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Is gas produced by bacteria always mainly methane? Or, are there bacteria out there that produce some biogas composed mainly of hydrogen, natural gas, propane, butane?
Microbes can produce several gasses other than methane.
- All microbes produce $CO_2$ through the oxidation of reduced carbon
Additionally some metabolic pathways produce other gases.
Photosynthetic microbes produce $O_2$
Sulfur reducing bacteria can produce $H_2S$ (as @ohcanada points out)
Denitrifying bacteria produce $NO$, $N_2O$, and $N_2$
Fermenters produce $H_2$ (as @mart indicates)
There may be others that I am not thinking of but these are some of the major players…
Well, some bacteria can produce Hydrogen Sulfide gas. For example, Proteus and Salmonella. The presence of $H_2S$ producing bacteria is actually clinically significant and we have a way to test for this, which is via the use of TSI (Triple Sugar Iron) media.
Assume you set up the test correctly, $H_2S$ producing bacteria will generate dark deposit within the media.
In the clinical setting, there are other choices beside TSI, such as SIM media and API20E.
Methane to bioproducts: the future of the bioeconomy?
Interest in the biological production of products from methane is rapidly growing.
The most-studied products are methanol, PHA, and single cell protein.
Genetic modification could open doors to many new products.
Methane is a promising substrate for the growing bioeconomy.
Methanotrophs have been studied since the 1970s, but interest has increased tremendously in recent years due to their potential to transform methane into valuable bioproducts. The vast quantity of available methane and the low price of methane as natural gas have helped to spur this interest. The most well-studied, biologically-derived products from methane include methanol, polyhydroxyalkanoates, and single cell protein. However, many other high-interest chemicals such as biofuels or high-value products such as ectoine could be made industrially relevant through metabolic engineering. Although challenges must be overcome to achieve commercialization of biologically manufactured methane-to-products, taking a holistic view of the production process or radically re-imagining pathways could lead to a future bioeconomy with methane as the primary feedstock.
Some abiogenic hypotheses have proposed that oil and gas did not originate from fossil deposits, but have instead originated from deep carbon deposits, present since the formation of the Earth.  Additionally, it has been suggested that hydrocarbons may have arrived on Earth from solid bodies such as comets and asteroids from the late formation of the Solar System, carrying hydrocarbons with them.  
The abiogenic hypothesis regained some support in 2009 when researchers at the Royal Institute of Technology (KTH) in Stockholm reported they believed they had proven that fossils from animals and plants are not necessary for crude oil and natural gas to be generated.  
An abiogenic hypothesis was first proposed by Georgius Agricola in the 16th century and various additional abiogenic hypotheses were proposed in the 19th century, most notably by Prussian geographer Alexander von Humboldt, [ when? ] the Russian chemist Dmitri Mendeleev (1877)  and the French chemist Marcellin Berthelot. [ when? ] Abiogenic hypotheses were revived in the last half of the 20th century by Soviet scientists who had little influence outside the Soviet Union because most of their research was published in Russian. The hypothesis was re-defined and made popular in the West by Thomas Gold, who developed his theories from 1979 to 1998 and published his research in English.
Abraham Gottlob Werner and the proponents of neptunism in the 18th century regarded basaltic sills as solidified oils or bitumen. While these notions proved unfounded, the basic idea of an association between petroleum and magmatism persisted. Alexander von Humboldt proposed an inorganic abiogenic hypothesis for petroleum formation after he observed petroleum springs in the Bay of Cumaux (Cumaná) on the northeast coast of Venezuela.  He is quoted as saying in 1804, "the petroleum is the product of a distillation from great depth and issues from the primitive rocks beneath which the forces of all volcanic action lie". [ citation needed ] Other early prominent proponents of what would become the generalized abiogenic hypothesis included Dmitri Mendeleev  and Berthelot.
In 1951, the Soviet geologist Nikolai Alexandrovitch Kudryavtsev proposed the modern abiotic hypothesis of petroleum.   On the basis of his analysis of the Athabasca Oil Sands in Alberta, Canada, he concluded that no "source rocks" could form the enormous volume of hydrocarbons, and therefore offered abiotic deep petroleum as the most plausible explanation. (Humic coals have since been proposed for the source rocks.  ) Others who continued Kudryavtsev's work included Petr N. Kropotkin, Vladimir B. Porfir'ev, Emmanuil B. Chekaliuk, Vladilen A. Krayushkin, Georgi E. Boyko, Georgi I. Voitov, Grygori N. Dolenko, Iona V. Greenberg, Nikolai S. Beskrovny, and Victor F. Linetsky.
Astronomer Thomas Gold was a prominent proponent of the abiogenic hypothesis in the West until his death in 2004. More recently, Jack Kenney of Gas Resources Corporation has come to prominence,    supported by studies by researchers at the Royal Institute of Technology in Stockholm. 
Within the mantle, carbon may exist as hydrocarbons—chiefly methane—and as elemental carbon, carbon dioxide, and carbonates.  The abiotic hypothesis is that the full suite of hydrocarbons found in petroleum can either be generated in the mantle by abiogenic processes,  or by biological processing of those abiogenic hydrocarbons, and that the source-hydrocarbons of abiogenic origin can migrate out of the mantle into the crust until they escape to the surface or are trapped by impermeable strata, forming petroleum reservoirs.
Abiogenic hypotheses generally reject the supposition that certain molecules found within petroleum, known as biomarkers, are indicative of the biological origin of petroleum. They contend that these molecules mostly come from microbes feeding on petroleum in its upward migration through the crust, that some of them are found in meteorites, which have presumably never contacted living material, and that some can be generated abiogenically by plausible reactions in petroleum. 
Some of the evidence used to support abiogenic theories includes:
|Gold||The presence of methane on other planets, meteors, moons and comets  |
|Gold, Kenney||Proposed mechanisms of abiotically chemically synthesizing hydrocarbons within the mantle   |
|Kudryavtsev, Gold||Hydrocarbon-rich areas tend to be hydrocarbon-rich at many different levels |
|Kudryavtsev, Gold||Petroleum and methane deposits are found in large patterns related to deep-seated large-scale structural features of the crust rather than to the patchwork of sedimentary deposits |
|Gold||Interpretations of the chemical and isotopic composition of natural petroleum |
|Kudryavtsev, Gold||The presence of oil and methane within non-sedimentary rocks upon the Earth |
|Gold||The existence of methane hydrate deposits |
|Gold||Perceived ambiguity in some assumptions and key evidence used in the conventional understanding of petroleum origin.  |
|Gold||Bituminous coal creation is based upon deep hydrocarbon seeps |
|Gold||Surface carbon budget and oxygen levels stable over geologic time scales |
|Kudryavtsev, Gold||The biogenic explanation does not explain some hydrocarbon deposit characteristics |
|Szatmari||The distribution of metals in crude oils fits better with upper serpentinized mantle, primitive mantle and chondrite patterns than oceanic and continental crust, and show no correlation with sea water |
|Gold||The association of hydrocarbons with helium, a noble gas [ clarification needed ] |
As of 2009 [update] , little research is directed towards establishing abiogenic petroleum or methane, although the Carnegie Institution for Science has reported that ethane and heavier hydrocarbons can be synthesized under conditions of the upper mantle.  Research mostly related to astrobiology and the deep microbial biosphere and serpentinite reactions, however, continues to provide insight into the contribution of abiogenic hydrocarbons into petroleum accumulations.
- rock porosity and migration pathways for abiogenic petroleum 
- mantle peridotiteserpentinization reactions and other natural Fischer–Tropsch analogs
- Primordial hydrocarbons in meteorites, comets, asteroids and the solid bodies of the Solar System 
- Primordial or ancient sources of hydrocarbons or carbon in Earth 
- Primordial hydrocarbons formed from hydrolysis of metal carbides of the iron peak of cosmic elemental abundance (chromium, iron, nickel, vanadium, manganese, cobalt) 
Most serious researchers view the theory as easily debunkable with basic scientific knowledge, often placing it in the realm of pseudoscience or conspiracy theories. Some common criticisms include:
- If oil was created in the mantle, it would be expected that oil would be most commonly found in fault zones, as that would provide the greatest opportunity for oil to migrate into the crust from the mantle. Additionally, the mantle near subduction zones tends to be more oxidizing than the rest. However, the locations of oil deposits have not been found to be correlated with fault zones.
