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5.9F: Anoxic Hydrocarbon Oxidation - Biology


Anoxic hydrocarbon oxidation can be used to degrade toxic hydrocarbons, such as crude oil, in anaerobic environments.

Learning Objectives

  • Describe the process of anoxic hydrocarbon oxidation in regards to marine environments

Key Points

  • Hydrocarbons are organic compounds consisting entirely of hydrogen and carbon.
  • The majority of hydrocarbons occur naturally in crude oil, where decomposed organic matter provides an abundance of carbon and hydrogen. The combustion of hydrocarbons is the primary energy source for current civilizations.
  • Anaerobic oxidation of methane (AOM) is a microbial process that occurs in anoxic marine sediments. AOM is considered to be a very important process, reducing the emission of methane (a greenhouse gas) from the ocean into the atmosphere by up to 90%.

Key Terms

  • methanotrophic: The ability to metabolize methane as an only source of carbon and energy.
  • syntrophic: When one species lives off the products of another species.
  • anoxic: Lacking oxygen.

Hydrocarbons are organic compounds consisting entirely of hydrogen and carbon. The majority of hydrocarbons occur naturally in crude oil, where decomposed organic matter provides an abundance of carbon and hydrogen. The combustion of hydrocarbons is the primary energy source for current civilizations.

Crude oil contains aromatic compounds that are toxic to most forms of life. Their release into the environment by human spills and natural seepages can have detrimental effects. Marine environments are especially vulnerable. Despite its toxicity, a considerable fraction of crude oil entering marine systems is eliminated by the hydrocarbon-degrading activities of microbial communities. Although it was once thought that hydrocarbon compounds could only be degraded in the presence of oxygen, the discovery of anaerobic hydrocarbon-degrading bacteria and pathways show that the anaerobic degradation of hydrocarbons occurs naturally.

The facultative denitrifying proteobacteria Aromatoleum aromaticum strain EbN1 was the first to be determined as an anaerobic hydrocarbon degrader, using toluene or ethylbenzene as substrates. Some sulfate-reducing bacteria can reduce hydrocarbons such as benzene, toluene, ethylbenzene, and xylene, and have been used to clean up contaminated soils. The genome of the iron-reducing and hydrocarbon degrading species Geobacter metallireducens was recently determined.

Anaerobic oxidation of methane (AOM) is a microbial process that occurs in anoxic marine sediments. During this process, the hydrocarbon methane is oxidized with sulfate as the terminal electron acceptor: CH4 + SO42- → HCO3- + HS + H2O. It is believed that AOM is mediated by a syntrophic aggregation of methanotrophic archaea and sulfate-reducing bacteria, although the exact mechanisms of this syntrophic relationship are still poorly understood. AOM is considered to be a very important process in reducing the emission of methane (a greenhouse gas) from the ocean into the atmosphere. It is estimated that almost 90% of all the methane that arises from marine sediments is oxidized anaerobically by this process. Recent investigations have shown that some syntrophic pairings are able to oxidize methane with nitrate instead of sulfate.


5.9F: Anoxic Hydrocarbon Oxidation - Biology

We know that ozone is photolyzed by light with a wavelength of 330 nm or less to make oxygen molecule and oxygen atom. Nitrogen oxides also produce oxygen atom upon photolysis.

In the stratosphere, oxygen atom most often reacts with molecular oxygen to regenerate ozone. The troposphere, unlike the stratosphere, contains considerable concentrations of water vapor and water reacts faster with O than does O2.

The product, OH, is a very reactive molecule. In the daytime when photolysis is possible, it is always present in a very small but constant concentration in air. Draw the Lewis structure. Does this tell you why it is so reactive?

Oxidation of Hydrocarbon

Hydrocarbons are released continually from living things or through the decomposition of living things on Earth. Only methane has a high enough concentration to be listed in the chart of molecules in the atmosphere. Why is that?

All hydrocarbons react in air to form carbon monoxide and then carbon dioxide through a series of reactions. The first step is always the reaction between the hydrocarbon and hydroxyl radical. With alkanes, the hydroxyl radical abstracts a hydrogen atom and forms a carbon-centered radical.

