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Are Basidiomycete Laccase Gene Abundance and Composition Related to Reduced Lignolytic Activity Under Elevated Atmospheric NO3 − Deposition in a Northern Hardwood Forest?

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Abstract

Anthropogenic release of biologically available N has increased atmospheric N deposition in forest ecosystems, which may slow decomposition by reducing the lignolytic activity of white-rot fungi. We investigated the potential for atmospheric N deposition to reduce the abundance and alter the composition of lignolytic basidiomycetes in a regional network of four northern hardwood forest stands receiving experimental NO3 − deposition (30 kg NO3 −−N ha−1 year−1) for a decade. To estimate the abundance of basidiomycetes with lignolytic potential, we used PCR primers targeting laccase (polyphenol oxidase) and quantitative fluorescence PCR to estimate gene copy number. Natural variation in laccase gene size permitted use of length heterogeneity PCR to profile basidiomycete community composition across two sampling dates in forest floor and mineral soil. Although past work has identified significant and consistent negative effects of NO3 − deposition on lignolytic enzyme activity, microbial biomass, soil respiration, and decomposition rate, we found no consistent effect of NO3 − deposition on basidiomycete laccase gene abundance or community profile. Rather, laccase abundance under NO3 − deposition was lower (−52%), higher (+223%), or unchanged, depending on stand. Only a single stand exhibited a significant change in basidiomycete laccase gene profile. Basidiomycete laccase genes occurring in mineral soil were a subset of the genes observed in the forest floor. Moreover, significant effects on laccase abundance were confined to the forest floor, suggesting that species composition plays some role in determining how lignolytic basidiomycetes are affected by N deposition. Community profiles differed between July and October sampling dates, and basidiomycete communities sampled in October had lower laccase gene abundance in the forest floor, but higher laccase abundance in mineral soil. Although experimental N deposition significantly suppresses lignolytic activity in these forests, this change is not related to the abundance or community composition of basidiomycete fungi with laccase genes. Understanding the expression of laccases and other lignolytic enzymes by basidiomycete fungi and other lignin-decaying organisms appears to hold promise for explaining the consistent decline in lignolytic activity elicited by experimental N deposition.

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Acknowledgments

This work was supported by grants from the NSF Ecosystem Studies Program (DEB 9629842, DEB 0315138, DEB 0614422), and by NSF-IGERT support to J.E. Hassett through the Biosphere Atmosphere Research Training program (DGE 0504552). Site access was made possible by the Manistee National Forest and the Michigan Department of Natural Resources. We thank the numerous contributors and collaborators who have supported this effort, especially Terrestrial Ecosystems Laboratory personnel at the University of Michigan. Nicole Seleno and Kirsten Hofmockel provided invaluable technical and analytical support. Editorial suggestions by Ivan Edwards were highly beneficial to manuscript development.

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  1. Christopher B. Blackwood

    Present address: Department of Biological Sciences, Kent State University, Kent, OH, USA

  2. Kurt S. Pregitzer

    Present address: Department of Natural Resources and Environmental Science, University of Nevada, Reno, NV, USA

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    John E. Hassett & Donald R. Zak

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Supplemental Table S1

Examples of length heterogeneity in published laccase sequences. Rows contain sequence information for specific laccase sequences presented in published reports, retrievable by GenBank accession number. For each sequence, columns indicate which of 18 identified sequence features is present between the Cu1F and Cu2R primer sites, as well as the total length of the expected PCR amplicon. Positions of sequence features are given in base pair, as measured 5′ to 3′ from the 5′ end of primer Cu1F on a consensus laccase sequence 142 bases long. For each sequence and feature, a numeric value indicates the length of a predicted intron in the sequence, (+) indicates a codon insertion/deletion, and (−) indicates no feature at the given position (PDF 13.6 KB)

Supplemental Figure S1

Intron map of partial basidiomycete laccase sequence, representing the 66% majority consensus amino acid sequence encoded by exons of 36 published laccase genes (see Supplemental Table 1). Sequence proceeds 5′→3′, enclosed areas represent PCR priming sites for primers Cu1F (left) and Cu2R (right). Tilde (~) indicates codon position without consensus. Open triangles (s) above sequence indicate the positions of 16 predicted introns; closed triangle (p) below sequence indicates position of a single codon insertion. Bar (−) spans the site of a single-codon deletion (PDF 28.5 KB)

Supplemental Figure S2

Examples of laccase LH-PCR profiles. Chromatograms were generated by capillary gel separation of PCR products amplified using basidiomycete laccase primers Cu1FFAM and Cu2R [S4]. Profiles display the results for single samples derived from the forest floor (A) and mineral soil (B) of stand A (PDF 191 KB)

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Hassett, J.E., Zak, D.R., Blackwood, C.B. et al. Are Basidiomycete Laccase Gene Abundance and Composition Related to Reduced Lignolytic Activity Under Elevated Atmospheric NO3 − Deposition in a Northern Hardwood Forest?. Microb Ecol 57, 728–739 (2009). https://doi.org/10.1007/s00248-008-9440-5

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