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Novel Insights into Bioremediation of Petroleum-Polluted Environments and Bacterial Catabolic Pathways
Published in Wael Ahmed Ismail, Jonathan Van Hamme, Hydrocarbon Biotechnology, 2023
Laura Rodríguez-Castro, Roberto E. Durán, Constanza C. Macaya, Flavia Dorochesi, Lisette Hernández, Felipe Salazar-Tapia, Vanessa Ayala-Espinoza, Patricio Santis-Cortés, Ximena Báez-Matus, Michael Seeger
Fumarate addition is the predominant activation mechanism of n-alkane degradation under anoxic conditions (Ji et al., 2019), and this occurs via two main mechanisms (Rojo, 2009; Sierra-Garcia and Oliveira, 2013) (Figure 3.4). The first mechanism involves activation of the alkane substrate by the addition of fumarate at the subterminal carbon, producing an alkylsuc-cinate derivative, whereas in the second mechanism, fumarate is added at the terminal carbon. Activation of alkanes by nitrate-, iron-, and sulfate-reducing and methanogenic alkane-degrading bacteria has been reported (Abbasian et al., 2015). Anaerobic HC-degrading bacteria that use fumarate in Proteobacteria (Pseudomonadota) and Firmicutes (Bacilliota) phyla were identified by metagenome analyses in marine sediments at seeps (Stagars et al., 2016). Metagenomic analyzes of oil reservoirs revealed that members of the Atribacteria (Atribacterota) phylum are also potentially capable of HC degradation via fumarate addition (Mbadinga et al., 2011; Liu et al., 2019a). Sulfidogenic and denitrifying Desulfatibacillum alkenivorans AK-01 and Aromatoleum sp. HxN1 are bacterial models to investigate the activation by fumarate addition (Grundmann et al., 2008; Bian et al., 2015). D. alkeniv- orans AK-01 is able to grow on C13–C18n-alkanes, while Aromatoleum sp. HxN1 is able to grow on C6–C8n-alkanes (Callaghan et al 2006; Grundmann et al., 2008). The addition of fumarate is catalyzed by strictly anaerobic glycyl radical enzymes such as alkylsuccinate synthase and (1-methylalkyl) succinate synthase (Grundmann et al., 2008; Callaghan et al 2012). Anaerobic alkane activation has been proposed based on cell fatty acids and isotope labeling analysis (Callaghan et al 2006, Grundmann et al., 2008; Zedelius et al., 2011). A carboxylate rearrangement is observed in the (methyl)alkylsuc-cinate, presumably as a CoA thioester, followed by a decarboxylation reaction (Widell and Grundmann, 2010; Rabus et al., 2016). The resulting fatty acid can then undergo ß-oxidation. If the degradation produces propionate, fumarate could be regenerated through the methylmalonyl-CoA pathway (Widdel et al., 2006; Mbadinga et al., 2011; Callaghan et al 2012; Fuentes et al., 2014) (Figure 3.4(A)). Although the D. alkenivorans AK-01 genome was sequenced, only the alkylsuccinate synthase genes have been identified (Callaghan et al., 2012). Alkylsuccinate metabolites are biochemical indicators for in situ anaerobic microbial degradation of oil alkanes. Alkylsuc-cinates have been reported in oil-contaminated environments as well as in oilfield facilities (Grundmann et al., 2008; Sierra-Garcia and Oliveira, 2013).
Taxonomic, metabolic traits and species description of aromatic compound degrading Indian soil bacterium Pseudomonas bharatica CSV86T
Published in Journal of Environmental Science and Health, Part A, 2023
Balaram Mohapatra, Prashant S. Phale
Pseudomonas belongs to gammaproteobacteria of phylum Proteobacteria which represents type genus of the group Pseudomonad-ales/ceae or recently proposed Pseudomonadota.[11] Various Pseudomonas spp. are reported to degrade aromatic pollutants and xenobiotics like pesticides, herbicides, drugs, etc.;[12] produce diverse secondary metabolites like alginate, pyoverdine, homoserine lactone, peptides;[13] form biofilm and displaying beneficial plant growth promoting activities.[13,14] As per the standing nomenclature (LPSN), till date (April, 2023), a total of 414 validly published Pseudomonas type species are reported from diverse habitat. The taxonomic status of Pseudomonas has been reviewed and amended by several scientists due to observed phenotypic versatility.[15–17] However, it has been observed that several of the Pseudomonas species reported in the recent past are found to be assigned with dubious taxonomic conclusions.[17,18] At present, the genus Pseudomonas is divided into two major lineages, i.e., P. fluorescens and P. aeruginosa, which are further sub-divided into several groups and subgroups. Members of P. putida are phylogenetically distant/diverse, suggesting partitioning of P. putida group members into other spp. or new species group.[17–19] Hence, many members of this group needs taxonomic revision and reclassification based on combined genomic provenance, metabolic traits and phenotypic demarcations.