Biodegradation - Hydrocarbons - Revision history

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Jhurley: /* Anaerobic Degradation */

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‎Anaerobic Degradation

Jhurley: /* Introduction */

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‎Introduction

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Jhurley: /* Aromatic Hydrocarbons */

2019-05-02T21:17:12Z

‎Aromatic Hydrocarbons

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 *[[Landfarming]]
 *[[Polycyclic Aromatic Hydrocarbons (PAHs)]]
 '''Contributor(s):''' [[Elisse Magnuson]] and [[Dr. Elizabeth Edwards]]
 '''Key Resource(s)''':

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 ==Anaerobic Degradation==
 </onlyinclude>
-[[File:Edwards Article 1-figure 2.PNG|600px|thumbnail|right|Figure 2. Comparison of the longitudinal redox zonation concept (A) and the plume fringe concept (B). Both concepts describe the spatial distribution of electron acceptors and respiration processes in a hydrocarbon contaminant plume. (B) Iron(III) reduction, manganese(IV) reduction, and methanogenesis may occur simultaneously in the core of the contaminant plume (reproduced with permission from &copy; 2015 American Chemical Society<ref>Meckenstock, R.U., Elsner, M., Griebler, C., Lueders, T., Stumpp, C., Aamand, J., Agathos, S.N., Albrechtsen, H.J., Bastiaens, L., Bjerg, P.L. and Boon, N., '''More Authors Here''', 2015. Biodegradation: updating the concepts of control for microbial cleanup in contaminated aquifers. Environmental Science & Technology, 49(12), 7073-7081. [https://doi.org/10.1021/acs.est.5b00715 doi: 10.1021/acs.est.5b00715]</ref>).]]
+[[File:Edwards Article 1-figure 2.PNG|600px|thumbnail|right|Figure 2. Comparison of the longitudinal redox zonation concept (A) and the plume fringe concept (B). Both concepts describe the spatial distribution of electron acceptors and respiration processes in a hydrocarbon contaminant plume. (B) Iron(III) reduction, manganese(IV) reduction, and methanogenesis may occur simultaneously in the core of the contaminant plume (reproduced with permission from &copy; 2015 American Chemical Society<ref>Meckenstock, R.U., Elsner, M., Griebler, C., Lueders, T., Stumpp, C., Aamand, J., Agathos, S.N., Albrechtsen, H.J., Bastiaens, L., Bjerg, P.L., Boon, N., Dejonghe, W., Huang, W.E., Schmidt, S.I., Smolders, E., Sørensen, S.R., Springael, D, and van Breukelen, B.M., 2015. Biodegradation: Updating the Concepts of Control for Microbial Cleanup in Contaminated Aquifers. Environmental Science and Technology, 49(12), pp. 7073-7081. [https://doi.org/10.1021/acs.est.5b00715 doi: 10.1021/acs.est.5b00715]</ref>).]]
 <onlyinclude>
 Hydrocarbon degradation under anaerobic conditions is often slower compared to aerobic degradation, due to less favorable reaction energetics with alternate electron acceptors. Despite this limitation, both facultative and obligately anaerobic bacteria and archaea are known to degrade hydrocarbons without oxygen. Such microorgansims develop readily at hydrocarbon-impacted sites owing to rapid consumption of oxygen, and therefore anaerobic processes significantly impact the fate of hydrocarbons in the environment. </onlyinclude>Initial steps in anoxic hydrocarbon degradation that involve adding an oxidized functional group to activate the molecule are typically rate-limiting. Doubling times of anaerobic hydrocarbon degraders range from days to months<ref>Meckenstock, R.U. and Mouttaki, H., 2011. Anaerobic degradation of non-substituted aromatic hydrocarbons. Current Opinion in Biotechnology, 22(3), 406-414. [https://doi.org/10.1016/j.copbio.2011.02.009 doi: 10.1016/j.copbio.2011.02.009]</ref>. Despite slow growth rates, complete degradation of many different types of hydrocarbons occurs in the absence of oxygen. For example, degradation of [[Polycyclic Aromatic Hydrocarbons (PAHs) | polycyclic aromatic hydrocarbons]] (compounds composed of multiple aromatic rings) has been reported to occur within 90 days, while benzene degradation occurred over a timescale of 120 weeks<ref name="Meckenstock2016">Meckenstock, R.U., Boll, M., Mouttaki, H., Koelschbach, J.S., Cunha Tarouco, P., Weyrauch, P., Dong, X. and Himmelberg, A.M., 2016. Anaerobic degradation of benzene and polycyclic aromatic hydrocarbons. Journal of Molecular Microbiology and Biotechnology, 26(1-3), 92-118. [https://doi.org/10.1159/000441358 doi: 10.1159/000441358]</ref>. Under methanogenic conditions, linear alkanes have reportedly been degraded in under 200 days<ref>Jiménez, N., Richnow, H.H., Vogt, C., Treude, T. and Krueger, M., 2016. Methanogenic hydrocarbon degradation: evidence from field and laboratory studies. Journal of Molecular Microbiology and Biotechnology, 26(1-3), 227-242. [https://doi.org/10.1159/000441679 doi: 10.1159/000441679]</ref>.
