Enzymatic and genetic characterization of lignin depolymerization by Streptomyces sp. S6 isolated from a tropical environment

Fatimah Azizah Riyadi,Zuriati Zakaria,Nurul Syazwani Ahmad Sabri,Nurtasbiyah Yusof,Hirofumi Hara,Nor'Azizi Othman,Megat Johari Megat Mohd Noor,Fazrena Nadia M D Akhir,Analhuda Abdullah Tahir

doi:10.1038/s41598-020-64817-4

Fatimah Azizah Riyadi, Zuriati Zakaria + Show 7 more

Open Access

https://doi.org/10.1038/s41598-020-64817-4

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Journal: Scientific Reports	Publication Date: May 8, 2020
Citations: 57	License type: open-access

Affiliation: University of Technology Malaysia

Abstract

The conversion of lignocellulosic biomass into bioethanol or biochemical products requires a crucial pretreatment process to breakdown the recalcitrant lignin structure. This research focuses on the isolation and characterization of a lignin-degrading bacterial strain from a decaying oil palm empty fruit bunch (OPEFB). The isolated strain, identified as Streptomyces sp. S6, grew in a minimal medium with Kraft lignin (KL) as the sole carbon source. Several known ligninolytic enzyme assays were performed, and lignin peroxidase (LiP), laccase (Lac), dye-decolorizing peroxidase (DyP) and aryl-alcohol oxidase (AAO) activities were detected. A 55.3% reduction in the molecular weight (Mw) of KL was observed after 7 days of incubation with Streptomyces sp. S6 based on gel-permeation chromatography (GPC). Gas chromatography-mass spectrometry (GC-MS) also successfully highlighted the production of lignin-derived aromatic compounds, such as 3-methyl-butanoic acid, guaiacol derivatives, and 4,6-dimethyl-dodecane, after treatment of KL with strain S6. Finally, draft genome analysis of Streptomyces sp. S6 also revealed the presence of strong lignin degradation machinery and identified various candidate genes responsible for lignin depolymerization, as well as for the mineralization of the lower molecular weight compounds, confirming the lignin degradation capability of the bacterial strain.

Highlights

The conversion of lignocellulosic biomass into bioethanol or biochemical products requires a crucial pretreatment process to breakdown the recalcitrant lignin structure
Strain S6 was successfully isolated from decaying oil palm empty fruit bunch (OPEFB) and grew well on the tested agar plate
To further confirm the ability of the strain to grow on lignin, the growth pattern was observed in liquid culture (in terms of optical density at 600 nm (OD600)) using 2.5 g/L Kraft lignin (KL) as the sole carbon source (Supplementary Fig. S2)

Summary

Introduction

The conversion of lignocellulosic biomass into bioethanol or biochemical products requires a crucial pretreatment process to breakdown the recalcitrant lignin structure. S6 revealed the presence of strong lignin degradation machinery and identified various candidate genes responsible for lignin depolymerization, as well as for the mineralization of the lower molecular weight compounds, confirming the lignin degradation capability of the bacterial strain. Cellulose and hemicellulose are chains of polysaccharides that can be degraded by microbial enzymes or by chemical hydrolysis and are considered the main candidates for bioethanol and biochemical production. The abundance of oil palm biomass in the country makes it a possible source of bacterial strains with lignin-degrading abilities. The potential lignin-degrading ability of the strain was evaluated by performing enzymatic assays and gel-permeation chromatography (GPC) using Kraft lignin (KL) as the lignin model compound. The draft genome sequence of the potential ligninolytic strain was obtained to confirm the degradation process and to reveal all the candidate genes responsible for lignin degradation

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Conclusion