| Methylobacillus flagellatus | |
|---|---|
Scientific classification  | |
| Domain: | Bacteria |
| Phylum: | Pseudomonadota |
| Class: | Betaproteobacteria |
| Order: | Methylophilaceae |
| Genus: | Methylobacillus |
| Species: | M. flagellatus |
| Binomial name | |
| Methylobacillus flagellatus Govorukhina et al. 1998 | |
Methylobacillus flagellatus is a species of aerobic bacteria.
Methylobacillus is a group of methylotrophic aerobic bacteria, and they can be found in large numbers in marine and fresh water ecosystems. [1] [2] These organisms are one of Earth's most important carbon recyclers, and they recycle such important carbon compounds as methane, methanol, and methylated amines on Earth. [3] [1] “In general methylotrophs can use green-house gases such as carbon dioxide and methane as substrates to fulfill their energy and carbon needs.” [4] Furthermore, strong scientific evidences indicate that a subset group of methylotrophs, the methanotrophs, play huge roles in global warming and groundwater contamination. According to Bonnie et al., methane gas is far more efficient at absorbing infrared radiation than carbon dioxide gas, and “the concentration of methane has been increasing at an alarming rate of 1% per year for the last 150 year to 200 years.” [3] The role that these methylotrophs play in carbon cycling may help us understand, and eventually combat global warming. Thus, it is imperative for researchers to classify, and study methylotrophic bacteria.
One such important methylotroph of interest is Methylobacillus flagellatus KT strain. Methylobacillus flagellatus was first isolated in the early 1980s in sewerage pipes of a metropolitan sanitary sewer. “M. flagellatus is most closely related to other members of the family Methylophilaceae.” [1] The shape of M. flagellatus is an oval shape, with multiple flagella originating from opposite poles of the bacteria. [5] Using small-subunit 16S rRNAs and comparing metabolic/phylogenic similarities and differences< between M. flagellatus and its relatives, scientists have determined that Methylobacillus flagellatus (betaproteobacteria) is more closely related to Methylobacterium extorquens (alphaproteobacteria) and Methylococcus capsulatus (gammaproteobacteria), than to Methylibium petroleiphilum (betaproteobacteria). [3] [1]
The genome of Methylobacillus flagellatus is a circular chromosome that is approximately 3Mbp long, and it encodes about 2,766 proteins. According to Chistoserdova et al., M. flagellatus’ genome does not code for three enzymes of the tricarboxylic acid cycle (TCA cycle). The failure of M. flagellatus to produce these three enzymes (dehydrogenases) means that it can only rely on one-carbon compounds as carbon substrates for the production of precursor molecules, and for its energy needs. The ability to use only one-carbon substrates automatically makes M. flagellatus an obligate methylotroph. [1]
Overall characteristics of the M. flagellatus genome include 53.7% GC content and 143,032 base pairs that are direct repeats. Furthermore, there are approximately 2,766 coding regions, and only 233 open reading frames (ORFs) are unique to M. flagellatus. [1] The genome also contains a CRISPR region, which is functionally linked to lateral gene transfer, host cell defense, replication, and regulation.
A recent attempt at phylogeny classification of obligate methylotrophs puts the genus Methylobacillus along with Methylophilus and Methylovorus as terrestrial methylobacteria, while marine obligate methylotrophs are assigned to the genus Methylophaga. [6] Methylobacillus flagellatus KT strain was found in a metropolitan sewer system, whereas Methylobacillus pratensis were isolated from meadow grass. [1] [6] The important point is that the methylotrophs are very adaptable and they can be found in diverse ecosystems.
As mentioned before, the importance of studying M. flagellatus and other closely related species of methylobacteria will help us better understand the recycling of carbon on Earth. More specifically a better understanding of how these methylotrophs affect the carbon cycle would undoubtedly help us shed light on the effects of methane gas on global warming. “Approximately 10^3 megatons of methane are produced globally each year by anaerobic micro-organisms.” [7] A subgroup of methylotrophs, the methanotrophs, oxidizes roughly %80-90 of the global methane. The significance of this fact cannot be overlooked, because without these methanotrophs the vast majority of atmospheric methane would not get degraded. [7] The accumulation of methane gas would cause the Earth's temperature to rise dramatically, because methane gas is far more efficient at absorbing infrared radiation than carbon-dioxide gas, and “may contribute more [than carbon dioxide] to global warming.” [3]
No known pathogenic quality of M. flagellatus has been discovered.
