An inoculum-dependent culturing strategy (IDC) for the cultivation of environmental microbiomes and the isolation of novel endophytic Actinobacteria

• Published in: Journal of antibiotics Vol. 73; no. 1; pp. 66 - 71
• Main Authors: Sarhan, Mohamed S., Mourad, Elhussein F., Nemr, Rahma A., Abdelfadeel, Mohamed R., Daanaa, Hassan-Sibroe A., Youssef, Hanan H., Goda, Hanan A., Hamza, Mervat A., Fayez, Mohamed, Eichler-Löbermann, Bettina, Ruppel, Silke, Hegazi, Nabil A.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.01.2020; Nature Publishing Group
• Subjects: 38/22; 45/23; 45/29; 45/77; 631/1647/2234; 631/326/1320; 631/326/2565/855; 82/29; Actinobacteria - chemistry; Bacteriological Techniques; Bacteriology; Biomedical and Life Sciences; Bioorganic Chemistry; Brief Communication; Colony Count, Microbial; Cultivation; Culture Media; Endophytes - chemistry; Life Sciences; Medicinal Chemistry; Microbiology; Microbiota; Nutrients; Organic Chemistry; Plant Roots - microbiology; Plant Shoots - microbiology; Plants - microbiology
• ISSN: 0021-8820; 1881-1469
• DOI: 10.1038/s41429-019-0226-4

The recent introduction of plant-only-based culture media enabled cultivation of not-yet-cultured bacteria that exceed 90% of the plant microbiota communities. Here, we further prove the competence and challenge of such culture media, and further introduce “the inoculum-dependent culturing strategy, IDC”. The strategy depends on direct inoculating plant serial dilutions onto plain water agar plates, allowing bacteria to grow only on the expense of natural nutrients contained in the administered inoculum. Developed colonies are successively transferred/subcultured onto plant-only-based culture media, which contains natural nutrients very much alike to those found in the prepared plant inocula. Because of its simplicity, the method is recommended as a powerful tool in screening programs that require microbial isolation from a large number of diverse plants. Here, the method comfortably and successfully recovered several isolates of endophytic Actinobacteria represented by the six genera of Curtobacterium spp., Plantibacter spp., Agreia spp., Herbiconiux spp., Rhodococcus spp., and Nocardioides spp. Furthermore, two of the isolates are most likely novel species belonging to Agreia spp. and Herbiconiux spp.