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Background <p>Ginger [<i>Zingiber officinale</i> Roscoe (Zo)], an important spice crop, is highly susceptible to soft rot caused by necrotrophic <i>Pythium</i> spp., unlike its wild congener <i>Z</i>. <i>zerumbet</i> (L.) Smith (<i>Zz</i>), which displays robust resistance. Despite the established role of root endophytes in host defense, very few studies have explored the differential endophytic microbiome composition in rhizomes of resistant <i>Zz</i> and susceptible <i>Zo</i>.</p> Method <p>The endophytic rhizome microbiome of <i>Zz</i> and <i>Zo</i> was analyzed using 16S rRNA (V3–V4) metabarcoding.</p> Result <p>16S rRNA (V3-V4) metabarcoding of endophytic rhizome microbiome of <i>Zz</i> and <i>Zo</i> identified Proteobacteria and Cyanobacteria as major phyla with differential Proteobacteria composition in <i>Zz</i> [α-proteobacteria- 81% and γ- proteobacteria- 8%] and <i>Zo</i> [α-proteobacteria- 50%; γ- proteobacteria- 40% and β-proteobacteria- 7%]. Higher bacterial diversity and species variability estimated as α- diversity was observed in <i>Zo</i> (123 species; chao1: 506.06 ± 27.2; ACE: 496.61 ± 11.19; Fisher: 60.57) compared to <i>Zz</i> (77 species; chao1: 410.37 ± 31.5; ACE: 403.32 ± 10.6; Fisher: 46.17) with genus specificity like predominance of <i>Bacillus</i> and <i>Streptomyces</i> in <i>Zz</i> while <i>Pseudomonas</i>, <i>Enterobacter</i>, <i>Chitinophaga</i>, <i>Chryseobacterium</i> and <i>Caulobacter</i> in <i>Zo</i>. Estimates of β- diversity revealed higher variability in endophyte composition in <i>Zo</i> compared to <i>Zz</i> rhizomes.</p> Conclusion <p>Distinct genera like <i>Bacillus</i> and <i>Streptomyces</i> identified in resistant <i>Zz</i> holds potential as candidates for development of synthetic microbial communities (SynComs). These can be harnessed to reshape the ginger rhizome microbiome for conferring resistance against <i>Pythium</i>, a pathogen whose virulence and host invasion are profoundly shaped by climate change.</p> Graphical Abstract <p></p>

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Microbial dysbiosis underlies soft-rot susceptibility in ginger (Zingiber officinale Roscoe) compared to resistant Z. zerumbet (L.) Smith as revealed by 16S rRNA metabarcoding

  • 期刊论文

  • 发表日期：

    2026年1月27日

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  • Aswati R. Nair,
  • Harsha K

摘要

Background

Ginger [Zingiber officinale Roscoe (Zo)], an important spice crop, is highly susceptible to soft rot caused by necrotrophic Pythium spp., unlike its wild congener Z. zerumbet (L.) Smith (Zz), which displays robust resistance. Despite the established role of root endophytes in host defense, very few studies have explored the differential endophytic microbiome composition in rhizomes of resistant Zz and susceptible Zo.

Method

The endophytic rhizome microbiome of Zz and Zo was analyzed using 16S rRNA (V3–V4) metabarcoding.

Result

16S rRNA (V3-V4) metabarcoding of endophytic rhizome microbiome of Zz and Zo identified Proteobacteria and Cyanobacteria as major phyla with differential Proteobacteria composition in Zz [α-proteobacteria- 81% and γ- proteobacteria- 8%] and Zo [α-proteobacteria- 50%; γ- proteobacteria- 40% and β-proteobacteria- 7%]. Higher bacterial diversity and species variability estimated as α- diversity was observed in Zo (123 species; chao1: 506.06 ± 27.2; ACE: 496.61 ± 11.19; Fisher: 60.57) compared to Zz (77 species; chao1: 410.37 ± 31.5; ACE: 403.32 ± 10.6; Fisher: 46.17) with genus specificity like predominance of Bacillus and Streptomyces in Zz while Pseudomonas, Enterobacter, Chitinophaga, Chryseobacterium and Caulobacter in Zo. Estimates of β- diversity revealed higher variability in endophyte composition in Zo compared to Zz rhizomes.

Conclusion

Distinct genera like Bacillus and Streptomyces identified in resistant Zz holds potential as candidates for development of synthetic microbial communities (SynComs). These can be harnessed to reshape the ginger rhizome microbiome for conferring resistance against Pythium, a pathogen whose virulence and host invasion are profoundly shaped by climate change.

Graphical Abstract