASVZ celebrated their 75th anniversary.

Traditions

The annual Polyball is the most prestigious public event at ETH, with a long tradition since the 1880s. The end of November, the Polyball welcomes around 10,000 dancers, music-lovers and partygoers in the extensively decorated main building of ETH. The Polyball is the biggest decorated ball in Europe. 

The amicable rivalry between ETH and the neighbouring University of Zürich has been cultivated since 1951 (Uni-Poly). There has been an annual rowing match between teams from the two institutions on the river Limmat. 

There are many regular symposia and conferences at ETH, most notably the annual Wolfgang Pauli Lectures, in honor of former ETH Professor Wolfgang Pauli. Distinct lecturers, among them 24 Nobel Laureates, have held lectures of the various fields of natural sciences at this conference since 1962.

Notable alumni and faculty

Albert Einstein, 1921

 

John von Neumann, graduated in chemical engineering, ETH Zurich 1925.

 

The names listed below are taken from the official record compiled by the ETH. It includes only graduates of the ETH and professors who have been awarded the Nobel Prize for their achievements at ETH.

Nobel Prize in Physics

• 1901 Wilhelm Conrad Röntgen (graduate)
• 1920 Charles-Edouard Guillaume (graduate)
• 1921 Albert Einstein (student and professor)
• 1943 Otto Stern (lecturer)
• 1945 Wolfgang Pauli (professor)
• 1952 Felix Bloch (graduate)
• 1986 Heinrich Rohrer (graduate)
• 1987 Georg Bednorz (graduate)
• 1987 Karl Alexander Müller (graduate)

Nobel Prize in Chemistry

• 1913 Alfred Werner (graduate)
• 1915 Richard Martin Willstätter (professor)
• 1918 Fritz Haber (attended for one semester)
• 1936 Peter Debye (professor)
• 1938 Richard Kuhn (professor)
• 1939 Leopold Ružička (professor)
• 1953 Hermann Staudinger (lecturer)
• 1975 Vladimir Prelog (professor)
• 1991 Richard Ernst (graduate and professor)
• 2002 Kurt Wüthrich (professor)
• 2010 Richard F. Heck (postdoctoral student)

Nobel Prize in Medicine

• 1950 Tadeus Reichstein (graduate)
• 1978 Werner Arber (graduate)

Other Nobel Laureates directly affiliated with the ETH

• 1912 Nils Gustaf Dalén (in collaboration with Aurel Stodola)
• 1943 George de Hevesy
• 1945 Artturi Ilmari Virtanen (in collaboration with Georg Wiegner)
• 1954 Max Born (in collaboration with Adolf Hurwitz)
• 1964 Konrad E. Bloch (in collaboration with Leopold Ružička and Vladimir Prelog)
• 1968 Lars Onsager (in collaboration with Peter Debye and Erich Hückel)
• 1968 Har Gobind Khorana (in collaboration with Vladimir Prelog)
• 1969 Max Delbrück (in collaboration with Wolfgang Pauli)
• 1987 Jean-Marie Lehn

ETH Rectors

• Sarah Springman 1 January 2015
• Lino Guzzella 2013 – 31 December 2014
• Heidi Wunderli-Allenspach September 2007 - August 2013
• Konrad Osterwalder 1995 - September 2007
• Albin Herzog 1895-1899

ETH Presidents

• Joël Mesot January 2019
• Lino Guzzella January 2015 - December 2018
• Ralph Eichler September 2007 – December 2014
• Konrad Osterwalder President Pro Tempore November 2006 – September 2007
• Ernst Hafen December 2005 – November 2006

ETH Zurich has produced and attracted many famous scientists in its short history, including Albert Einstein. More than twenty Nobel laureates have either studied at ETH or were awarded the Nobel Prize for their work achieved at ETH. Other alumni include scientists who were distinguished with the highest honours in their respective fields, amongst them Fields Medal, Pritzker Prize and Turing Award winners. Academic achievements aside, ETH has been Alma Mater to many Olympic Medalists and world champions.