Specific characteristics of M. flagellatus such as its high coefficient of conversion of oxidizers (methanol) to its own biomass [8] allows for practical applications such as inexpensive industrial productions of commercially needed compounds. [1] These compounds can range from heterologous proteins and amino-acids to vitamins. Some methylotrophs within the genus of Methylobacillus can even use organic compounds such as the pesticide carbofuran and choline as carbon raw materials; they use these carbon sources to fulfill their energy and carbon requirements. [4] As early as the late 1980s researchers had known that some methylotrophs possess enzymes such as dichloromethane dehalogenase, or methane monooxygenase (MMO), which degrade various environmental pollutants (i.e.: alkanes, alkenes, and mono- and poly-substituted aromatic compounds). [7] Another common environmental pollutant that results from industrial processes is formaldehyde. Recently, a company called BIP Ltd has been cultivating a pink-pigmented methylotroph, strain BIP, for the specific purpose of remediating formaldehyde-contaminated industrial wastes. [9]
Since there are not a lot of published researches on M. flagellatus in particular, hence, there are not a lot of data available about this organism on the topic of application to biotechnology. We can still look at M. flagellatus’ close relatives, the methanotrophs, to help us better understand the genus Methylobacillus. Methanotrophs are a subset of a physiological group of methylotrophs, and its sole assimilatory/dissmilatory carbon source is methane. [4] Methanotrophs also possess MMO, it is known that this enzyme has a broad substrate specificity and it can catalyzes the oxidation of a wide variety of water pollutants, such as trichloroethylene, vinyl chloride, and other halogenated hydrocarbons. [7] MMO’s primary role is to convert methane to methanol, and any methyltrophs that can synthesize MMO are most likely classified as methanotrophs. [4]
M. flagellatus is closely related to members of the family Methylophilaceae. Most of its genes are dedicated to its methylotrophy functions (i.e.: breaking down one-carbon compounds), and these genes are present in more than one identical or non-identical copy. [10] M. flagellatus is an obligate methylotroph; this is the direct consequence of an incomplete set of genes that cannot encode 3 critical enzymes (dehydrogenases) of the TCA cycle. [10] Its genome does not code for any secondary metabolite synthesis pathways such as antibiotic biosynthesis, and no known xenobiotic degradation pathways are encoded. [1] The absence of these self-defense mechanisms may help explain why M. flagellatus has no pathogenic qualities.
In June 2006 Kalyuzhaya et al. published a paper (“Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations”) detailing more precise methods for separating organisms of interests within a natural sample. Their experiment focused on separating Type I and Type II Methanotrophs using combined techniques of FISH/FC (fluorescence in situ hybridization-flow cytometry) and FACS (fluorescence-activated FC analysis and cell sorting). FISH/FC employs oligonucleotide attached to florescein, or Alexa for targeting 16S rRNA. The fluoresced microbe can then be subjected to analysis and cell sorting. The detection phase involves putting the detected sample to “functional gene analysis to indicate specific separation using 16S rRNA, pmoA (encoding a subunit of particulate methane monooxygenase), and fae (encoding formaldehyde activating enzyme) genes.” [11] The data indicate that FISH/FC/FACS is a method that can “provide significant enrichment of microbial populations of interest from complex natural communities.” [11] Lastly, Kalyuzhaya et al. tested the reliability of whole genome amplification (WGA) using limited numbers of sorted cells. They found that WGA would give more “specific” results if a rough threshold number of 10^4 or more cells are in a sample. Having proven FISH/FC/FACS’ effectiveness to detect microbial populations, Kalyuzhay et al. used mixed samples of M. flagellatus along with other members of the methylotrophs genus to test their method's effectiveness.
In “Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT strain, a ribulose monophosphate cycle methylotroph” Chistoserdova et al. studied different pathways of formaldehyde oxidation in M. flagellatus KT strain to asset the importance of these pathways relating to dissimilatory metabolism, and, or formaldehyde detoxification.