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 '''3. Carboxylation'''<br />
 All mechanisms described to date only apply to hydrocarbons with alkyl groups, and not to unsubstituted aromatic hydrocarbons like benzene or naphthalene. In fact, anaerobic degradation of benzene is much slower than that of toluene, or xylenes, and may not occur at all sites<ref name="Lawrence2006" />. One mechanism for naphthalene degradation and postulated for anaerobic benzene degradation is [[wikipedia: Carboxylation | carboxylation]]. In this process, CO<sub>2</sub> is added directly to aliphatic and aromatic hydrocarbons<ref name="Abbasian2015" />. The process is thought to be somewhat analogous to the mechanism of anaerobic phenol (=hydroxybenzene) degradation where phenol is first activated using energy from ATP to phosphophenol prior to carboxylation to para-hydroxybenzoate. Enzymes called carboxylases catalyze the reaction that adds a carboxyl (-COOH) group to their substrate, although the mechanism is still under investigation. Activation of benzene is thought to occur by carboxylation to benzoate under iron- and nitrate-reducing conditions<ref name="Meckenstock2016" />. Benzene ring activation is difficult due to the stability of the ring and the correspondingly high dissociation energy. While no biochemical evidence for benzene carboxylation yet exists, gene expression and proteomic studies correlate expression of the putative anaerobic benzene carboxylase (called AbcDA) with benzene degradation<ref>Luo, F., Gitiafroz, R., Devine, C.E., Gong, Y., Hug, L.A., Raskin, L. and Edwards, E.A., 2014. Metatranscriptome of an anaerobic benzene-degrading, nitrate-reducing enrichment culture reveals involvement of carboxylation in benzene ring activation. Applied and Environmental Microbiology, 80(14), 4095-4107. [https://doi.org/10.1128/aem.00717-14 doi:10.1128/AEM.00717-14]</ref><ref>Abu Laban, N., Selesi, D., Rattei, T., Tischler, P. and Meckenstock, R.U., 2010. Identification of enzymes involved in anaerobic benzene degradation by a strictly anaerobic iron‐reducing enrichment culture. Environmental Microbiology, 12(10), 2783-2796. [http://dx.doi.org/10.1111/j.1462-2920.2010.02248.x doi:10.1111/j.1462-2920.2010.02248.x]</ref>. Naphthalene carboxylation has been demonstrated in crude cell extracts<ref>Mouttaki, H., Johannes, J. and Meckenstock, R.U., 2012. Identification of naphthalene carboxylase as a prototype for the anaerobic activation of non‐substituted aromatic hydrocarbons. Environmental Microbiology, 14(10), 2770-2774. [http://doi.org/10.1111/j.1462-2920.2012.02768.x doi: 10.1111/j.1462-2920.2012.02768.x]</ref>. The active sites of aromatic ring carboxylases are thought to be similar to the UbiD family of carboxylases<ref name="Boll2014" /> involved in general aromatic metabolism.
 ==Implications for Remediation==

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 [[File:Edwards Article 1-figure 1.PNG|400 px|thumbnail|left|Figure 1. Components of hydrocarbon biodegradation. Understanding and facilitating biodegradation at a contaminated site requires knowledge of the environmental conditions, compound properties, and microorganisms present (adapted after Sutherson, 1999)<ref name="Suthersan1999" />.]]
