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Ji C, Guo J, Ma Y, Xu X, Zang T, Liu S, An Z, Yang M, He X, Zheng W. Application Progress of Culturomics in the Isolated Culture of Rhizobacteria: A Review. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:7586-7595. [PMID: 38530921 DOI: 10.1021/acs.jafc.3c08885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
Comprehending the structure and function of rhizobacteria components and their regulation are crucial for sustainable agricultural management. However, obtaining comprehensive species information for most bacteria in the natural environment, particularly rhizobacteria, presents a challenge using traditional culture methods. To obtain diverse and pure cultures of rhizobacteria, this study primarily reviews the evolution of rhizobacteria culturomics and associated culture methods. Furthermore, it explores new strategies for enhancing the application of culturomics, providing valuable insights into efficiently enriching and isolate target bacterial strains/groups from the environment. The findings will help improve rhizobacteria's culturability and enrich the functional bacterial library.
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Affiliation(s)
- Chao Ji
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Junli Guo
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Ying Ma
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Xiangfu Xu
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Tongyu Zang
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Sentao Liu
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Zhenzhen An
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Min Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, National Engineering Research Center for Applied Technology of Agricultural Biodiversity, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Xiahong He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, National Engineering Research Center for Applied Technology of Agricultural Biodiversity, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan 650201, China
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Landscape Architecture Engineering Research Center of National Forestry and Grassland Administration, Southwest Forestry University, Kunming, Yunnan 650224, China
| | - Wenjie Zheng
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, National Engineering Research Center for Applied Technology of Agricultural Biodiversity, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan 650201, China
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Landscape Architecture Engineering Research Center of National Forestry and Grassland Administration, Southwest Forestry University, Kunming, Yunnan 650224, China
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Cross Cultivation on Homologous/Heterologous Plant-Based Culture Media Empowers Host-Specific and Real Time In Vitro Signature of Plant Microbiota. DIVERSITY 2022. [DOI: 10.3390/d15010046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Alliances of microbiota with plants are masked by the inability of in vitro cultivation of their bulk. Pure cultures piled in international centers originated from dissimilar environments/hosts. Reporting that plant root/leaf-based culture media support the organ-specific growth of microbiota, it was of interest to further investigate if a plant-based medium prepared from homologous (maize) supports specific/adapted microbiota compared to another prepared from heterologous plants (sunflower). The culture-independent community of maize phyllosphere was compared to communities cross-cultivated on plant broth-based media: CFU counts and taxa prevalence (PCR-DGGE; Illumina MiSeq amplicon sequencing). Similar to total maize phyllospheric microbiota, culture-dependent communities were overwhelmed by Proteobacteria (>94.3–98.3%); followed by Firmicutes (>1.3–3.7%), Bacteroidetes (>0.01–1.58%) and Actinobacteria (>0.06–0.34%). Differential in vitro growth on homologous versus heterologous plant-media enriched/restricted various taxa. In contrast, homologous cultivation over represented members of Proteobacteria (ca. > 98.0%), mainly Pseudomonadaceae and Moraxellaceae; heterologous cultivation and R2A enriched Firmicutes (ca. > 3.0%). The present strategy simulates/fingerprints the chemical composition of host plants to expand the culturomics of plant microbiota, advance real-time in vitro cultivation and lab-keeping of compatible plant microbiota, and identify preferential pairing of plant-microbe partners toward future synthetic community (SynComs) research and use in agriculture.
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Chandel A, Mann R, Kaur J, Tannenbaum I, Norton S, Edwards J, Spangenberg G, Sawbridge T. Australian native Glycine clandestina seed microbiota hosts a more diverse bacterial community than the domesticated soybean Glycine max. ENVIRONMENTAL MICROBIOME 2022; 17:56. [PMID: 36384698 PMCID: PMC9670509 DOI: 10.1186/s40793-022-00452-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 11/11/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Plant microbiome composition has been demonstrated to change during the domestication of wild plants and it is suggested that this has resulted in loss of plant beneficial microbes. Recently, the seed microbiome of native plants was demonstrated to harbour a more diverse microbiota and shared a common core microbiome with modern cultivars. In this study the composition of the seed-associated bacteria of Glycine clandestina is compared to seed-associated bacteria of Glycine max (soybean). RESULTS The seed microbiome of the native legume Glycine clandestina (crop wild relative; cwr) was more diverse than that of the domesticated Glycine max and was dominated by the bacterial class Gammaproteobacteria. Both the plant species (cwr vs domesticated) and individual seed accessions were identified as the main driver for this diversity and composition of the microbiota of all Glycine seed lots, with the effect of factor "plant species" exceeded that of "geographical location". A core microbiome was identified between the two Glycine species. A high percentage of the Glycine microbiome was unculturable [G. clandestina (80.8%) and G. max (75.5%)] with only bacteria of a high relative abundance being culturable under the conditions of this study. CONCLUSION Our results provided novel insights into the structure and diversity of the native Glycine clandestina seed microbiome and how it compares to that of the domesticated crop Glycine max. Beyond that, it also increased our knowledge of the key microbial taxa associated with the core Glycine spp. microbiome, both wild and domesticated. The investigation of this commonality and diversity is a valuable and essential tool in understanding the use of native Glycine spp. for the discovery of new microbes that would be of benefit to domesticated Glycine max cultivars or any other economically important crops. This study has isolated microbes from a crop wild relative that are now available for testing in G. max for beneficial phenotypes.
