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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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Gerna D, Clara D, Allwardt D, Mitter B, Roach T. Tailored Media Are Key to Unlocking the Diversity of Endophytic Bacteria in Distinct Compartments of Germinating Seeds. Microbiol Spectr 2022; 10:e0017222. [PMID: 35867396 PMCID: PMC9431621 DOI: 10.1128/spectrum.00172-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 07/01/2022] [Indexed: 11/24/2022] Open
Abstract
Seeds offer an internal microbial niche, termed the endosphere, colonized by communities of endophytic bacteria. To elucidate the functions of seed endophytes during germination and early plant growth, studies with culturable isolates are essential. Conventional growth media favor few fast-growing taxa, while micro organisms with restricted nutrient requirements are usually outcompeted prior to isolation. Consequently, current knowledge of the interaction between seeds and their endophytes remains limited to only few bacterial taxa, despite a "black box" of unculturable isolates colonizing the endosphere. Here, we designed various solid media to mimic the endosphere of germinating soybean (Glycine max L.) seeds and assessed their effect on the diversity of culturable endophytic bacteria. The embryonic axis (i.e., the future plant) possessed higher richness and harbored more unique genera (i.e., Brevundimonas, Methylobacterium, Microbacterium, Pseudoclavibacter, and Rathayibacter) than cotyledons (i.e., seed storage organs). Overall, media containing germinating and ground seeds enabled culturing and isolation of the broadest diversity of endophytic bacteria, viewed through the molecular identification of 246 isolates. The use of multiple tailored media helped uncover trophic adaptation of the core taxa. Furthermore, comparison of seeds from four lots of distinct cultivars and origin revealed few overlapping taxa, indicating that the parental environment, including soil and fertilization regime, influenced seed endophytic diversity. Extended diversity of native seed endophytic bacteria revealed the functional relevance of unique Arthrobacter, Bacillus, and Curtobacterium strains to seed germination under salt stress, exemplifying the importance of enhanced culturing approaches to elucidate the role of microbiota in seed germination. IMPORTANCE Plant growth-promoting endophytic isolates that appear to advance seed germination are often obtained from plant niches other than the seed endosphere. Isolating pure cultures of native endophytes from seeds during germination is crucial to investigate their function during early plant growth. Here, the diversity of endophytic bacteria isolated from seeds during soybean germination was enhanced by combining media tailored to the nutritional composition of the seed endosphere, including pregerminated seeds themselves. Our results show that isolation from distinct soybean seed compartments affected such diversity, with the embryonic axis harboring more unique taxa while displaying higher endophytic richness. Furthermore, using pools of seeds from separate lots, each corresponding to a certain cultivar and field site, supported isolation of further unique strains that often unveiled substantial effects on germination performance. Such findings are relevant to assist studies on the interactions between seeds and their native endophytic bacteria.
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Affiliation(s)
- Davide Gerna
- Department of Botany and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - David Clara
- Department of Botany and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Dorothee Allwardt
- Bioresources Unit, Austrian Institute of Technology GmbH, Tulln, Austria
| | - Birgit Mitter
- Bioresources Unit, Austrian Institute of Technology GmbH, Tulln, Austria
| | - Thomas Roach
- Department of Botany and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
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Designing a Waste-Based Culture Medium for the Production of Plant Growth Promoting Microorganisms Based on Cladodes Juice from Opuntia ficus-indica Pruning. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8050225] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The production of beneficial microorganisms is the first step to obtain a commercial-based product for application in agriculture. In this study, prickly pear (Opuntia ficus-indica) pruning waste was evaluated as a raw material for the production of large amounts of Plant Growth Promoting Microorganisms (PGPMs) reducing the number of generated wastes. Specifically, five PGPMs constituting a synthetic microbial consortium with complementing plant growth-promoting traits were grown on a laboratory scale and, subsequently, on a pilot scale using a 21-L bioreactor. Primarily, the physical-chemical characterization of the culture medium obtained from the juice of Opuntia cladodes was carried out, revealing the presence of sugars and organic acids with different molar ratios. Compared to conventional media, the waste medium did not show significant differences in bacterial growth efficiency. Instead, the survival rates of the bacteria grown in cladodes juice media, after air-drying on zeolite or freeze-drying, were significantly higher than those observed when they were grown in conventional media. The present work is the first conducted on a pilot-scale that maximizes the production of PGPMs in submerged fermentation using cladodes juice from Opuntia, reducing both economic and environmental impacts associated with the generation of wastes.