-Many bioremediation efforts involve injection and circulation of oxygen to subsurface environments in order to increase the availability of oxygen as both reactant and electron acceptor. Common methods include using a vacuum pump to promote air circulation<ref name="NRC1993">National Research Council, 1993. In Situ Bioremediation – When does it work? Committee on In Situ Bioremediation, Water Science and Technology Board, Commission on Engineering and Technical Systems, National Academy Press, Washington D.C. [https://doi.org/10.17226/2131 doi: 10.17226/2131]</ref>, bioventing or biosparging that add air to the subsurface<ref>US Environmental Protection Agency, 1994. How to evaluate alternative cleanup technologies for underground storage tank sites. [//www.enviro.wiki/images/7/74/USEPA-1994-How_to_evalutate_alternative_cleanup_tech_for_UST_Sites.pdf Report pdf]</ref>, water circulation aboveground to add oxygen<ref name="NRC1993" />, and the introduction of substances that release oxygen like peroxides or ozone. Remediation may also involve introduction of bacterial strains (bioaugmentation) as well as nutrients to stimulate hydrocarbon degradation. This strategy is most often used at sites with mid-weight or heavier petroleum products, as lighter compounds volatilize<ref name="Contsitecleanup2016">'''Contaminated Site Clean-Up Information, 2016. Bioremediation'''</ref>. Related commercial products include microbial culture, enzyme, and nutrient additives. These products may be less viable in the field than in laboratory settings due to varying site conditions such that field testing is necessary to determine their effectiveness<ref name="das2011">Das, N. and Chandran, P., 2011. Microbial degradation of petroleum hydrocarbon contaminants: an overview. Biotechnology Research International, 941810, 13 pgs. [https://doi.org/10.4061/2011/941810 doi: 10.4061/2011/941810]</ref>. As the biochemical processes of anaerobic hydrocarbon biotransformation have become more clearly established, bioremediation efforts have shifted towards adding nitrate or sulfate as electron acceptors instead of oxygen because these electron acceptors are much more soluble than oxygen and easier to deliver, particularly for in situ applications<ref>Cunningham, J.A., Hopkins, G.D., Lebron, C.A. and Reinhard, M., 2000. Enhanced anaerobic bioremediation of groundwater contaminated by fuel hydrocarbons at Seal Beach, California. Biodegradation, 11(2-3), 159-170. [https://doi.org/10.1023/a:1011167709913 doi: 10.1023/A:1011167709913]</ref>.
+Many bioremediation efforts involve injection and circulation of oxygen to subsurface environments in order to increase the availability of oxygen as both reactant and electron acceptor. Common methods include using a vacuum pump to promote air circulation<ref name="NRC1993">National Research Council, 1993. In Situ Bioremediation – When does it work? Committee on In Situ Bioremediation, Water Science and Technology Board, Commission on Engineering and Technical Systems, National Academy Press, Washington D.C. [https://doi.org/10.17226/2131 doi: 10.17226/2131]</ref>, bioventing or biosparging that add air to the subsurface<ref>US Environmental Protection Agency, 1994. How to evaluate alternative cleanup technologies for underground storage tank sites. [//www.enviro.wiki/images/7/74/USEPA-1994-How_to_evalutate_alternative_cleanup_tech_for_UST_Sites.pdf Report pdf]</ref>, water circulation aboveground to add oxygen<ref name="NRC1993" />, and the introduction of substances that release oxygen like peroxides or ozone. Remediation may also involve introduction of bacterial strains (bioaugmentation) as well as nutrients to stimulate hydrocarbon degradation. This strategy is most often used at sites with mid-weight or heavier petroleum products, as lighter compounds volatilize<ref name="Contsitecleanup2016">US EPA, CLU-IN, Bioremediation. [https://clu-in.org/techfocus/default.focus/sec/Bioremediation/cat/Overview/ Website]</ref>. Related commercial products include microbial culture, enzyme, and nutrient additives. These products may be less viable in the field than in laboratory settings due to varying site conditions such that field testing is necessary to determine their effectiveness<ref name="das2011">Das, N. and Chandran, P., 2011. Microbial degradation of petroleum hydrocarbon contaminants: an overview. Biotechnology Research International, 941810, 13 pgs. [https://doi.org/10.4061/2011/941810 doi: 10.4061/2011/941810]</ref>. As the biochemical processes of anaerobic hydrocarbon biotransformation have become more clearly established, bioremediation efforts have shifted towards adding nitrate or sulfate as electron acceptors instead of oxygen because these electron acceptors are much more soluble than oxygen and easier to deliver, particularly for in situ applications<ref>Cunningham, J.A., Hopkins, G.D., Lebron, C.A. and Reinhard, M., 2000. Enhanced anaerobic bioremediation of groundwater contaminated by fuel hydrocarbons at Seal Beach, California. Biodegradation, 11(2-3), 159-170. [https://doi.org/10.1023/a:1011167709913 doi: 10.1023/A:1011167709913]</ref>.