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Affiliation(s)
- Ankush Chandel
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia.
| | - Ross Mann
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Jatinder Kaur
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Ian Tannenbaum
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Sally Norton
- Agriculture Victoria Research, Australian Grains Genebank, Horsham, VIC, 3400, Australia
| | - Jacqueline Edwards
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | - German Spangenberg
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | - Timothy Sawbridge
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
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Abdelfadil MR, Taha MH, El-Hadidi M, Hamza MA, Youssef HH, Khalil M, Henawy AR, Nemr RA, Elsawey H, Tchuisseu Tchakounte GV, Abbas M, Youssef GH, Witzel K, Shawky ME, Fayez M, Kolb S, Hegazi NA, Ruppel S. Clay chips and beads capture in situ barley root microbiota and facilitate in vitro long-term preservation of microbial strains. FEMS Microbiol Ecol 2022; 98:fiac064. [PMID: 35641146 PMCID: PMC9249396 DOI: 10.1093/femsec/fiac064] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/18/2022] [Accepted: 05/25/2022] [Indexed: 11/23/2022] Open
Abstract
Capturing the diverse microbiota from healthy and/or stress resilient plants for further preservation and transfer to unproductive and pathogen overloaded soils, might be a tool to restore disturbed plant-microbe interactions. Here, we introduce Aswan Pink Clay as a low-cost technology for capturing and storing the living root microbiota. Clay chips were incorporated into the growth milieu of barley plants and developed under gnotobiotic conditions, to capture and host the rhizospheric microbiota. Afterward, it was tested by both a culture-independent (16S rRNA gene metabarcoding) and -dependent approach. Both methods revealed no significant differences between roots and adjacent clay chips in regard total abundance and structure of the present microbiota. Clay shaped as beads adequately supported the long-term preservation of viable pure isolates of typical rhizospheric microbes, i.e. Bacillus circulans, Klebsiella oxytoca, Sinorhizobium meliloti, and Saccharomyces sp., up to 11 months stored at -20°C, 4°C, and ambient temperature. The used clay chips and beads have the capacity to capture the root microbiota and to long-term preserve pure isolates. Hence, the developed approach is qualified to build on it a comprehensive strategy to transfer and store complex and living environmental microbiota of rhizosphere toward biotechnological application in sustainable plant production and environmental rehabilitation.
