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Diversity, Interaction, and Bioprospecting of Plant-Associated Microbiomes
Article

Plant Broth- (Not Bovine-) Based Culture Media Provide the Most Compatible Vegan Nutrition for In Vitro Culturing and In Situ Probing of Plant Microbiota

1
ESRU, Department of Microbiology, Faculty of Agriculture, Cairo University, Giza 12613, Egypt
2
Algorithms in Bioinformatics, Center for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany
3
Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Shizuoka 411-8540, Japan
4
Regional Center for Food and Feed (RCFF), Agricultural Research Center (ARC), Giza 12613, Egypt
5
Department of Microbiology, Faculty of Agriculture & Natural Resources, Aswan University, Aswan 81528, Egypt
6
Department of Plant Microbe Systems, Leibniz Institute of Vegetable and Ornamental Crops, 14979 Großbeeren, Germany
*
Author to whom correspondence should be addressed.
Diversity 2020, 12(11), 418; https://doi.org/10.3390/d12110418
Received: 9 September 2020 / Revised: 23 October 2020 / Accepted: 29 October 2020 / Published: 4 November 2020
Plant microbiota support the diversity and productivity of plants. Thus, cultivation-dependent approaches are indispensable for in vitro manipulation of hub taxa. Despite recent advances in high-throughput methods, cultivability is lagging behind other environmental microbiomes, notably the human microbiome. As a plant-based culturing strategy, we developed culture media based on a broth of cooked aqueous mixtures of host plants. This improved the in vitro growth of representative isolates of plant microbiota and extended the in situ recovery of plant microbiota. With clover, 16S rRNA gene sequencing of representative isolates confirmed the predominance of Firmicutes, Alphaproteobacteria and Gammaproteobacteria, and less frequently Bacteroidetes and Actinobacteria. Whereas bovine-based culture media (modified R2A) confined the diversity to Firmicutes, the plant broth-based culture media revealed a wider scope of endophytes beyond rhizobia, i.e., multiple genera such as Chryseobacterium, Cronobacter, Kosakonia, Tsukamurella, and a potentially/presumptive novel species. Matrix-assisted laser desorption/ionization time-of-flight (MADI-TOF) analysis clustered isolates according to their plant niches, the endo-phyllosphere/endo-rhizosphere. We recommend the plant broth for simplicity, reproducibility and perdurable storage, supporting future culturomics applications, good laboratory practice (GLP) and good manufacturing practice (GMP). The strategy creates an “in-situ-similis” vegan nutritional matrix to analyze microbial diversity and reveal novel microbial resources pertinent to biotechnological and environmental applications. View Full-Text
Keywords: plant microbiota; cultivation-dependent of plant microbiota; plant broth-based culture media; “in-situ-similis” culturing strategy; vegan nutrition; clover bacterial endophytes plant microbiota; cultivation-dependent of plant microbiota; plant broth-based culture media; “in-situ-similis” culturing strategy; vegan nutrition; clover bacterial endophytes
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MDPI and ACS Style

Elsawey, H.; Patz, S.; Nemr, R.A.; Sarhan, M.S.; Hamza, M.A.; Youssef, H.H.; Abdelfadeel, M.R.; Daanaa, H.-S.A.; El-Tahan, M.; Abbas, M.; Fayez, M.; Witzel, K.; Ruppel, S.; Hegazi, N.A. Plant Broth- (Not Bovine-) Based Culture Media Provide the Most Compatible Vegan Nutrition for In Vitro Culturing and In Situ Probing of Plant Microbiota. Diversity 2020, 12, 418. https://doi.org/10.3390/d12110418

AMA Style

Elsawey H, Patz S, Nemr RA, Sarhan MS, Hamza MA, Youssef HH, Abdelfadeel MR, Daanaa H-SA, El-Tahan M, Abbas M, Fayez M, Witzel K, Ruppel S, Hegazi NA. Plant Broth- (Not Bovine-) Based Culture Media Provide the Most Compatible Vegan Nutrition for In Vitro Culturing and In Situ Probing of Plant Microbiota. Diversity. 2020; 12(11):418. https://doi.org/10.3390/d12110418

Chicago/Turabian Style

Elsawey, Hend, Sascha Patz, Rahma A. Nemr, Mohamed S. Sarhan, Mervat A. Hamza, Hanan H. Youssef, Mohamed R. Abdelfadeel, Hassan-Sibroe A. Daanaa, Mahmoud El-Tahan, Mohamed Abbas, Mohamed Fayez, Katja Witzel, Silke Ruppel, and Nabil A. Hegazi 2020. "Plant Broth- (Not Bovine-) Based Culture Media Provide the Most Compatible Vegan Nutrition for In Vitro Culturing and In Situ Probing of Plant Microbiota" Diversity 12, no. 11: 418. https://doi.org/10.3390/d12110418

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