 Site conditions affect the occurrence and rate of biodegradation in contaminated environments (Fig. 1). Nitrogen, phosphorus, and iron are important nutrients for bacteria and may become limiting in certain environments, particularly in seawater and freshwater wetlands which can be nutrient deficient. Addition of inorganic nutrients can bolster biodegradation rates. However, high levels of nitrogen, phosphorus, and potassium may inhibit biodegradation, particularly of [[Polycyclic Aromatic Hydrocarbons (PAHs) | aromatics]]<ref name="das2011" />. Nitrogen at reported levels of 200-4000 mg N/kg soil have been shown to reduce hydrocarbon loss, while lower levels stimulated degradation. This may depend on site-specific conditions such as soil type and contaminants<ref>Braddock, J.F., Ruth, M.L., Catterall, P.H., Walworth, J.L. and McCarthy, K.A., 1997. Enhancement and inhibition of microbial activity in hydrocarbon-contaminated arctic soils: implications for nutrient-amended bioremediation. Environmental Science & Technology, 31(7), 2078-2084. [https://doi.org/10.1021/es960904d doi: 10.1021/es960904d]</ref><ref>Chaineau, C.H., Rougeux, G., Yepremian, C. and Oudot, J., 2005. Effects of nutrient concentration on the biodegradation of crude oil and associated microbial populations in the soil. Soil Biology and Biochemistry, 37(8), 1490-1497. [http://dx.doi.org/10.1016/j.soilbio.2005.01.012 doi: 10.1016/j.soilbio.2005.01.012]</ref>. In addition, the pH of a site affects the solubility and availability of nutrients, and must be in the tolerant range for the responsible microorganisms, generally between pH 6-8<ref name="Contsitecleanup2016" /><ref name="Suthersan1999">Suthersan, S.S. 1999. Soil vapor extraction. In: Remediation Engineering Design Concepts. CRC Press, S.S. Suthersan, ed., Boca Raton, Florida. [https://www.crcpress.com/Remediation-Engineering-Design-Concepts/Suthersan/p/book/9781566701372 ISBN: 978-1-5667-0137-2]</ref>. The presence of organic matter may increase persistence of contaminants due to contaminant partitioning into the organic phase, reducing their bioavailability to microorganisms<ref name="Chikere2011">Chikere, C.B., Okpokwasili, G.C. and Chikere, B.O., 2011. Monitoring of microbial hydrocarbon remediation in the soil. 3 Biotech, 1(3), 117-138. [https://doi.org/10.1007/s13205-011-0014-8 doi: 10.1007/s13205-011-0014-8]</ref>.
 <onlyinclude>
 ==Aerobic Degradation==
 Hydrocarbons are readily degraded under aerobic conditions. Bacteria, fungi, and algae are all capable of aerobic hydrocarbon degradation</onlyinclude><ref name="Haritash2009" /><onlyinclude>. In general, [[wikipedia: Alkene | alkenes]] (hydrocarbons containing double bonds) and short-chain [[wikipedia: Alkane | alkanes]] (hydrocarbons containing only single bonds) are the most easily degraded, followed by branched alkanes (alkanes with side chains) and then aromatics (hydrocarbons in a stable ring structure)</onlyinclude><ref name="Xue2015" /><onlyinclude>.</onlyinclude> However, degradation rates vary based on environmental parameters and decrease as hydrocarbon complexity increases. Reported degradation rates vary considerably because hydrocarbon composition depends on the source of the petroleum and age of the spill. For example, compound degradation varies from 5% to 30% in 28 days, while up to 100% degradation occurrs with nitrogen addition<ref>Röling, W.F., Milner, M.G., Jones, D.M., Lee, K., Daniel, F., Swannell, R.J. and Head, I.M., 2002. Robust hydrocarbon degradation and dynamics of bacterial communities during nutrient-enhanced oil spill bioremediation. Applied and Environmental Microbiology, 68(11), 5537-5548. [https://doi.org/10.1128/aem.68.11.5537-5548.2002 doi: 10.1128/AEM.68.11.5537-5548.2002]</ref>. Degradation rates by fungal species reportedly range from ~ 30-100% degradation over 28 days or less<ref>Zafra, G. and Cortés-Espinosa, D.V., 2015. Biodegradation of polycyclic aromatic hydrocarbons by Trichoderma species: a mini review. Environmental Science and Pollution Research, 22(24), 19426-19433. [https://doi.org/10.1007/s11356-015-5602-4 doi: 10.1007/s11356-015-5602-4]</ref>. As discussed above, the primary rate-limiting factor in aerobic biodegradation is delivery of oxygen. Oxygen availability is dependent on the ability of oxygen to move or diffuse through the site environment as well as on the uptake rate by microorganisms. Addition of oxygen can increase degradation rates several orders of magnitude over naturally occurring rates<ref name="Contsitecleanup2016" />.

