The Frankia actinorhizal plant symbiosis plays an important role in colonization of soils contaminated with toxic aromatic hydrocarbons. Our understanding of the bacterial partner, Frankia, in the actinorhizal symbiosis has been greatly facilitated by the availability of sequenced genomes. The analysis of these Frankia genomes has suggested that these bacteria are metabolically diverse and have potential for toxic aromatic hydrocarbon degradation. In this chapter, we explore what is known about that metabolic potential.
- Frankia s-triazines
- aromatic hydrocarbon degradation
Frankiagenomics and identification of metabolic potential
Based on phylogenetic analysis,
In this chapter, we will describe what is known about the degradation properties of these bacteria.
Among bacteria with bioremediation potential,
S- triazines degradation
Triazines are a class of herbicides composed of a heterocyclic six-membered ring with alternating carbon and nitrogen atoms joined by double bonds. These herbicides have been used extensively for control of broadleaf and grassy weeds in corn, sorghum, and sugarcane cultivation. Atrazine and simazine are the most ubiquitous members of the s-triazine family. Biodegradation of atrazine is a complex process and depends on the nature and amount of atrazine in soil or water [39-41]. There are four major steps in atrazine degradation: hydrolysis, dealkylation, deamination, and ring cleavage. For the hydrolysis step, an amidohydrolase enzyme (AtzA) cleaves the carbon-chlorine (C-Cl) bond and thus dechlorinates atrazine to hydroxylatrazine. This intermediate is dealkylated and deaminated at the ethyl and isopropyl groups by the amidohydrolase enzymes, AtzB and AtzC, to produce cyanuric acid. This product is converted to ammonia and carbon dioxide by the AtzD, AtzE, and AtzF enzymes [42-44].
S-triazine degradation pathway in Frankia
Bioinformatics analysis of the
4. Aromatic compounds degradation
4.1. Biphenyl and polychlorinated biphenyl
Biphenyls and polychlorinated biphenyls (PCBs) are some of the most recalcitrant xenobiotics found in the environment. The degree of chlorination differs greatly among the PCBs, ranging from 1 to 10, as does their position on the carbon atoms. Since the mid-1980s, the use of PCBs has been phased out in many countries. However, due to their toxicity, persistence in the environment, and potential carcinogenicity, they are still a major global environmental problem [46-48].
Bacteria degrade biphenyl and PCBs via the
4.1.1. Biphenyl degradation pathway in Frankia
At least four
4.2. Phenol degradation
Phenol (or hydroxybenzene) consists of a benzene ring substituted with a hydroxyl group. Derivatives of this molecule are colloquially known as phenolic compounds. Phenolic compounds are ubiquitous chemicals with diverse properties and uses. The simplest phenolic compound, phenol, is widely used in oil and coal processing, tinctorial and metallurgic industries, and many other industrial applications. Phenol also enters the environment via vehicle exhaust and as the product of natural metabolic processes, and chlorophenols are widely used as biocides in agricultural applications [for a review see 55]. While anthropogenic phenolics are often hazardous, natural phenolic compounds are mostly harmless in the concentrations that are found in foods such as coffee and tea, and some are used as antibiotics [56, 57]. However, the toxicity of some phenolics, particularly phenol and chlorinated phenols, has prompted considerable research activity devoted to phenol remediation. Acute and chronic exposure to phenol and chlorophenol has serious health effects. Phenol and chlorophenol cause lipid peroxidation which ultimately leads to tissue necrosis, and liver and kidney damage . Additionally, chlorophenol exposure is associated with elevated risks of cancer, immune deficiencies, and teratogenic effects [59-61].
4.2.2. General phenol degradation pathway
One of the most promising techniques for removing anthropogenic phenolics from the environment is bioremediation. As was the case for many compounds, the degradation pathway for phenol was first elucidated in a
4.2.3. Phenolic compounds and
4.3. Naphthalene degradation
Naphthalene is a ubiquitous polyaromatic hydrocarbon composed of two benzene rings joined at the 9 and 10 carbons (Figure 5). Naphthalene is produced by distilling and crystallizing coal tar, and also as by-product of fossil fuel combustion and cigarette smoke . Naphthalene is used in a number of industrial applications including as feed stock for the production of plastics and resins, and as a component of creosote-based wood preservatives. Naphthalene is also used in tincture and leather tanning industries . Unlike many organic pollutants, naphthalene does not bioaccumulate. Instead, naphthalene is metabolized and excreted in the urine of rats and humans [72, 73]. Nonetheless, naphthalene is a problematic pollutant with numerous toxic effects. Acute exposure to naphthalene causes hemolytic anemia, and liver and neurological damage . Chronic naphthalene exposure is associated with elevated cancer risk [75, 76]. The toxicity of naphthalene and its prevalence as a pollutant has spurred research on remediation techniques, including bioremediation and biodegradation.
4.3.2. Degradation pathway
The naphthalene biodegradation pathway was first studied in a strain of
In the lower pathway, salicylate hydroxylase hydroxylates salicylate to produce catechol. The remaining benzene ring is then cleaved by catechol-2,3-dioxygenase to produce 2-hydroxymuconic semialdehyde . Hydroxymuconic semialdehyde dehydrogenase then produces 2-hydroxyhexa-2,4-diene-1,6-dioate which is subsequently isomerized by 4-oxalocrotmate isomerase to produce 2-oxohexa-3-ene-1,6-dioate. This is then transformed into 2-oxopent-4-enoate by 4-oxalocrotomate decarboxylase. 2-oxopent-4-enole hydratase produces 4-hydroxy-2-oxovalerate, which is subsequently split into acetaldehyde and pyruvate by 2-oxo-4-hydroxypentanoate aldolase. Finally, acetaldehyde dehydrogenase converts acetaldehyde into acetyl Co-A . Both of these pathways are also found in
4.3.3. Naphthalene degradation in Frankia
Under oxic conditions, microbial degradation of many aromatic compounds occurs through the catechol or protocatechuate branch of the ß-ketoadipate pathway via either
4.4.2. Potential protocatechuate degradation pathway in Frankia
Besides the protochatechuate pathway found in
Petroleum-based energy and products are used extensively around the world. The pervasiveness of petroleum inevitably leads to serious environmental pollution. Petroleum is a complex mixture of hydrocarbons, cycloalkanes, aromatic hydrocarbons, and more complex chemicals like asphaltenes. These chemicals and their derivatives, which are termed petrogenic compounds, are released into the environment as a result of oil spills and combustion of petroleum-based products . Oil spills are one of the most serious sources of petroleum pollution and devastate aquatic and marine environments. Ongoing research to identify new methods for petroleum remediation is important because oil spills and other types of petroleum-derived pollution continue to pose environmental health risks.
Hydrocarbon-degrading bacteria and fungi are widely distributed in marine and freshwater environments, as well as soil habitats [83, 84]. In
A bioinformatics approach was used to identify these potential hydrocarbon degradation pathways among the sequenced
6. Future aspects
Clearly, we have only begun to scratch the surface of the metabolism of
From limited field studies, actinorhizal nodule occupancy seems to be under control by environmental conditions. The presence of
We thank Michele Greenleaf, Teal Furnholm, and Kaci B. Kus for their efforts on our degradation studies. Partial funding was provided by the New Hampshire Agricultural Experiment Station. This is scientific Contribution Number 2613. This work was supported by USDA National Institute of Food and Agriculture Hatch Project NH585. MR was supported by an Egyptian Channel Fellowship from The Egyptian Cultural Affairs and Missions Sectors.
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