Selective Isolation and Polyphasic Characterization of Culturable Endophytes from Tuber Crops: A Critical Appraisal of Methodologies, Challenges, and Evidence-Based Recommendations
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Abstract
Endophytic microorganisms in tuber crops (yam, cassava, sweet potato, potato, and taro) are valuable reservoirs of genetic and metabolic diversity for plant health and sustainable agriculture. However, selective isolation and accurate characterization of culturable endophytes from these subterranean organs are challenging due to high starch and phenolic content, the co-occurrence of fastidious and slow-growing taxa, epiphytic contamination risks, and loss of culturability upon subcultivation. This review synthesizes methodological developments from 87 eligible studies (2020–2026) identified via systematic searches of PubMed, Scopus, and Web of Science. Optimized surface sterilization using 70% ethanol (1–3 min) followed by 1–5% sodium hypochlorite (2–10 min) with validated sterility checks remains standard, though crop-specific adjustments are essential. Multi-media strategies combining low-nutrient media (R2A, 1/10 TSA) with selective media significantly improve recovery breadth. Extended incubation (4–12 weeks) and microaerophilic conditions are critical for recovering slow-growing and facultative anaerobic taxa. Polyphasic characterization integrating MALDI-TOF MS, multilocus sequence analysis, and whole-genome sequencing with average nucleotide identity calculations provides superior taxonomic resolution compared to single-gene approaches. Evidence for crop-specific recommendations remains uneven, with potato and cassava better studied than yam, sweet potato, and taro. Critical knowledge gaps include limited comparative studies across crops, insufficient validation of best practices, and the need for standardized reporting. We provide recommendations for protocol standardization, quality control implementation, effective culture preservation, and integration of culture-omic strategies to maximize recovery and taxonomic resolution of beneficial endophytes from tuber crops.
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