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      Ectomycorrhizal fungi decompose soil organic matter using oxidative mechanisms adapted from saprotrophic ancestors

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          • Ectomycorrhizal fungi are thought to have a key role in mobilizing organic nitrogen that is trapped in soil organic matter ( SOM). However, the extent to which ectomycorrhizal fungi decompose SOM and the mechanism by which they do so remain unclear, considering that they have lost many genes encoding lignocellulose‐degrading enzymes that are present in their saprotrophic ancestors.

          • Spectroscopic analyses and transcriptome profiling were used to examine the mechanisms by which five species of ectomycorrhizal fungi, representing at least four origins of symbiosis, decompose SOM extracted from forest soils.

          • In the presence of glucose and when acquiring nitrogen, all species converted the organic matter in the SOM extract using oxidative mechanisms. The transcriptome expressed during oxidative decomposition has diverged over evolutionary time. Each species expressed a different set of transcripts encoding proteins associated with oxidation of lignocellulose by saprotrophic fungi. The decomposition ‘toolbox’ has diverged through differences in the regulation of orthologous genes, the formation of new genes by gene duplications, and the recruitment of genes from diverse but functionally similar enzyme families.

          • The capacity to oxidize SOM appears to be common among ectomycorrhizal fungi. We propose that the ancestral decay mechanisms used primarily to obtain carbon have been adapted in symbiosis to scavenge nutrients instead.

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          ProtTest: selection of best-fit models of protein evolution.

          Using an appropriate model of amino acid replacement is very important for the study of protein evolution and phylogenetic inference. We have built a tool for the selection of the best-fit model of evolution, among a set of candidate models, for a given protein sequence alignment. ProtTest is available under the GNU license from http://darwin.uvigo.es
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            Ectomycorrhizal fungi - potential organic matter decomposers, yet not saprotrophs.

            Although hypothesized for many years, the involvement of ectomycorrhizal fungi in decomposition of soil organic matter remains controversial and has not yet been fully acknowledged as an important factor in the regulation of soil carbon (C) storage. Here, we review recent findings, which support the view that some ectomycorrhizal fungi have the capacity to oxidize organic matter, either by 'brown-rot' Fenton chemistry or using 'white-rot' peroxidases. We propose that ectomycorrhizal fungi benefit from organic matter decomposition primarily through increased nitrogen mobilization rather than through release of metabolic C and question the view that ectomycorrhizal fungi may act as facultative saprotrophs. Finally, we discuss how mycorrhizal decomposition may influence organic matter storage in soils and mediate responses of ecosystem C sequestration to environmental changes. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.
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              Characterization and genomic analysis of kraft lignin biodegradation by the beta-proteobacterium Cupriavidus basilensis B-8

              Background Lignin materials are abundant and among the most important potential sources for biofuel production. Development of an efficient lignin degradation process has considerable potential for the production of a variety of chemicals, including bioethanol. However, lignin degradation using current methods is inefficient. Given their immense environmental adaptability and biochemical versatility, bacterial could be used as a valuable tool for the rapid degradation of lignin. Kraft lignin (KL) is a polymer by-product of the pulp and paper industry resulting from alkaline sulfide treatment of lignocellulose, and it has been widely used for lignin-related studies. Results Beta-proteobacterium Cupriavidus basilensis B-8 isolated from erosive bamboo slips displayed substantial KL degradation capability. With initial concentrations of 0.5–6 g L-1, at least 31.3% KL could be degraded in 7 days. The maximum degradation rate was 44.4% at the initial concentration of 2 g L-1. The optimum pH and temperature for KL degradation were 7.0 and 30°C, respectively. Manganese peroxidase (MnP) and laccase (Lac) demonstrated their greatest level of activity, 1685.3 U L-1 and 815.6 U L-1, at the third and fourth days, respectively. Many small molecule intermediates were formed during the process of KL degradation, as determined using GC-MS analysis. In order to perform metabolic reconstruction of lignin degradation in this bacterium, a draft genome sequence for C. basilensis B-8 was generated. Genomic analysis focused on the catabolic potential of this bacterium against several lignin-derived compounds. These analyses together with sequence comparisons predicted the existence of three major metabolic pathways: β-ketoadipate, phenol degradation, and gentisate pathways. Conclusion These results confirmed the capability of C. basilensis B-8 to promote KL degradation. Whole genomic sequencing and systematic analysis of the C. basilensis B-8 genome identified degradation steps and intermediates from this bacterial-mediated KL degradation method. Our findings provide a theoretical basis for research into the mechanisms of lignin degradation as well as a practical basis for biofuel production using lignin materials.
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                Author and article information

                Journal
                New Phytol
                New Phytol
                10.1111/(ISSN)1469-8137
                NPH
                The New Phytologist
                John Wiley and Sons Inc. (Hoboken )
                0028-646X
                1469-8137
                March 2016
                03 November 2015
                : 209
                : 4 ( doiID: 10.1111/nph.2016.209.issue-4 )
                : 1705-1719
                Affiliations
                [ 1 ] Department of Biology Microbial Ecology GroupLund University Ecology Building SE‐223 62 LundSweden
                [ 2 ] Centre for Environmental SciencesHasselt University Building D Agoralaan 3590 Diepenbeek LimburgBelgium
                [ 3 ] Biology Department Lasry Center for BioscienceClark University 950 Main Street Worcester MA 01610‐1477USA
                [ 4 ] Department of Pharmaceutical Microbiology at the Hans Knöll InstituteFriedrich‐Schiller‐Universität Beutenbergstrasse 11a 07745 JenaGermany
                [ 5 ] Centre National de la Recherche Scientifique (CNRS)UMR7257 Université Aix‐Marseille Marseille 13288France
                [ 6 ] Department of Biological SciencesKing Abdulaziz University JeddahSaudi Arabia
                [ 7 ] Bioinformatics Infrastructures for Life Sciences (BILS) Department of BiologyLund University Ecology Building SE‐223 62 LundSweden
                [ 8 ] Institut de la Recherche Agronomique (INRA) Laboratory of Excellence ARBREUMR INRA‐Université de Lorraine ‘Interactions Arbres/Micro‐organismes’ INRA‐Nancy 54280 ChampenouxFrance
                [ 9 ] Centre for Environmental and Climate Research (CEC)Lund University Ecology Building SE‐223 62 LundSweden
                Author notes
                [*] [* ] Author for correspondence:

                Anders Tunlid

                Tel: +46 46 222 37 57

                Email: anders.tunlid@ 123456biol.lu.se

                Author information
                http://orcid.org/0000-0002-4737-3715
                Article
                NPH13722 2015-19899
                10.1111/nph.13722
                5061094
                26527297
                70a1c492-6c3f-423b-9360-cd80d4133d42
                © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust

                This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 08 June 2015
                : 22 September 2015
                Page count
                Pages: 15
                Funding
                Funded by: Swedish Research Council
                Funded by: Knut and Alice Wallenberg Foundation
                Funded by: Biodiversity and Ecosystem Services in a Changing Climate
                Funded by: French National Research Agency
                Funded by: Laboratory of Excellence ARBRE
                Award ID: ANR‐11‐LABX‐0002‐01
                Funded by: Office of Science of the US Department of Energy
                Categories
                Full Paper
                Research
                Full Papers
                Custom metadata
                2.0
                nph13722
                March 2016
                Converter:WILEY_ML3GV2_TO_NLMPMC version:4.9.4 mode:remove_FC converted:12.10.2016

                Plant science & Botany
                decomposition,ectomycorrhizal fungi,evolution,soil organic matter,spectroscopy,transcriptome

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