Fungi Unearthed: Transcripts Encoding Lignocellulolytic and Chitinolytic Enzymes in Forest Soil

Abstract

BackgroundFungi are the main organisms responsible for the degradation of biopolymers such as lignin, cellulose, hemicellulose, and chitin in forest ecosystems. Soil surveys largely target fungal diversity, paying less attention to fungal activity.Methodology/Principal FindingsHere we have focused on the organic horizon of a hardwood forest dominated by sugar maple that spreads widely across Eastern North America. The sampling site included three plots receiving normal atmospheric nitrogen deposition and three that received an extra 3 g nitrogen m−2 y−1 in form of sodium nitrate pellets since 1994, which led to increased accumulation of organic matter in the soil. Our aim was to assess, in samples taken from all six plots, transcript-level expression of fungal genes encoding lignocellulolytic and chitinolytic enzymes. For this we collected RNA from the forest soil, reverse-transcribed it, and amplified cDNAs of interest, using both published primer pairs as well as 23 newly developed ones. We thus detected transcript-level expression of 234 genes putatively encoding 26 different groups of fungal enzymes, notably major ligninolytic and diverse aromatic-oxidizing enzymes, various cellulose- and hemicellulose-degrading glycoside hydrolases and carbohydrate esterases, enzymes involved in chitin breakdown, N-acetylglucosamine metabolism, and cell wall degradation. Among the genes identified, 125 are homologous to known ascomycete genes and 105 to basidiomycete genes. Transcripts corresponding to all 26 enzyme groups were detected in both control and nitrogen-supplemented plots.Conclusions/SignificanceMany of these enzyme groups are known to be important in soil turnover processes, but the contribution of some is probably underestimated. Our data highlight the importance of ascomycetes, as well as basidiomycetes, in important biogeochemical cycles. In the nitrogen-supplemented plots, we have detected no transcript-level gap likely to explain the observed increased carbon storage, which is more likely due to community changes and perhaps transcriptional and/or post-transcriptional down-regulation of relevant genes.

Distribution of Extracellular Enzymes in Soils: Spatial Heterogeneity and Determining Factors at Various Scales

“…These approaches have been combined in studies that specifically target laccase (Luis et al, 2005a), exocellulase Eichorst and Kuske, 2012), or a range of various glycosyl hydrolases and oxidases (Kellner and Vandenbol, 2010) in forest soils and are highly attractive due to their theoretical potential to assign gene sequences to specific groups of soil microorganisms. Single-gene-oriented surveys suffer from limitations, however, due to their limited applicability to only highly similar gene sequences (often a single protein family) and varying specificity of polymerase chain reaction (PCR) primers.…”

Enzymatic Degradation of Lignin in Soil: A Review

“…Degradation studies are mainly biotic, aerobic, and co-metabolic. Studies have shown that certain bacteria [10] and fungi [11] are able to break down various biopolymers in soil. Lignocellulosic biomass degradation has been widely studied in wood-rotting Baciomycetes fungi due to their potential to degrade lignin.…”

Atmospheric N Deposition Increases Bacterial Laccase-Like Multicopper Oxidases: Implications for Organic Matter Decay

“…Lignin decay is mediated by lignin-peroxidases (LiP), manganese-peroxidases (MnP), and laccases thought to be of largely fungal origin and can result in complete metabolism to CO 2 (26)(27)(28). The high redox potential of LiP and MnP enables the oxidation of both phenolic and nonphenolic lignin units (ϳ90% of the polymer), whereas the lower redox potential of laccases oxidize phenolic lignin units, often comprising ϳ10% of the polymer (29).…”