@@ Line 43: / Line 43: @@
 Anaerobic microbes use terminal electron acceptors other than oxygen in respiration, including compounds such as nitrate, sulfate, carbon dioxide, oxidized metals, or even certain organic compounds<ref name= "Contsitecleanup2016"/>. At a contaminated site, microbes tend to use electron acceptors sequentially as a function of decreasing reduction potential in the order of oxygen, nitrate, ferric iron, sulfate, and H<sub>2</sub> (Fig. 2)<ref name= "Abbasian2015"/>. In a few cases, specific species of denitrifying or sulfate reducing microorganisms have been shown to metabolise certain hydrocarbons completely to CO<sub>2</sub> and water. However, anaerobic degradation of hydrocarbons more often occurs via syntrophy, where the degradation of a substrate by one microbe is dependent on the activity of another microbe responsible for keeping intermediate products such as formate and H<sub>2</sub> at low concentrations. Low product concentrations drive otherwise thermodynamically unfavorable reactions. Syntrophy is more common under anaerobic conditions because the use of oxygen as a terminal electron acceptor is more energetically favorable<ref>Morris, B.E., Henneberger, R., Huber, H. and Moissl-Eichinger, C., 2013. Microbial syntrophy: interaction for the common good. FEMS Microbiology Reviews, 37(3), 384-406. [https://doi.org/10.1111/1574-6976.12019 doi: 10.1111/1574-6976.12019]</ref>. Syntrophic processes are absolutely necessary for complete degradation to methane and carbon dioxide, since methanogens (archaea that produce methane) are only able to metabolize simple substrates like acetate and hydrogen. Multiple syntrophic relationships may be present in any given environment, based on available substrates and conditions (Fig. 3). In methanogenic environments, where all other electron acceptors are used up, primary degraders such as ''Peptococcaceae'' and ''Clostridium'' degrade hydrocarbons to intermediates like H<sub>2</sub> and acetate, which are consumed by methanogens<ref name= "Gieg2014">Gieg, L.M., Fowler, S.J. and Berdugo-Clavijo, C., 2014. Syntrophic biodegradation of hydrocarbon contaminants. Current Opinion in Biotechnology, 27, 21-29. [https://doi.org/10.1016/j.copbio.2013.09.002 doi: 10.1016/j.copbio.2013.09.002]</ref>.
-[[File:Edwards Article 1-figure 3.PNG|550px|thumbnail|center|Figure 3. Conceptual model for syntrophic anaerobic degradation of benzene and alkylbenzenes. Acetate and H<sub>2</sub> are consumed in reactions 1, 2, and 3, keeping the fermentation reaction energetically favorable. When external electron acceptors (e.g., nitrate, iron, or sulphate) are no longer available, methanogens consume acetate and hydrogen (adapted from<ref name= "Gieg2014"/>).]]
+[[File:Edwards Article 1-figure 3.PNG|550px|thumbnail|left|Figure 3. Conceptual model for syntrophic anaerobic degradation of benzene and alkylbenzenes. Acetate and H<sub>2</sub> are consumed in reactions 1, 2, and 3, keeping the fermentation reaction energetically favorable. When external electron acceptors (e.g., nitrate, iron, or sulphate) are no longer available, methanogens consume acetate and hydrogen (adapted from<ref name= "Gieg2014"/>).]]
