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Microbial genomics, transcriptomics and proteomics: new discoveries in decomposition research using complementary methods

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Abstract

Molecular methods for the analysis of biomolecules have undergone rapid technological development in the last decade. The advent of next-generation sequencing methods and improvements in instrumental resolution enabled the analysis of complex transcriptome, proteome and metabolome data, as well as a detailed annotation of microbial genomes. The mechanisms of decomposition by model fungi have been described in unprecedented detail by the combination of genome sequencing, transcriptomics and proteomics. The increasing number of available genomes for fungi and bacteria shows that the genetic potential for decomposition of organic matter is widespread among taxonomically diverse microbial taxa, while expression studies document the importance of the regulation of expression in decomposition efficiency. Importantly, high-throughput methods of nucleic acid analysis used for the analysis of metagenomes and metatranscriptomes indicate the high diversity of decomposer communities in natural habitats and their taxonomic composition. Today, the metaproteomics of natural habitats is of interest. In combination with advanced analytical techniques to explore the products of decomposition and the accumulation of information on the genomes of environmentally relevant microorganisms, advanced methods in microbial ecophysiology should increase our understanding of the complex processes of organic matter transformation.

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Acknowledgments

This work was supported by the Ministry of Education, Youth and Sports of the Czech Republic projects LD12048 and CZ.1.07/2.3.00/30.0003 and by the Research Concept of the Institute of Microbiology ASCR (RVO61388971).

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The authors declare that they have no conflict of interest.

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  1. Laboratory of Environmental Microbiology, Institute of Microbiology of the ASCR, Vídeňská 1083, 14220, Prague 4, Czech Republic

    Petr Baldrian & Rubén López-Mondéjar

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  1. Petr Baldrian
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Correspondence to Petr Baldrian.

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Baldrian, P., López-Mondéjar, R. Microbial genomics, transcriptomics and proteomics: new discoveries in decomposition research using complementary methods. Appl Microbiol Biotechnol 98, 1531–1537 (2014). https://doi.org/10.1007/s00253-013-5457-x

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