Characterization of Trapped Lignin-Degrading Microbes in Tropical Forest Soil

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

A study of soil methane sink regulation in two grasslands exposed to drought and N fertilization

Oxidation by soil bacteria is the only biological sink for atmospheric methane (CH4). There are substantial uncertainties regarding the global size of this sink, in part because the ecological controls of the involved processes are not well understood to date. We have investigated effects of severe summer drought and of nitrogen inputs (ammonium nitrate or cattle urine) on soil CH4 fluxes in a field experiment. Soil moisture was the most important factor regulating the temporal dynamics of CH4 fluxes. Simulated drought episodes altered the soil’s water balance throughout the year, increasing CH4 oxidation by 50% on an annual basis. N fertilizers exerted only small and transient effects at the ecosystem level. Laboratory incubations suggested that effects differed between soil layers, with larger effects of drought and N application in the top soil than in deeper layers. With soil moisture being the primary controlling factor of methanotrophy, a detailed understanding of the ecosystem’s water balance is required to predict CH4 budgets under future climatic conditions

Subterranean atmospheres may act as daily methane sinks

In recent years, methane (CH4) has received increasing scientific attention because it is the most abundant non-CO2 atmospheric greenhouse gas (GHG) and controls numerous chemical reactions in the troposphere and stratosphere. However, there is much that is unknown about CH4 sources and sinks and their evolution over time. Here we show that near-surface cavities in the uppermost vadose zone are now actively removing atmospheric CH4. Through seasonal geochemical tracing of air in the atmosphere, soil and underground at diverse geographic and climatic locations in Spain, our results show that complete consumption of CH4 is favoured in the subsurface atmosphere under near vapour-saturation conditions and without significant intervention of methanotrophic bacteria. Overall, our results indicate that subterranean atmospheres may be acting as sinks for atmospheric CH4 on a daily scale. However, this terrestrial sink has not yet been considered in CH4 budget balances

Clostridiaceae and Enterobacteriaceae as active fermenters in earthworm gut content

The earthworm gut provides ideal in situ conditions for ingested heterotrophic soil bacteria capable of anaerobiosis. High amounts of mucus- and plant-derived saccharides such as glucose are abundant in the earthworm alimentary canal, and high concentrations of molecular hydrogen (H2) and organic acids in the alimentary canal are indicative of ongoing fermentations. Thus, the central objective of this study was to resolve potential links between fermentations and active fermenters in gut content of the anecic earthworm Lumbricus terrestris by 16S ribosomal RNA (rRNA)-based stable isotope probing, with [13C]glucose as a model substrate. Glucose consumption in anoxic gut content microcosms was rapid and yielded soluble organic compounds (acetate, butyrate, formate, lactate, propionate, succinate and ethanol) and gases (carbon dioxide and H2), products indicative of diverse fermentations in the alimentary canal. Clostridiaceae and Enterobacteriaceae were users of glucose-derived carbon. On the basis of the detection of 16S rRNA, active phyla in gut contents included Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Cyanobacteria, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, Proteobacteria, Tenericutes and Verrucomicrobia, taxa common to soils. On the basis of a 16S rRNA gene similarity cutoff of 87.5%, 82 families were detected, 17 of which were novel family-level groups. These findings (a) show the large diversity of soil taxa that might be active during gut passage, (b) show that Clostridiaceae and Enterobacteriaceae (fermentative subsets of these taxa) are selectively stimulated by glucose and might therefore be capable of consuming mucus- and plant-derived saccharides during gut passage and (c) indicate that ingested obligate anaerobes and facultative aerobes from soil can concomitantly metabolize the same source of carbon