Because an O-H bond is stronger than a C-H, this step is exothermic.

With alkenes and alkynes, the electron-deficient hydroxyl radical adds to the multiple bond.

The carbon-centered radical then reacts with molecular oxygen. There are many steps after this that, ultimately, gives carbon dioxide and water.

Enthalpy of Combustion

The reactions that produce carbon and dioxide and water from hydrocarbons in the atmosphere release the same amount of energy as the combustion of those hydrocarbons. We can measure the enthalpy of combustion by burning the hydrocarbons in a calorimeter. This enthalpy can also be calculated using Hf values.

Let's consider the combustion (or air oxidation) of ethane. How much heat is released by transforming 1 mol of ethane to carbon dioxide and water? The first step is to show the balanced equation for the reaction of 1 equivalent of ethane.

Next we consult a table of enthalpy of formation values.

Using those values, we compute the enthalpy of the reaction. Because the enthalpy is a thermodynamic state function, it doesn't depend on the pathway. The combustion of ethane in a boiler and the air oxidation of ethane must release the same amount of energy because they reactions start from the same molecules and finish with the same molecules.


Abstract

The biodegradation of two crude oils by microorganisms from an anoxic aquifer previously contaminated by natural gas condensate was examined under methanogenic and sulfate-reducing conditions. Artificially weathered Alaska North Slope crude oil greatly stimulated both methanogenesis and sulfate reduction. Gas chromatographic analysis revealed the entire n-alkane fraction of this oil (C13−C34) was consumed under both conditions. Naphthalene, 2-methylnaphthalene, and 2-ethylnaphthalene were also biodegraded but only in the presence of sulfate. Alba crude oil, which is naturally depleted in n-alkanes, resulted in a relatively modest stimulation of methanogenesis and sulfate reduction. Polycyclic aromatic hydrocarbon biodegradation was similar to that found for the Alaska North Slope crude oil, but a broader range of compounds was metabolized, including 2,6-dimethylnaphthalene and 2,7-dimethylnaphthalene in the presence of sulfate. These results indicate that n-alkanes are relatively labile, and their biodegradation in terrestrial environments is not necessarily limited by electron acceptor availability. Polycyclic aromatic hydrocarbons are relatively more recalcitrant, and the biodegradation of these substrates appeared to be sulfate-dependent and homologue-specific. This information should be useful for assessing the limits of in situ crude oil biodegradation in terrestrial environments and for making decisions regarding risk-based corrective actions.

Current address: AstraZeneca R&D Lund, S-221 87 Lund, Sweden.

ExxonMobil Research and Engineering Co.

Corresponding author phone: (405)325-5761 fax: (405)325-7541 e-mail: [email protected]


Examples of hydrocarbon in the following topics:

Anoxic Hydrocarbon Oxidation

  • Anoxic hydrocarbon oxidation can be used to degrade toxic hydrocarbons, such as crude oil, in anaerobic environments.
  • Hydrocarbons are organic compounds consisting entirely of hydrogen and carbon.
  • The combustion of hydrocarbons is the primary energy source for current civilizations.
  • Although it was once thought that hydrocarbon compounds could only be degraded in the presence of oxygen, the discovery of anaerobic hydrocarbon-degrading bacteria and pathways show that the anaerobic degradation of hydrocarbons occurs naturally.
  • Microbes may be used to degrade toxic hydrocarbons in anaerobic environments.

Aerobic Hydrocarbon Oxidation

  • Microbes can utilize hydrocarbons via a stepwise oxidation of a hydrocarbon by oxygen produces water and, successively, an alcohol, an aldehyde or a ketone, a carboxylic acid, and then a peroxide.
  • Note the presence of oxygen, thus defining this as aerobic hydrocarbon oxidation.
  • There are examples of anaerobic hydrocarbon oxidation, which will not be discussed here.
  • Biosurfactants enhance the emulsification of hydrocarbons, have the potential to solubilize hydrocarbon contaminants, and increase their availability for microbial degradation.
  • Discuss the advantages of organisms that can undergo aerobic hydrocarbon oxidation