- If oil were naturally generated in the earth, it would follow that depleted oil reserves would refill themselves over time. Proponents of the abiogenic theory often claim that the supply of oil from the earth is effectively limitless. However, it is possible (and relatively easy) to deplete oil deposits, and, once depleted, they do not appear to refill.
Primordial deposits Edit
Thomas Gold's work was focused on hydrocarbon deposits of primordial origin. Meteorites are believed to represent the major composition of material from which the Earth was formed. Some meteorites, such as carbonaceous chondrites, contain carbonaceous material. If a large amount of this material is still within the Earth, it could have been leaking upward for billions of years. The thermodynamic conditions within the mantle would allow many hydrocarbon molecules to be at equilibrium under high pressure and high temperature. Although molecules in these conditions may disassociate, resulting fragments would be reformed due to the pressure. An average equilibrium of various molecules would exist depending upon conditions and the carbon-hydrogen ratio of the material. 
Creation within the mantle Edit
Russian researchers concluded that hydrocarbon mixes would be created within the mantle. Experiments under high temperatures and pressures produced many hydrocarbons—including n-alkanes through C10H22—from iron oxide, calcium carbonate, and water.  Because such materials are in the mantle and in subducted crust, there is no requirement that all hydrocarbons be produced from primordial deposits.
Hydrogen generation Edit
Hydrogen gas and water have been found more than 6,000 metres (20,000 ft) deep in the upper crust in the Siljan Ring boreholes and the Kola Superdeep Borehole. Data from the western United States suggests that aquifers from near the surface may extend to depths of 10,000 metres (33,000 ft) to 20,000 metres (66,000 ft). Hydrogen gas can be created by water reacting with silicates, quartz, and feldspar at temperatures in the range of 25 °C (77 °F) to 270 °C (518 °F). These minerals are common in crustal rocks such as granite. Hydrogen may react with dissolved carbon compounds in water to form methane and higher carbon compounds. 
One reaction not involving silicates which can create hydrogen is:
The above reaction operates best at low pressures. At pressures greater than 5 gigapascals (49,000 atm) almost no hydrogen is created. 
Thomas Gold reported that hydrocarbons were found in the Siljan Ring borehole and in general increased with depth, although the venture was not a commercial success. 
However, several geologists analysed the results and said that no hydrocarbon was found.     
Serpentinite mechanism Edit
In 1967, the Ukrainian scientist Emmanuil B. Chekaliuk proposed that petroleum could be formed at high temperatures and pressures from inorganic carbon in the form of carbon dioxide, hydrogen and/or methane.
This mechanism is supported by several lines of evidence which are accepted by modern scientific literature. This involves synthesis of oil within the crust via catalysis by chemically reductive rocks. A proposed mechanism for the formation of inorganic hydrocarbons  is via natural analogs of the Fischer–Tropsch process known as the serpentinite mechanism or the serpentinite process.  
Serpentinites are ideal rocks to host this process as they are formed from peridotites and dunites, rocks which contain greater than 80% olivine and usually a percentage of Fe-Ti spinel minerals. Most olivines also contain high nickel concentrations (up to several percent) and may also contain chromite or chromium as a contaminant in olivine, providing the needed transition metals.
However, serpentinite synthesis and spinel cracking reactions require hydrothermal alteration of pristine peridotite-dunite, which is a finite process intrinsically related to metamorphism, and further, requires significant addition of water. Serpentinite is unstable at mantle temperatures and is readily dehydrated to granulite, amphibolite, talc–schist and even eclogite. This suggests that methanogenesis in the presence of serpentinites is restricted in space and time to mid-ocean ridges and upper levels of subduction zones. However, water has been found as deep as 12,000 metres (39,000 ft),  so water-based reactions are dependent upon the local conditions. Oil being created by this process in intracratonic regions is limited by the materials and temperature.
Serpentinite synthesis Edit
A chemical basis for the abiotic petroleum process is the serpentinization of peridotite, beginning with methanogenesis via hydrolysis of olivine into serpentine in the presence of carbon dioxide.  Olivine, composed of Forsterite and Fayalite metamorphoses into serpentine, magnetite and silica by the following reactions, with silica from fayalite decomposition (reaction 1a) feeding into the forsterite reaction (1b).
Fayalite + water → magnetite + aqueous silica + hydrogen
Forsterite + aqueous silica → serpentinite
When this reaction occurs in the presence of dissolved carbon dioxide (carbonic acid) at temperatures above 500 °C (932 °F) Reaction 2a takes place.
Olivine + water + carbonic acid → serpentine + magnetite + methane
However, reaction 2(b) is just as likely, and supported by the presence of abundant talc-carbonate schists and magnesite stringer veins in many serpentinised peridotites
Olivine + water + carbonic acid → serpentine + magnetite + magnesite + silica
( F e , M g ) 2 S i O 4 + n H 2 O + C O 2 → M g 3 S i 2 O 5 ( O H ) 4 + F e 3 O 4 + M g C O 3 + S i O 2
SiO_<4>+nH_<2>O+CO_<2> ightarrow Mg_<3>Si_<2>O_<5>(OH)_<4>+Fe_<3>O_<4>+MgCO_<3>+SiO_<2>> >
The upgrading of methane to higher n-alkane hydrocarbons is via dehydrogenation of methane in the presence of catalyst transition metals (e.g. Fe, Ni). This can be termed spinel hydrolysis.
Spinel polymerization mechanism Edit
Magnetite, chromite and ilmenite are Fe-spinel group minerals found in many rocks but rarely as a major component in non-ultramafic rocks. In these rocks, high concentrations of magmatic magnetite, chromite and ilmenite provide a reduced matrix which may allow abiotic cracking of methane to higher hydrocarbons during hydrothermal events.
Chemically reduced rocks are required to drive this reaction and high temperatures are required to allow methane to be polymerized to ethane. Note that reaction 1a, above, also creates magnetite.
Methane + magnetite → ethane + hematite
Reaction 3 results in n-alkane hydrocarbons, including linear saturated hydrocarbons, alcohols, aldehydes, ketones, aromatics, and cyclic compounds. 
Carbonate decomposition Edit
Calcium carbonate may decompose at around 500 °C (932 °F) through the following reaction: 
Hydrogen + calcium carbonate → methane + calcium oxide + water
Note that CaO (lime) is not a mineral species found within natural rocks. Whilst this reaction is possible, it is not plausible.
Evidence of abiogenic mechanisms Edit
- Theoretical calculations by J.F. Kenney using scaled particle theory (a statistical mechanical model) for a simplified perturbed hard-chain predict that methane compressed to 30,000 bars (3.0 GPa) or 40,000 bars (4.0 GPa) kbar at 1,000 °C (1,830 °F) (conditions in the mantle) is relatively unstable in relation to higher hydrocarbons. However, these calculations do not include methane pyrolysis yielding amorphous carbon and hydrogen, which is recognized as the prevalent reaction at high temperatures. 
- Experiments in diamond anvil high pressure cells have resulted in partial conversion of methane and inorganic carbonates into light hydrocarbons., 
The "deep biotic petroleum hypothesis", similar to the abiogenic petroleum origin hypothesis, holds that not all petroleum deposits within the Earth's rocks can be explained purely according to the orthodox view of petroleum geology. Thomas Gold used the term the deep hot biosphere to describe the microbes which live underground.  
This hypothesis is different from biogenic oil in that the role of deep-dwelling microbes is a biological source for oil which is not of a sedimentary origin and is not sourced from surface carbon. Deep microbial life is only a contaminant of primordial hydrocarbons. Parts of microbes yield molecules as biomarkers.
Deep biotic oil is considered to be formed as a byproduct of the life cycle of deep microbes. Shallow biotic oil is considered to be formed as a byproduct of the life cycles of shallow microbes.
Microbial biomarkers Edit
Thomas Gold, in a 1999 book, cited the discovery of thermophile bacteria in the Earth's crust as new support for the postulate that these bacteria could explain the existence of certain biomarkers in extracted petroleum.  A rebuttal of biogenic origins based on biomarkers has been offered by Kenney, et al. (2001). 
Isotopic evidence Edit
Methane is ubiquitous in crustal fluid and gas.  Research continues to attempt to characterise crustal sources of methane as biogenic or abiogenic using carbon isotope fractionation of observed gases (Lollar & Sherwood 2006). There are few clear examples of abiogenic methane-ethane-butane, as the same processes favor enrichment of light isotopes in all chemical reactions, whether organic or inorganic. δ 13 C of methane overlaps that of inorganic carbonate and graphite in the crust, which are heavily depleted in 12 C, and attain this by isotopic fractionation during metamorphic reactions.