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Affiliation(s)
- Mohamed R Abdelfadil
- Thaer-Institute, Faculty of Life Sciences, Humboldt University of Berlin, 10115 Berlin, Germany
- Department of Microbiology, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
- Department of Plant Microbe Systems, Leibniz Institute of Vegetable and Ornamental Crops, 14979 Großbeeren, Germany
- RA Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, D-15374 Müncheberg, Germany
| | - Manar H Taha
- Bioinformatics Group, Center of Informatics Sciences (CIS), Nile University, 12677 Giza, Egypt
| | - Mohamed El-Hadidi
- Bioinformatics Group, Center of Informatics Sciences (CIS), Nile University, 12677 Giza, Egypt
| | - Mervat A Hamza
- Department of Microbiology, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Hanan H Youssef
- Department of Microbiology, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Mohab Khalil
- Department of Microbiology, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Ahmed R Henawy
- Department of Microbiology, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Rahma A Nemr
- Department of Microbiology, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Hend Elsawey
- Faculty of Organic Agriculture, Heliopolis University, 11785 Cairo, Egypt
| | | | - Mohamed Abbas
- Department of Microbiology, Faculty of Agriculture and Natural Resources, Aswan University, 81528 Aswan, Egypt
| | - Gehan H Youssef
- Department of Soil Chemistry and Physics, Soil, Water and Environment Research Institute, Agricultural Research Centre (ARC), 12112 Giza, Egypt
| | - Katja Witzel
- Department of Plant Microbe Systems, Leibniz Institute of Vegetable and Ornamental Crops, 14979 Großbeeren, Germany
| | - Mohamed Essam Shawky
- Department of Soil Science, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Mohamed Fayez
- Department of Microbiology, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Steffen Kolb
- Thaer-Institute, Faculty of Life Sciences, Humboldt University of Berlin, 10115 Berlin, Germany
- RA Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, D-15374 Müncheberg, Germany
| | - Nabil A Hegazi
- Department of Microbiology, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Silke Ruppel
- Department of Plant Microbe Systems, Leibniz Institute of Vegetable and Ornamental Crops, 14979 Großbeeren, Germany
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Nemr RA, Patz S, Abdelwakeel SM, Khalil M, Ben Djadid A, Abdelfadeel MR, Morsi AT, Goda HA, Youssef HH, Hamza M, Abbas M, Fayez M, El-Sahhar KF, Becker M, Ruppel S, Hegazi NA. Culture Media Based on Leaf Strips/Root Segments Create Compatible Host/Organ Setup for in vitro Cultivation of Plant Microbiota. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.660790] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Plant microbiota have co-evolved with their associated plants in the entire holobiont, and their assemblages support diversity and productivity on our planet. Of importance is in vitro cultivation and identification of their hub taxa for possible core microbiome modification. Recently, we introduced the in situ-similis culturing strategy, based on the use of plant leaves as a platform for in vitro growth of plant microbiota. Here, the strategy is further extended by exploring plant organ compatible cultivation of plant microbiota when grown on corresponding leaf/root-based culture media. Pooling the advantages of MPN enrichment methodology together with natural plant-only-based culture media, the introduced method efficiently constructed a nutritional milieu governed by vegan nutrients of plant origin, i.e., leaf strips/root segments, immersed in plain semi-solid water agar. MPN estimates exceeded log 7.0 and 4.0 g−1 of endo-rhizosphere and endo-phyllosphere, respectively, of maize and sunflower; being proportionate to those obtained for standard culture media. With sunflower, PCR-DGGE analyses indicated divergence in community composition of cultivable endophytes primarily attributed to culture media, signaling a certain degree of plant organ affinity/compatibility. Based on 16S rRNA gene sequencing of bacterial isolates, 20 genera comprising 32 potential species were enriched; belonged to Bacteroidetes, Firmicutes, and Alpha-/Gammaproteobacteria. The described cultivation strategy furnished diversified nutritive platform in terms of homologous/heterologous plant organ-based medium and ambient/limited oxygenic cultivation procedure. Duly, cultivability extended to > 8 genera: Bosea, Brevundimonas, Chitinophaga, Pseudoxanthomonas, Sphingobacterium Caulobacter, Scandinavium, and Starkeya; the latter three genera were not yet reported for Sunflower, and possible unknown species or even one new putative genus. Thus, both potential members of the major microbiome and rare isolates of satellite microbiomes can be isolated using the presented method. It is a feasible addition to traditional cultivation methods to explore new potential resources of PGPB for future biotechnological applications.
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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. [DOI: 10.3390/d12110418] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
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.
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Papik J, Folkmanova M, Polivkova-Majorova M, Suman J, Uhlik O. The invisible life inside plants: Deciphering the riddles of endophytic bacterial diversity. Biotechnol Adv 2020; 44:107614. [PMID: 32858117 DOI: 10.1016/j.biotechadv.2020.107614] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/14/2020] [Accepted: 08/15/2020] [Indexed: 10/25/2022]
Abstract
Endophytic bacteria often promote plant growth and protect their host plant against pathogens, herbivores, and abiotic stresses including drought, increased salinity or pollution. Current agricultural practices are being challenged in terms of climate change and the ever-increasing demand for food. Therefore, the rational exploitation of bacterial endophytes to increase the productivity and resistance of crops appears to be very promising. However, the efficient and larger-scale use of bacterial endophytes for more effective and sustainable agriculture is hindered by very little knowledge on molecular aspects of plant-endophyte interactions and mechanisms driving bacterial communities in planta. In addition, since most of the information on bacterial endophytes has been obtained through culture-dependent techniques, endophytic bacterial diversity and its full biotechnological potential still remain highly unexplored. In this study, we discuss the diversity and role of endophytic populations as well as complex interactions that the endophytes have with the plant and vice versa, including the interactions leading to plant colonization. A description of biotic and abiotic factors influencing endophytic bacterial communities is provided, along with a summary of different methodologies suitable for determining the diversity of bacterial endophytes, mechanisms governing the assembly and structure of bacterial communities in the endosphere, and potential biotechnological applications of endophytes in the future.
