Culturomics of the plant prokaryotic microbiome and the dawn of plant-based culture media – A review

Sarhan, Mohamed S.; Hamza, M.; Youssef, Hanan H.; Patz, Sascha; Becker, Matthias; Elsawey, Hend; Nemr, Rahma A.; Daanaa, Hassan-Sibroe A.; Mourad, Elhussein F.; Morsi, Ahmed; Abdelfadeel, Mohamed R.; Abbas, Mohamed; Fayez, M. B. E.; Ruppel, Silke; Hegazi, N. A.

doi:10.1016/j.jare.2019.04.002

Cited by 108 publications

(98 citation statements)

References 121 publications

(168 reference statements)

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“…Multi-omic approaches are the future the field but conceptual frameworks should develop in parallel A multitude of -omics toolsincluding (meta)genomics, (meta)transcriptomics, (meta)proteomics, metabolomics, and also culturomicsare now available to understand the functional role of endophytic communities (Kaul et al, 2016;Levy et al, 2018;Sarhan et al, 2019). Levy et al (2018) recently reviewed the objectives, strengths and limitations of each of these tools.…”

Section: Methodological Challenges and Limitations To Study Endophytesmentioning

confidence: 99%

The plant endosphere world – bacterial life within plants

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Cambon

Vacher

et al. 2020

Environmental Microbiology

206

104

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The plant endosphere is colonized by complex microbial communities and microorganisms, which colonize the plant interior at least part of their lifetime and are termed endophytes. Their functions range from mutualism to pathogenicity. All plant organs and tissues are generally colonized by bacterial endophytes and their diversity and composition depend on the plant, the plant organ and its physiological conditions, the plant growth stage as well as on the environment. Plant-associated microorganisms, and in particular endophytes, have lately received high attention, because of the increasing awareness of the importance of host-associated microbiota for the functioning and performance of their host. Some endophyte functions are known from mostly lab assays, genome prediction and few metagenome analyses; however, we have limited understanding on in planta activities, particularly considering the diversity of micro-environments and the dynamics of conditions. In our review, we present recent findings on endosphere environments, their physiological conditions and endophyte colonization. Furthermore, we discuss microbial functions, the interaction between endophytes and plants as well as methodological limitations of endophyte research. We also provide an outlook on needs of future research to improve our understanding on the role of microbiota colonizing the endosphere on plant traits and ecosystem functioning.

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Section: Methodological Challenges and Limitations To Study Endophytesmentioning

confidence: 99%

The plant endosphere world – bacterial life within plants

Compant

Cambon

Vacher

et al. 2020

Environmental Microbiology

206

104

View full text Add to dashboard Cite

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“…To gain insights into their unknown functions and exploit their potentials, different approaches were recently introduced to culture such not-yet-cultured bacteria [2,3]. In this respect, the plantonly-based culture media were presented as natural culture media to replace myriad formulas of synthetic culture media, and strongly recommended to increase the cultivability of the plant microbiota [4][5][6][7][8][9][10]. To alleviate the stress of disproportionate nutrients, present in common culture media, we aimed at culturing maize and sunflower microbiota on the natural nutrients present in the plant inoculum itself, compared to highly diluted plant-only-based culture media and standard R2A.…”

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confidence: 99%

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

et al. 2019

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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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“…Our previous investigations, recently reviewed by Sarhan et al (2019), provided evidence that plant materials, such as crude slurry homogenates, juices, saps, and dehydrated powders, as such, without any supplement, can be successfully used to enhance the culturability of plant-associated microbiota. In the present study, we further advance the leaf-based culture strategy for the growth of epiphytic and endophytic microbiota of sunflower grown in fields in Giza, Egypt, in semi-arid land environments.…”

Section: Discussionmentioning

confidence: 99%

“…Throughout the present study, we investigated the cultivable community of bacteria residing in both the phyllosphere and rhizosphere compartments of sunflower plants. We compared the introduced leaf-based culture media to other forms of plant-based culture media recently presented by Sarhan et al (2019) as well as the standard chemically synthetic R2A culture medium. To shed light on the diversity of the culturable community, representative isolates were subjected to 16S rRNA gene sequencing and matrix-assisted laser desorption/ionization timeof-flight mass spectrometry (MALDI-TOF MS) for identification and classification.…”

Section: Introductionmentioning

confidence: 99%

“In situ similis” Culturing of Plant Microbiota: A Novel Simulated Environmental Method Based on Plant Leaf Blades as Nutritional Pads

et al. 2020

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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

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Culturomics of the plant prokaryotic microbiome and the dawn of plant-based culture media – A review

Abstract: Graphical abstract

Cited by 108 publications

References 121 publications

The plant endosphere world – bacterial life within plants

The plant endosphere world – bacterial life within plants

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

“In situ similis” Culturing of Plant Microbiota: A Novel Simulated Environmental Method Based on Plant Leaf Blades as Nutritional Pads

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