One argument for abiogenic oil cites the high carbon depletion of methane as stemming from the observed carbon isotope depletion with depth in the crust. However, diamonds, which are definitively of mantle origin, are not as depleted as methane, which implies that methane carbon isotope fractionation is not controlled by mantle values. 
Commercially extractable concentrations of helium (greater than 0.3%) are present in natural gas from the Panhandle-Hugoton fields in the US, as well as from some Algerian and Russian gas fields.  
Helium trapped within most petroleum occurrences, such as the occurrence in Texas, is of a distinctly crustal character with an Ra ratio of less than 0.0001 that of the atmosphere.  
Biomarker chemicals Edit
Certain chemicals found in naturally occurring petroleum contain chemical and structural similarities to compounds found within many living organisms. These include terpenoids, terpenes, pristane, phytane, cholestane, chlorins and porphyrins, which are large, chelating molecules in the same family as heme and chlorophyll. Materials which suggest certain biological processes include tetracyclic diterpane and oleanane. [ citation needed ]
The presence of these chemicals in crude oil is a result of the inclusion of biological material in the oil these chemicals are released by kerogen during the production of hydrocarbon oils, as these are chemicals highly resistant to degradation and plausible chemical paths have been studied. Abiotic defenders state that biomarkers get into oil during its way up as it gets in touch with ancient fossils. However a more plausible explanation is that biomarkers are traces of biological molecules from bacteria (archaea) that feed on primordial hydrocarbons and die in that environment. For example, hopanoids are just parts of the bacterial cell wall present in oil as contaminant. 
Trace metals Edit
Nickel (Ni), vanadium (V), lead (Pb), arsenic (As), cadmium (Cd), mercury (Hg) and others metals frequently occur in oils. Some heavy crude oils, such as Venezuelan heavy crude have up to 45% vanadium pentoxide content in their ash, high enough that it is a commercial source for vanadium. Abiotic supporters argue that these metals are common in Earth's mantle, but relatively high contents of nickel, vanadium, lead and arsenic can be usually found in almost all marine sediments.
Analysis of 22 trace elements in oils correlate significantly better with chondrite, serpentinized fertile mantle peridotite, and the primitive mantle than with oceanic or continental crust, and shows no correlation with seawater. 
Reduced carbon Edit
Sir Robert Robinson studied the chemical makeup of natural petroleum oils in great detail, and concluded that they were mostly far too hydrogen-rich to be a likely product of the decay of plant debris, assuming a dual origin for Earth hydrocarbons.  However, several processes which generate hydrogen could supply kerogen hydrogenation which is compatible with the conventional explanation. 
Olefins, the unsaturated hydrocarbons, would have been expected to predominate by far in any material that was derived in that way. He also wrote: "Petroleum . [seems to be] a primordial hydrocarbon mixture into which bio-products have been added."
This hypothesis was later demonstrated to have been a misunderstanding by Robinson, related to the fact that only short duration experiments were available to him. Olefins are thermally very unstable (which is why natural petroleum normally does not contain such compounds) and in laboratory experiments that last more than a few hours, the olefins are no longer present. [ citation needed ]
The presence of low-oxygen and hydroxyl-poor hydrocarbons in natural living media is supported by the presence of natural waxes (n=30+), oils (n=20+) and lipids in both plant matter and animal matter, for instance fats in phytoplankton, zooplankton and so on. These oils and waxes, however, occur in quantities too small to significantly affect the overall hydrogen/carbon ratio of biological materials. However, after the discovery of highly aliphatic biopolymers in algae, and that oil generating kerogen essentially represents concentrates of such materials, no theoretical problem exists anymore. [ citation needed ] Also, the millions of source rock samples that have been analyzed for petroleum yield by the petroleum industry have confirmed the large quantities of petroleum found in sedimentary basins.
Occurrences of abiotic petroleum in commercial amounts in the oil wells in offshore Vietnam are sometimes cited, as well as in the Eugene Island block 330 oil field, and the Dnieper-Donets Basin. However, the origins of all these wells can also be explained with the biotic theory.  Modern geologists think that commercially profitable deposits of abiotic petroleum could be found, but no current deposit has convincing evidence that it originated from abiotic sources. 
The Soviet school of thought saw evidence of their [ clarification needed ] hypothesis in the fact that some oil reservoirs exist in non-sedimentary rocks such as granite, metamorphic or porous volcanic rocks. However, opponents noted that non-sedimentary rocks served as reservoirs for biologically originated oil expelled from nearby sedimentary source rock through common migration or re-migration mechanisms. 
The following observations have been commonly used to argue for the abiogenic hypothesis, however each observation of actual petroleum can also be fully explained by biotic origin: 
Lost City hydrothermal vent field Edit
The Lost City hydrothermal field was determined to have abiogenic hydrocarbon production. Proskurowski et al. wrote, "Radiocarbon evidence rules out seawater bicarbonate as the carbon source for FTT reactions, suggesting that a mantle-derived inorganic carbon source is leached from the host rocks. Our findings illustrate that the abiotic synthesis of hydrocarbons in nature may occur in the presence of ultramafic rocks, water, and moderate amounts of heat." 
Siljan Ring crater Edit
The Siljan Ring meteorite crater, Sweden, was proposed by Thomas Gold as the most likely place to test the hypothesis because it was one of the few places in the world where the granite basement was cracked sufficiently (by meteorite impact) to allow oil to seep up from the mantle furthermore it is infilled with a relatively thin veneer of sediment, which was sufficient to trap any abiogenic oil, but was modelled as not having been subjected to the heat and pressure conditions (known as the "oil window") normally required to create biogenic oil. However, some geochemists concluded by geochemical analysis that the oil in the seeps came from the organic-rich Ordovician Tretaspis shale, where it was heated by the meteorite impact. 
In 1986–1990 The Gravberg-1 borehole was drilled through the deepest rock in the Siljan Ring in which proponents had hoped to find hydrocarbon reservoirs. It stopped at the depth of 6,800 metres (22,300 ft) due to drilling problems, after private investors spent $40 million.  Some eighty barrels of magnetite paste and hydrocarbon-bearing sludge were recovered from the well Gold maintained that the hydrocarbons were chemically different from, and not derived from, those added to the borehole, but analyses showed that the hydrocarbons were derived from the diesel fuel-based drilling fluid used in the drilling.     This well also sampled over 13,000 feet (4,000 m) of methane-bearing inclusions. 
In 1991–1992, a second borehole, Stenberg-1, was drilled a few miles away to a depth of 6,500 metres (21,300 ft), finding similar results.
Bacterial mats Edit
Direct observation of bacterial mats and fracture-fill carbonate and humin of bacterial origin in deep boreholes in Australia are also taken as evidence for the abiogenic origin of petroleum. 
Examples of proposed abiogenic methane deposits Edit
Panhandle-Hugoton field (Anadarko Basin) in the south-central United States is the most important gas field with commercial helium content. Some abiogenic proponents interpret this as evidence that both the helium and the natural gas came from the mantle.    
The Bạch Hổ oil field in Vietnam has been proposed as an example of abiogenic oil because it is 4,000 m of fractured basement granite, at a depth of 5,000 m.  However, others argue that it contains biogenic oil which leaked into the basement horst from conventional source rocks within the Cuu Long basin.  
A major component of mantle-derived carbon is indicated in commercial gas reservoirs in the Pannonian and Vienna basins of Hungary and Austria. 
Natural gas pools interpreted as being mantle-derived are the Shengli Field  and Songliao Basin, northeastern China.  
The Chimaera gas seep, near Çıralı, Antalya (southwest Turkey), has been continuously active for millennia and it is known to be the source of the first Olympic fire in the Hellenistic period. On the basis of chemical composition and isotopic analysis, the Chimaera gas is said to be about half biogenic and half abiogenic gas, the largest emission of biogenic methane discovered deep and pressurized gas accumulations necessary to sustain the gas flow for millennia, posited to be from an inorganic source, may be present.  Local geology of Chimaera flames, at exact position of flames, reveals contact between serpentinized ophiolite and carbonate rocks. [ citation needed ] Fischer–Tropsch process can be suitable reaction to form hydrocarbon gases.