Bacterial genome

From Wikipedia, the free encyclopedia

Bacterial genomes are generally smaller and less variant in size among species when compared with genomes of animals and single cell eukaryotes. Bacterial genomes can range in size anywhere from about 130 kbp to over 14 Mbp. A study that included, but was not limited to, 478 bacterial genomes, concluded that as genome size increases, the number of genes increases at a disproportionately slower rate in eukaryotes than in non-eukaryotes. Thus, the proportion of non-coding DNA goes up with genome size more quickly in non-bacteria than in bacteria. This is consistent with the fact that most eukaryotic nuclear DNA is non-gene coding, while the majority of prokaryotic, viral, and organellar genes are coding. Right now, we have genome sequences from 50 different bacterial phyla and 11 different archaeal phyla. Second-generation sequencing has yielded many draft genomes (close to 90% of bacterial genomes in GenBank are currently not complete); third-generation sequencing might eventually yield a complete genome in a few hours. The genome sequences reveal much diversity in bacteria. Analysis of over 2000 Escherichia coli genomes reveals an E. coli core genome of about 3100 gene families and a total of about 89,000 different gene families. Genome sequences show that parasitic bacteria have 500–1200 genes, free-living bacteria have 1500–7500 genes, and archaea have 1500–2700 genes. A striking discovery by Cole et al. described massive amounts of gene decay when comparing Leprosy bacillus to ancestral bacteria. Studies have since shown that several bacteria have smaller genome sizes than their ancestors did. Over the years, researchers have proposed several theories to explain the general trend of bacterial genome decay and the relatively small size of bacterial genomes. Compelling evidence indicates that the apparent degradation of bacterial genomes is owed to a deletional bias.

Methods and techniques

As of 2014, there are over 30,000 sequenced bacterial genomes publicly available and thousands of metagenome projects. Projects such as the Genomic Encyclopedia of Bacteria and Archaea (GEBA) intend to add more genomes.

The single gene comparison is now being supplanted by more general methods. These methods have resulted in novel perspectives on genetic relationships that previously have only been estimated.

A significant achievement in the second decade of bacterial genome sequencing was the production of metagenomic data, which covers all DNA present in a sample. Previously, there were only two metagenomic projects published.

Bacterial genomes

Log-log plot of the total number of annotated proteins in genomes submitted to GenBank as a function of genome size. Based on data from NCBI genome reports.

 

Bacteria possess a compact genome architecture distinct from eukaryotes in two important ways: bacteria show a strong correlation between genome size and number of functional genes in a genome, and those genes are structured into operons. The main reason for the relative density of bacterial genomes compared to eukaryotic genomes (especially multicellular eukaryotes) is the presence of noncoding DNA in the form of intergenic regions and introns. Some notable exceptions include recently formed pathogenic bacteria. This was initially described in a study by Cole et al. in which Mycobacterium leprae was discovered to have a significantly higher percentage of pseudogenes to functional genes (~40%) than its free-living ancestors.

Furthermore, amongst species of bacteria, there is relatively little variation in genome size when compared with the genome sizes of other major groups of life. Genome size is of little relevance when considering the number of functional genes in eukaryotic species. In bacteria, however, the strong correlation between the number of genes and the genome size makes the size of bacterial genomes an interesting topic for research and discussion.

The general trends of bacterial evolution indicate that bacteria started as free-living organisms. Evolutionary paths led some bacteria to become pathogens and symbionts. The lifestyles of bacteria play an integral role in their respective genome sizes. Free-living bacteria have the largest genomes out of the three types of bacteria; however, they have fewer pseudogenes than bacteria that have recently acquired pathogenicity. 

Facultative and recently evolved pathogenic bacteria exhibit a smaller genome size than free-living bacteria, yet they have more pseudogenes than any other form of bacteria. 

Obligate bacterial symbionts or pathogens have the smallest genomes and the fewest pseudogenes of the three groups. The relationship between life-styles of bacteria and genome size raises questions as to the mechanisms of bacterial genome evolution. Researchers have developed several theories to explain the patterns of genome size evolution amongst bacteria.

Genome comparisons and phylogeny

As single-gene comparisons have largely given way to genome comparisons, phylogeny of bacterial genomes have improved in accuracy. The Average Nucleotide Identity method quantifies genetic distance between entire genomes by taking advantage of regions of about 10,000 bp. With enough data from genomes of one genus, algorithms are executed to categorize species. This has been done for the Pseudomonas avellanae species in 2013.

To extract information about bacterial genomes, core- and pan-genome sizes have been assessed for several strains of bacteria. In 2012, the number of core gene families was about 3000. However, by 2015, with an over tenfold increased in available genomes, the pan-genome has increased as well. There is roughly a positive correlation between the number of genomes added and the growth of the pan-genome. On the other hand, the core genome has remain static since 2012. Currently, the E. coli pan-genome is composed of about 90,000 gene families. About one-third of these exist only in a single genome. Many of these, however, are merely gene fragments and the result of calling errors. Still, there are probably over 60,000 unique gene families in E. coli.

Theories of bacterial genome evolution

Bacteria lose a large amount of genes as they transition from free-living or facultatively parasitic life cycles to permanent host-dependent life. Towards the lower end of the scale of bacterial genome size are the mycoplasmas and related bacteria. Early molecular phylogenetic studies revealed that mycoplasmas represented an evolutionary derived state, contrary to prior hypotheses. Furthermore, it is now known that mycoplasmas are just one instance of many of genome shrinkage in obligately host-associated bacteria. Other examples are Rickettsia, Buchnera aphidicola, and Borrelia burgdorferi.

