Diverse alkane hydroxylase genes in microorganisms and environments

Abstract

AlkB and CYP153 are important alkane hydroxylases responsible for aerobic alkane degradation in bioremediation of oil-polluted environments and microbial enhanced oil recovery. Since their distribution in nature is not clear, we made the investigation among thus-far sequenced 3,979 microbial genomes and 137 metagenomes from terrestrial, freshwater, and marine environments. Hundreds of diverse alkB and CYP153 genes including many novel ones were found in bacterial genomes, whereas none were found in archaeal genomes. Moreover, these genes were detected with different distributional patterns in the terrestrial, freshwater, and marine metagenomes. Hints for horizontal gene transfer, gene duplication, and gene fusion were found, which together are likely responsible for diversifying the alkB and CYP153 genes adapt to the ubiquitous distribution of different alkanes in nature. In addition, different distributions of these genes between bacterial genomes and metagenomes suggested the potentially important roles of unknown or less common alkane degraders in nature.

Contribution of cyanobacterial alkane production to the ocean hydrocarbon cycle

“…Therefore, the majority of cyanobacterially produced hydrocarbons are likely to be released into the environment and subsequently degraded by bacteria (34). Obligate hydrocarbon-degrading bacteria, including Cycloclasticus, Thalassolituus, Oleiphilus, Oleispira, and Alcanivorax species, have been isolated from geographically diverse coastal and open-ocean regions in all seas, in sediments and both surface and deep waters, including areas with minimal oil pollution (9)(10)(11)35). Alcanivorax species are typically among the dominant bacteria found metabolizing crude oil during large spill events (34)(35)(36)(37)(38).…”

“…Populations of hydrocarbon-degrading bacteria, referred to as hydrocarbonoclastic bacteria, including many species that cannot use other carbon sources, are present in marine systems and play an important role in turnover of these compounds (5)(6)(7)(8)(9). Because obligate hydrocarbon-degrading bacteria are found in waters without significant levels of crude oil pollution, these organisms must use an alternate hydrocarbon source (9)(10)(11).…”

Detection of Horizontal Transfer of Housekeeping and Hydrocarbons Catabolism Genes in Bacterial Genus with Potential to Application in Bioremediation Process

“…In addition the possibility of horizontal gene transfer involving housekeeping genes not very likely, it must be taken into account. Because these doubts, the study of several housekeeping gene sequences and multilocus analysis has already been recommended for improving the reliability of phylogenetic inference [36] Bacterial alkane degradation is important for the bioremediation of petroleum-contaminated environments since these compounds are predominant in crude oil [43] [44]. A number of bacteria have multiple alkane hydroxylase genes which proven to potentially expand the n-alkane range of the host strain [45].…”

Plant <i>n</i>-alkane production from litterfall altered the diversity and community structure of alkane degrading bacteria in litter layer in lowland subtropical rainforest in Taiwan

“…To date, alkane monooxygenase gene (alkB) hydroxylases are the most commonly found alkane hydroxylases in both Gram-negative and Grampositive bacteria. More than 60 genera of aerobic bacteria and 5 genera of anaerobic bacteria are known to degrade n-alkanes (Nie et al, 2014). Although alkanes can be metabolized anaerobically, the growth of anaerobic alkane degraders is significantly slower than that of aerobic ones, especially in the litter layer environment where the oxygen supply is adequate (Wentzel et al, 2007).…”