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

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.

SUBMITTER: DeAngelis KM

PROVIDER: S-EPMC3084812 | biostudies-other | 2011

REPOSITORIES: biostudies-other

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

DeAngelis Kristen M KM Allgaier Martin M Chavarria Yaucin Y Fortney Julian L JL Hugenholtz Phillip P Simmons Blake B Sublette Kerry K Silver Whendee L WL Hazen Terry C TC

PloS one 20110429 4

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 orga ...[more]

PMID: 21559391

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Project description:Soil characteristics have been hypothesised as one of the possible mechanisms leading to monodominance of Gilbertiodendron dewerei in some areas of Central Africa where higher-diversity forest would be expected. However, the differences in soil characteristics between the G. dewevrei-dominated forest and its adjacent mixed forest are still poorly understood. Here we present the soil characteristics of the G. dewevrei forest and quantify whether soil physical and chemical properties in this monodominant forest are significantly different from the adjacent mixed forest.We sampled top soil (0-5, 5-10, 10-20, 20-30 cm) and subsoil (150-200 cm) using an augur in 6 × 1 ha areas of intact central Africa forest in SE Cameroon, three independent patches of G. dewevrei-dominated forest and three adjacent areas (450-800 m apart), all chosen to be topographically homogeneous. Analysis--subjected to Bonferroni correction procedure--revealed no significant differences between the monodominant and mixed forests in terms of soil texture, median particle size, bulk density, pH, carbon (C) content, nitrogen (N) content, C:N ratio, C:total NaOH-extractable P ratio and concentrations of labile phosphorous (P), inorganic NaOH-extractable P, total NaOH-extractable P, aluminium, barium, calcium, copper, iron, magnesium, manganese, molybdenum, nickel, potassium, selenium, silicon, sodium and zinc. Prior to Bonferroni correction procedure, there was a significant lower level of silicon concentration found in the monodominant than mixed forest deep soil; and a significant lower level of nickel concentration in the monodominant than mixed forest top soil. Nevertheless, these were likely to be the results of multiple tests of significance.Our results do not provide clear evidence of soil mediation for the location of monodominant forests in relation to adjacent mixed forests. It is also likely that G. dewevrei does not influence soil chemistry in the monodominant forests.

Dataset Information

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

Publications

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

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