Small genome size in such species is associated with certain particularities, such as rapid evolution of polypeptide sequences and low GC content in the genome. The convergent evolution of these qualities in unrelated bacteria suggests that an obligate association with a host promotes genome reduction.

Given that over 80% of almost all of the fully sequenced bacterial genomes consist of intact ORFs, and that gene length is nearly constant at ~1 kb per gene, it is inferred that small genomes have few metabolic capabilities. While free-living bacteria, such as E. coli, Salmonella species, or Bacillus species, usually have 1500 to 6000 proteins encoded in their DNA, obligately pathogenic bacteria often have as few as 500 to 1000 such proteins.

One candidate explanation is that reduced genomes maintain genes that are necessary for vital processes pertaining to cellular growth and replication, in addition to those genes that are required to survive in the bacteria's ecological niche. However, sequence data contradicts this hypothesis. The set of universal orthologs amongst eubacteria comprises only 15% of each genome. Thus, each lineage has taken a different evolutionary path to reduced size. Because universal cellular processes require over 80 genes, variation in genes imply that the same functions can be achieved by exploitation of nonhomologous genes.

Host-dependent bacteria are able to secure many compounds required for metabolism from the host's cytoplasm or tissue. They can, in turn, discard their own biosynthetic pathways and associated genes. This removal explains many of the specific gene losses. For example, the Rickettsia species, which relies on specific energy substrate from its host, has lost many of its native energy metabolism genes. Similarly, most small genomes have lost their amino acid biosynthesizing genes, as these are found in the host instead. One exception is the Buchnera, an obligate maternally transmitted symbiont of aphids. It retains 54 genes for biosynthesis of crucial amino acids, but no longer has pathways for those amino acids that the host can synthesize. Pathways for nucleotide biosynthesis are gone from many reduced genomes. Those anabolic pathways that evolved through niche adaptation remain in particular genomes.

The hypothesis that unused genes are eventually removed does not explain why many of the removed genes would indeed remain helpful in obligate pathogens. For example, many eliminated genes code for products that are involved in universal cellular processes, including replication, transcription, and translation. Even genes supporting DNA recombination and repair are deleted from every small genome. In addition, small genomes have fewer tRNAs, utilizing one for several amino acids. So, a single codon pairs with multiple codons, which likely yields less-than-optimal translation machinery. It is unknown why obligate intracellular pathogens would benefit by retaining fewer tRNAs and fewer DNA repair enzymes.

Another factor to consider is the change in population that corresponds to an evolution towards an obligately pathogenic life. Such a shift in lifestyle often results in a reduction in the genetic population size of a lineage, since there is a finite number of hosts to occupy. This genetic drift may result in fixation of mutations that inactivate otherwise beneficial genes, or otherwise may decrease the efficiency of gene products. Hence, not will only useless genes be lost (as mutations disrupt them once the bacteria has settled into host dependency), but also beneficial genes may be lost if genetic drift enforces ineffective purifying selection.

The number of universally maintained genes is small and inadequate for independent cellular growth and replication, so that small genome species must achieve such feats by means of varying genes. This is done partly through nonorthologous gene displacement. That is, the role of one gene is replaced by another gene that achieves the same function. Redundancy within the ancestral, larger genome is eliminated. The descendant small genome content depends on the content of chromosomal deletions that occur in the early stages of genome reduction.

The very small genome of M. genitalium possesses dispensable genes. In a study in which single genes of this organism were inactivated using transposon-mediated mutagenesis, at least 129 of its 484 ORGs were not required for growth. A much smaller genome than that of the M. genitalium is therefore feasible.

Doubling time

One theory predicts that bacteria have smaller genomes due to a selective pressure on genome size to ensure faster replication. The theory is based upon the logical premise that smaller bacterial genomes will take less time to replicate. Subsequently, smaller genomes will be selected preferentially due to enhanced fitness. A study done by Mira et al. indicated little to no correlation between genome size and doubling time. The data indicates that selection is not a suitable explanation for the small sizes of bacterial genomes. Still, many researchers believe there is some selective pressure on bacteria to maintain small genome size.

Deletional bias

Selection is but one process involved in evolution. Two other major processes (mutation and genetic drift) can account for the genome sizes of various types of bacteria. A study done by Mira et al. examined the size of insertions and deletions in bacterial pseudogenes. Results indicated that mutational deletions tend to be larger than insertions in bacteria in the absence of gene transfer or gene duplication. Insertions caused by horizontal or lateral gene transfer and gene duplication tend to involve transfer of large amounts of genetic material. Assuming a lack of these processes, genomes will tend to reduce in size in the absence of selective constraint. Evidence of a deletional bias is present in the respective genome sizes of free-living bacteria, facultative and recently derived parasites and obligate parasites and symbionts. 

