Characterization of trapped lignin-degrading microbes in tropical forest soil

Deangelis, Kristen M., Allgaier, Martin, Chavarria, Yaucin, Fortney, Julian L., Hugenholtz, Philip, Simmons, Blake, Sublette, Kerry, Silver, Whendee L. and Hazen, Terry C. (2011) Characterization of trapped lignin-degrading microbes in tropical forest soil. Plos One, 6 4: e19306.1-e19306.9. doi:10.1371/journal.pone.0019306

Author Deangelis, Kristen M.
Allgaier, Martin
Chavarria, Yaucin
Fortney, Julian L.
Hugenholtz, Philip
Simmons, Blake
Sublette, Kerry
Silver, Whendee L.
Hazen, Terry C.
Title Characterization of trapped lignin-degrading microbes in tropical forest soil
Journal name Plos One   Check publisher's open access policy
ISSN 1932-6203
Publication date 2011-04-01
Year available 2011
Sub-type Article (original research)
DOI 10.1371/journal.pone.0019306
Open Access Status DOI
Volume 6
Issue 4
Start page e19306.1
End page e19306.9
Total pages 9
Place of publication San Francisco, CA, United States
Publisher Public Library of Science
Language eng
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.
Keyword 16S Ribosomal RNA
Polymerase Chain Reaction
Phosphorus Availability
Litter Decomposition
Q-Index Code C1
Q-Index Status Confirmed Code
Grant ID DE-AC02-05CH11231
DEB 0543558
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Non HERDC
School of Chemistry and Molecular Biosciences
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