Assessment of the Degradation Potential and Genomic Insights towards Phenanthrene by Dietzia psychralcaliphila JI1D

Abstract

Extreme marine environments are potential sources of novel microbial isolations with dynamic metabolic activity. Dietzia psychralcaliphila J1ID was isolated from sediments originated from Deception Island, Antarctica, grown over phenanthrene. This strain was also assessed for its emulsifying activity. In liquid media, Dietzia psychralcaliphila J1ID showed 84.66% degradation of phenanthrene examined with HPLC-PDA. The identification of metabolites by GC-MS combined with its whole genome analysis provided the pathway involved in the degradation process. Whole genome sequencing indicated a genome size of 4,216,480 bp with 3961 annotated genes. The presence of a wide range of monooxygenase and dioxygenase, as well as dehydrogenase catabolic genes provided the genomic basis for the biodegradation. The strain possesses the genetic compartments for a wide range of toxic aromatic compounds, which includes the benABCD and catABC clusters. COG2146, COG4638, and COG0654 through COG analysis confirmed the genes involved in the oxygenation reaction of the hydrocarbons by the strain. Insights into assessing the depletion of phenanthrene throughout the incubation process and the genetic components involved were obtained. This study indicates the degradation potential of the strain, which can also be further expanded to other model polyaromatic hydrocarbons.

Antimicrobial Biosynthetic Potential and Phylogenetic Analysis of Culturable Bacteria Associated with the Sponge Ophlitaspongia sp. from the Yellow Sea, China

“…Chemically diverse products such as new alkaloids and α-pyrones have recently been isolated from Saccharomonospora [ 54 , 55 ]. Genera such as Dietzia , Rothia , Leeuwenhoekiella , and Polaribacter have served as specific degraders of chemically diverse carbohydrates and may play crucial roles in the marine food web and energy metabolism [ 56 , 57 , 58 , 59 ]. Specifically, the genus Dietzia is known for degrading hydrocarbons such as polycyclic aromatic compounds [ 56 ].…”

“…Genera such as Dietzia , Rothia , Leeuwenhoekiella , and Polaribacter have served as specific degraders of chemically diverse carbohydrates and may play crucial roles in the marine food web and energy metabolism [ 56 , 57 , 58 , 59 ]. Specifically, the genus Dietzia is known for degrading hydrocarbons such as polycyclic aromatic compounds [ 56 ]. Members of the genus Rothia have diverse metabolic capacities, including carbohydrate and peptide fermentation, to primary metabolites, while Leeuwenhoekiella species have been found to hydrolyse esters, glucose, and amides, as well as utilise labile carbon sources [ 60 , 61 ].…”

Molecular characterization of a polycyclic aromatic hydrocarbons (PAHs) degrader, Burkholderia contaminans strain P14, isolated from aged oil-contaminated soil in Kuwait

“…The PAH compounds can have two or seven benzene rings depending on their aromatic ring structure. They are excellent lubricants and intermediates for thermosetting polymers because of their unique physiochemical characteristics (Mackay and Callcott, 1998;Ausuri et al, 2021). Despite these characteristics, several bacteria can metabolize these molecules as a carbon and energy source through their biosyn-thetic processes, playing a significant role in recycling the carbon of aromatic rings and decomposing such contaminants (Cauduro et al, 2020).…”

“…The development of molecular biology tools has recently made it possible to monitor this process directly. Catechol-based intermediates are formed during PAHs degradation through dioxygenases, leading to intermediates in the TCA cycle (Nogales et al, 2017;Ausuri et al, 2021). A prototypical model for biodegradation investigations is phenanthrene, which shares its structural backbone with other PAHs and is often used to identify PAH contamination (Mallick et al, 2010).…”

“…A prototypical model for biodegradation investigations is phenanthrene, which shares its structural backbone with other PAHs and is often used to identify PAH contamination (Mallick et al, 2010). Phenanthrene breakdown has been monitored in a wide variety of microbes, which includes the bacterial genera from Pseudomonas, Bacillus, Arthobacter, Serratia, Stenotrophomonas, Shewanella, Spingobium, Acidovorax, Rhodococcus, Ralsonia, Brevibacterium, and Burkholderia (Seemann, 2014;Alegbeleye et al, 2017;Morya et al, 2020;Ausuri et al, 2021).…”