Based on null mutant experiments of 6-phosphogluconate dehydrogenase (Gnd) (a key enzyme of the cyclic oxidation pathway), and methenyl H4MPT cyclohydrolase (CH) (participating in the direct oxidation of formaldehyde via H4MPT derivatives), Chistoserdova et al. have found that Gnd null mutants were not obtained, but CH null mutants were obtained. The experimental result suggests “that this pathway [cyclic oxidation] is essential for growth on methylotrophic substrates”, [12] and that linear oxidation of formaldehyde via H4MPT derivatives is not required for growth. More specifically, “results confirm previous suggestions that the cyclic formaldehyde oxidation pathway plays a crucial role in C1 metabolism of M. flagellatus KT strain, most probably as the major energy-generating pathway.” [12]
Metabolic comparisons between M. flagellatus (beta-proteobacteria) and Methylobacterium extorquens (alpha-proteobacteria) indicated that these species utilize the linear oxidation pathway via H4MPT linked derivatives differently. M. flagellatus “mutants defective in this (linear oxidation) pathway were more sensitive to formaldehyde than wild-type for cells grown on solid media but not in shaken liquid cultures.” The result provided clues that this pathway may serve to protect the M. flagellatus from excess formaldehyde, whereas Methylobacterium extorquens uses this pathway as its “main energy-generating pathway for methylotrophic growth.” [12]
Methanogens are microorganisms that produce methane as a metabolic byproduct in hypoxic conditions. They are prokaryotic and belong to the domain Archaea. All known methanogens are members of the archaeal phylum Euryarchaeota. Methanogens are common in wetlands, where they are responsible for marsh gas, and in the digestive tracts of animals such as ruminants and many 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.
The Methylocystaceae are a family of bacteria that are capable of obtaining carbon and energy from methane. Such bacteria are called methanotrophs, and in particular the Methylocystaceae comprise the type II methanotrophs, which are structurally and biochemically distinct from the Methylococcaceae or type I methanotrophs.
Methanotrophs are prokaryotes that metabolize methane as their source of carbon and chemical energy. They are bacteria or archaea, can grow aerobically or anaerobically, and require single-carbon compounds to survive.
Methylotrophs are a diverse group of microorganisms that can use reduced one-carbon compounds, such as methanol or methane, as the carbon source for their growth; and multi-carbon compounds that contain no carbon-carbon bonds, such as dimethyl ether and dimethylamine. This group of microorganisms also includes those capable of assimilating reduced one-carbon compounds by way of carbon dioxide using the ribulose bisphosphate pathway. These organisms should not be confused with methanogens which on the contrary produce methane as a by-product from various one-carbon compounds such as carbon dioxide. Some methylotrophs can degrade the greenhouse gas methane, and in this case they are called methanotrophs. The abundance, purity, and low price of methanol compared to commonly used sugars make methylotrophs competent organisms for production of amino acids, vitamins, recombinant proteins, single-cell proteins, co-enzymes and cytochromes.
Methane monooxygenase (MMO) is an enzyme capable of oxidizing the C-H bond in methane as well as other alkanes. Methane monooxygenase belongs to the class of oxidoreductase enzymes.
Microbial metabolism is the means by which a microbe obtains the energy and nutrients it needs to live and reproduce. Microbes use many different types of metabolic strategies and species can often be differentiated from each other based on metabolic characteristics. The specific metabolic properties of a microbe are the major factors in determining that microbe's ecological niche, and often allow for that microbe to be useful in industrial processes or responsible for biogeochemical cycles.
Oxalosuccinic acid is a substrate of the citric acid cycle. It is acted upon by isocitrate dehydrogenase. Salts and esters of oxalosuccinic acid are known as oxalosuccinates.
Methylorubrum extorquens is a Gram-negative bacterium. Methylorubrum species often appear pink, and are classified as pink-pigmented facultative methylotrophs, or PPFMs. The wild type has been known to use both methane and multiple carbon compounds as energy sources. Specifically, M. extorquens has been observed to use primarily methanol and C1 compounds as substrates in their energy cycles. It has been also observed that use lanthanides as a cofactor to increase its methanol dehydrogenase activity
In enzymology, a methanol dehydrogenase (MDH) is an enzyme that catalyzes the chemical reaction:
Methylocella silvestris is a bacterium from the genus Methylocella spp which are found in many acidic soils and wetlands. Historically, Methylocella silvestris was originally isolated from acidic forest soils in Germany, and it is described as Gram-negative, aerobic, non-pigmented, non-motile, rod-shaped and methane-oxidizing facultative methanotroph. As an aerobic methanotrophic bacteria, Methylocella spp use methane (CH4), and methanol as their main carbon and energy source, as well as multi compounds acetate, pyruvate, succinate, malate, and ethanol. They were known to survive in the cold temperature from 4° to 30° degree of Celsius with the optimum at around 15° to 25 °C, but no more than 36 °C. They grow better in the pH scale between 4.5 to 7.0. It lacks intracytoplasmic membranes common to all methane-oxidizing bacteria except Methylocella, but contain a vesicular membrane system connected to the cytoplasmic membrane. BL2T (=DSM 15510T=NCIMB 13906T) is the type strain.
