Agricultural and Biosystems Engineering Publications

Campus Units

Agricultural and Biosystems Engineering, Bioinformatics and Computational Biology

Document Type


Publication Version

Published Version

Publication Date


Journal or Book Title

Soil Biology and Biochemistry



First Page


Research Focus Area(s)

Biological and Process Engineering and Technology




Temperate coniferous forests sustain the highest levels of biomass of all terrestrial ecosystems and belong to the major carbon sinks on Earth. However, the community composition and its functional diversity depending on the habitat have yet to be unveiled. Here, we analyzed the proteomes from litter, plant roots, rhizosphere, and bulk soil in a temperate coniferous forest at two time points to improve the understanding of the interplay between bacterial and eukaryotic communities in different habitats. Our metaproteomic approach yielded a total of 139,127 proteins that allowed to differentiate the contribution of microbial taxa to protein expression as well as the general functionality based on KEGG Orthology in each habitat. The pool of expressed carbohydrate-active enzymes (CAZymes) was dominated by fungal proteins. While CAZymes in roots and litter targeted mostly the structural biopolymers of plant origin such as lignin and cellulose, the majority of CAZymes in bulk and rhizosphere soil targeted oligosaccharides, starch, and glycogen. Proteins involved in nitrogen cycling were mainly of bacterial origin. Most nitrogen cycling proteins in litter and roots participated in ammonium assimilation while those performing nitrification were the most abundant in bulk and rhizosphere soil. Together, our results indicated niche differentiation of the microbial involvement in carbon and nitrogen cycling in a temperate coniferous forest topsoil.


This article is published as Robert Starke, Rubén López Mondéjar, Zander Rainer Human, Diana Navrátilová, Martina Štursová, Tomáš Větrovský, Heather M. Olson, Daniel J. Orton, Stephen J. Callister, Mary S. Lipton, Adina Howe, Lee Ann McCue, Christa Pennacchio, Igor Grigoriev, and Petr Baldrian. "Niche differentiation of bacteria and fungi in carbon and nitrogen cycling of different habitats in a temperate coniferous forest: A metaproteomic approach." Soil Biology and Biochemistry (2021): 108170. DOI: 10.1016/j.soilbio.2021.108170.




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