Incidental arguments for abiogenic oil Edit
Given the known occurrence of methane and the probable catalysis of methane into higher atomic weight hydrocarbon molecules, various abiogenic theories consider the following to be key observations in support of abiogenic hypotheses:
- the serpentinite synthesis, graphite synthesis and spinel catalysation models prove the process is viable 
- the likelihood that abiogenic oil seeping up from the mantle is trapped beneath sediments which effectively seal mantle-tapping faults 
- outdated  mass-balance calculations [when?] for supergiant oilfields which argued that the calculated source rock could not have supplied the reservoir with the known accumulation of oil, implying deep recharge. 
- the presence of hydrocarbons encapsulated in diamonds 
The proponents of abiogenic oil also use several arguments which draw on a variety of natural phenomena in order to support the hypothesis:
- the modeling of some researchers shows the Earth was accreted at relatively low temperature, thereby perhaps preserving primordial carbon deposits within the mantle, to drive abiogenic hydrocarbon production 
- the presence of methane within the gases and fluids of mid-ocean ridge spreading centre hydrothermal fields. 
- the presence of diamond within kimberlites and lamproites which sample the mantle depths proposed as being the source region of mantle methane (by Gold et al.). 
Incidental arguments against abiogenic oil Edit
Arguments against chemical reactions, such as the serpentinite mechanism, being a source of hydrocarbon deposits within the crust include:
- the lack of available pore space within rocks as depth increases. 
- this is contradicted by numerous studies which have documented the existence of hydrologic systems operating over a range of scales and at all depths in the continental crust. 
- The Gravberg-1 well only produced 84 barrels (13.4 m 3 ) of oil, which later was shown to derive from organic additives, lubricants and mud used in the drilling process. 
Field test evidence Edit
What unites both theories of oil origin is the low success rate in predicting the locations of giant oil/gas fields: according to the statistics discovering a giant demands drilling 500+ exploration wells. A team of American-Russian scientists (mathematicians, geologists, geophysicists, and computer scientists) developed an Artificial Intelligence software and the appropriate technology for geological applications, and used it for predicting places of giant oil/gas deposits.     In 1986 the team published a prognostic map for discovering giant oil and gas fields at the Ands in South America  based on abiogenic petroleum origin theory. The model proposed by Prof. Yury Pikovsky (Moscow State University) assumes that petroleum moves from the mantle to the surface through permeable channels created at the intersection of deep faults.  The technology uses 1) maps of morphostructural zoning, which outlines the morphostructural nodes (intersections of faults), and 2) pattern recognition program that identify nodes containing giant oil/gas fields. It was forecast that eleven nodes, which had not been developed at that time, contain giant oil or gas fields. These 11 sites covered only 8% of the total area of all the Andes basins. 30 years later (in 2018) was published the result of comparing the prognosis and the reality.  Since publication of the prognostic map in 1986 only six giant oil/gas fields were discovered in the Andes region: Cano- Limon, Cusiana, Capiagua, and Volcanera (Llanos basin, Colombia), Camisea (Ukayali basin, Peru), and Incahuasi (Chaco basin, Bolivia). All discoveries were made in places shown on the 1986 prognostic map as promising areas. The result is convincingly positive, and this is a strong contribution in support of abiogenic theory of oil origin.
The presence of methane on Saturn's moon Titan and in the atmospheres of Jupiter, Saturn, Uranus and Neptune is cited as evidence of the formation of hydrocarbons without biological intermediate forms,  for example by Thomas Gold.  (Terrestrial natural gas is composed primarily of methane). Some comets contain massive amounts of organic compounds, the equivalent of cubic kilometers of such mixed with other material  for instance, corresponding hydrocarbons were detected during a probe flyby through the tail of Comet Halley in 1986.  Drill samples from the surface of Mars taken in 2015 by the Curiosity rover's Mars Science Laboratory have found organic molecules of benzene and propane in 3 billion year old rock samples in Gale Crater. 
Methane Production in Ecosystems
There are two known forms of methane production on Earth, called non-biological and biological methane sources. Non-biological methane production occurs without the participation of living organisms. Non-biological methane can be released by volcanoes or formed underground, under high pressures and temperatures. These geological processes normally involve the transformation of rocks that are melted with heat and water (Figure 1). Biological methane production is only done by microorganisms. The current estimates suggest that 90% of the methane released into the atmosphere has a biological origin and is produced exclusively as a result of microbial activity!
- Figure 1 - Diagram of the methane cycle showing sources of methane production and methane breakdown on Earth.
The process of biological methane production is called methano-genesis. The best studied methane-producing microorganisms are named methanogenic archaea or simply methanogens. Methanogens have a complex metabolism that allows them to create methane as they produce the energy they need to survive. Interestingly, atmospheric oxygen which we need to breath and obtain energy, is toxic to some methanogens, so these microorganisms are generally found in areas where oxygen is limited or absent, such as underground, in the sediments at the bottom of lakes, lagoons, wetlands, and oceans, and even inside the intestines of all types of animals, including worms, termites, cows, and humans.
Methanogenesis is the terminal step in the food chain that occurs in the absence of atmospheric oxygen. This gas is produced as a consequence of the total degradation of organic matter, where complex molecules are degraded into their most basic compounds and then are converted to methane by methanogens. This means that in all kinds of environments, the remains of dead organisms, such as plants and animals are slowly decomposed by microbes (Figure 1). This allows the return of the nutrients to the food chain, and the last step involves methane production [ 3 ].
Some species of bacteria produce methane
Nitrogen-fixing bacteria contain a previously unrecognised pathway for producing methane, researchers have discovered. The ability appears to be a by-product of an enzyme reaction that brings about another gas transformation.
Nitrogen-fixing bacteria are critically important for life on Earth, because they convert atmospheric nitrogen into a form that can be exploited by plants and animals.
However, microbiologists Caroline Harwood and Yanning Zheng of the University of Washington School of Medicine, and published in the journal Nature Microbiology , have uncovered other, more complex chemical feats performed by some of the microbes.
About 10% of nitrogen-fixing species manufacture an enzyme called “iron-only nitrogenase”. The primary function of the enzyme is to convert nitrogen gas into ammonia. Harwood and Zheng, however, discovered that the same enzyme also converts carbon dioxide into methane.
Although iron-only nitrogenase was identified in the mid-Twentieth Century, until now its methane-producing capacity had gone unnoticed.
“It’s been a neglected enzyme,” Zheng says.
Microbes, primarily archaea, are responsible for producing and consuming around a billion tonnes of methane at all. However, nitrogen-fixing bacteria have until now not been seen as involved in the cycle.
“Methane is potent greenhouse gas,” says Harwood. “That is why it is important to account for all of its sources.”
The scientists made their discovery while working with a bacterial species known as Rhodopseudomonas palustris.
To make sure it was not a property unique to the species, they then tested three other nitrogen-fixing varieties and found the same result. They then checked DNA data and found the genes that produce iron-only nitrogenase in several – indicating that they too are unacknowledged sources of methane.
“There is now recent evidence that iron-only nitrogenase is active in microbes more often and in more conditions than we had previously thought,” Zheng says.
Andrew Masterson is a former editor of Cosmos.
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Common symptoms of SIBO include:
- Abdominal pain
- Acid Reflux
- Bad Breath
Bloating From SIBO – The Annoying SIBO Symptom
One of the primary complaints and symptoms of SIBO is bloating. When you have an overgrowth of bacteria in the small intestine, the bacteria will start fermenting the undigested starches and fiber. Gas is produced as a by-product of fermentation.
The excessive fermentation and production of gas in the small intestine can cause mild to severe bloating. Even a skinny person can look as though they are pregnant.
It can feel as though you are walking around with a bloated stomach full of air. Not fun. I used to be constantly bloated. I remember looking in the mirror one day thinking, all I ate was a salad? Why I am so bloated?
In the morning, I would feel less bloated, but as the day progressed, I would slowly watch my stomach blow up like a balloon. I had a whole lot of upper abdominal gas production with a noisy growling stomach that was always talking to me.
SIBO and Burping
Burping and belching can also be symptoms of SIBO. When bacteria ferment upon fibres in the colon the gas is released through lower flatulence.
But when bacteria produce gas in the small intestine, the gas builds up pressure in the upper abdomen leading to burping and belching. What are you burping up? A whole lot of gas, produced by bacteria in the small intestine.
People with SIBO often experience constant burping or belching due to the excess gas production in the small intestine.