Polycyclic Aromatic Hydrocarbons

  • It can degrade high molecular mass polycyclic aromatic hydrocarbons of 4 and 5 rings.
  • Polycyclic aromatic hydrocarbons (PAHs), also known as poly-aromatic hydrocarbons or polynuclear aromatic hydrocarbons, are seen in .
  • It can degrade high molecular mass polycyclic aromatic hydrocarbons of 4 and 5 rings.
  • An image showing three examples of polycyclic aromatic hydrocarbons.
  • Recognize various sources of polycyclic aromatic hydrocarbons and means of removal (bio-, phy

Industrial Microorganisms

  • Corynebacterium can also be used in steroid conversion and in the degradation of hydrocarbons.
  • Degradation of hydrocarbons is key in the breakdown and elimination of environmental toxins.
  • Items such as plastics and oils are hydrocarbons the use of microorganisms which exhibit the ability to breakdown these compounds is critical for environmental protection .

Endophytes and Plants

  • Inoculating crop plants with certain endophytes may provide increased disease or parasite resistance while others may possess metabolic processes that convert cellulose and other carbon sources into "myco-diesel" hydrocarbons and hydrocarbon derivatives.

Petroleum Biodegradation

  • Some microorganisms produce enzymes that can degrade a variety of chemical compounds, including hydrocarbons like oil.
  • Aside from hydrocarbons, crude oil contains additional toxic compounds, such as pyridine.

The Degradation of Synthetic Chemicals in Soils and Water

  • Examples of such contaminants are polychlorinated biphenyls (PCBs), polyaromatic hydrocarbons (PAHs), chloroethenes, and pharmaceutical substances.
  • Hydrocarbons and their derivatives were long believed to be degraded only in the presence of oxygen.

Cold-Seep Ecosystems

  • A cold seep is an area of the ocean floor where hydrogen sulfide, methane, and other hydrocarbon-rich fluid seepage occurs.
  • A cold seep (sometimes called a cold vent) is an area of the ocean floor where hydrogen sulfide, methane, and other hydrocarbon-rich fluid seepage occurs, often in the form of a brine pool.

Iron Oxidation

  • G. metallireducens) can use toxic hydrocarbons such as toluene as a carbon source, there is significant interest in using these organisms as bioremediation agents in ferric iron-rich contaminated aquifers .

Carotenoids and Phycobilins

  • Carotenoids generally cannot be manufactured by species in the animal kingdom so animals obtain carotenoids in their diets, and may employ them in various ways in metabolism.There are over 600 known carotenoids they are split into two classes, xanthophylls (which contain oxygen) and carotenes (which are purely hydrocarbons, and contain no oxygen).
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Methanogenesis

Methanogenesis is a form of anaerobic respiration that uses carbon as a electron acceptor and results in the production of methane.

Learning Objectives

Recognize the characteristics associated with methanogenesis

Key Takeaways

Key Points

  • Carbon dioxide or acetic acid are the most commonly used electron acceptor in methanogenesis.
  • Microbes capable of producing methane are called methanogens. They have been identified only from the domain Archaea – a group that is phylogenetically distinct from eukaryotes and bacteria.
  • The production of methane is an important and widespread form of microbial metabolism. In most environments, it is the final step in the decomposition of biomass.
  • Methane is a major greenhouse gas. The average cow emits around 250 liters of methane a day as a result of the breakdown of cellulose by methanogens. Therefore, the large scale raising of cattle for meat is a considerable contributor to global warming.

Key Terms

  • methanethiol: A colourless gas, a thiol with a smell like rotten cabbage, found naturally in plants and animals.
  • cofactor: A substance, especially a coenzyme or a metal, that must be present for an enzyme to function.
  • fermentation: Any of many anaerobic biochemical reactions in which an enzyme (or several enzymes produced by a microorganism) catalyses the conversion of one substance into another especially the conversion (using yeast) of sugars to alcohol or acetic acid with the evolution of carbon dioxide.

