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      Who is who in litter decomposition? Metaproteomics reveals major microbial players and their biogeochemical functions

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          Abstract

          Leaf-litter decomposition is a central process in carbon cycling; however, our knowledge about the microbial regulation of this process is still scarce. Metaproteomics allows us to link the abundance and activity of enzymes during nutrient cycling to their phylogenetic origin based on proteins, the ‘active building blocks' in the system. Moreover, we employed metaproteomics to investigate the influence of environmental factors and nutrients on the decomposer structure and function during beech litter decomposition. Litter was collected at forest sites in Austria with different litter nutrient content. Proteins were analyzed by 1-D-SDS-PAGE followed by liquid-chromatography and tandem mass-spectrometry. Mass spectra were assigned to phylogenetic and functional groups by a newly developed bioinformatics workflow, assignments being validated by complementary approaches. We provide evidence that the litter nutrient content and the stoichiometry of C:N:P affect the decomposer community structure and activity. Fungi were found to be the main producers of extracellular hydrolytic enzymes, with no bacterial hydrolases being detected by our metaproteomics approach. Detailed investigation of microbial succession suggests that it is influenced by litter nutrient content. Microbial activity was stimulated at higher litter nutrient contents via a higher abundance and activity of extracellular enzymes.

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          Most cited references 34

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          Global analysis of nitrogen and phosphorus limitation of primary producers in freshwater, marine and terrestrial ecosystems.

          The cycles of the key nutrient elements nitrogen (N) and phosphorus (P) have been massively altered by anthropogenic activities. Thus, it is essential to understand how photosynthetic production across diverse ecosystems is, or is not, limited by N and P. Via a large-scale meta-analysis of experimental enrichments, we show that P limitation is equally strong across these major habitats and that N and P limitation are equivalent within both terrestrial and freshwater systems. Furthermore, simultaneous N and P enrichment produces strongly positive synergistic responses in all three environments. Thus, contrary to some prevailing paradigms, freshwater, marine and terrestrial ecosystems are surprisingly similar in terms of N and P limitation.
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            TANDEM: matching proteins with tandem mass spectra.

            Tandem mass spectra obtained from fragmenting peptide ions contain some peptide sequence specific information, but often there is not enough information to sequence the original peptide completely. Several proprietary software applications have been developed to attempt to match the spectra with a list of protein sequences that may contain the sequence of the peptide. The application TANDEM was written to provide the proteomics research community with a set of components that can be used to test new methods and algorithms for performing this type of sequence-to-data matching. The source code and binaries for this software are available at http://www.proteome.ca/opensource.html, for Windows, Linux and Macintosh OSX. The source code is made available under the Artistic License, from the authors.
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              Comparative metagenomics of microbial communities.

              The species complexity of microbial communities and challenges in culturing representative isolates make it difficult to obtain assembled genomes. Here we characterize and compare the metabolic capabilities of terrestrial and marine microbial communities using largely unassembled sequence data obtained by shotgun sequencing DNA isolated from the various environments. Quantitative gene content analysis reveals habitat-specific fingerprints that reflect known characteristics of the sampled environments. The identification of environment-specific genes through a gene-centric comparative analysis presents new opportunities for interpreting and diagnosing environments.
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                Author and article information

                Journal
                ISME J
                ISME J
                The ISME Journal
                Nature Publishing Group
                1751-7362
                1751-7370
                September 2012
                08 March 2012
                1 September 2012
                : 6
                : 9
                : 1749-1762
                Affiliations
                [1 ]Department of Microbiology, Institute of Plant Biology, University of Zurich , Zurich, Switzerland
                [2 ]Institute for Soil Research, Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences (BOKU) , Vienna, Austria
                [3 ]Institute of Applied Microbiology, Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) , Vienna, Austria
                [4 ]Functional Genomics Center, University & ETH Zurich , Zurich, Switzerland
                [5 ]Chemical Ecology and Ecosystem Research, University of Vienna , Vienna, Austria
                [6 ]School of Earth and Environment, The University of Western Australia , Crawley, Perth, Australia
                [7 ]Institute of Microbiology , Greifswald, Germany
                Author notes
                [* ]Current address: Department of Molecular Plant Physiology, Institute of Plant Biology, University of Zurich , Zollikerstrase 107, 8008 Zurich, Switzerland. E-mail: Thomas.Schneider@ 123456botinst.uzh.ch
                [8]

                These authors contributed equally to this work.

                Article
                ismej201211
                10.1038/ismej.2012.11
                3498922
                22402400
                Copyright © 2012 International Society for Microbial Ecology

                This work is licensed under the Creative Commons Attribution-NonCommercial-No Derivative Works 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-nd/3.0/

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