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Affiliation(s)
- Jakub Papik
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Magdalena Folkmanova
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Marketa Polivkova-Majorova
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Jachym Suman
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Ondrej Uhlik
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic.
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Nemr RA, Khalil M, Sarhan MS, Abbas M, Elsawey H, Youssef HH, Hamza MA, Morsi AT, El-Tahan M, Fayez M, Patz S, Witzel K, Ruppel S, El-Sahhar KF, Hegazi NA. " In situ similis" Culturing of Plant Microbiota: A Novel Simulated Environmental Method Based on Plant Leaf Blades as Nutritional Pads. Front Microbiol 2020; 11:454. [PMID: 32318031 PMCID: PMC7154060 DOI: 10.3389/fmicb.2020.00454] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 03/03/2020] [Indexed: 01/22/2023] Open
Abstract
High-throughput cultivation methods have recently been developed to accelerate the recovery of microorganisms reluctant to cultivation. They simulate in situ environmental conditions for the isolation of environmental microbiota through the exchange of growth substrates during cultivation. Here, we introduce leaf-based culture media adopting the concept of the plant being the master architect of the composition of its microbial community. Pre-physical treatments of sunflower plant leaves, namely punching, freezing, and/or autoclavation, allowed the diffusion of electrolytes and other nutrients to configure the leaf surface as a natural pad, i.e., creating an “in situ similis” environment suitable for the growth of rarely isolated microbiota. We used surface inoculation and membrane-filtration methods to assess the culturability of endophytic bacteria from the sunflower phyllosphere and rhizosphere. Both methods supported excellent colony-forming unit (CFU) development when compared to standard R2A medium, with a special affinity to support better growth of epiphytic and endophytic populations of the phyllosphere compared with the rhizosphere. A 16S rRNA gene analysis of >122 representative isolates indicated the cultivation of a diverse set of microorganisms by application of the new methods. It indicated the predominance of 13 genera of >30 potential species, belonging to Firmicutes, Proteobacteria, and Actinobacteria, and especially genera not commonly reported for sunflower, e.g., Rhizobium, Aureimonas, Sphingomonas, Paracoccus, Stenotrophomonas, Pantoea, Kosakonia, and Erwinia. The strategy successfully extended diversity and richness in the endophyllosphere compared to the endorhizosphere, while CFUs grown on the standard R2A medium mainly pertain to Firmicutes, especially Bacillus spp. MALDI-TOF MS analysis clustered the isolates according to their niche and potential functions, where the majority of isolates of the endorhizosphere were clustered away from those of the endophyllosphere. Isolates identified as Gammaproteobacteria and Alphaproteobacteria were distinguishably sub-clustered, which was in contrast to the heterogeneous isolates of Firmicutes (Bacillus spp.). In conclusion, leaf in situ similis cultivation is an effective strategy to support the future application of culturomics of plant microbiota. This is an effort to access novel isolates that are more adapted and competitive in their natural environments, especially those subjected to abiotic stresses like those prevailing in arid/semi-arid zones, and, consequently, to support the application of agro-biotechnologies, among other technologies, to improving agriculture in such zones.
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Affiliation(s)
- Rahma A Nemr
- Environmental Studies and Research Unit, Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Mohab Khalil
- Environmental Studies and Research Unit, Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Mohamed S Sarhan
- Environmental Studies and Research Unit, Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Mohamed Abbas
- Department of Microbiology, Faculty of Agriculture and Natural Resources, Aswan University, Aswan, Egypt
| | - Hend Elsawey
- Environmental Studies and Research Unit, Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Hanan H Youssef
- Environmental Studies and Research Unit, Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Mervat A Hamza
- Environmental Studies and Research Unit, Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Ahmed T Morsi
- Environmental Studies and Research Unit, Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Mahmoud El-Tahan
- Regional Center for Food and Feed, Agricultural Research Center, Giza, Egypt
| | - Mohamed Fayez
- Environmental Studies and Research Unit, Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Sascha Patz
- Algorithms in Bioinformatics, Center for Bioinformatics, University of Tübingen, Tübingen, Germany
| | - Katja Witzel
- Department of Plant Microbe Systems, Leibniz Institute of Vegetable and Ornamental Crops, Großbeeren, Germany
| | - Silke Ruppel
- Department of Plant Microbe Systems, Leibniz Institute of Vegetable and Ornamental Crops, Großbeeren, Germany
| | - Kassem F El-Sahhar
- Department of Botany, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Nabil A Hegazi
- Environmental Studies and Research Unit, Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
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9
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Sarhan MS, Mourad EF, Nemr RA, Abdelfadeel MR, Daanaa HSA, Youssef HH, Goda HA, Hamza MA, Fayez M, Eichler-Löbermann B, Ruppel S, Hegazi NA. An inoculum-dependent culturing strategy (IDC) for the cultivation of environmental microbiomes and the isolation of novel endophytic Actinobacteria. J Antibiot (Tokyo) 2019; 73:66-71. [PMID: 31467444 PMCID: PMC8075983 DOI: 10.1038/s41429-019-0226-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 07/25/2019] [Accepted: 08/04/2019] [Indexed: 02/04/2023]
Abstract
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.