Free-living bacteria tend to have large population-sizes and are subject to more opportunity for gene transfer. As such, selection can effectively operate on free-living bacteria to remove deleterious sequences resulting in a relatively small number of pseudogenes. Continually, further selective pressure is evident as free-living bacteria must produce all gene-products independent of a host. Given that there is sufficient opportunity for gene transfer to occur and there are selective pressures against even slightly deleterious deletions, it is intuitive that free-living bacteria should have the largest bacterial genomes of all bacteria types. 

Recently-formed parasites undergo severe bottlenecks and can rely on host environments to provide gene products. As such, in recently-formed and facultative parasites, there is an accumulation of pseudogenes and transposable elements due to a lack of selective pressure against deletions. The population bottlenecks reduce gene transfer and as such, deletional bias ensures the reduction of genome size in parasitic bacteria. 

Obligatory parasites and symbionts have the smallest genome sizes due to prolonged effects of deletional bias. Parasites which have evolved to occupy specific niches are not exposed to much selective pressure. As such, genetic drift dominates the evolution of niche-specific bacteria. Extended exposure to deletional bias ensures the removal of most superfluous sequences. Symbionts occur in drastically lower numbers and undergo the most severe bottlenecks of any bacterial type. There is almost no opportunity for gene transfer for endosymbiotic bacteria, and thus genome compaction can be extreme. One of the smallest bacterial genomes ever to be sequenced is that of the endosymbiont Carsonella rudii. At 160 kbp, the genome of Carsonella is one of the most streamlined examples of a genome examined to date.

Genomic reduction

Molecular phylogenetics has revealed that every clade of bacteria with genome sizes under 2 Mb was derived from ancestors with much larger genomes, thus refuting the hypothesis that bacteria evolved by the successive doubling of small-genomed ancestors. Recent studies performed by Nilsson et al. examined the rates of bacterial genome reduction of obligate bacteria. Bacteria were cultured introducing frequent bottlenecks and growing cells in serial passage to reduce gene transfer so as to mimic conditions of endosymbiotic bacteria. The data predicted that bacteria exhibiting a one-day generation time lose as many as 1,000 kbp in as few as 50,000 years (a relatively short evolutionary time period). Furthermore, after deleting genes essential to the methyl-directed DNA mismatch repair (MMR) system, it was shown that bacterial genome size reduction increased in rate by as much as 50 times. These results indicate that genome size reduction can occur relatively rapidly, and loss of certain genes can speed up the process of bacterial genome compaction.

This is not to suggest that all bacterial genomes are reducing in size and complexity. While many types of bacteria have reduced in genome size from an ancestral state, there are still a huge number of bacteria that maintained or increased genome size over ancestral states. Free-living bacteria experience huge population sizes, fast generation times and a relatively high potential for gene transfer. While deletional bias tends to remove unnecessary sequences, selection can operate significantly amongst free-living bacteria resulting in evolution of new genes and processes.

Horizontal gene transfer

Unlike eukaryotes, which evolve mainly through the modification of existing genetic information, bacteria have acquired a large percentage of their genetic diversity by the horizontal transfer of genes. This creates quite dynamic genomes, in which DNA can be introduced into and removed from the chromosome.

Bacteria have more variation in their metabolic properties, cellular structures, and lifestyles than can be accounted for by point mutations alone. For example, none of the phenotypic traits that distinguish E. coli from Salmonella enterica can be attributed to point mutation. On the contrary, evidence suggests that horizontal gene transfer has bolstered the diversification and speciation of many bacteria.

Horizontal gene transfer is often detected via DNA sequence information. DNA segments obtained by this mechanism often reveal a narrow phylogenetic distribution between related species. Furthermore, these regions sometimes display an unexpected level of similarity to genes from taxa that are assumed to be quite divergent.

Although gene comparisons and phylogenetic studies are helpful in investigating horizontal gene transfer, the DNA sequences of genes are even more revelatory of their origin and ancestry within a genome. Bacterial species differ widely in overall GC content, although the genes in any one species' genome are roughly identical with respect to base composition, patterns of codon usage, and frequencies of di- and trinucleotides. As a result, sequences that are newly acquired through lateral transfer can be identified via their characteristics, which remains that of the donor. For example, many of the S. enterica genes that are not present in E. coli have base compositions that differ from the overall 52% GC content of the entire chromosome. Within this species, some lineages have more than a megabase of DNA that is not present in other lineages. The base compositions of these lineage-specific sequences imply that at least half of these sequences were captured through lateral transfer. Furthermore, the regions adjacent to horizontally obtained genes often have remnants of translocatable elements, transfer origins of plasmids, or known attachment sites of phage integrases.

In some species, a large proportion of laterally transferred genes originate from plasmid-, phage-, or transposon-related sequences.

Although sequence-based methods reveal the prevalence of horizontal gene transfer in bacteria, the results tend to be underestimates of the magnitude of this mechanism, since sequences obtained from donors whose sequence characteristics are similar to those of the recipient will avoid detection.