Methylomonas scandinavica is a species of Gram-negative gammaproteobacteria found in deep igneous rock ground water in Sweden. As a member of the Methylomonas genus, M. scandinavica has the ability to use methane as a carbon source.
Methanohalophilus mahii is an obligately anaerobic, methylotrophic, methanogenic cocci-shaped archaeon of the genus Methanohalophilus that can be found in high salinity aquatic environments. The name Methanohalophilus is said to be derived from methanum meaning "methane" in Latin; halo meaning "salt" in Greek; and mahii meaning "of Mah" in Latin, after R.A. Mah, who did substantial amounts of research on aerobic and methanogenic microbes. The proper word in ancient Greek for "salt" is however hals (ἅλς). The specific strain type was designated SLP and is currently the only identified strain of this species.
Methylosinus trichosporium is an obligate aerobic and methane-oxidizing bacterium species from the genus of Methylosinus. Its native habitat is generally in the soil, but the bacteria has been isolated from fresh water sediments and groundwater as well. Because of this bacterium's ability to oxidize methane, M. trichosporium has been popular for identifying both the structure and function of enzymes involved with methane oxidation since it was first isolated in 1970 by Roger Whittenbury and colleagues. Since its discovery, M. trichosporium and its soluble monooxygenase enzyme have been studied in detail to see if the bacterium could help in bioremediation treatments.
Methylacidiphilum fumariolicum is an autotrophic bacterium first described in 2007 growing on volcanic pools near Naples, Italy. It grows in mud at temperatures between 50 °C and 60 °C and an acidic pH of 2–5. It is able to oxidize methane gas. It uses ammonium, nitrate or atmospheric nitrogen as a nitrogen source and fixes carbon dioxide.
Methylacidiphilum infernorum is an extremely acidophilic methanotrophic aerobic bacteria first isolated and described in 2007 growing on soil and sediment on Hell's Gate, New Zealand. Similar organisms have also been isolated from geothermal sites on Italy and Russia.
Methylophaga thiooxydans is a methylotrophic bacterium that requires high salt concentrations for growth. It was originally isolated from a culture of the algae Emiliania huxleyi, where it grows by breaking down dimethylsulfoniopropionate from E. hexleyi into dimethylsulfide and acrylate. M. thiooxydans has been implicated as a dominant organism in phytoplankton blooms, where it consumes dimethylsulfide, methanol and methyl bromide released by dying phytoplankton. It was also identified as one of the dominant organisms present in the plume following the Deepwater Horizon oil spill, and was identified as a major player in the breakdown of methanol in coastal surface water in the English channel.
Mary E. Lidstrom is a Professor of Microbiology at the University of Washington. She also holds the Frank Jungers Chair of Engineering, in the Department of Chemical Engineering. She currently is a fellow of the American Academy of Microbiology, a member of the National Academy of Sciences and serves on the editorial boards of the Journal of Bacteriology and FEMS Microbial Ecology.
Ann Patricia Wood is a retired British biochemist and bacteriologist who specialized in the ecology, taxonomy and physiology of sulfur-oxidizing chemolithoautotrophic bacteria and how methylotrophic bacteria play a role in the degradation of odour causing compounds in the human mouth, vagina and skin. The bacterial genus Annwoodia was named to honor her contributions to microbial research in 2017.
John Rodney (Rod) Quayle FRS (1926–2006) was a microbial biochemist, West Riding Professor of Microbiology and Head of Department at University of Sheffield (1965–1983) and then Vice-Chancellor of Bath University (1983–1992). He adopted techniques for dissecting enzymic reactions using radioactive carbon-14. He focused on microbes that used compounds containing one atom of carbon as their sources of energy and biomass.
Formatotrophs are organisms that can assimilate formate or formic acid to use as a carbon source or for reducing power. Some authors classify formatotrophs as one of the five trophic groups of methanogens, which also include hydrogenotrophs, acetotrophs, methylotrophs, and alcoholotrophs. Formatotrophs have garnered attention for applications in biotechnology as part of a "formate bioeconomy" in which synthesized formate could be used as a nutrient for microoganisms. Formate can be electrochemically synthesized from CO2 and renewable energy, and formatotrophs may be genetically modified to enhance production of biochemical products to be used as biofuels. Technical limitations in culturing formatotrophs have limited the discovery of natural formatotrophs and impeded research on their formate-metabolizing enzymes, which are of interest for applications in carbon sequestration and astrobiology.