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Affiliation(s)
- Mohamed S Sarhan
- Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt.,Faculty of Agricultural and Environmental Sciences, Rostock University, Rostock, Germany
| | - Elhussein F Mourad
- Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Rahma A Nemr
- Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | | | - Hassan-Sibroe A Daanaa
- Department of Genetics, School of Life Science, the Graduate University for Advanced Studies (SOKENDAI), 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Hanan H Youssef
- Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Hanan A Goda
- Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Mervat A Hamza
- Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Mohamed Fayez
- Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | | | - Silke Ruppel
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Großbeeren, Germany
| | - Nabil A Hegazi
- Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt.
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10
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Culturomics of the plant prokaryotic microbiome and the dawn of plant-based culture media - A review. J Adv Res 2019; 19:15-27. [PMID: 31341666 PMCID: PMC6630032 DOI: 10.1016/j.jare.2019.04.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 04/11/2019] [Accepted: 04/12/2019] [Indexed: 12/22/2022] Open
Abstract
The plant microbiome culturomics is substantially lagging behind the human microbiome. Conventional chemically-synthetic culture media recover < 10% of plant-associated microbiota. Plant-based culture media (PCM) are introduced as a novel tool for plant microbiome culturomics. PCM extended the microbiota culturability to recover unculturable bacterial taxa. Streamlined- and large-genomes conspicuously contribute to the dilemma of unculturability.
Improving cultivability of a wider range of bacterial and archaeal community members, living natively in natural environments and within plants, is a prerequisite to better understanding plant-microbiota interactions and their functions in such very complex systems. Sequencing, assembling, and annotation of pure microbial strain genomes provide higher quality data compared to environmental metagenome analyses, and can substantially improve gene and protein database information. Despite the comprehensive knowledge which already was gained using metagenomic and metatranscriptomic methods, there still exists a big gap in understanding in vivo microbial gene functioning in planta, since many differentially expressed genes or gene families are not yet annotated. Here, the progress in culturing procedures for plant microbiota depending on plant-based culture media, and their proficiency in obtaining single prokaryotic isolates of novel and rapidly increasing candidate phyla are reviewed. As well, the great success of culturomics of the human microbiota is considered with the main objective of encouraging microbiologists to continue minimizing the gap between the microbial richness in nature and the number of species in culture, for the benefit of both basic and applied microbiology. The clear message to fellow plant microbiologists is to apply plant-tailored culturomic techniques that might open up novel procedures to obtain not-yet-cultured organisms and extend the known plant microbiota repertoire to unprecedented levels.
