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<p><i>Paraburkholderia sabiae</i> LMG24235<sup>T</sup> is a beta-proteobacterium originally isolated from <i>Mimosa caesalpiniifolia</i> nodules that efficiently outcompetes phytopathogens both in vitro and <i>in planta</i>. Here we show that <i>P. sabiae</i> LMG24235<sup>T</sup> can spontaneously lose a 2.3-Mbp replicon, resulting in a reduction of genome size by approximately one quarter and representing the first reported case of a bacterium losing 23% of its genome in a single event. Phylogenetic analysis of the replication initiation protein A (RepA) revealed that this replicon is closely related to megaplasmids found in other <i>Paraburkholderia</i> strains and a randomly barcoded transposon mutagenesis (RB-TnSeq) analysis showed that it contains very few predicted likely-essential genes, all of which are dispensable for growth. In contrast to the wild-type strain, <i>P. sabiae</i> lacking the second replicon (Δ2) exhibited a growth defect on D-trehalose and L-leucine, reduced motility and decreased survival under low-oxygen conditions. While growth in rich medium was otherwise unaffected, <i>P. sabiae</i> Δ2 was outcompeted by the wild type in vitro, and <i>M. caesalpiniifolia</i> nodules occupied by Δ2 fixed 40% less nitrogen compared to wild-type nodules. These results suggest that the second replicon is not an essential chromosomal element but rather a dispensable large megaplasmid that confers a competitive advantage to <i>P. sabiae</i> LMG24235<sup>T</sup> in its natural environment.</p>

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Extensive spontaneous genome reduction in Paraburkholderia sabiae

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年4月29日

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  • Kim Bolli,
  • Colin Waichler,
  • Yilei Liu,
  • Daphné Golaz,
  • Adam M. Deutschbauer,
  • Leo Eberl,
  • Sebastian J. Hug,
  • Marta Torres,
  • Gabriella Pessi

摘要

Paraburkholderia sabiae LMG24235T is a beta-proteobacterium originally isolated from Mimosa caesalpiniifolia nodules that efficiently outcompetes phytopathogens both in vitro and in planta. Here we show that P. sabiae LMG24235T can spontaneously lose a 2.3-Mbp replicon, resulting in a reduction of genome size by approximately one quarter and representing the first reported case of a bacterium losing 23% of its genome in a single event. Phylogenetic analysis of the replication initiation protein A (RepA) revealed that this replicon is closely related to megaplasmids found in other Paraburkholderia strains and a randomly barcoded transposon mutagenesis (RB-TnSeq) analysis showed that it contains very few predicted likely-essential genes, all of which are dispensable for growth. In contrast to the wild-type strain, P. sabiae lacking the second replicon (Δ2) exhibited a growth defect on D-trehalose and L-leucine, reduced motility and decreased survival under low-oxygen conditions. While growth in rich medium was otherwise unaffected, P. sabiae Δ2 was outcompeted by the wild type in vitro, and M. caesalpiniifolia nodules occupied by Δ2 fixed 40% less nitrogen compared to wild-type nodules. These results suggest that the second replicon is not an essential chromosomal element but rather a dispensable large megaplasmid that confers a competitive advantage to P. sabiae LMG24235T in its natural environment.