World Bank Africa Centre of Excellence, Centre for Oilfield Chemical Research, University of Port Harcourt, Port Harcourt 500272, Nigeria.
Laboratory of Extraterrestrial Ocean Systems (LEOS), Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China; Department of Environmental Science, University of South Africa, Florida Campus, 1710, South Africa.
Sci Total Environ. 2023 Jun 15;877:162951. doi: 10.1016/j.scitotenv.2023.162951. Epub 2023 Mar 21.
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 services. 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 C-C medium-chain alkane metabolism. These enzymes 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 bioremediation, 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 limitation 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 explanation 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 biodegradation pathways.
环境中的碳氢化合物足迹，通过生物合成、自然渗漏、人为活动和事故，影响生态系统并引发健康生物地球化学平衡的转变，从而推动所需的生态服务。此外，这些失衡会导致人类疾病并减少动物和微生物的多样性。利用功能基因的微生物生物修复是清洁受碳氢化合物影响的环境的一种可持续缓解选择。本综述重点介绍细菌 alkB 功能基因，该基因编码一种非血红素二铁单加氧酶（AlkB），具有二铁活性位点，可催化 C-C 中链烷烃代谢。这些酶是普遍存在的，具有共同的属性，例如受全局转录调节剂控制，是大多数超级碳氢化合物降解物的组成部分，其分布与水平基因转移（HGT）事件有关。用于 HGT 检测的系统发育方法表明，AlkB 树拓扑结构按功能聚类细菌，并且优先梯度决定基因分布。alkB 基因也可用作生物修复的生物标志物，尽管它存在于原始环境中，而在一些碳氢化合物降解物中不存在。例如，定量分子方法未能将 alkB 拷贝数与污染浓度水平联系起来。这种局限性可能是由于 AlkB 同源物除了同化 n-烷烃之外还有其他功能。因此，本综述重点介绍恶臭假单胞菌 GPo1 alkB，表明 AlkB 蛋白多种多样，但在碳氢化合物降解细菌周围具有一些统一的趋势；仅依赖 alkB 检测作为碳氢化合物降解的监测参数是错误的，alkB 基因分布优先分布于细菌中，并且迄今为止报道的超级降解物中碳氢化合物广谱代谢与 AlkB 关联的合理解释。总的来说，本综述提供了携带 alkB 的细菌及其定向生物降解途径的生态广泛视角。