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Sarhan MS, Patz S, Hamza MA, Youssef HH, Mourad EF, Fayez M, Murphy B, Ruppel S, Hegazi NA. G3 PhyloChip Analysis Confirms the Promise of Plant-Based Culture Media for Unlocking the Composition and Diversity of the Maize Root Microbiome and for Recovering Unculturable Candidate Divisions/Phyla. Microbes Environ 2018; 33:317-325. [PMID: 30210099 PMCID: PMC6167109 DOI: 10.1264/jsme2.me18023] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 07/09/2018] [Indexed: 12/22/2022] Open
Abstract
The rapid development of high-throughput techniques and expansion of bacterial databases have accelerated efforts to bring plant microbiomes into cultivation. We introduced plant-only-based culture media as a successful candidate to mimic the nutritional matrices of plant roots. We herein employed a G3 PhyloChip microarray to meticulously characterize the culture-dependent and -independent bacterial communities of the maize root compartments, the endo- and ecto-rhizospheres. An emphasis was placed on the preference of the growth of unculturable candidate divisions/phyla on plant-only-based culture media over standard culture media (nutrient agar). A total of 1,818 different operational taxonomic units (OTUs) were resolved representing 67 bacterial phyla. Plant-only-based culture media displayed particular affinity towards recovering endophytic over ectophytic rhizobacteria. This was shown by the slightly higher recovery of CFUs for endophytes on plant-only-based culture media (26%) than on standard culture media (10%) as well as the higher taxa richness and numbers of exclusive families of unculturable divisions/phyla. Out of 30 bacterial phyla (comprising >95% of the whole population), 13 were of a significantly higher incidence on plant-only-based culture media, 6 phyla of which were not-yet-cultured (Atribacteria, OP9; Dependentiae, TM6; Latescibacteria, WS3; Marinimicrobia, SAR406; Omnitrophica, OP3; BRC1). Furthermore, plant-only-based culture media significantly enriched less abundant and/or hard-to-culture bacterial phyla (Acidobacteria, Gemmatimonadetes, and Tenericutes). These results present conclusive evidence of the ability of plant-only-based culture media to bring the plant-fed in situ microbiome into the status of plant-fed in vitro cultures, and to widen the scope of cultivation of heretofore-unculturable bacterial divisions/phyla.
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Affiliation(s)
- Mohamed S. Sarhan
- Environmental Studies and Research Unit (ESRU), Department of Microbiology, Faculty of Agriculture, Cairo UniversityGiza, 12613Egypt
| | - Sascha Patz
- Algorithms in Bioinformatics, Center for Bioinformatics, University of TübingenTübingen, 72076Germany
| | - Mervat A. Hamza
- Environmental Studies and Research Unit (ESRU), Department of Microbiology, Faculty of Agriculture, Cairo UniversityGiza, 12613Egypt
| | - Hanan H. Youssef
- Environmental Studies and Research Unit (ESRU), Department of Microbiology, Faculty of Agriculture, Cairo UniversityGiza, 12613Egypt
| | - Elhussein F. Mourad
- Environmental Studies and Research Unit (ESRU), Department of Microbiology, Faculty of Agriculture, Cairo UniversityGiza, 12613Egypt
| | - Mohamed Fayez
- Environmental Studies and Research Unit (ESRU), Department of Microbiology, Faculty of Agriculture, Cairo UniversityGiza, 12613Egypt
| | - Brian Murphy
- Department of Botany, School of Natural Sciences, Trinity College DublinDublin 2Ireland
| | - Silke Ruppel
- Leibniz Institute of Vegetable and Ornamental Crops Großbeeren/Erfurt e.V. (IGZ)Großbeeren, 14979Germany
| | - Nabil A. Hegazi
- Environmental Studies and Research Unit (ESRU), Department of Microbiology, Faculty of Agriculture, Cairo UniversityGiza, 12613Egypt
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Mourad EF, Sarhan MS, Daanaa HSA, Abdou M, Morsi AT, Abdelfadeel MR, Elsawey H, Nemr R, El-Tahan M, Hamza MA, Abbas M, Youssef HH, Abdelhadi AA, Amer WM, Fayez M, Ruppel S, Hegazi NA. Plant Materials are Sustainable Substrates Supporting New Technologies of Plant-Only-Based Culture Media for in vitro Culturing of the Plant Microbiota. Microbes Environ 2018; 33:40-49. [PMID: 29479006 PMCID: PMC5877342 DOI: 10.1264/jsme2.me17135] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In order to improve the culturability and biomass production of rhizobacteria, we previously introduced plant-only-based culture media. We herein attempted to widen the scope of plant materials suitable for the preparation of plant-only-based culture media. We chemically analyzed the refuse of turfgrass, cactus, and clover. They were sufficiently rich to support good in vitro growth by rhizobacteria isolates representing Proteobacteria and Firmicutes. They were also adequate and efficient to produce a cell biomass in liquid batch cultures. These culture media were as sufficient as artificial culture media for the cultivation and recovery of the in situ rhizobacteria of barley (Hordeum murinum L.). Based on culture-dependent (CFU plate counting) and culture-independent analyses (qPCR), mowed turfgrass, in particular, supported the highest culturable population of barley endophytes, representing >16% of the total bacterial number quantified with qPCR. This accurately reflected the endophytic community composition, in terms of diversity indices (S', H', and D') based on PCR-DGGE, and clustered the plant culture media together with the qPCR root populations away from the artificial culture media. Despite the promiscuous nature of the plant materials tested to culture the plant microbiome, our results indicated that plant materials of a homologous nature to the tested host plant, at least at the family level, and/or of the same environment were more likely to be selected. Plant-only-based culture media require further refinements in order to provide selectivity for the in vitro growth of members of the plant microbiome, particularly difficult-to-culture bacteria. This will provide insights into their hidden roles in the environment and support future culturomic studies.
