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Comparative Genomics Reveal the High Conservation and Scarce Distribution of Nitrogen Fixation nif Genes in the Plant-Associated Genus Herbaspirillum

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Abstract

The genus Herbaspirillum gained the spotlight due to the several reports of diazotrophic strains and promising results in plant-growth field assays. However, as diversity exploration of Herbaspirillum species gained momentum, it became clearer that the plant beneficial lifestyle was not the only form of ecological interaction in this genus, due to reports of phytopathogenesis and nosocomial infections. Here we performed a deep search across all publicly available Herbaspirillum genomes. Using a robust core genome phylogeny, we have found that all described species are well delineated, being the only exception H. aquaticum and H. huttiense clade. We also uncovered that the nif genes are only highly prevalent in H. rubrisubalbicans; however, irrespective to the species, all nif genes share the same gene arrangement with high protein identity, and are present in only two main types, in inverted strands. By means of a NifHDKENB phylogenetic tree, we have further revealed that the Herbaspirillum nif sequences may have been acquired from the same last common ancestor belonging to the Nitrosomonadales order.

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Authors and Affiliations

  1. CAL CCA UFSC, Food Science and Technology Department, Federal University of Santa Catarina, Rod. Admar Gonzaga, Florianopolis, SC, 1346, 88034-001, Brazil

    Ana Marina Pedrolo & Ana Carolina Maisonnave Arisi

  2. ESALQ USP, Soil Science Department, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, 13418-900, Brazil

    Filipe Pereira Matteoli

  3. MIP CCB UFSC, Microbiology, Immunology and Parasitology Department, Federal University of Santa Catarina, Av. Prof. Henrique da Silva Fontes, Florianopolis, SC, 2754, 88040-900, Brazil

    Cláudio Roberto Fônseca Sousa Soares

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A. M. P., conceptualization, writing, original draft, methodology, and investigation. F. P. M., writing — final draft, methodology, data curation, investigation, and visualization. A. C. M. A. and C. R. F. S. S., conceptualization, supervision, and writing — review and editing.

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Pedrolo, A.M., Matteoli, F.P., Soares, C.R.F.S. et al. Comparative Genomics Reveal the High Conservation and Scarce Distribution of Nitrogen Fixation nif Genes in the Plant-Associated Genus Herbaspirillum. Microb Ecol 86, 563–574 (2023). https://doi.org/10.1007/s00248-022-02084-8

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