 Anaerobic microbes use diverse strategies to activate hydrocarbons without requiring molecular oxygen (O<sub>2</sub>). Each strategy is discussed separately below, and is applicable to both aliphatic and aromatic compounds. The general strategy is to insert a more oxidized group into the molecule to make it more reactive to further transformation to more common intermediates (typically fatty acids and other carboxylic acids) that can enter central metabolic pathways. Most aromatic compounds are activated and funnelled towards the central anaerobic intermediate, benzoate, or more accurately, its coenzyme A (CoA) thioester derivative, benzoyl-CoA.

@@ Line 38: / Line 38: @@
 ==Anaerobic Degradation==</onlyinclude>
 [[File:Edwards Article 1-figure 2.PNG|600px|thumbnail|right|Figure 2. Comparison of the longitudinal redox zonation concept (A) and the plume fringe concept (B). Both concepts describe the spatial distribution of electron acceptors and respiration processes in a hydrocarbon contaminant plume. (B) Iron(III) reduction, manganese(IV) reduction, and methanogenesis may occur simultaneously in the core of the contaminant plume (reproduced with permission from &copy; 2015 American Chemical Society<ref>Meckenstock, R.U., Elsner, M., Griebler, C., Lueders, T., Stumpp, C., Aamand, J., Agathos, S.N., Albrechtsen, H.J., Bastiaens, L., Bjerg, P.L. and Boon, N., '''More Authors Here''', 2015. Biodegradation: updating the concepts of control for microbial cleanup in contaminated aquifers. Environmental Science & Technology, 49(12), 7073-7081. [https://doi.org/10.1021/acs.est.5b00715 doi: 10.1021/acs.est.5b00715]</ref>).]]
 <onlyinclude>
-<onlyinclude>Hydrocarbon degradation under anaerobic conditions is often slower compared to aerobic degradation, due to less favorable reaction energetics with alternate electron acceptors. Despite this limitation, both facultative and obligately anaerobic bacteria and archaea are known to degrade hydrocarbons without oxygen. Such microorgansims develop readily at hydrocarbon-impacted sites owing to rapid consumption of oxygen, and therefore anaerobic processes significantly impact the fate of hydrocarbons in the environment. </onlyinclude>Initial steps in anoxic hydrocarbon degradation that involve adding an oxidized functional group to activate the molecule are typically rate-limiting. Doubling times of anaerobic hydrocarbon degraders range from days to months<ref>Meckenstock, R.U. and Mouttaki, H., 2011. Anaerobic degradation of non-substituted aromatic hydrocarbons. Current Opinion in Biotechnology, 22(3), 406-414. [https://doi.org/10.1016/j.copbio.2011.02.009 doi: 10.1016/j.copbio.2011.02.009]</ref>. Despite slow growth rates, complete degradation of many different types of hydrocarbons occurs in the absence of oxygen. For example, degradation of [[Polycyclic Aromatic Hydrocarbons (PAHs) | polycyclic aromatic hydrocarbons]] (compounds composed of multiple aromatic rings) has been reported to occur within 90 days, while benzene degradation occurred over a timescale of 120 weeks<ref name= "Meckenstock2016">Meckenstock, R.U., Boll, M., Mouttaki, H., Koelschbach, J.S., Cunha Tarouco, P., Weyrauch, P., Dong, X. and Himmelberg, A.M., 2016. Anaerobic degradation of benzene and polycyclic aromatic hydrocarbons. Journal of Molecular Microbiology and Biotechnology, 26(1-3), 92-118. [https://doi.org/10.1159/000441358 doi: 10.1159/000441358]</ref>. Under methanogenic conditions, linear alkanes have reportedly been degraded in under 200 days<ref>Jiménez, N., Richnow, H.H., Vogt, C., Treude, T. and Krueger, M., 2016. Methanogenic hydrocarbon degradation: evidence from field and laboratory studies. Journal of Molecular Microbiology and Biotechnology, 26(1-3), 227-242. [https://doi.org/10.1159/000441679 doi: 10.1159/000441679]</ref>.
