Medium-chain alkane biodegradation and its link to some unifying attributes of alkB genes diversity

Hydrocarbon footprints in the environment, via biosynthesis, natural seepage, anthropogenic activities and accidents, affect the ecosystem and induce a shift in the healthy biogeochemical equilibrium that drives needed ecological ser-vices. In addition, these imbalances cause human diseases and reduce animal and microorganism diversity. Microbial bioremediation, which capitalizes on functional genes, is a sustainable mitigation option for cleaning hydrocarbon-impacted environments. This review focuses on the bacterial alkB functional gene, which codes for a non-heme di-iron monooxygenase (AlkB) with a di-iron active site that catalyzes C8-C16 medium-chain alkane metabolism. These en-zymes are ubiquitous and share common attributes such as being controlled by global transcriptional regulators, being a component of most super hydrocarbon degraders, and their distributions linked to horizontal gene transfer (HGT) events. The phylogenetic approach used in the HGT detection suggests that AlkB tree topology clusters bacteria functionally and that a preferential gradient dictates gene distribution. The alkB gene also acts as a biomarker for bio-remediation, although it is found in pristine environments and absent in some hydrocarbon degraders. For instance, a quantitative molecular method has failed to link alkB copy number to contamination concentration levels. This limita-tion may be due to AlkB homologues, which have other functions besides n-alkane assimilation. Thus, this review, which focuses on Pseudomonas putida GPo1 alkB, shows that AlkB proteins are diverse but have some unifying trends around hydrocarbon-degrading bacteria; it is erroneous to rely on alkB detection alone as a monitoring parameter for hydrocarbon degradation, alkB gene distribution are preferentially distributed among bacteria, and the plausible ex-planation for AlkB affiliation to broad-spectrum metabolism of hydrocarbons in super-degraders hitherto reported. Overall, this review provides a broad perspective of the ecology of alkB-carrying bacteria and their directed biodegra-dation pathways.

Automated summary

Hydrocarbon footprints in the environment affect the ecosystem and result in imbalances that lead to human diseases and reduced biodiversity. Microbial bioremediation using functional genes, such as the bacterial alkB gene, is a sustainable option for cleaning hydrocarbon-impacted environments. However, relying solely on alkB detection as a monitoring parameter for hydrocarbon degradation is erroneous due to its distribution among bacteria and limitations in linking copy number to contamination concentration levels.