Comparisons of completely sequenced genomes confirm that bacterial chromosomes are amalgams of ancestral and laterally acquired sequences. The hyperthermophilic Eubacteria Aquifex aeolicus and Thermotoga maritima each has many genes that are similar in protein sequence to homologues in thermophilic Archaea. 24% of Thermotoga's 1,877 ORFs and 16% of Aquifex's 1,512 ORFs show high matches to an Archaeal protein, while mesophiles such as E. coli and B. subtilis have far lesser proportions of genes that are most like Archaeal homologues.

Mechanisms of lateral transfer

The genesis of new abilities due to horizontal gene transfer has three requirements. First, there must exist a possible route for the donor DNA to be accepted by the recipient cell. Additionally, the obtained sequence must be integrated with the rest of the genome. Finally, these integrated genes must benefit the recipient bacterial organism. The first two steps can be achieved via three mechanisms: transformation, transduction and conjugation.

Transformation involves the uptake of named DNA from the environment. Through transformation, DNA can be transmitted between distantly related organisms. Some bacterial species, such as Haemophilus influenzae and Neisseria gonorrhoeae, are continuously competent to accept DNA. Other species, such as Bacillus subtilis and Streptococcus pneumoniae, become competent when they enter a particular phase in their lifecycle. 

Transformation in N. gonorrhoeae and H. influenzae is effective only if particular recognition sequences are found in the recipient genomes (5'-GCCGTCTGAA-3' and 5'-AAGTGCGGT-3'. respectively). Although the existence of certain uptake sequences improve transformation capability between related species, many of the inherently competent bacterial species, such as B. subtilis and S. pneumoniae, do not display sequence preference.

New genes may be introduced into bacteria by a bacteriophage that has replicated within a donor through generalized transduction or specialized transduction. The amount of DNA that can be transmitted in one event is constrained by the size of the phage capsid (although the upper limit is about 100 kilobases). While phages are numerous in the environment, the range of microorganisms that can be transduced depends on receptor recognition by the bacteriophage. Transduction does not require both donor and recipient cells to be present simultaneously in time nor space. Phage-encoded proteins both mediate the transfer of DNA into the recipient cytoplasm and assist integration of DNA into the chromosome.

Conjugation involves physical contact between donor and recipient cells and is able to mediate transfers of genes between domains, such as between bacteria and yeast. DNA is transmitted from donor to recipient either by self-transmissible or mobilizable plasmid. Conjugation may mediate the transfer of chromosomal sequences by plasmids that integrate into the chromosome. 

Despite the multitude of mechanisms mediating gene transfer among bacteria, the process's success is not guaranteed unless the received sequence is stably maintained in the recipient. DNA integration can be sustained through one of many processes. One is persistence as an episome, another is homologous recombination, and still another is illegitimate incorporation through lucky double-strand break repair.

Traits introduced through lateral gene transfer

Antimicrobial resistance genes grant an organism the ability to grow its ecological niche, since it can now survive in the presence of previously lethal compounds. As the benefit to a bacterium earned from receiving such genes are time- and space-independent, those sequences that are highly mobile are selected for. Plasmids are quite mobilizable between taxa and are the most frequent way by which bacteria acquire antibiotic resistance genes. 

Adoption of a pathogenic lifestyle often yields a fundamental shift in an organism's ecological niche. The erratic phylogenetic distribution of pathogenic organisms implies that bacterial virulence is a consequence of the presence, or obtainment of, genes that are missing in avirulent forms. Evidence of this includes the discovery of large 'virulence' plasmids in pathogenic Shigella and Yersinia, as well as the ability to bestow pathogenic properties onto E. coli via experimental exposure to genes from other species.

Computer-made form

In April 2019, scientists at ETH Zurich reported the creation of the world's first bacterial genome, named Caulobacter ethensis-2.0, made entirely by a computer, although a related viable form of C. ethensis-2.0 does not yet exist.

Methanogen / Methanotroph

From Wikipedia, the free encyclopedia

Methanogen

Methanogens are microorganisms that produce methane as a metabolic byproduct in hypoxic conditions. They are prokaryotic and belong to the domain of archaea. They are common in wetlands, where they are responsible for marsh gas, and in the digestive tracts of animals such as ruminants and humans, where they are responsible for the methane content of belching in ruminants and flatulence in humans. In marine sediments the biological production of methane, also termed methanogenesis, is generally confined to where sulfates are depleted, below the top layers. Moreover, methanogenic archaea populations play an indispensable role in anaerobic wastewater treatments. Others are extremophiles, found in environments such as hot springs and submarine hydrothermal vents as well as in the "solid" rock of Earth's crust, kilometers below the surface.