Acid Reflux and SIBO
Acid reflux is another SIBO symptom that can be caused by the excessive overgrowth of bacteria in the small intestine. Often stomach acid levels are low when acid reflux occurs. The gas produced by bacteria in the small intestine can put pressure on the stomach causing acid to reflux up into the esophagus.
Acid reflux was one of the SIBO symptoms that I used to experience. Here are some natural remedies for anyone with acid reflux.
Abdominal Pain From SIBO
Abdominal pain or cramping frequently occurs as a symptom of SIBO. The severity of abdominal pain caused by SIBO can range from mild to severe. The pain can be constant or come and go.
I noticed abdominal tenderness when palpating my upper mid-abdomen. I have also heard the pain described as a constant gnawing sensation.
Abdominal pain can be associated with too many histamine producing bacteria located in the small intestine. Often high histamine foods such as fermented foods, citrus, tomatoes, and alcohol will trigger abdominal pain or cramping.
I always like to ask the question, do you notice any trigger foods that aggravate your pain, such as onion and garlic? High fodmap foods will frequently trigger abdominal pain in people with SIBO.
Keeping a food journal with foods eaten and notes on any SIBO symptoms can help you to connect the dots to find out which foods aggravate your SIBO symptoms the most.
Constipation and Diarrhea
Constipation and diarrhea are common symptoms of SIBO. I know confusing, both diarrhea and constipation?!
Constipation is more common in people with methane-producing bacteria. Diarrhea is more common in people with hydrogen-producing bacteria.
A sluggish gallbladder and poor bile flow can be the root cause of constipation, diarrhea, and SIBO as well.
One of the most crucial properties of bile is that bile is antimicrobial and helps to prevent small intestinal bacterial overgrowth. Bile also stimulates peristalsis to keep food moving along the intestinal tract.
The other function of bile is to emulsify and break down fats. Fat malabsorption can cause loose, floating stools, and diarrhea.
Anytime someone is experiencing constipation or diarrhea, I am always thinking about a sluggish gallbladder as the root cause. If anyone has trouble digesting fats and symptoms of poor fat digestion, the gallbladder is most likely in need of support.
Bad Breath and SIBO
Bad breath is another embarrassing symptom of SIBO that no one wants to admit too. Yet no one wants bad breath. When bacteria ferment upon foods gas is produced.
Some of the gases produced can include hydrogen sulfide, which is a stinky smelling gas. When there is an overgrowth of bacteria in the small intestine, those gases can come out through the breath causing bad breath. I have seen stinky breath alongside SIBO that got worse with the use of antimicrobials before getting better. Often the exact symptoms of SIBO can flare during the healing process before getting better.
Symptoms of SIBO can vary in presentation and severity. The best way to determine if SIBO is causing your symptoms is by doing a breath test.
Here are some additional SIBO resources to heal SIBO. Grab my gut health guide to start improving your gut health today!
If you are struggling with SIBO Dr Nirala Jacobi from the SIBO Doctor has a very informative patient SIBO success course to beat SIBO for good. This course covers
- underlying causes of SIBO
- testing for SIBO
- Symptoms of SIBO
- types of SIBO
- biphasic SIBO diet
- antimicrobials for SIBO
Dr Nirala Jacobi has been my go-to resource for information on SIBO. There is so much to know about SIBO and the SIBO success plan covers all the essentials that you need to know about SIBO so you can beat SIBO for good.
Flatulence is Embarrassing, but it doesn't have to be!
Flatulence ( fart, flatus, intestinal gas, breaking wind, SBD)- we all have flatulence, and it is a normal part of life. It is a natural result of good digestion. Passing gas is a more familiar term to many people. Most of us try to make light of flatulance so as to not be embarrassed by its occurrence. Gas pains can be uncomfortable and malodorous for many people but you can reduce the symptoms and find relief with proper diet control.
The average person expels flatulence gas 14 times every day. The amount of actual gas released ranges from as little as one cup to as much as one half gallon per day. Gas is made primarily of odorless vapors such as carbon dioxide, oxygen, nitrogen, hydrogen, and sometimes methane. The unpleasant noxious odor of flatulence comes from bacteria in the large intestine that release small amounts of gases that contain hydrogen sulfide.(sulfur smell) Contrary to popular belief, women have just as many passages as men, and older people, have no more gas than younger individuals.
Flatulance occurs when a food does not break down completely in the stomach and small intestine. As a result, the food makes it into the large intestine in an undigested state. Most lower intestinal gas is produced when bacteria in your colon ferment carbohydrates that aren't digested in your small intestine. The body does not digest and absorb some carbohydrates (the sugar, starches, and fiber found in many foods) in the small intestine because of a shortage or absence of certain enzymes.
This undigested food then passes from the small intestine into the large intestine, where normal, harmless bacteria break down the food, producing gases such as hydrogen, carbon dioxide, and, in about one-third of all people, methane. As much as 80 to 90 percent of rectal gas (flatulence) is formed by bacteria. Eventually these gases exit through the rectum. Certain foods produce more flatulence than others because they contain more indigestible carbohydrates than others. Beans are well known gas producers. The beans pass through the small intestine and arrive in the large intestine without being digested, which causes flatulence to occur.
Unfortunately, healthy foods such as fruits, vegetables, oatmeal and legumes (beans and peas) are often the worst offenders. That's because these foods are high in soluble fiber. Soluble fiber dissolves in water forming a gelatinous substance in the bowel. Fiber has many health benefits, including keeping your digestive tract in good working order, regulating blood sugar and cholesterol levels, and helping prevent heart attacks and other heart problems. But it can also lead to the formation of gas. In the colon the bacteria thrive on the undigestible fiber. These bacteria are harmless but for those who have an intestinal gas or flatus problem it is probably best to avoid or carefully test soluble fibers to see if they are contributing to intestinal gas.
On the other hand, insoluble fiber as found in wheat, rye, bran, and other grains does not dissolve in water. It is not used by intestinal colon bacteria as a food source, so the bacteria generally do not produce intestinal gas. Both soluble and insoluble fiber should be eaten on a daily basis.
By contrast, fats and proteins cause little gas. They are absorbed in the digestive tract before they get to the colon.
Sugars are known to create gas. Fructose is naturally present in onions, artichokes and, pears. It is also used as a sweetener in some soft drinks and fruit drinks. Sorbitol is a sugar found naturally in fruits, including apples, pears, peaches, and prunes. It is also used as an artificial sweetener in many dietetic foods and sugarfree candies and gums.
Foods that may cause excessive and smelly gas include:
-Most beans, especially dried beans and peas, baked beans, soy beans, lima beans,
-Vegetables, such as Cabbage radishes onions broccoli Brussels sprouts cauliflower cucumbers sauerkraut kohlrabi asparagus, potatoes
-Fruits such as Prunes apricots apples raisins bananas.
-Carbonated beverages- Soft drinks, fruit drinks, milk and milk products, such as cheese and ice cream.
-Packaged foods prepared with lactose, such as bread, cereal, and salad dressing.
-Foods containing sorbitol, such as dietetic foods and sugarfree candies and gums
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Methane is a greenhouse gas (GHG) with a global warming potential 28-fold that of carbon dioxide . Agriculture makes a significant contribution to total GHG production, with estimates varying according to country and calculation method . Nonetheless, a global contribution of between 7 and 18% of total anthropogenic GHG emissions is generally accepted . Ruminant production accounts for about 81% of GHG from the livestock sector (calculated from Hristov et al. ), 90% of which results from rumen microbial methanogenesis . Ruminal CH4 production also represents a loss of energy (from 2 to 12% of gross energy intake ), which could in principle otherwise be available for animal growth or milk production. Lowering CH4 emissions therefore would benefit the environment and possibly the efficiency of livestock production. More than 87% of the CH4 produced by sheep has been estimated to be derived from the rumen , where a population of methanogenic archaea converts the H2 and CO2 produced by a complex community of ciliate protozoa, bacteria and anaerobic fungi to CH4 [6, 7]. A massive worldwide research effort has investigated various mitigation strategies. Changes in management practices can be simple and very effective , while feed additives that might inhibit H2 production, provide an alternative metabolic H sink or inhibit the archaea themselves offer opportunities beyond those straightforward management changes [6–11]. Other opportunities include chemogenomics and immunization [12–14]. One strategy that is foremost in several investigations is genetic selection of the livestock. If we can demonstrate that persistently different CH4 emissions in different animals [14–16] can be explained by their individual ruminal microbiomes, and that the characteristic is heritable, it should be possible to select future generations of ruminants that have intrinsically lower CH4 emissions. All the strategies potentially involve changing the ruminal microbiome. The aim of this short review is to assess our current understanding of the role of different members of the microbiome in determining the extent of methanogenesis in the rumen.