+Hydrocarbon degradation under anaerobic conditions is often slower compared to aerobic degradation, due to less favorable reaction energetics with alternate electron acceptors. Despite this limitation, both facultative and obligately anaerobic bacteria and archaea are known to degrade hydrocarbons without oxygen. Such microorgansims develop readily at hydrocarbon-impacted sites owing to rapid consumption of oxygen, and therefore anaerobic processes significantly impact the fate of hydrocarbons in the environment. </onlyinclude>Initial steps in anoxic hydrocarbon degradation that involve adding an oxidized functional group to activate the molecule are typically rate-limiting. Doubling times of anaerobic hydrocarbon degraders range from days to months<ref>Meckenstock, R.U. and Mouttaki, H., 2011. Anaerobic degradation of non-substituted aromatic hydrocarbons. Current Opinion in Biotechnology, 22(3), 406-414. [https://doi.org/10.1016/j.copbio.2011.02.009 doi: 10.1016/j.copbio.2011.02.009]</ref>. Despite slow growth rates, complete degradation of many different types of hydrocarbons occurs in the absence of oxygen. For example, degradation of [[Polycyclic Aromatic Hydrocarbons (PAHs) | polycyclic aromatic hydrocarbons]] (compounds composed of multiple aromatic rings) has been reported to occur within 90 days, while benzene degradation occurred over a timescale of 120 weeks<ref name= "Meckenstock2016">Meckenstock, R.U., Boll, M., Mouttaki, H., Koelschbach, J.S., Cunha Tarouco, P., Weyrauch, P., Dong, X. and Himmelberg, A.M., 2016. Anaerobic degradation of benzene and polycyclic aromatic hydrocarbons. Journal of Molecular Microbiology and Biotechnology, 26(1-3), 92-118. [https://doi.org/10.1159/000441358 doi: 10.1159/000441358]</ref>. Under methanogenic conditions, linear alkanes have reportedly been degraded in under 200 days<ref>Jiménez, N., Richnow, H.H., Vogt, C., Treude, T. and Krueger, M., 2016. Methanogenic hydrocarbon degradation: evidence from field and laboratory studies. Journal of Molecular Microbiology and Biotechnology, 26(1-3), 227-242. [https://doi.org/10.1159/000441679 doi: 10.1159/000441679]</ref>.
 Anaerobic microbes use terminal electron acceptors other than oxygen in respiration, including compounds such as nitrate, sulfate, carbon dioxide, oxidized metals, or even certain organic compounds<ref name= "Contsitecleanup2016"/>. At a contaminated site, microbes tend to use electron acceptors sequentially as a function of decreasing reduction potential in the order of oxygen, nitrate, ferric iron, sulfate, and H<sub>2</sub> (Fig. 2)<ref name= "Abbasian2015"/>. In a few cases, specific species of denitrifying or sulfate reducing microorganisms have been shown to metabolise certain hydrocarbons completely to CO<sub>2</sub> and water. However, anaerobic degradation of hydrocarbons more often occurs via syntrophy, where the degradation of a substrate by one microbe is dependent on the activity of another microbe responsible for keeping intermediate products such as formate and H<sub>2</sub> at low concentrations. Low product concentrations drive otherwise thermodynamically unfavorable reactions. Syntrophy is more common under anaerobic conditions because the use of oxygen as a terminal electron acceptor is more energetically favorable<ref>Morris, B.E., Henneberger, R., Huber, H. and Moissl-Eichinger, C., 2013. Microbial syntrophy: interaction for the common good. FEMS Microbiology Reviews, 37(3), 384-406. [https://doi.org/10.1111/1574-6976.12019 doi: 10.1111/1574-6976.12019]</ref>. Syntrophic processes are absolutely necessary for complete degradation to methane and carbon dioxide, since methanogens (archaea that produce methane) are only able to metabolize simple substrates like acetate and hydrogen. Multiple syntrophic relationships may be present in any given environment, based on available substrates and conditions (Fig. 3). In methanogenic environments, where all other electron acceptors are used up, primary degraders such as ''Peptococcaceae'' and ''Clostridium'' degrade hydrocarbons to intermediates like H<sub>2</sub> and acetate, which are consumed by methanogens<ref name= "Gieg2014">Gieg, L.M., Fowler, S.J. and Berdugo-Clavijo, C., 2014. Syntrophic biodegradation of hydrocarbon contaminants. Current Opinion in Biotechnology, 27, 21-29. [https://doi.org/10.1016/j.copbio.2013.09.002 doi: 10.1016/j.copbio.2013.09.002]</ref>.