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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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Zahra T, Hamedi J, Mahdigholi K. Endophytic actinobacteria of a halophytic desert plant Pteropyrum olivieri: promising growth enhancers of sunflower. 3 Biotech 2020; 10:514. [PMID: 33184598 DOI: 10.1007/s13205-020-02507-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 10/24/2020] [Indexed: 01/30/2023] Open
Abstract
In the present study, 40 actinobacterial isolates were obtained from the roots of a desert plant, Pteropyrum olivieri and tested for extracellular hydrolytic enzyme activities, hydrogen cyanide, and siderophore production. Based on these activities, three isolates designated UTMC 2482, UTMC 2483, and UTMC 3136 were selected with an aim of developing bio-fertilizing agent to improve the growth of sunflower plants under normal conditions. The selected isolates showed 98.2, 98.4, and 100% similarities in the 16S rRNA gene sequences to Streptomyces chromofuscus, Streptomyces ambofaciens, and Streptomyces gardneri, respectively. These isolates exhibited indole acetic acid production while UTMC 2483 was found to produce 1-aminocyclopropane-1-carboxylate deaminase, as well. Sunflower seeds soaked in the bacterial spore suspensions increased the tolerance of sunflower seedlings to the stresses of salinity and water deficiency up to 270 mM of NaCl and - 2Mpa of PEG6000, respectively. Under normal conditions, inoculation with individual isolates and their consortia enhanced the yield (plant length, weight, and flower diameter) and biochemical contents (i.e. chlorophyll, protein, and oil) up to 5.3, 1.7, and 2.4 times higher than that of un-inoculated plants, significantly (p < 0.05) in greenhouse and field experiments. This is the first study demonstrating that endophytic actinobacteria from the desert plant, P. olivieri, have profound bio-fertilizing effects on the growth of sunflower.
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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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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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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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11
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Uppala SS, Zhou XG, Liu B, Wu M. Plant-Based Culture Media for Improved Growth and Sporulation of Cercospora janseana. PLANT DISEASE 2019; 103:504-508. [PMID: 30657430 DOI: 10.1094/pdis-05-18-0814-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Cercospora janseana is the causal agent of narrow brown leaf spot, one of the major diseases of rice in the United States. In vitro studies were conducted to evaluate various plant-based agar media in comparison with potato dextrose agar (PDA) for their effects on radial growth and sporulation of C. janseana. The agar media were evaluated individually with the following plant-extract ingredients: fresh rice leaves, dried rice leaves, dried rice stems, dried rice roots, dried rice hulls, dried rice straw, rice bran, dried sorghum leaves, and dried barnyard grass leaves. Plant-based extracts obtained from 25, 50, 100, or 200 g/liter (plant material/water) were tested either alone or in combination with 10 and 20% clarified V8 juice. PDA served as the control medium. Media with 10 and 20% V8 juice were also included for comparison. Media were inoculated with a disc of 1-week-old actively growing C. janseana at the center of Petri plates and incubated at 28°C with a 12/12-h (light/dark) cycle for 2 weeks. Radial growth was measured at 7 and 14 days after inoculation (DAI), whereas sporulation was measured at 14 DAI. Radial growth and sporulation differed among various media and their amendment concentrations. Media with extracts of fresh rice leaves, dried rice leaves, dried rice stems, dried barnyard grass leaves, and clarified V8 juice enhanced radial growth compared with the PDA control. Of all the agar media evaluated, fresh rice leaf extract amendment at 25 g/liter with no V8 supplementation consistently supported the greatest radial growth, and 10% V8-only medium resulted in greater sporulation of C. janseana than other media evaluated.