The rumen microbial community
The rumen is home to a vast array of ciliate protozoa, anaerobic fungi, anaerobic bacteria and archaea. The protozoa can comprise up to half the rumen microbial biomass [17, 18], the fungi were originally estimated to be about 8% of the biomass  but may reach 20% in sheep , the archaea comprise 0.3–4%  and the bacteria form the remainder, typically the largest component of the microbial biomass. Our present understanding of ruminal microbiology was built initially upon a few epoch-changing advances made many years ago: Gruby & Delafond’s  microscopic observations of protozoa Hungate’s  appreciation of the anaerobic nature of the rumen that led to new, truly anaerobic culture techniques for the bacteria Orpin’s  realization that some flagellate protozoa were in fact zoospores of anaerobic fungi, until then a contradiction in terms. The isolation and study of pure cultures was and remains invaluable in understanding the likely role of different species of bacteria, protozoa or fungi in the overall fermentation. Drawbacks of cultivation techniques are that only a very small number of samples can be tested, and that they suffer from bias, whereby the composition of the growth medium, generally too rich, determines which species can grow . Development of molecular techniques, based mainly on ssu rRNA gene and intergenic spacer sequence (for the fungi) analyses, opened new opportunities in rumen research. Cloning and sequencing provided community analyses that were not prone to the biases imposed by cultivation techniques, although different bias was introduced by other factors, like storage conditions , the differential efficiency of DNA extraction from different species and amplification bias [27–29]. Related techniques for microbiome analysis quickly followed (DGGE, TGGE, T-RFLP, ARISA). Quantitative PCR and FISH enabled microbial groups or species to be quantified . Now, metagenomic sequencing enables rapid community analysis to be carried out, without the cultivation bias or variation associated with primer selection or PCR amplification irregularities [25, 31]. The problem of DNA extraction remains, however, and databases are relatively weak where ruminal organisms are concerned . Nevertheless, if we can use this approach to determine how the functional activity of the rumen microbial community influences methane emissions, the knowledge should enable strategies to decrease the environmental impact of livestock agriculture. Furthermore, it might be expected to improve animal production efficiency.
Ruminal community analysis relating to methane emissions
There are two main routes for methanogenesis in the rumen, both carried out by archaea. The hydrogenotrophic pathway converts H2 and CO2 produced by the protozoa, bacteria and fungi to CH4 [3, 6]. It is usually assumed that formate, which can be used by all the most abundant ruminal archaea, is equivalent to H2 + CO2, so formate is included in the hydrogenotrophic category [21, 33]. A second category of substrate for methanogenesis is methyl groups, such as those present in methylamines and methanol [34, 35]. Methylamines are derived from glycine betaine (from beet) and choline (from plant membranes), while methanol is derived from the hydrolysis of methanolic side-groups in plant polysaccharides. The most common hydrogenotrophic archaea are from the genus Methanobrevibacter, which has been divided into two subgroups, one known as the SGMT clade (Mbb. smithii, Mbb. gottschalkii, Mbb. millerae and Mbb. thaueri), the other (RO) clade comprising principally Mbb. ruminantium and Mbb. olleyae [21, 36]. Other significant hydrogenotrophic genera include Methanosphaera, Methanimicrococcus and Methanobacterium. The less abundant methylotrophs (Methanosarcinales, Methanosphaera, Methanomassiliicoccaceae) can use methylamines and methanol, and there are archaea (Methanosarcinales) that produce methane via the aceticlastic pathway (reviewed in Morgavi et al. ). Rumen methanogenic archaeal diversity is restricted to four orders  and is highly conserved across 32 ruminant species collected worldwide .
Intuitively, archaea should be the microbial group most closely correlated with methane emissions. However, some studies have shown no such correlation with their overall abundance while in others the correlation has been weak. Morgavi et al. , Zhou et al. , Danielsson et al.  and Danielsson  found no correspondence between the numbers of methanogens and methane emissions from dairy cows when measured using metagenomics and qPCR techniques. Kittelmann et al.  and Shi et al.  formed a similar conclusion in sheep. A weak correlation between archaeal abundance relative to bacteria was found in beef steers  but none was found with dairy cows in the RuminOmics project [http://www.ruminomics.eu/] when expressed as the archaea:bacteria ratio (Fig. 1). Shi et al.  also observed that archaeal gene expression rather than gene abundance was correlated to methane emissions from individual sheep. It is easy to see why gene expression might be a useful proxy for methanogenesis in a static system like soil , but less so in a flowing system like the rumen, where for physiological reasons biomass must be directly correlated to gene abundance unless other processes, such as uncoupled CH4 production occur .
Archaea:bacteria relative abundance in relation to methane emissions, preliminary data from the 1000-cow RuminOmics project. Dairy cows on different farms throughout Europe received grass or maize silage:concentrate diets of similar nutrient composition. Feed intake was measured either directly or calculated from faecal long-chain hydrocarbons. Samples of rumen contents were removed by stomach tube and DNA was extracted by the Yu & Morrison method . Abundances were calculated from qPCR of 16S rRNA genes using universal primers for archaea and bacteria
Given the high variability of the relationship with overall archaeal abundance, it may be that the composition of the archaeal community rather than just its size may have greater significance with regard to methane emissions. Zhou et al. , Danielsson et al. , Shi et al.  and Danielsson  all found a positive correlation between the relative abundance of Methanobrevibacter SGMT clade and methane emissions. Danielsson  interpreted this correlation in terms of different affinities for H2 in the two groups, with the SGMT clade possessing methyl coenzyme M reductase isozymes McrI and McrII , which enables the archaea to utilise H2 at higher concentrations, against the RO clade that possess only McrI [3, 12]. The dynamics of the of the archaeal community composition and thus the efficiency of H2 utilization would in turn would be a consequence of differing H2 production by different bacteria [33, 41] and presumably also protozoal and fungal communities. Furthermore, the proportion of Methanosphaera spp. in total archaea was negatively associated with methane production in sheep , although not in beef cattle . Thus, differing methane emissions are at least partly due to varying relative abundances within the community of methanogenic archaea.
Other observations regarding the archaeal community, sometimes called the archaeome, include those of Pitta et al. , who found that archaeal abundance increased in steers suffering frothy bloat, and Pei et al. , who discovered archaea associated with the rumen epithelium. In the former case, the CH4 content of the gas was not measured, so it is unclear the impact the bloat would have on methanogenesis. In the latter, the finding was surprising because the rumen wall is considered to be an aerobic/anaerobic interface, and the relative abundance of O2 might be considered to suppress the growth of the extremely O2-sensitive methanogens. In fact, one might have possibly expected CH4 oxidisers to be present, in spite of their absence from the deep ruminal digesta .
Ruminal ciliates are intimately involved in methanogenesis, partly via their abundant H2 production  and, taking advantage of this, their associated methanogens, which are found both as intracytoplasmic commensals and on the exterior surface of the protozoa [3, 18, 51–53]. Several studies suggested a correlation between the abundance of protozoa and methane emissions (collated in [18, 54, 55]), while others do not [37, 43]. Guyader et al.  conducted a meta-analysis containing 28 experiments and 91 treatments. This meta-analysis showed a linear positive relationship between log10 protozoal numbers and methane emissions expressed per unit DMI. An r = 0.96 showed that there is indeed a reasonably strong relationship (Fig. 2).
Relationship between methane emission and rumen protozoa concentration in a meta-analysis of 28 different experiments. The black dashed line represents the average within-experiment relationship. Reproduced from  with permission
Defaunation (the removal of the ciliates from the rumen) has therefore been investigated in relation to methane production. Although in some cases the results of defaunation on CH4 emissions have not been encouraging [57–60], Newbold et al.  carried out a meta-analysis of defaunation studies and concluded that CH4 was decreased on average by 11%. Despite the lower CH4 production, the total archaeal abundance was not significantly decreased in the Newbold et al. meta-analysis, suggesting that the archaeal community in defaunated animals may have a lower CH4-emitting specific activity than that of the protozoa-associated community.
