HYDROTHERMAL VENT ALKANOTROPHS USING MECHANISMS AND ENZYMES SIMILAR TO SURFACE WATER BACTERIA FOR ALKANE METABOLISM

Alkanes are a class of saturated hydrocarbon (carbon and hydrogen containing) compounds.  The simplest, possible alkane, with which most of us are familiar, is methane (CH₄). They are key energy source for various human activities as they are a major component of petroleum and natural gas. They are toxic to some organisms whereas source of energy and carbon for others. In nature, alkanes originate from various biological, especially microbial, as well as geochemical activities. Nevertheless, major source is through microbial activities. Thus, understanding microbial transformations of alkanes is very important. The bacteria that use hydrocarbons as their sole source of carbon and energy are called “Hydrocarbonoclastic bacteria”. Oxidation of alkanes involves breaking of a strong non-polar C-H bond, which is chemically very difficult. In marine bacteria, eight different families of enzymes employed in aerobic alkane oxidation, have been identified. These include monooxygenases, hydroxylases, cytochrome P450 (CYPs) and others.

High to moderate amounts of hydrocarbons, including n-alkanes are found in hydrothermal vent fluids. Hydrothermal vent fluids are usually highly reducing and anoxic, which are mixed with colder oxygenated waters of depths, forming thermal and redox gradients. Microbes exploit these gradients and support complex vent ecosystems. For example, there is experimental evidence for microbial oxidation of methane and other short-chain alkanes – playing critical role in supporting higher trophic levels in the vent ecosystem. Similarly, anaerobic oxidation of methane in vent sediments is critical in carbon cycling. Microbes that oxidize long chain alkanes have also been isolated from plume waters and vent sediments. Nevertheless, little is known about the diversity and ecological role of long chain-alkane oxidizers of hydrothermal vents. There is also industrial potential for finding powerful enzymes from vent microbes that can transform alkanes into other organics in more efficient ways.

This study explores reaction mechanisms of alkane metabolism in six different bacteria isolated from deep sea vents. Norcarane (a mid-chain alkane) was used to culture the tested strains of bacteria. It is called as “diagnostic substrate” because its enzymatic oxidation produces distinct profile depending upon the enzyme which has been used.

This study confirms presence of medium-chain alkane oxidizing mesophilic bacteria among hydrothermal vents. Alkane oxidation may be a key component of microbial metabolism in this extreme environment. The enzymes involved in this are AlkB like hydroxylase and CYPs, both of

which are thought to be involved in hydroxylation of medium-chain alkanes in surface waters.  Thus, mechanisms for medium-chain alkane oxidation are similar among hydrothermal vents, surface waters and other environments. 

Interestingly, there is a redundancy among different classes of alkane-oxidizing enzymes; rendered by having more than one enzyme for oxidizing same sort of alkane. Some bacteria express only one kind of enzyme but they still possess multiple genes for its isozymes whereas others have multiple types of enzymes (e.g. CYPs & AlkBs) employed in the same job and expressed simultaneously. Metal availability and subcellular enzyme localization could be the explanations for such redundancies.

This study found two different enzymes (CYPs & AlkBs) potentially doing same task, where only one strain expressed CYPs and others expressed AlkB-like hydroxylases. Both are iron-containing metalloenzymes and as the strains are from hydrothermal vent – an iron-rich environment; metal availability is unlikely to be a factor. Slightly different substrate ranges could be a cause for coexistence of these enzymes. 

In my opinion, in an evolutionary perspective, this redundancy or having more than one enzyme for doing the same task may characterize acclimatory abilities of an organism to different environmental conditions such as different temperature and salinity regimes, resource availability (e.g. metal availability). Gene-knock out experiments could resolve the question of redundancy where under certain conditions; all the isozymes of an enzyme may be knocked-out to see if desired reaction can be catalysed by that particular enzyme under those certain condition!

In summary, this is the first study to investigate mechanisms of medium- to long-chain alkane oxidation and metalloenzymes involved in it by aerobic vent bacteria. Although being from an extreme environment, vent bacteria do not seem to have novel alkane oxidising mechanisms; but express enzymes, functionally similar to bacteria from other environments. It is intriguing to see that extreme environment has not prompted its resident microbes to do things differently, at least alkane oxidation.

Bertrand, E. M., Keddis, R., Groves, J. T., Vetriani, C. & Austin, R. N. (2013). Identity and mechanisms of alkane-oxidizing metalloenzymes from deep-sea hydrothermal vents. Frontiers in Microbiology, 4 (109), 1-11.