Physical description

Methanogens are coccoid (spherical shaped) or bacilli (rod shaped). There are over 50 described species of methanogens, which do not form a monophyletic group, although all known methanogens belong to Archaea. They are mostly anaerobic organisms that cannot function under aerobic conditions, but recently a species (Candidatus Methanothrix paradoxum) has been identified that can function in anoxic microsites within aerobic environments. They are very sensitive to the presence of oxygen even at trace level. Usually, they cannot sustain oxygen stress for a prolonged time. However, Methanosarcina barkeri is exceptional in possessing a superoxide dismutase (SOD) enzyme, and may survive longer than the others in the presence of O₂. Some methanogens, called hydrogenotrophic, use carbon dioxide (CO₂) as a source of carbon, and hydrogen as a reducing agent.

The reduction of carbon dioxide into methane in the presence of hydrogen can be expressed as follows:

CO₂ + 4 H₂ → CH₄ + 2H₂O

Some of the CO₂ reacts with the hydrogen to produce methane, which creates an electrochemical gradient across the cell membrane, used to generate ATP through chemiosmosis. In contrast, plants and algae use water as their reducing agent.

Methanogens lack peptidoglycan, a polymer that is found in the cell walls of Bacteria but not in those of Archaea. Some methanogens have a cell wall that is composed of pseudopeptidoglycan. Other methanogens do not, but have at least one paracrystalline array (S-layer) made up of proteins that fit together like a jigsaw puzzle.

Extreme living areas

Methanogens play a vital ecological role in anaerobic environments of removing excess hydrogen and fermentation products that have been produced by other forms of anaerobic respiration. Methanogens typically thrive in environments in which all electron acceptors other than CO₂ (such as oxygen, nitrate, ferriciron (Fe(III)), and sulfate) have been depleted. In deep basaltic rocks near the mid ocean ridges, they can obtain their hydrogen from the serpentinisation reaction of olivine as observed in the hydrothermal field of Lost City. 

The thermal breakdown of water and water radiolysis are other possible sources of hydrogen. 

Methanogens are key agents of remineralization of organic carbon in continental margin sediments and other aquatic sediments with high rates of sedimentation and high sediment organic matter. Under the correct conditions of pressure and temperature, biogenic methane can accumulate in massive deposits of methane clathrates, which account for a significant fraction of organic carbon in continental margin sediments and represent a key reservoir of a potent greenhouse gas.

Methanogens have been found in several extreme environments on Earth – buried under kilometres of ice in Greenland and living in hot, dry desert soil. They are known to be the most common archaebacteria in deep subterranean habitats. Live microbes making methane were found in a glacial ice core sample retrieved from about three kilometres under Greenland by researchers from the University of California, Berkeley. They also found a constant metabolism able to repair macromolecular damage, at temperatures of 145 to –40 °C.

Another study has also discovered methanogens in a harsh environment on Earth. Researchers studied dozens of soil and vapour samples from five different desert environments in Utah, Idaho and California in the United States, and in Canada and Chile. Of these, five soil samples and three vapour samples from the vicinity of the Mars Desert Research Station in Utah were found to have signs of viable methanogens.

Some scientists have proposed that the presence of methane in the Martian atmosphere may be indicative of native methanogens on that planet.

Closely related to the methanogens are the anaerobic methane oxidizers, which utilize methane as a substrate in conjunction with the reduction of sulfate and nitrate. Most methanogens are autotrophic producers, but those that oxidize CH₃COO⁻ are classed as chemotroph instead.

Comparative genomics and molecular signatures

Comparative genomic analysis has led to the identification of 31 signature proteins which are specific for methanogens (also known as Methanoarchaeota). Most of these proteins are related to methanogenesis, and they could serve as potential molecular markers for methanogens. Additionally, 10 proteins found in all methanogens which are shared by Archaeoglobus, suggest that these two groups are related. In phylogenetic trees, methanogens are not monophyletic and they are generally split into three clades. Hence, the unique shared presence of large numbers of proteins by all methanogens could be due to lateral gene transfers.

Metabolism

Methane production

Methanogens are known to produce methane from substrates such as H₂/CO₂, acetate, formate, methanol and methylamines in a process called methanogenesis. Different methanogenic reactions are catalyzed by unique sets of enzymes and coenzymes. While reaction mechanism and energetics vary between one reaction and another, all of these reactions contribute to net positive energy production by creating ion concentration gradients that are used to drive ATP synthesis. The overall reaction for H₂/CO₂ methanogenesis is:

${\displaystyle {\ce {CO2 + 4 H2 -> CH4 + 2 H2O}}}$
  (∆G˚’ = -134 kJ/mol CH₄)

Well-studied organisms that produce methane via H2/CO₂ methanogenesis include Methanosarcina barkeri, Methanobacterium thermoautotrophicum, and Methanobacterium wolfei. These organism are typically found in anaerobic environments.

In the earliest stage of H₂/CO₂ methanogenesis, CO₂ binds to methylfuran (MF) and is reduced to formyl-MF. This endergonic reductive process (∆G˚’= +16 kJ/mol) is dependent on the availability of H₂ and is catalyzed by the enzyme formyl-MF dehydrogenase.

