Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass

PLoS One. 2013 Jul 19;8(7):e68465. doi: 10.1371/journal.pone.0068465. Print 2013.

Abstract

Thermophilic bacteria are a potential source of enzymes for the deconstruction of lignocellulosic biomass. However, the complement of proteins used to deconstruct biomass and the specific roles of different microbial groups in thermophilic biomass deconstruction are not well-explored. Here we report on the metagenomic and proteogenomic analyses of a compost-derived bacterial consortium adapted to switchgrass at elevated temperature with high levels of glycoside hydrolase activities. Near-complete genomes were reconstructed for the most abundant populations, which included composite genomes for populations closely related to sequenced strains of Thermus thermophilus and Rhodothermus marinus, and for novel populations that are related to thermophilic Paenibacilli and an uncultivated subdivision of the little-studied Gemmatimonadetes phylum. Partial genomes were also reconstructed for a number of lower abundance thermophilic Chloroflexi populations. Identification of genes for lignocellulose processing and metabolic reconstructions suggested Rhodothermus, Paenibacillus and Gemmatimonadetes as key groups for deconstructing biomass, and Thermus as a group that may primarily metabolize low molecular weight compounds. Mass spectrometry-based proteomic analysis of the consortium was used to identify >3000 proteins in fractionated samples from the cultures, and confirmed the importance of Paenibacillus and Gemmatimonadetes to biomass deconstruction. These studies also indicate that there are unexplored proteins with important roles in bacterial lignocellulose deconstruction.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Adaptation, Biological*
  • Bacteria / genetics*
  • Bacteria / metabolism*
  • Base Composition
  • Biomass
  • Carbohydrate Metabolism
  • Genomics
  • Lignin / metabolism
  • Metabolomics
  • Metagenomics
  • Molecular Sequence Annotation
  • Panicum / microbiology*
  • Phylogeny
  • Proteomics
  • RNA, Bacterial
  • RNA, Ribosomal, 16S

Substances

  • RNA, Bacterial
  • RNA, Ribosomal, 16S
  • lignocellulose
  • Lignin

Grants and funding

This work was performed as part of the DOE Joint BioEnergy Institute (http://www.jbei.org) supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, through contract DE-AC02-05CH11231 between Lawrence Berkeley National Laboratory and the U.S. Department of Energy. Metagenomic sequencing was conducted by the DOE Joint Genome Institute which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. A portion of the research was performed using the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.