Digging a Little Deeper- Investigation of Anaerobic Lignin Degradation from Soil Bacteria For The Improvement of Biopulping and the Conversion of Lignin to Lignocellulosic Biofuel

EPA Grant Number: FP917823
Title: Digging a Little Deeper- Investigation of Anaerobic Lignin Degradation from Soil Bacteria For The Improvement of Biopulping and the Conversion of Lignin to Lignocellulosic Biofuel
Investigators: Chaput, Gina M
Institution: University of Massachusetts - Amherst
EPA Project Officer: Lee, Sonja
Project Period: September 1, 2015 through August 31, 2018
Project Amount: $132,000
RFA: STAR Graduate Fellowships (2015) RFA Text |  Recipients Lists
Research Category: Academic Fellowships


The overarching goal of this investigation is to improve the sustainability of the pulping process in the paper industry through the application of pathways and enzymes of microbes that can degrade lignin. This greener approach to pulping is also known as biopulping. In previous work, biopulping focused solely on fungal cultures; however, fungi need constant aeration, which is costly to supply. A solution to this issue is to alternatively use anaerobic bacteria in replace of fungi, which would be amenable to industrial engineering, can be cultured to high cell density, and would not require aeration. The main objective of this research is to investigate soil communities that have been adapted anaerobically onto lignin as a sole carbon source and elucidate their mechanisms by which they utilize lignin. The communities of study were collected from soil plots at Harvard Forest (Petersham, MA), which have been adapted to 23 years of soil warming in a replicated field soil warming experiment. During this time, labile carbon substrate that the original communities were adapted to have been depleted, and previous studies have shown that the resident soil microbes are able to more efficiently degrade more complex carbon sources compared to the control communities. The hypothesis is that there are a variety of genes relating to lignin degradation in these communities that are novel and can be used for applications such as biopulping and biofuel production from lignin waste. This research proposes to work in two aims: (1) identify the community members degrading lignin under anaerobic conditions, and, (2) characterize the genes and pathways involved in anaerobic lignin degradation.


This project will follow anaerobic lignin degradation of microbial communities that have been adapted onto lignin as a sole carbon source. The first aim of this study is to identify the community members degrading lignin. To do so, communities will be serially diluted until single isolates are obtained for culturing. DNA will then be extracted from these isolates in order to identify the community members and whether their genomes are publicly available. Novel isolates found will have their complete genomes sequenced in order to better understand their physiology and define how they may degrade lignin. The second aim is to elucidate how the community is utilizing lignin. Isolates will be cultured individually onto various lignin-related aromatic monomers. Growth will be monitored and samples will be harvested at early, mid, and late growth phases. Monomer degradation and metabolites produced will be analyzed from each sample. Using the genomes of the isolates, the metabolites found in the cultures, and knowing which of the monomers were the initial substrate, it will be possible to model potential lignin degradation pathways. Finally, to confirm these pathways, genes of interest will metabolically engineered into Escherichia coli to determine the roles in lignin degradation mechanisms. If functional predictions are correct, lignin degradation activity should be seen, which will be confirmed with enzyme assays.

Expected Results:

It has been suggested that paper pulping using microbes could replace current chemical processes due to having low energy consumption, effective delignification, and being sustainable. Currently, few bacteria are known to degrade lignin anaerobically and soil microbial functional diversity is still largely not well understood. This research provides the foundational work in uncovering the ability of soil communities to utilize lignin as a sole carbon source. Based on this work, organisms, genes, and pathways used by these efficient anaerobic lignin degraders will be incorporated into improving biopulping processes and biofuel production from lignin.

Supplemental Keywords:

Anaerobic bacteria, Anaerobic lignin degradation, Biodegradation, Biopulping, Lignin, Lignin-related aromatics, Microbial Communities, Metabolic Engineering

Progress and Final Reports:

  • 2016
  • 2017
  • Final