${\displaystyle {\ce {CO2 + H2 + MF -> HCO-MF + H2O}}}$

The formyl constituent of formyl-MF is then transferred to the coenzyme tetrahydromethanopterin (H4MPT) and is catalyzed by a soluble enzyme known as formyl transferase. This results in the formation of formyl-H4MPT.

${\displaystyle {\ce {HCO-MF + H4MPT -> HCO-H4MPT + MF}}}$

Formyl-H4MPT is subsequently reduced to methenyl-H4MPT. Methenyl-H4MPT then undergoes a one-step hydrolysis followed by a two-step reduction to methyl-H4MPT. The two-step reversible reduction is assisted by coenzyme F₄₂₀ whose hydride acceptor spontaneously oxidizes. Once oxidized, F₄₂₀’s electron supply is replenished by accepting electrons from H₂. This step is catalyzed by methylene H4MPT dehydrogenase.

${\displaystyle {\ce {HCO-H4MPT + H+ -> CH-H4MPT+ + H2O}}}$ 

(Formyl-H4MPT reduction)

${\displaystyle {\ce {CH-H4MPT+ + F420H2 -> CH2=H4MPT + F420 + H+}}}$

 

(Methenyl-H4MPT hydrolysis)

${\displaystyle {\ce {CH2=H4MPT + H2 -> CH3-H4MPT + H+}}}$ 

(H4MPT reduction)

Next, the methyl group of methyl-M4MPT is transferred to coenzyme M via a methyltransferase-catalyzed reaction.

${\displaystyle {\ce {CH3-H4MPT + HS-CoM -> CH3-S-CoM + H4MPT}}}$

The final step of H₂/CO₂ methanogenic involves methyl-coenzyme M reductase and two coenzymes: N-7 mercaptoheptanoylthreonine phosphate (HS-HTP) and coenzyme F₄₃₀. HS-HTP donates electrons to methyl-coenzyme M allowing the formation of methane and mixed disulfide of HS-CoM.^[24] F₄₃₀, on the other hand, serves as a prosthetic group to the reductase. H₂ donates electrons to the mixed disulfide of HS-CoM and regenerates coenzyme M.

${\displaystyle {\ce {CH3-S-CoM + HS-HTP -> CH4 + CoM-S-S-HTP}}}$ 

  (Formation of methane)

${\displaystyle {\ce {CoM-S-S-HTP + H2 -> HS-CoM + HS-HTP}}}$ 

(Regeneration of coenzyme M)

Wastewater treatment

Methanogens are widely used in anaerobic digestors to treat wastewater as well as aqueous organic pollutants. Industries have selected methanogens for their ability to perform biomethanation during wastewater decomposition thereby rendering the process sustainable and cost-effective.

Bio-decomposition in the anaerobic digester involves a four-staged cooperative action performed by different microorganisms. The first stage is the hydrolysis of insoluble polymerized organic matter by anaerobes such as Streptococcus and Enterobacterium. In the second stage, acidogens breakdown dissolved organic pollutants in wastewater to fatty acids. In the third stage, acetogens convert fatty acids to acetates. In the final stage, methanogens metabolize acetates to gaseous methane. The byproduct methane leaves the aqueous layer and serves as an energy source to power wastewater-processing within the digestor, thus generating a self-sustaining mechanism.

Methanogens also effectively decrease the concentration of organic matter in wastewater run-off. For instance, agricultural wastewater, highly rich in organic material, has been a major cause of aquatic ecosystem degradation. The chemical imbalances can lead to severe ramifications such as eutrophication. Through anaerobic digestion, the purification of wastewater can prevent unexpected blooms in water systems as well as trap methanogenesis within digesters. This allocates biomethane for energy production and prevents a potent greenhouse gas, methane, from being released into the atmosphere. 

The organic components of wastewater vary vastly. Chemical structures of the organic matter select for specific methanogens to perform anaerobic digestion. An example is the members of Methanosaeta genus dominate the digestion of palm oil mill effluent (POME) and brewery waste. Modernizing wastewater treatment systems to incorporate higher diversity of microorganisms to decrease organic content in treatment is under active research in the field of microbiological and chemical engineering. Current new generations of Staged Multi-Phase Anaerobic reactors and Upflow Sludge Bed reactor systems are designed to have innovated features to counter high loading wastewater input, extreme temperature conditions, and possible inhibitory compounds.

Methanotroph

Methanotrophs (sometimes called methanophiles) are prokaryotes that metabolize methane as their only source of carbon and energy. They can be either bacteria or archaea and can grow aerobically or anaerobically, and require single-carbon compounds to survive.

General

Methanotrophs are especially common in or near environments where methane is produced, although also methanotrophs exist that can oxidize atmospheric methane. Their habitats include wetlands, soils, marshes, rice paddies, landfills, aquatic systems (lakes, oceans, streams) and more. They are of special interest to researchers studying global warming, as they play a significant role in the global methane budget, by reducing the amount of methane emitted to the atmosphere.