Methanogenesis, or biomethanation, is a form of anaerobic respiration that uses carbon as the terminal electron acceptor, resulting in the production of methane. The carbon is sourced from a small number of low molecular weight organic compounds, such as carbon dioxide, acetic acid, formic acid (formate), methanol, methylamines, dimethyl sulfide, and methanethiol. The two best described pathways of methanogenesis use carbon dioxide or acetic acid as the terminal electron acceptor:

Methanogenesis of acetate: Acetate is broken down to methane by methanogenesis, a type of anaerobic respiration.

The biochemistry of methanogenesis is relatively complex. It involves the coenzymes and cofactors F420, coenzyme B, coenzyme M, methanofuran, and methanopterin.

Microbes capable of producing methane are called methanogens. They have been identified only from the domain Archaea – a group that is phylogenetically distinct from eukaryotes and bacteria – though many live in close association with anaerobic bacteria. The production of methane is an important and widespread form of microbial metabolism, and in most environments, it is the final step in the decomposition of biomass.

During the decay process, electron acceptors (such as oxygen, ferric iron, sulfate, and nitrate) become depleted, while hydrogen (H2), carbon dioxide, and light organics produced by fermentation accumulate. During advanced stages of organic decay, all electron acceptors become depleted except carbon dioxide, which is a product of most catabolic processes. It is not depleted like other potential electron acceptors.

Only methanogenesis and fermentation can occur in the absence of electron acceptors other than carbon. Fermentation only allows the breakdown of larger organic compounds, and produces small organic compounds. Methanogenesis effectively removes the semi-final products of decay: hydrogen, small organics, and carbon dioxide. Without methanogenesis, a great deal of carbon (in the form of fermentation products) would accumulate in anaerobic environments.

Methanogenesis also occurs in the guts of humans and other animals, especially ruminants. In the rumen, anaerobic organisms, including methanogens, digest cellulose into forms usable by the animal. Without these microorganisms, animals such as cattle would not be able to consume grass. The useful products of methanogenesis are absorbed by the gut. Methane is released from the animal mainly by belching (eructation). The average cow emits around 250 liters of methane per day. Some, but not all, humans emit methane in their flatus!

Some experiments even suggest that leaf tissues of living plants emit methane, although other research indicates that the plants themselves do not actually generate methane they are just absorbing methane from the soil and then emitting it through their leaf tissues. There may still be some unknown mechanism by which plants produce methane, but that is by no means certain.

Methane is one of the earth’s most important greenhouse gases, with a global warming potential 25 times greater than carbon dioxide (averaged over 100 years). Therefore, the methane produced by methanogenesis in livestock is a considerable contributor to global warming.

Methanogenesis can also be beneficially exploited. It is the primary pathway that breaks down organic matter in landfills (which can release large volumes of methane into the atmosphere if left uncontrolled), and can be used to treat organic waste and to produce useful compounds. Biogenic methane can be collected and used as a sustainable alternative to fossil fuels.


Anaerobic oxidation of short-chain alkanes in hydrothermal sediments: potential influences on sulfur cycling and microbial diversity

Short-chain alkanes play a substantial role in carbon and sulfur cycling at hydrocarbon-rich environments globally, yet few studies have examined the metabolism of ethane (C-2), propane (C-3), and butane (C-4) in anoxic sediments in contrast to methane (C-1). In hydrothermal vent systems, short-chain alkanes are formed over relatively short geological time scales via thermogenic processes and often exist at high concentrations. The sediment-covered hydrothermal vent systems at Middle Valley (MV Juan de Fuca Ridge) are an ideal site for investigating the anaerobic oxidation of C-1-C-4 alkanes, given the elevated temperatures and dissolved hydrocarbon species characteristic of these metalliferous sediments. We examined whether MV microbial communities oxidized C-1-C-4 alkanes under mesophilic to thermophilic sulfate-reducing conditions. Here we present data from discrete temperature (25, 55, and 75 degrees C) anaerobic batch reactor incubations of MV sediments supplemented with individual alkanes. Co-registered alkane consumption and sulfate reduction (SR) measurements provide clear evidence for C-1-C-4 alkane oxidation linked to SR over time and across temperatures. In these anaerobic batch reactor sediments, 16S ribosomal RNA pyrosequencing revealed that Deltaproteobacteria, particularly a novel sulfate-reducing lineage, were the likely phylotypes mediating the oxidation of C-2-C-4 alkanes. Maximum C-1-C-4 alkane oxidation rates occurred at 55 degrees C, which reflects the mid-core sediment temperature profile and corroborates previous studies of rate maxima for the anaerobic oxidation of methane (AOM). Of the alkanes investigated, C-3 was oxidized at the highest rate over time, then C-4, C-2, and C-1, respectively. The implications of these results are discussed with respect to the potential competition between the anaerobic oxidation of C-2-C(4)alkanes with AOM for available oxidants and the influence on the fate of C-1 derived from these hydrothermal systems.