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Affiliation(s)
- Sai Sree Uppala
- 1 Texas A&M University System, AgriLife Research and Extension Center, Beaumont, TX, U.S.A.; and
| | - Xin-Gen Zhou
- 1 Texas A&M University System, AgriLife Research and Extension Center, Beaumont, TX, U.S.A.; and
| | - Baohua Liu
- 2 Hunan Agricultural University, Changsha, Hunan, China
| | - Mingliang Wu
- 2 Hunan Agricultural University, Changsha, Hunan, China
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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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13
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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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14
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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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15
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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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16
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Sarhan MS, Mourad EF, Hamza MA, Youssef HH, Scherwinski AC, El-Tahan M, Fayez M, Ruppel S, Hegazi NA. Plant powder teabags: a novel and practical approach to resolve culturability and diversity of rhizobacteria. PHYSIOLOGIA PLANTARUM 2016; 157:403-413. [PMID: 27178359 DOI: 10.1111/ppl.12469] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 03/24/2016] [Accepted: 04/18/2016] [Indexed: 06/05/2023]
Abstract
We have developed teabags packed with dehydrated plant powders, without any supplements, for preparation of plant infusions necessary to develop media for culturing rhizobacteria. These bacteria are efficiently cultivated on such plant teabag culture media, with better progressive in situ recoverability compared to standard chemically synthetic culture media. Combining various plant-based culture media and incubation conditions enabled us to resolve unique denaturing gradient gel electrophoresis (DGGE) bands that were not resolved by tested standard culture media. Based on polymerase chain reaction PCR-DGGE of 16S rDNA fingerprints and sequencing, the plant teabag culture media supported higher diversity and significant increases in the richness of endo-rhizobacteria, namely Gammaproteobacteria (Enterobacteriaceae) and predominantly Alphaproteobacteria (Rhizobiaceae). This culminated in greater retrieval of the rhizobacteria taxa associated with the plant roots. We conclude that the plant teabag culture medium by itself, without any nutritional supplements, is sufficient and efficient for recovering and mirroring the complex and diverse communities of rhizobacteria. Our message to fellow microbial ecologists is: simply dehydrate your plant canopy, teabag it and soak it to prepare your culture media, with no need for any additional supplementary nutrients.
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Affiliation(s)
- Mohamed S Sarhan
- Environmental Studies and Research Unit (ESRU), Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Elhussein F Mourad
- Environmental Studies and Research Unit (ESRU), Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Mervat A Hamza
- Environmental Studies and Research Unit (ESRU), Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Hanan H Youssef
- Environmental Studies and Research Unit (ESRU), Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Ann-Christin Scherwinski
- Leibniz Institute of Vegetable and Ornamental Crops Grossbeeren/Erfurt e.V. (IGZ), Grossbeeren, Germany
| | - Mahmoud El-Tahan
- Regional Center for Food and Feed (RCFF), Agricultural Research Center (ARC), Giza, Egypt
| | - Mohamed Fayez
- Environmental Studies and Research Unit (ESRU), Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Silke Ruppel
- Leibniz Institute of Vegetable and Ornamental Crops Grossbeeren/Erfurt e.V. (IGZ), Grossbeeren, Germany
| | - Nabil A Hegazi
- Environmental Studies and Research Unit (ESRU), Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
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17
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Boakye-Boaten NA, Xiu S, Shahbazi A, Wang L, Li R, Schimmel K. Uses of miscanthus press juice within a green biorefinery platform. BIORESOURCE TECHNOLOGY 2016; 207:285-292. [PMID: 26896712 DOI: 10.1016/j.biortech.2016.02.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 02/03/2016] [Accepted: 02/04/2016] [Indexed: 06/05/2023]
Abstract
This study assesses some uses of nutrient-rich juice mechanically extracted from freshly harvested Miscanthus x giganteus (MxG) as part of a green biorefinery system. The juice was used for culturing Saccharomyces cerevisiae and lactic acid bacteria. MxG juice was further used as substrate for fermentation to produce lactic acid using Lactobacillus brevis and Lactobacillus plantarum. The results show that MxG juice was a highly nutritious source for the cultivation of bacteria. Higher concentrations of MxG juice used as culture media, resulted in higher cell growth both aerobically and anaerobically. The highest ethanol yield of 70% theoretical and concentration of 0.75g/100ml were obtained from S. cerevisiae cultivated with 90% (v/v) MxG juice media and used for miscanthus solid fraction fermentation. 11.91g/L of lactic acid was also successfully produced from MxG juice through SSF.
