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 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.
[edit] Microbial biomarkers

Extremophile organisms living within the crust (deep heat-loving bacteria thermophiles) are considered a plausible source of biomarkers which are not sourced from kerogen.

Hopanoids, called the "most abundant natural products on Earth", were believed to be indicators of oil derived from ferns and lichens but are now known to be created by many bacteria, including archaea.

Sterane was thought to have come from processes involving surface deposits but is now known to be produced by several prokaryotes including methanotrophic proteobacteria.

The case for shallow bacterial life creating petroleum is apparent from circumstantial evidence at "tar seeps" in sandstone outcrops where live oil is encountered down-dip (e.g. Midway-Sunset field, San Joaquin Valley, California). Bacteria are considered to have "degraded" higher gravity oil to bitumens.

Extrapolation of bacterial degradation to still higher gravity oils and finally to methane leads to the suggestion that all petroleum up to tar and most of the carbon in coal are derivatives of methane, which is progressively stripped of its hydrogen by bacteria and archaea. The resultant partial methane molecules, CH3, CH2, CH, may be called "an-hydrides". Anhydride hypothesis, a New Theory of Petroleum and Coal Generation, is offered by C. Warren Hunt (1999).[citation needed]

Due to the difficulty in culturing and sampling thermophilic bacteria little was known of their chemistry. As more is learned of bacterial chemistry, more biomarker chemicals can be attributed to bacterial sources. Although extremophile micro-organisms exist deep underground and some metabolize carbon, some of these biomarkers are so far only known from surface plants and remain the most reliable chemical evidence of biogenic genesis of petroleum.

This evidence is consistent with the biogenic hypothesis, although it might be true that these hydrocarbons have merely been in contact with ancient plant residues. There also is evidence that low-temperature relatives of hyperthermophiles are widespread, so it is also possible for biological deposits to have been altered by low-temperature bacteria which are similar to deeper heat-loving relatives.

It must also be acknowledged that, if extremophilic bacteria prove to be the source of some parts of known oils, that this remains a biological process.

Thorough rebuttal of biogenic origins based on biomarkers has been offered by Kenney, et al. (2001).[10]
[edit] Isotopic evidence

Methane is ubiquitous in crustal fluid and gas [3]. 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. δ13C of methane overlaps that of inorganic carbonate and graphite in the crust, which are heavily depleted in 12C, 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.[33]

Commercially extractable concentrations of helium (greater than 0.3%) are present in natural gas from the Panhandle-Hugoton fields in the USA, as well as from some Algerian and Russian gas fields.[citation needed]

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.[34][35]

The Chimaera gas seep, near Antalya (SW Turkey), new and thorough molecular and isotopic analyses including methane (~87% v/v; D13C1 from -7.9 to -12.3 ‰; D13D1 from -119 to -124 ‰), light alkanes (C2+C3+C4+C5 = 0.5%; C6+: 0.07%; D13C2 from -24.2 to -26.5 ‰; D13C3 from -25.5 to -27 ‰), hydrogen (7.5 to 11 %), carbon dioxide (0.01-0.07%; D13CCO2: -15 ‰), helium (~80 ppmv; R/Ra: 0.41) and nitrogen (2-4.9%; D15N from -2 to -2.8 ‰) converge to indicate that the seep releases a mixture of organic thermogenic gas, related to mature Type III kerogen occurring in Paleozoic and Mesozoic organic rich sedimentary rocks, and abiogenic gas produced by low temperature serpentinization in the Tekirova ophiolitic unit.[36] [1]
[edit] Biomarker chemicals

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.

The presence of these chemicals in crude oil is assumed to be as a result of the inclusion of biological material in the oil. This is predicated upon the theory that these chemicals are released by kerogen during the production of hydrocarbon oils.

However, since the advent of abiogenic hypothesis, the veracity of these assumptions has been called into question and new lines of evidence used to provide alternative explanations. Some are provided by many scientists from around the world including Russia.
[edit] Trace metals

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. These metals are common in Earth's mantle, thus their compounds in oils are often called as abiomarkers.[citation needed]

Analysis of 22 trace elements in 77 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.[23]
[edit] Reduced carbon

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.[25] However, several processes which generate hydrogen could supply kerogen hydrogenation which is compatible with conventional petroleum generation theories.[37]

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 has however been demonstrated later to be a misunderstanding by Robinson, related to the fact that only short duration experiments were available to him. Olefins are thermally very unstable (that 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.

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 represent concentrates of such materials, no theoretical problem exists anymore. Furthermore, the millions of source rock samples that have been analyzed for petroleum yield by the petroleum industry have eliminated any pre-existing doubt about the enormous quantities of petroleum generated in sedimentary basins by thermal cracking of kerogen.