As with the archaea, the questions then revert to whether some individual protozoal genera or species, and their associated archaea, are more linked with methanogenesis than others. In general, the protozoa harbour an archaeal population that, like the general archaeal community, is dominated by Methanobrevibacter spp. [61–64], although differences were observed in the abundance of different archaea found in the protozoa and in the non-associated archaea [18, 61, 65] that might lead to different methanogenic specific activities in the two populations. Furthermore, archaeal colonisation abundance may differ between different protozoal species  and each may be associated with different predominant archaeal genera/species. Holotrichs in particular had an archaeal community that differed from entodiniomorphid protozoa . Larger ciliates appear to be more heavily colonized by methanogens than smaller ciliates [53, 66], and also by bacteria, suggesting that there is not a selective colonisation by archaea . The lower metabolic activity in terms of H2 production of the larger protozoal species per unit biomass [50, 54, 58] presumably explains that smaller protozoa, and their associated archaea, will be relatively more active in methanogenesis than larger species. Indeed, in vitro studies indicated that the smaller Entodinium spp. were more associated with methane production than larger species like Polyplastron multivesiculatum [50, 58]. In vivo studies are inconsistent, however. Refaunation experiments indicated that the abundance of Entodinium spp. [67, 68] or holotrichs  correlated with higher methane emissions. A large amplicon sequencing study in sheep nevertheless found no relationship between the relative abundance of different ciliates and methane emissions . Furthermore, ciliate communities fall into a small number of types (A, AB, B and O ) depending on interactions, principally inter-species predation. Despite the large differences in relative abundance of different protozoa types in the different community types, methane emissions could not be correlated with protozoal community structure . The varying colonisation by archaea depending on the time after feeding  is another confounding factor in trying to evaluate the role of protozoa in methanogenesis.
Ruminal bacteria form the most diverse group within the rumen, capable of utilizing fibre, starch, protein and sugars . Among numerous bacterial phyla found in different studies, Firmicutes, Bacteroidetes and Proteobacteria are the most abundant . Fibrolytic bacteria, especially cellulolytic Ruminococcus and several Eubacterium spp (Firmicutes), are well studied H2 producers. On the other hand, the prominent cellulolytic genus, Fibrobacter, does not produce H2, while Bacteroidetes are net H2 utilizers . Microbiome analysis has identified three different ‘ruminotypes’ that seemed to be associated with variations in methane production by sheep . The low-CH4 production ruminotype Q was characterised by high relative abundances of the propionate-producing Quinella ovalis. Low-CH4 ruminotype S had higher abundances of lactate- and succinate-producing Fibrobacter spp., Kandleria vitulina, Olsenella spp., Prevotella bryantii, and Sharpea azabuensis. The high-CH4 production ruminotype H had higher relative abundances of species belonging to Ruminococcus, other Ruminococcaceae, Lachnospiraceae, Catabacteriaceae, Coprococcus, other Clostridiales, Prevotella, other Bacteroidales, and Alphaproteobacteria. The overall interpretation would be that methane emissions depend on the abundance of the H2-producing bacteria present a corollary to this is the observation that chemical inhibition of methanogenesis in goats led to increases in the abundance of H2-consuming Prevotella and Selenomonas spp. . Proteobacteria were 4-fold less abundant (2.7 vs. 11.2% of bacteria) in high emitting beef cattle  and a similar finding was made in dairy cows . The dominant family among Proteobacteria was Succinivibrionaceae. This finding seems to parallel the high numbers of Succinivibrionaceae in the Tammar wallaby , which, like the ruminant, is a herbivorous foregut fermenter. It produces only about one-fifth of the methane per unit of feed intake of ruminants, which is attributed to the large community of Succinovibrionaceae. An intriguing additional observation common to these studies [40, 41] was that within different Prevotella OTUs, some were correlated with a high CH4 phenotype, while others were associated with low emissions. The different OTUs seem to cluster together (Fig. 3), suggesting functional versatility within the Prevotella genus. Further investigation of the phenotypes of these dominant ruminal bacteria is needed, which may well provide clues for future exploitation, particularly as some Prevotella are reported to produce formate .
Neighbor Joining tree of Prevotella-like OTUs that had a negative (blue dots) or positive (red dots) relation to methane (expressed in terms of g methane/kg DMI) in the 1,000-cow RuminOmics project. Multiple alignment was done using MUSCLE . The Neighbor Joining tree was constructed using p-distance and pairwise-deletion parameters. The tree was resampled 1,000 times and bootstrap values are indicated. The linearized tree was computed using MEGA v5.1  by using most abundant Bacteroidales OTUs to create an “outgroup”
In a dairy cattle study  with two CH4-mitigating feed additives, grapemarc and a combination of lipids and tannins, it was found that the microbiome differed from the control diet in a similar way. Faecalibacterium prausnitzii was over-represented in the low- CH4 diets, and other microbiome markers that could be predictive of low-CH4 phenotypes were identified. F. prausnitzii is a bacterial species that is abundant in the human colon  but is seldom mentioned in the context of the rumen. It may prove a useful marker, but it is not obvious how its properties could be mechanistically connected to the low-CH4 phenotype.
The anaerobic fungi, like the protozoa, produce abundant amounts of H2, along with CO2, formate and acetate as metabolic end products . Six fungal genera have been detected in the rumen but recent molecular research suggests existence of several new taxa , with functions still to be understood. Methanogens are found in close association with fungal hyphae . Although there is reason to suppose that fungal abundance might be related to methane emissions, reports are few. Kittelmann et al.  noted no difference in fungal community structure in relation to methane emissions from sheep. In the RuminOmics project, however, preliminary results suggest that two fungal species, Caecomyces communis and Neocallimastix frontalis, are negatively related to methanogenesis (r = -0.50 and -0.45, P < 0.001 R.J. Wallace et al., unpublished]. The meta-analysis of Newbold et al.  noted that one of largest effects of defaunation, which leads to lower CH4 production, was a decrease in fungal abundance. Whether this decrease is a major or direct cause of lower CH4 production in defaunated animals is unclear.
General considerations on variations in methanogenesis and the microbiome
Contribution of non-hydrogenotrophic methanogenesis
The main substrates for methanogenesis in the rumen are known to be H2 + CO2, formate and compounds containing methyl groups like the methylamines and methanol . In the reviews already mentioned here, formate and H2 + CO2 are usually considered to be equivalent as substrates for methanogenesis and formate is not treated separately. Formate feeds directly into the methanogenesis pathway at the very beginning via formate dehydrogenase . Hungate et al.  estimated that 18% of methane was formed via formate rather than H2 + CO2. Yet there are some important aspects of formate metabolism about which our understanding is incomplete. The relationship between bacterial abundances from microbiome estimates, above, was discussed in relation to whether bacteria form H2, as in other analyses [33, 41, 43, 46], with little indication about formate producers. There is a large uncertainty about bacterial formate production, reflected in the summary tables of Stewart et al. . Although many species produce some formate, precise amounts are not known and therefore the importance of this production is difficult to estimate. Perhaps the Hungate 1000 collection (www.rmgnetwork.org/hungate1000.html) could be used as a resource to make such measurements. At present, the Hungate 1000 project has its emphasis on strengthening genetic databases , but much phenotypic information is being collected alongside the main thrust of the project. Assessing bacterial formate production is further complicated by the knowledge that co-culture experiments demonstrate that the metabolism of some bacteria and fungi grown in the presence of methanogens can be pulled in the direction of H2 or formate production [82–85], so it is very difficult to be sure what the role of different species might be in the mixed rumen community. And perhaps most crucially, methanogenesis is not the sole fate of formate in the rumen. Hungate et al.  noted formate utilisation in the absence of methanogenesis, presumably by bacteria. Species like Wolinella succinogenes use formate as an energy source . So, although it is usually stated that ruminal archaea utilise either H2 + CO2 or formate , it is unclear whether they are indeed equivalent for different archaea. For example, in co-cultures between rumen anaerobic fungi and three methanogens, all the methanogens used H2 but formate was only utilised simultaneously by M. smithii . The differential expression of formate dehydrogenase was one of the largest differences between high- and low-emitting sheep . The formate dehydrogenase of M. ruminantium M1 was induced by co-culture with the formate-producing Butyrivibrio proteoclasticus . Thus there are several reasons to conclude that thinking about formate as a substrate in the context of microbiomes differing in their methanogenic activity might prove fruitful. Furthermore, despite the emphasis on H2 produced by ciliate protozoa, the quantity of formate produced seems to be many times greater than H2 .