Methanotrophy is a special case of methylotrophy, using single-carbon compounds that are more reduced than carbon dioxide. Some methylotrophs, however, can also make use of multi-carbon compounds which differentiates them from methanotrophs that are usually fastidious methane and methanol oxidizers. The only facultative methanotrophs isolated to date are members of the genus Methylocella and Methylocystis.

In functional terms, methanotrophs are referred to as methane-oxidizing bacteria, however, methane-oxidizing bacteria encompass other organisms that are not regarded as sole methanotrophs. For this reason methane-oxidizing bacteria have been separated into four subgroups: two methane-assimilating bacteria (MAB) groups, the methanotrophs, and two autotrophic ammonia-oxidizing bacteria (AAOB).

Methanotroph classification

Methantrophs can be either bacteria or archaea. Which methanotroph species is present, is mainly determined by the availability of electron acceptors. Many types of methane oxidizing bacteria (MOB) are known. Differences in the method of formaldehyde fixation and membrane structure divide these bacterial methanotrophs into several groups. These include the Methylococcaceae and Methylocystaceae. Although both are included among the Proteobacteria, they are members of different subclasses. Other methanotroph species are found in the Verrucomicrobiae. Among the methanotrophic archaea, several subgroups are determined.

Aerobic methanotrophs

Under aerobic conditions, methanotrophs combine oxygen and methane to form formaldehyde, which is then incorporated into organic compounds via the serine pathway or the ribulose monophosphate (RuMP) pathway, and [Carbon dioxide], which is released. Type I and type X methanotrophs are part of the Gammaproteobacteria and they use the RuMP pathway to assimilate carbon. Type II methanotrophs are part of the Alphaproteobacteria and utilize the serine pathway of carbon assimilation. They also characteristically have a system of internal membranes within which methane oxidation occurs. No methanotrophic archaea are capable of using oxygen.

Anaerobic methanotrophs

Under anoxic conditions, methanotrophs use different electron acceptors for methane oxidation. This can happen in anoxic habitats such as marine or lake sediments, oxygen minimum zones, anoxic water columns, rice paddies and soils. Some specific methanotrophs can reduce nitrate or nitrite, and couple that to methane oxidation. Investigations in marine environments revealed that methane can be oxidized anaerobically by consortia of methane oxidizing archaea and sulfate-reducing bacteria. This type of Anaerobic oxidation of methane (AOM) mainly occurs in anoxic marine sediments. The exact mechanism behind this is still a topic of debate but the most widely accepted theory is that the archaea use the reversed methanogenesis pathway to produce carbon dioxide and another, unknown substance. This unknown intermediate is then used by the sulfate-reducing bacteria to gain energy from the reduction of sulfate to hydrogen sulfide. The anaerobic methanotrophs are not related to the known aerobic methanotrophs; the closest cultured relative to the anaerobic methanotrophs are the methanogens in the order Methanosarcinales. Metal-oxides, such as manganese and iron, can also be used as terminal electron acceptors by ANME. For this, no consortium is needed. ANME shuttle electrons directly to the abiotic particles, which get reduced chemically. 

In some cases, aerobic methane oxidation can take place in anoxic (no oxygen) environments. Candidatus Methylomirabilis oxyfera belongs to the phylum NC10 bacteria, and can catalyze nitrite reduction through an “intra-aerobic” pathway, in which internally produced oxygen is used to oxidise methane. In clear water lakes, methanotrophs can live in the anoxic water column, but receive oxygen from photosynthetic organisms, that they then directly consume to oxidise methane aerobically.

Special methanotroph species

Methylococcus capsulatus is utilised to produce animal feed from natural gas.

Recently, a new bacterium Candidatus Methylomirabilis oxyfera was identified that can couple the anaerobic oxidation of methane to nitrite reduction without the need for a syntrophic partner. Based on the studies of Ettwig et al., it is believed that M. oxyfera oxidizes methane anaerobically by utilizing the oxygen produced internally from the dismutation of nitric oxide into nitrogen and oxygen gas.

Properties

RuMP pathway in type I methanotrophs

 

Serine pathway in type II methanotrophs

 

Methanotrophs oxidize methane by first initiating reduction of an oxygen atom to H₂O₂ and transformation of methane to CH₃OH using methane monooxygenases (MMOs). Furthermore, two types of MMO have been isolated from methanotrophs: soluble methane monooxygenase (sMMO) and particulate methane monooxygenase (pMMO). Cells containing pMMO have demonstrated higher growth capabilities and higher affinity for methane than sMMO containing cells. It is suspected that copper ions may play a key role in both pMMO regulation and the enzyme catalysis, thus limiting pMMO cells to more copper-rich environments than sMMO producing cells.