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Affiliation(s)
- Nana Abayie Boakye-Boaten
- Energy and Environmental Systems Program, College of Arts and Science, North Carolina A & T State University, 1601 East Market Street, Greensboro, NC 27411, United States; Biological Engineering Program, Department of Natural Resources and Environmental Design, North Carolina A & T State University, 1601 East Market Street, Greensboro, NC 27411, United States
| | - Shuangning Xiu
- Biological Engineering Program, Department of Natural Resources and Environmental Design, North Carolina A & T State University, 1601 East Market Street, Greensboro, NC 27411, United States.
| | - Abolghasem Shahbazi
- Biological Engineering Program, Department of Natural Resources and Environmental Design, North Carolina A & T State University, 1601 East Market Street, Greensboro, NC 27411, United States
| | - Lijun Wang
- Biological Engineering Program, Department of Natural Resources and Environmental Design, North Carolina A & T State University, 1601 East Market Street, Greensboro, NC 27411, United States
| | - Rui Li
- Joint School of Nanoscience and Nanoengineering, North Carolina A & T State University, 2907 E. Gate City Blvd, Greensboro, NC 27401, United States; Biological Engineering Program, Department of Natural Resources and Environmental Design, North Carolina A & T State University, 1601 East Market Street, Greensboro, NC 27411, United States
| | - Keith Schimmel
- Energy and Environmental Systems Program, College of Arts and Science, North Carolina A & T State University, 1601 East Market Street, Greensboro, NC 27411, United States
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18
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Plant-based culture media: Efficiently support culturing rhizobacteria and correctly mirror their in-situ diversity. J Adv Res 2015; 7:305-16. [PMID: 26966571 PMCID: PMC4767806 DOI: 10.1016/j.jare.2015.07.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 07/25/2015] [Accepted: 07/28/2015] [Indexed: 11/21/2022] Open
Abstract
Our previous publications and the data presented here provide evidences on the ability of plant-based culture media to optimize the cultivability of rhizobacteria and to support their recovery from plant-soil environments. Compared to the tested chemically-synthetic culture media (e.g. nutrient agar and N-deficient combined-carbon sources media), slurry homogenates, crude saps, juices and powders of cactus (Opuntia ficus-indica) and succulent plants (Aloe vera and Aloe arborescens) were rich enough to support growth of rhizobacteria. Representative isolates of Enterobacter spp., Klebsiella spp., Bacillus spp. and Azospirillum spp. exhibited good growth on agar plates of such plant-based culture media. Cell growth and biomass production in liquid batch cultures were comparable to those reported with the synthetic culture media. In addition, the tested plant-based culture media efficiently recovered populations of rhizobacteria associated to plant roots. Culturable populations of >106–108 cfu g−1 were recovered from the ecto- and endo-rhizospheres of tested host plants. More than 100 endophytic culture-dependent isolates were secured and subjected to morphophysiological identification. Factor and cluster analyses indicated the unique community structure, on species, genera, class and phyla levels, of the culturable population recovered with plant-based culture media, being distinct from that obtained with the chemically-synthetic culture media. Proteobacteria were the dominant (78.8%) on plant-based agar culture medium compared to only 31% on nutrient agar, while Firmicutes prevailed on nutrient agar (69%) compared to the plant-based agar culture media (18.2%). Bacteroidetes, represented by Chryseobacterium indologenes, was only reported (3%) among the culturable rhizobacteria community of the plant-based agar culture medium.
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Bone- and cartilage-forming tumors and ewing sarcoma: an update with a gnathic emphasis. Head Neck Pathol 2014; 8:454-62. [PMID: 25409851 PMCID: PMC4245414 DOI: 10.1007/s12105-014-0587-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 11/03/2014] [Indexed: 12/16/2022]
Abstract
Over the past decade, there have been remarkable advances in bone tumor pathology. Insights into the genetic basis and pathobiology of many tumor types have impacted diagnosis, classification, and treatment. However, because gnathic lesions may comprise only a small proportion of cases overall for many tumors, clinicopathologic features and management considerations specific to this subset may be overlooked. Here we provide a summary of recent developments in the following tumor types: osteosarcoma (OS), chondrosarcoma (CS), osteoid osteoma (OO), osteoblastoma (OB), and Ewing sarcoma (ES). In particular, we will give special consideration to cases arising in the jaws.
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HIDAYATI ERNIN, TRI WAHYUDI ARIS, SUWANTO ANTONIUS, WIDYASTUTI RAHAYU. Abundance of Culturable Bacteria Isolated from Maize Rhizosphere Soil Using Four Different Culture Media. MICROBIOLOGY INDONESIA 2014. [DOI: 10.5454/mi.8.1.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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