@@ Line 28: / Line 28: @@
 <onlyinclude>
 ==Aerobic Degradation==
-Hydrocarbons are readily degraded under aerobic conditions. Bacteria, fungi, and algae are all capable of aerobic hydrocarbon degradation</onlyinclude><ref name="Haritash2009"/><onlyinclude>. In general, [[wikipedia: Alkene | alkenes]] (hydrocarbons containing double bonds) and short-chain [[wikipedia: Alkane | alkanes]] (hydrocarbons containing only single bonds) are the most easily degraded, followed by branched alkanes (alkanes with side chains) and then aromatics (hydrocarbons in a stable ring structure)</onlyinclude><ref name="Xue2015"/>. However, degradation rates vary based on environmental parameters and decrease as hydrocarbon complexity increases. Reported degradation rates vary considerably because hydrocarbon composition depends on the source of the petroleum and age of the spill. For example, compound degradation varies from 5% to 30% in 28 days, while up to 100% degradation occurrs with nitrogen addition<ref>Röling, W.F., Milner, M.G., Jones, D.M., Lee, K., Daniel, F., Swannell, R.J. and Head, I.M., 2002. Robust hydrocarbon degradation and dynamics of bacterial communities during nutrient-enhanced oil spill bioremediation. Applied and Environmental Microbiology, 68(11), 5537-5548. [https://doi.org/10.1128/aem.68.11.5537-5548.2002 doi: 10.1128/AEM.68.11.5537-5548.2002]</ref>. Degradation rates by fungal species reportedly range from ~ 30-100% degradation over 28 days or less<ref>Zafra, G. and Cortés-Espinosa, D.V., 2015. Biodegradation of polycyclic aromatic hydrocarbons by Trichoderma species: a mini review. Environmental Science and Pollution Research, 22(24), 19426-19433. [https://doi.org/10.1007/s11356-015-5602-4 doi: 10.1007/s11356-015-5602-4]</ref>. As discussed above, the primary rate-limiting factor in aerobic biodegradation is delivery of oxygen. Oxygen availability is dependent on the ability of oxygen to move or diffuse through the site environment as well as on the uptake rate by microorganisms. Addition of oxygen can increase degradation rates several orders of magnitude over naturally occurring rates<ref name= "Contsitecleanup2016"/>.
+Hydrocarbons are readily degraded under aerobic conditions. Bacteria, fungi, and algae are all capable of aerobic hydrocarbon degradation</onlyinclude><ref name="Haritash2009"/><onlyinclude>. In general, [[wikipedia: Alkene | alkenes]] (hydrocarbons containing double bonds) and short-chain [[wikipedia: Alkane | alkanes]] (hydrocarbons containing only single bonds) are the most easily degraded, followed by branched alkanes (alkanes with side chains) and then aromatics (hydrocarbons in a stable ring structure)</onlyinclude><ref name="Xue2015"/><onlyinclude>.</onlyinclude> However, degradation rates vary based on environmental parameters and decrease as hydrocarbon complexity increases. Reported degradation rates vary considerably because hydrocarbon composition depends on the source of the petroleum and age of the spill. For example, compound degradation varies from 5% to 30% in 28 days, while up to 100% degradation occurrs with nitrogen addition<ref>Röling, W.F., Milner, M.G., Jones, D.M., Lee, K., Daniel, F., Swannell, R.J. and Head, I.M., 2002. Robust hydrocarbon degradation and dynamics of bacterial communities during nutrient-enhanced oil spill bioremediation. Applied and Environmental Microbiology, 68(11), 5537-5548. [https://doi.org/10.1128/aem.68.11.5537-5548.2002 doi: 10.1128/AEM.68.11.5537-5548.2002]</ref>. Degradation rates by fungal species reportedly range from ~ 30-100% degradation over 28 days or less<ref>Zafra, G. and Cortés-Espinosa, D.V., 2015. Biodegradation of polycyclic aromatic hydrocarbons by Trichoderma species: a mini review. Environmental Science and Pollution Research, 22(24), 19426-19433. [https://doi.org/10.1007/s11356-015-5602-4 doi: 10.1007/s11356-015-5602-4]</ref>. As discussed above, the primary rate-limiting factor in aerobic biodegradation is delivery of oxygen. Oxygen availability is dependent on the ability of oxygen to move or diffuse through the site environment as well as on the uptake rate by microorganisms. Addition of oxygen can increase degradation rates several orders of magnitude over naturally occurring rates<ref name= "Contsitecleanup2016"/>.
 ===Alkanes and Alkenes===