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<p>Continuous ratooning has adversely affected microbial diversity and sugarcane productivity. However, studies on the dynamic effects of ongoing sugarcane ratooning shape its microbial structure and functional genes are limited. This study employed shotgun metagenomic analysis to investigate the microbial structure and its functional profiles in sugarcane’s endophyte and rhizosphere microbiome across three ratoon cycles: non-ratoon (L0), third ratoon (L3), and ninth ratoon (L9). Soil and sugarcane root samples were collected from a dry cultivation area at the Dompu site in West Nusa Tenggara, Indonesia, in August 2023. Our findings revealed significant shifts in functional composition across ratoon cycles and sample types, as determined by PERMANOVA analysis (<i>p</i> &lt; 0.01). Further examinations focused on functional genes related to macro- and micronutrient cycling, plant-promoting hormones, and drought stress resilience. Pathways associated with nutrient limitations and drought stress resilience exhibited notable abundance, including nitrogen limitation sensing, responses to phosphorus starvation, ROS scavenging, and the biosynthesis of EPS and proline. Multiple bacterial species were found to regulate these pathways, emphasizing the importance of preserving key functions. Notably, we observed distinct patterns of bacterial species across ratoon cycles: <i>Enterobacter bugandensis</i> and <i>Herbaspirillum frisingense</i> were predominant in L0 and L3; <i>Paraburkholderia caribensis, Bradyrhizobium arachidis,</i> and <i>Variovorax paradoxus</i> were more pronounced in L3 and L9; and <i>Serratia nematodiphila</i> uniquely found in L9. These changes underscore how continuous ratooning alters the microbial and functional composition, aiding sugarcane in coping with nutrient limitations and stress accumulation.</p>

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Unraveling Microbial and Functional Gene Dynamics Across Continuous Ratoon Cycles of Sugarcane

  • 期刊论文

  • 发表日期：

    2025年12月20日

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  • Sulastri Sulastri,
  • Lina Herlıana,
  • Rika Sri Rahmawati,
  • Nur Alfi Saryanah,
  • Yuda Purwana Roswanjaya,
  • R. Bambang Sukmadi,
  • Ana Feronika Cindra Irawati,
  • Nia Asiani

摘要

Continuous ratooning has adversely affected microbial diversity and sugarcane productivity. However, studies on the dynamic effects of ongoing sugarcane ratooning shape its microbial structure and functional genes are limited. This study employed shotgun metagenomic analysis to investigate the microbial structure and its functional profiles in sugarcane’s endophyte and rhizosphere microbiome across three ratoon cycles: non-ratoon (L0), third ratoon (L3), and ninth ratoon (L9). Soil and sugarcane root samples were collected from a dry cultivation area at the Dompu site in West Nusa Tenggara, Indonesia, in August 2023. Our findings revealed significant shifts in functional composition across ratoon cycles and sample types, as determined by PERMANOVA analysis (p < 0.01). Further examinations focused on functional genes related to macro- and micronutrient cycling, plant-promoting hormones, and drought stress resilience. Pathways associated with nutrient limitations and drought stress resilience exhibited notable abundance, including nitrogen limitation sensing, responses to phosphorus starvation, ROS scavenging, and the biosynthesis of EPS and proline. Multiple bacterial species were found to regulate these pathways, emphasizing the importance of preserving key functions. Notably, we observed distinct patterns of bacterial species across ratoon cycles: Enterobacter bugandensis and Herbaspirillum frisingense were predominant in L0 and L3; Paraburkholderia caribensis, Bradyrhizobium arachidis, and Variovorax paradoxus were more pronounced in L3 and L9; and Serratia nematodiphila uniquely found in L9. These changes underscore how continuous ratooning alters the microbial and functional composition, aiding sugarcane in coping with nutrient limitations and stress accumulation.