The methylamines and methanol are methyl donors for methanogenesis by methylotrophic archaea, as described above. Their contribution to methanogenesis will depend to some extent on the concentration of methylamines in the diet [34, 35]. But how efficient is the process? Are methylamines converted quantitatively to CH4, and are methylamine, dimethylamine and trimethylamine equivalent in that respect? It is possible that variation in CH4 emissions between individual animals on some diets may be due to different efficiencies whereby methylamines are released from feed materials and converted to CH4.
One of the more surprising findings in the Mbb. ruminantium M1 genome was the presence of three genes encoding alcohol dehydrogenase . It has been demonstrated that ethanol can be used as a C source, but not as sole C source . Thus, the availability of ethanol from bacterial fermentation may influence the dependence of archaea on methanogenesis for ATP production, and therefore affect the quantity of CH4 produced.
Influence of diet and mitigation measures
An important principle underlying this review is that some microbiomes lead to different CH4 emissions when other factors remain constant. Thus, key members of the microbiome leading to high or low emissions should be able to be identified. In the RuminOmics project, all dairy cows received diets that were as nutritionally similar as was possible given the different locations. Only by keeping as many other factors as possible unchanged will it be possible to dissect the role of different members of the microbial community in determining low- and high-emitting individuals. It should be noted here that we have chosen to express CH4 production in terms of DMI, for the simple reason that it makes it easier to identify a low-CH4 microbiome rather than a microbiome that forms less CH4 only because the host animal eats less.
The results of microbiome analysis so far were expected in some respects, in the sense that diets high in starch content are known to lead to lower methane emissions, because starch utilising bacteria tend to produce less H2 than others, for example [33, 72]. In a similar way, the changed fermentation stoichiometry linked with methane emissions is a very long established observation [87, 88]. New questions have been highlighted regarding different species associated with high and low CH4 emissions under similar conditions. Unexpected correlations have been found. But many questions remain. It is also worth noting that widely different taxa may have similar metabolic activities , so there are several different microbiota that could lead to similar metabolic properties.
Mitigation measures have been described comprehensively elsewhere [2, 3, 6–10]. Perhaps the most promising of these is 3-nitrooxypropanol, a molecule obtained rationally by its structural similarity to methyl-CoM [90–92]. As yet we do not know the full implications of 3-nitrooxypropanol, but encouragement can be obtained that the concern that H2 accumulation might inhibit overall fermentation does not seem to be such a problem as was suggested by some in vitro experiments [33, 93]. It is also worth noting that a 50% reduction in the growth rate of methanogens would be sufficient to cause their washout from the rumen [3, 33]. Complete inhibition of growth is therefore not necessary.
Methane and feed efficiency
CH4 production and feed efficiency are linked, in the sense that a low feed efficiency, expressed as residual feed intake (RFI), is accompanied by lower CH4 production [94–96]. The reverse does not apply, however, as has been found in dairy cows in the RuminOmics project. The findings that the abundance of certain Prevotella changes according to feed efficiency in beef cattle [97, 98] and many other taxa change in abundance  further emphasises our need to understand the role of Prevotella and its different biotypes on ruminal fermentation and methanogenesis. Shabat et al.  discovered that Megasphaera elsdenii was more abundant in low-efficiency cows, as were genes of the acrylate pathway, used by M. elsdenii in propionate formation. The explanation for lower efficiency was that M. elsdenii introduced a type of futile cycle in the production and subsequent utilisation of lactate, an energetically inefficient process.
The influence of the host animal
Many researchers believe, and some studies are beginning to show, that the host animal exerts a controlling effect on its own gut microbiota [100–102]. The mechanism could conceivably be at a molecular level, perhaps via complex interactions with receptors in the rumen wall [103, 104] or antibodies in saliva [3, 105, 106]. More likely, however, is that the physical structure and dynamics of gut digesta are different in different animals. Goopy et al  found that lower methanogenesis in sheep was heritable and accompanied by the animals’ having smaller rumen volumes and therefore altered fluxes of nutrients through the tract. This would have the effect that less feed would be fermented in the rumen, leading to lower methanogenesis. Variations in saliva production could lead to a similar result . Both would likely influence the ruminal microbiome. Therefore, caution should be exercised in interpreting microbiome analyses – the changed microbiome may be associated with, but not cause, a decrease in methanogenesis.
Ross et al.  found good correlations between CH4 emissions and the broad characteristics of the microbiome. Now, metagenomics has shown that the abundance of certain groups of microbial genes can be highly predictive of CH4 emissions [46, 109] and feed efficiency . For example, 20 microbial genes explained 81% of variation in CH4 emissions from beef cattle, while 49 genes explained 86% of variation in RFI . Furthermore, the animal’s genetic background was a factor in determining these gene abundances . This is the early phase of what is sure to be a fertile area in which animal-microbiome-emissions can be delineated by metagenomics profiling, and animal breeding based on these gene abundances may lead to animals with lower CH4 emissions.
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Mooooove Over, Cows! Kangaroo Farts Warm the Earth, Too
Since the 1970s, it has been suggested that kangaroos don't fart — or rather, the (ahem!) gas they emit contains very little, if any, methane. But now, new research suggests this isn’t true.
Methane is naturally created by bacteria in an animal's gut. Kangaroos, cows and many other plant eaters use these bacteria to help them digest grass and leaves. In the 1970s and 1980s, research suggested that kangaroos don't produce much methane, which made scientists think they might have special low-methane-emitting bacteria living in their guts.
"The idea that kangaroos have unique gut microbes has been floating around for some time and a great deal of research has gone into discovering these apparently unique microbes," said study co-author Adam Munn, a professor in the School of Biological Sciences at the University of Wollongong in Australia. [See how animal farts impact global warming (infographic)]
The new findings, however, suggest that kangaroos actually produce about the same amount of methane as other animals of their size. Kangaroos do emit lower levels of methane than some animals, such as cows, but the marsupials are roughly on the same level as horses, the researchers said. This means kangaroos likely don't have special bacteria, after all.
One of the reasons this research is important is because understanding methane could help mitigate the effects of climate change, according to Alex Hristov, a professor of animal nutrition and diet at Pennsylvania State University.
Methane is a greenhouse gas that comes from natural sources, such as decomposing organic matter and human activities, ranging from farm animals (and the manure they produce) to oil and gas operations. Methane is less abundant in the atmosphere than carbon dioxide, but it is more effective at trapping heat (infrared radiation).
"It has a global-warming potential [about] 25 times — depends on how you look at it — that of carbon dioxide. So it's an important greenhouse gas," Hristov told Live Science. And while carbon dioxide is still the most abundant greenhouse gas produced by humans, methane emissions should not be ignored, he added.
Cows can produce up to 200 liters of methane every day and there are an estimated 1.4 billion of them in the world, so figuring out a way to reduce those emissions could potentially help address some climate-change concerns.
In the past, scientists have tried to introduce bacteria from kangaroos into cows, in hopes of reducing methane emissions from cows. In 2004 in the United States, manure and expelled body gas from livestock (predominantly cows and pigs) contributed more than 13 millions tons of methane, according to a 2014 study published in the Journal of Geophysical Research: Atmospheres. To put that figure into context, oil and gas operations contributed 7 million tons of methane.
This kind of research could also be important to farmers, Munn said. When the bacteria break down food into methane, they’re essentially robbing the cow of some of the food's nutrients. If farmers could somehow reduce methane emissions from livestock, more nutrients would go to the cow itself, which could help them grow better.
For the new study, the scientists put 10 kangaroos inside individual sealed rooms at the University of New South Wales' Fowlers Gap Research Station and fed them food. The rooms were set up so that the scientists could measure what gases were emitted in the air. The researchers also collected the animals’ poop to measure how many nutrients were left behind, and experimented with giving the animals different amounts of food.
It may still be the case that kangaroo guts actually do hold special secrets, the researchers said. How the marsupials maintain their bacterial garden, for instance, may work differently than other plant eaters.
"What we've done here is to really show that kangaroos probably don’t have a unique microbiome," Munn said, "it''s simply that that biome interacts with the food in a different way." The next steps would be to compare these results to those of other animals, he added.
This research was published online yesterday (Nov. 4) in the Journal of Experimental Biology.
Watch the video: Νέα ανατριχίλα στην Ευρώπη από τη διακοπή ρώσικου φυσικού αερίου (August 2022).
- Primordial or ancient sources of hydrocarbons or carbon in Earth