Screening and Phylogenetic Analysis of Deep-Sea Bacteria Capable of Metabolizing Lignin-Derived Aromatic Compounds

Abstract

Lignin is one of the most abundant biomasses in nature. It is composed of aromatic moieties and has great potential for use in the production of chemical alternatives to petroleum products. Because of increasing interest in biocatalysis, the potential for industrial application of microbial metabolism of lignin-derived compounds has gained considerable recent attention. Functional screenings of culturable bacteria isolated from sediments and sunken wood collected from the deep sea revealed the existence of a number of previously unidentified bacteria capable of metabolizing lignin-related aromatic compounds. Of the 510 isolates obtained in the present study, 208 completely or partially metabolized these compounds. The 208 isolates were classified into diverse phyla, including Firmicutes, Actinobacteria, Bacteroidetes, and Proteobacteria. Among the 208 isolates, 61 unique 16S rRNA gene sequences were detected including previously unidentified marine lineage isolates. The metabolites of the isolates were analysed using liquid chromatography/mass spectrometry (LC/MS) or gas chromatography/mass spectrometry (GC/MS). Most of the representative 61 isolates non-oxidatively decarboxylated the substrates to produce the corresponding aromatic vinyl monomers, which are used as feed stocks for bio-based plastics production. Oxidative metabolism of the lignin-related compounds for assimilation was frequently observed. Our study showed that the deep-sea environment contains an abundance of microorganisms capable of both non-oxidative and oxidative bioconversion of lignin-derived aromatic compounds. The ability for bio-conversion of aromatic compounds found in this study will facilitate the development of future biotechnological applications

Combination of six enzymes of a marine Novosphingobium converts the stereoisomers of β-O-4 lignin model dimers into the respective monomers

“…We previously isolated several deep-sea bacteria capable of metabolizing lignin-derived aromatic monomers 27 . Here, we screened the isolates for strains capable of cleaving the β -O- 4 ether linkage of the dimeric lignin model compound GGGE ( Fig.…”

“…To gain deeper insight into the involvment of microbes to lignin degradation in marine environments, we previously conducted functional screening of microbes isolated from deep-sea sediments and highly decomposed submerged wood, and identified a number of bacterial strains capable of degrading lignin-derived aromatic monomeric compounds 27 . Here, we screened this collection of marine isolates for microbes with β -O- 4 ether linkage cleavage activity and mined the genes required for the reaction from the genomic sequence 28 of one identified strain.…”

Hydrazidase, a Novel Amidase Signature Enzyme That Hydrolyzes Acylhydrazides

“…Several actinomycetes strains such as Streptomyces setonii, Rhodococcus opacus, and Corynebacterium glutamicum have this mechanism and catabolize HBA as well as other lignin derivatives (45)(46)(47)(48)(49). Microbacterium lacus isolated from deep-sea sediments can metabolize HBA (50), although, to the best of our knowledge, a Microbacterium mechanism for metabolizing HBA has not been reported. Database searches revealed that some Microbacterium strains possess a complete set of genes for the ␤-ketoadipate pathway (data not shown), indicating that Microbacterium sp.…”

Draft Genome Sequence of Novosphingobium sp. Strain MBES04, Isolated from Sunken Wood from Suruga Bay, Japan

“…The evolution of microbial pathways for using a wide variety of aromatic molecules as carbon sources was likely triggered by naturally produced aromatic compounds during lignin decomposition by some microorganisms ( 5 ). We recently isolated a marine Novosphingobium strain, isolated from sunken wood recovered from a depth of 260 m in Suruga Bay, off the Pacific coast of Shizuoka Prefecture, central Japan ( 6 ). The strain was found to metabolize a wide range of lignin-related aromatic monomers.…”