PhD project in Hydrocarbon metabolism in Archaea

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Employer

Job description

In this project we will study microbial key players in subsurface environments – members of the domain Archaea that can consume methane or other natural oil and gas constituents under anoxic conditions. Many of those taxa cooperate with sulfate-reducing bacteria to carry out hydrocarbon degradation. The successful applicant gets to work with natural enrichments of these enigmatic microbes and can apply a variety of molecular methods and biogeochemical approaches to identify relevant environmental processes in microbial hydrocarbon metabolism. There are several novel biomolecules to discover that are produced exclusively by this group of microorganisms.

Anaerobic oxidation of methane, carbon metabolism, alkanes, methanogenesis, Archaea

The applicants needs a MSc. degree (or equivalent) in biological sciences or related fields. Skills and interests in microbiology, molecular biology/bioinformatics and biochemistry are important. The applicant should be willing to join ship-based research expeditions and work in an interdisciplinary team at MPI Bremen and partner institutions.


FUTURE ISSUES

How are hydrocarbon seeps connected with the surrounding benthic and pelagic environments? Is this connectivity changing?

More sophisticated biogeochemical and analytical chemical approaches are needed to track and partition microbial metabolism at seeps under quasi in situ conditions.

Development of in situ instrumentation and measurement tools to document the rates and capacity of biogeochemical processing at hydrocarbon seeps (see the sidebar titled Outlook).

How will ocean acidification and warming deep waters influence the biogeochemistry of hydrocarbon seeps?

What factors limit the ability of seep microbial communities to respond to changing hydrocarbon flux regimes?

OUTLOOK

The impact of cold seeps is not limited to the seabed, as evidenced by recent reports linking seafloor seepage and surficial processes at water depths of >1,000 m, underscoring the role that cold seeps play in modulating benthic-pelagic coupling. Connectivity is not a new concept, but such benthic-driven dynamics require that we fundamentally revise the scales upon which we consider seep impact(s) and the way we incorporate these impacts into models. Quantifying seep fluxes requires development of improved chemical (methane, oxygen, and sulfide) sensors integrated in platforms with acoustic Doppler current profilers. The importance of metabolic phasing is a step forward, but much remains to be discovered regarding how anaerobic oxidation of methane is coupled to different electron-accepting processes over space and time. To understand the regulation and dynamics of microbial processes at seeps requires in situ assessment of activity and experiments conducted under realistic conditions [i.e., quasi in situ T, (substrate), pressure].

Cold seeps are uniquely prone to perturbation resulting from global change. Ocean acidification, warming waters, and the spread of hypoxic/anoxic conditions may fundamentally alter seep ecosystems. Warming waters may destabilize surficial methane hydrate deposits and increase fluxes of both methane and oil to the oceanic water column. Surface-breaching gas hydrates not only stymie methane flux but also slow oil discharge. Destabilization of these hydrates could increase the flux of hydrocarbons through the sediments, reducing the efficiency of consumption and promoting exchange between benthic and pelagic compartments. It is critical to identify the factors that regulate the ability of seep microbial communities to respond to increased hydrocarbon fluxes. Since cold seeps are often nutrient limited, increased hydrocarbon fluxes could exacerbate nutrient limitation and reduce the efficiency of the benthic hydrocarbon biofilter.