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Affiliation(s)
| | - Mohamed S Sarhan
- Department of Microbiology, Faculty of Agriculture, Cairo University
| | | | - Mennatullah Abdou
- Department of Microbiology, Faculty of Agriculture, Cairo University
| | - Ahmed T Morsi
- Department of Microbiology, Faculty of Agriculture, Cairo University
| | | | - Hend Elsawey
- Department of Microbiology, Faculty of Agriculture, Cairo University
| | - Rahma Nemr
- Department of Microbiology, Faculty of Agriculture, Cairo University
| | - Mahmoud El-Tahan
- Regional Center for Food & Feed (RCFF), Agricultural Research Center
| | - Mervat A Hamza
- Department of Microbiology, Faculty of Agriculture, Cairo University
| | - Mohamed Abbas
- Department of Microbiology, Faculty of Agriculture & Natural Resources, Aswan University
| | - Hanan H Youssef
- Department of Microbiology, Faculty of Agriculture, Cairo University
| | | | - Wafaa M Amer
- Department of Botany and Microbiology, Faculty of Science, Cairo University
| | - Mohamed Fayez
- Department of Microbiology, Faculty of Agriculture, Cairo University
| | - Silke Ruppel
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ)
| | - Nabil A Hegazi
- Department of Microbiology, Faculty of Agriculture, Cairo University
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Saleh MY, Sarhan MS, Mourad EF, Hamza MA, Abbas MT, Othman AA, Youssef HH, Morsi AT, Youssef GH, El-Tahan M, Amer WA, Fayez M, Ruppel S, Hegazi NA. A novel plant-based-sea water culture media for in vitro cultivation and in situ recovery of the halophyte microbiome. J Adv Res 2017; 8:577-590. [PMID: 28794903 PMCID: PMC5540709 DOI: 10.1016/j.jare.2017.06.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 06/24/2017] [Accepted: 06/26/2017] [Indexed: 11/29/2022] Open
Abstract
The plant-based-sea water culture medium is introduced to in vitro cultivation and in situ recovery of the microbiome of halophytes. The ice plant (Mesembryanthemum crystallinum) was used, in the form of juice and/or dehydrated plant powder packed in teabags, to supplement the natural sea water. The resulting culture medium enjoys the combinations of plant materials as rich source of nutrients and sea water exercising the required salt stress. As such without any supplements, the culture medium was sufficient and efficient to support very good in vitro growth of halotolerant bacteria. It was also capable to recover their in situ culturable populations in the phyllosphere, ecto-rhizosphere and endo-rhizosphere of halophytes prevailing in Lake Mariout, Egypt. When related to the total bacterial numbers measured for Suaeda pruinosa roots by quantitative-PCR, the proposed culture medium increased culturability (15.3-19.5%) compared to the conventional chemically-synthetic culture medium supplemented with (11.2%) or without (3.8%) NaCl. Based on 16S rRNA gene sequencing, representative isolates of halotolerant bacteria prevailed on such culture medium were closely related to Bacillus spp., Halomonas spp., and Kocuria spp. Seed germination tests on 25-50% sea water agar indicated positive interaction of such bacterial isolates with the germination and seedlings' growth of barley seeds.
