Abstract

Ratooning in sugarcane is crucial for agriculture sustainability, but the changes in microbial communities during consecutive ratooning remain unclear. We employed a shotgun metagenomic approach using Illumina 454 sequencing to investigate the root-associated microbial community in four sugarcane plantation sites, with three sites in the Dompu Regency and one in the Madiun Regency. The results revealed variations in the root-associated microbiome between ratoon and plant cane, as well as across different sites. pH, total organic carbon, and nitrogen were found to influence the community structure. Across the four sites, we identified 395 species, including 382 species of bacteria, 10 species of archaea, and 3 species of eukaryotes. In the ratoon plants of Dompu, the most abundant species was Paraburkholderia caribensis (40%), whereas in the plant cane dominated by Rhizobium pusense (16%)., In Madiun, the predominant species in ratoon plants was Rhodanobacter sp. DHG33 (20%) and Paraburkholderia sp. SOS3 (16%). These bacterial species may serve as key contributors to plant growth in ratooning plantations in these regions. The fungal community declined during the ratooning cycle but increased at later stages, possibly indicating a more stable fungal community in mature ratoon crops. The community structure varied, with bacteria more abundant in Dompu Regency's ratoon plants and archaea in Madiun Regency's ratoon plants. Understanding microbial dynamics across these four sites will support the development of sustainable strategies for ratooning practices in sugarcane production.

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