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A metaproteomic approach dissecting major bacterial functions in the rhizosphere of plants living in serpentine soil

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Abstract

A metaproteomic approach, based on liquid chromatography-high resolution mass spectrometry (LC-HRMS) analysis, was followed to map the major bacterial metabolic functions associated with the rhizosphere of metal-tolerant and metal hyperaccumulator plants, growing in a serpentine soil naturally contaminated by heavy metals such as Ni, Co and Cr. In particular, an “in-house” bacterial protein database was built based on the genera recognised by 16S rDNA profiling, then it was used for protein identification from LC-MS data. The combination of the information arising from three different extraction protocols, applied to each soil sample, permitted the identification of almost 800 proteins, corresponding to functions assigned to proper Gene Ontology categories. Mainly proteins involved in response to stimulus or in transport of metals and nutrients revealed variability of bacteria responses to microenvironment conditions. As for taxonomy, Phyllobacterium, Microbacterium oxidans, Pseudomonas oryzihabitans, Stenotrophomonas rhizophila and Bacillus methylotrophicus bacterial species were more represented in the rhizosphere samples of the metal-tolerant Biscutella laevigata and of the Ni hyperaccumulator Noccaea caerulescens with respect to bulk soil. Combining 16S rRNA gene-based sequencing and metaproteomic analysis, we get insights into microbial community functions and their interaction with plants colonising the stressful environment of serpentine soils.

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Authors and Affiliations

  1. Dipartimento di Chimica, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy

    Monica Mattarozzi & Maria Careri

  2. Dipartimento di Scienze e Innovazione Tecnologica, University of Piemonte Orientale, Viale Teresa Michel 11, 15121, Alessandria, Italy

    Marcello Manfredi, Fabio Gosetti & Emilio Marengo

  3. ISALIT S.r.l., via Bovio 6, 28100, Novara, Italy

    Marcello Manfredi

  4. Dipartimento di Bioscienze, University of Parma, Parco Area delle Scienze 11/A, 43124, Parma, Italy

    Barbara Montanini, Anna Maria Sanangelantoni & Giovanna Visioli

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  1. Monica Mattarozzi
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  2. Marcello Manfredi
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  3. Barbara Montanini
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  4. Fabio Gosetti
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  5. Anna Maria Sanangelantoni
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  6. Emilio Marengo
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  7. Maria Careri
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  8. Giovanna Visioli
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Correspondence to Giovanna Visioli.

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This research was in part supported by funding to Prof. Anna Maria Sanangelantoni and to Dr. Giovanna Visioli from FIL of the University of Parma Local Funding for Research.

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Mattarozzi, M., Manfredi, M., Montanini, B. et al. A metaproteomic approach dissecting major bacterial functions in the rhizosphere of plants living in serpentine soil. Anal Bioanal Chem 409, 2327–2339 (2017). https://doi.org/10.1007/s00216-016-0175-8

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