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Affiliation(s)
- Mohamed Y. Saleh
- Department of Microbiology, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Mohamed S. Sarhan
- Department of Microbiology, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Elhussein F. Mourad
- Department of Microbiology, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Mervat A. Hamza
- Department of Microbiology, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Mohamed T. Abbas
- Microbiology Department, Faculty of Agriculture and Natural Resources, Aswan University, P.O. Box 81528, Aswan, Egypt
| | - Amal A. Othman
- Hydrobiology Laboratory, Inland Water and Lake Division, National Institute of Oceanography and Fisheries (NIOF), 11516 Cairo, Egypt
| | - Hanan H. Youssef
- Department of Microbiology, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Ahmed T. Morsi
- Department of Microbiology, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Gehan H. Youssef
- Soils, Water and Environment Research Institute, Agricultural Research Center, 12112 Giza, Egypt
| | - Mahmoud El-Tahan
- Institute of Feed Research, Agricultural Research Center, 12112 Giza, Egypt
| | - Wafaa A. Amer
- Department of Botany and Microbiology, Faculty of Science, Cairo University, 12613 Giza, Egypt
| | - Mohamed Fayez
- Department of Microbiology, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Silke Ruppel
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), 14979 Grossbeeren, Germany
| | - Nabil A. Hegazi
- Department of Microbiology, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
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Younginger BS, Ballhorn DJ. Fungal endophyte communities in the temperate fern Polystichum munitum show early colonization and extensive temporal turnover. AMERICAN JOURNAL OF BOTANY 2017; 104:1188-1194. [PMID: 28814407 DOI: 10.3732/ajb.1700149] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 07/24/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF THE STUDY Fungal endophytes have been shown to colonize all land plants, yet surprisingly little attention has been given to their community composition in ferns. We examined the diversity and temporal turnover of fungal endophytes in foliar tissue of the temperate western sword fern, Polystichum munitum, comparing taxa in newly emerged leaflets and in the same fronds after 1 mo of exposure in the field. METHODS Utilizing next-generation sequencing, we sampled pinnae from P. munitum in spring, 2-3 d after they emerged. We additionally sampled pinnae 30 d later from the same fern blades. From these samples, we sequenced fungal DNA to characterize the initial colonization and temporal turnover of endophytes in the host. KEY RESULTS We demonstrate that P. munitum is abundantly colonized by endophytes in newly emerged foliar tissue. However, 1 mo later, the community composition undergoes a marked shift: the overall richness of endophytes increases, but the evenness of the community wanes as a single taxon, Flagellospora fusarioides, comes to dominate. CONCLUSIONS We conclude that P. munitum hosts a variety of fungal endophyte taxa, similarly to other land plants. However, the rapid shift of the endophyte community we report is an unprecedented observation. Therefore, we further conclude that repeated sampling should be the standard in endophyte studies, because single sampling events are not sufficient to capture the dynamic nature of these cryptic microfungi.
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Affiliation(s)
- Brett S Younginger
- Department of Biology, Portland State University, Portland, Oregon 97201, USA
| | - Daniel J Ballhorn
- Department of Biology, Portland State University, Portland, Oregon 97201, USA
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Hegazi NA, Sarhan MS, Fayez M, Patz S, Murphy BR, Ruppel S. Plant-fed versus chemicals-fed rhizobacteria of Lucerne: Plant-only teabags culture media not only increase culturability of rhizobacteria but also recover a previously uncultured Lysobacter sp., Novosphingobium sp. and Pedobacter sp. PLoS One 2017; 12:e0180424. [PMID: 28686606 PMCID: PMC5501534 DOI: 10.1371/journal.pone.0180424] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 06/15/2017] [Indexed: 11/19/2022] Open
Abstract
In an effort to axenically culture the previously uncultivable populations of the rhizobacteria of Lucerne (Medicago sativa L.), we propose plant-only teabags culture media to mimic the nutritional matrix available in the rhizosphere. Here, we show that culture media prepared from Lucerne powder teabags substantially increased the cultivability of Lucerne rhizobacteria compared with a standard nutrient agar, where we found that the cultivable populations significantly increased by up to 60% of the total bacterial numbers as estimated by Quantitative Real-time Polymerase Chain Reaction (qRT-PCR). Cluster analysis of 16S rDNA Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) of cultivable Colony-Forming Units (CFUs) revealed a more distinct composition and separation of bacterial populations recovered on the plant-only teabags culture media than those developed on a standard nutrient agar. Further, the new plant medium gave preference to the micro-symbiont Sinorhizobium meliloti, and succeeded in isolating a number of not-yet-cultured bacteria, most closely matched to Novosphingobium sp., Lysobacter sp. and Pedobacter sp. The present study may encourage other researchers to consider moving from the well-established standard culture media to the challenging new plant-only culture media. Such a move may reveal previously hidden members of rhizobacteria, and help to further explore their potential environmental impacts.
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Affiliation(s)
- Nabil A. Hegazi
- Environmental Studies and Research Unit (ESRU), Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
- * E-mail:
| | - Mohamed S. Sarhan
- Environmental Studies and Research Unit (ESRU), Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Mohamed Fayez
- Environmental Studies and Research Unit (ESRU), Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Sascha Patz
- Leibniz Institute of Vegetable and Ornamental Crops Großbeeren/ Erfurt e.V. (IGZ), Großbeeren, Germany
| | - Brian R. Murphy
- Department of Botany, School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | - Silke Ruppel
- Leibniz Institute of Vegetable and Ornamental Crops Großbeeren/ Erfurt e.V. (IGZ), Großbeeren, Germany
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