Characterization of trapped lignin-degrading microbes in tropical forest soil.

Kristen M Deangelis,Terry C Hazen,Yaucin Chavarria,Whendee L Silver,Blake Simmons,Kerry Sublette,Martin Allgaier,Julian L Fortney,Phillip Hugenholtz,Christopher V. Rao

doi:10.1371/journal.pone.0019306

Abstract

Lignin is often the most difficult portion of plant biomass to degrade, with fungi generally thought to dominate during late stage decomposition. Lignin in feedstock plant material represents a barrier to more efficient plant biomass conversion and can also hinder enzymatic access to cellulose, which is critical for biofuels production. Tropical rain forest soils in Puerto Rico are characterized by frequent anoxic conditions and fluctuating redox, suggesting the presence of lignin-degrading organisms and mechanisms that are different from known fungal decomposers and oxygen-dependent enzyme activities. We explored microbial lignin-degraders by burying bio-traps containing lignin-amended and unamended biosep beads in the soil for 1, 4, 13 and 30 weeks. At each time point, phenol oxidase and peroxidase enzyme activity was found to be elevated in the lignin-amended versus the unamended beads, while cellulolytic enzyme activities were significantly depressed in lignin-amended beads. Quantitative PCR of bacterial communities showed more bacterial colonization in the lignin-amended compared to the unamended beads after one and four weeks, suggesting that the lignin supported increased bacterial abundance. The microbial community was analyzed by small subunit 16S ribosomal RNA genes using microarray (PhyloChip) and by high-throughput amplicon pyrosequencing based on universal primers targeting bacterial, archaeal, and eukaryotic communities. Community trends were significantly affected by time and the presence of lignin on the beads. Lignin-amended beads have higher relative abundances of representatives from the phyla Actinobacteria, Firmicutes, Acidobacteria and Proteobacteria compared to unamended beads. This study suggests that in low and fluctuating redox soils, bacteria could play a role in anaerobic lignin decomposition.

Highlights

There is a strong impetus both nationally and internationally for devising new, non-fossil based fuels that are generated in a sustainable way with minimum greenhouse gas production [1]
This study demonstrates that the lignin-amended biosep beads are an effective method for trapping soil populations with the specific capability of decomposing lignin
Substantial phenol oxidase and peroxidase accompanied by depressed carbohydrate-active enzyme activity and low microbial community richness after one week suggests the capture of a fairly specialized group of microorganisms adapted to the lignin-amended bead environment

Summary

Introduction

There is a strong impetus both nationally and internationally for devising new, non-fossil based fuels that are generated in a sustainable way with minimum greenhouse gas production [1]. While pretreatment eliminates most of the lignin during biofuels production, lignin can pose a challenge due to its ability to inhibit cellulosic enzymes and as a potentially viable waste feedstock [4,5]. Phenol-degrading bacteria such as Kocuria and Staphylococcus [9], peroxidase-producing Flavobacterium meningosepticum [10], and bacterial degraders of polyaromatic hydrocarbons [6] may have a natural ability for degrading lignin derived from decomposing plant biomass. Discovery of novel anaerobic bacterial lignin-degrading enzymes would be beneficial to the industrial production of next-generation biofules, due to their potential application to microbial engineered biofuelsproducing organisms, lack of requirement of oxygen, and range of specificity or environmental conditions

Methods

Results

Conclusion