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Ginnan N, Bordenstein SR. It is time to authenticate the Microbiome Sciences with accredited educational programs and departments. PLoS Biol 2023; 21:e3002420. [PMID: 38060452 PMCID: PMC10703218 DOI: 10.1371/journal.pbio.3002420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023] Open
Abstract
The Microbiome Sciences are at a crucial maturation stage. Scientists and educators should now view the Microbiome Sciences as a flourishing and autonomous discipline, creating degree programs and departments that are conducive to cohesive growth.
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Affiliation(s)
- Nichole Ginnan
- The One Health Microbiome Center, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Seth R. Bordenstein
- The One Health Microbiome Center, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Entomology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
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Kurbessoian T, Heimlich-Villalta G, Ginnan N, Vieira FC, Rolshausen PE, Roper MC, Stajich JE. Genome Sequence and Assembly of 18 Fusarium Isolates from Florida Citrus under High Huanglongbing Disease Pressure and California Citrus under Low Huanglongbing Disease Pressure. Microbiol Resour Announc 2023; 12:e0010123. [PMID: 37042758 DOI: 10.1128/mra.00101-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023] Open
Abstract
The genomes of eighteen Fusarium isolates cultured from diseased and healthy citrus trees were sequenced, assembled, and annotated. Isolate species identification was confirmed using single marker (TEF1-alpha) phylogenetic assessment. Studies of the traits and genotypes of plant-associated isolates are important to understanding the fungal contribution to phytobiomes of citrus.
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Affiliation(s)
- Tania Kurbessoian
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, USA
- Institute for Integrative Genome Biology, University of California, Riverside, California, USA
| | - Gretchen Heimlich-Villalta
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, USA
- Institute for Integrative Genome Biology, University of California, Riverside, California, USA
| | - Nichole Ginnan
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, USA
- Institute for Integrative Genome Biology, University of California, Riverside, California, USA
| | - Flavia Campos Vieira
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, USA
- Institute for Integrative Genome Biology, University of California, Riverside, California, USA
| | - Philippe E Rolshausen
- Department of Botany and Plant Sciences, University of California, Riverside, California, USA
| | - M Caroline Roper
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, USA
- Institute for Integrative Genome Biology, University of California, Riverside, California, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, USA
- Institute for Integrative Genome Biology, University of California, Riverside, California, USA
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Blacutt A, Ginnan N, Dang T, Bodaghi S, Vidalakis G, Ruegger P, Peacock B, Viravathana P, Vieira FC, Drozd C, Jablonska B, Borneman J, McCollum G, Cordoza J, Meloch J, Berry V, Salazar LL, Maloney KN, Rolshausen PE, Roper MC. An In Vitro Pipeline for Screening and Selection of Citrus-Associated Microbiota with Potential Anti-" Candidatus Liberibacter asiaticus" Properties. Appl Environ Microbiol 2020; 86:e02883-19. [PMID: 32086307 PMCID: PMC7117939 DOI: 10.1128/aem.02883-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 02/11/2020] [Indexed: 12/13/2022] Open
Abstract
Huanglongbing (HLB) is a destructive citrus disease that is lethal to all commercial citrus plants, making it the most serious citrus disease and one of the most serious plant diseases. Because of the severity of HLB and the paucity of effective control measures, we structured this study to encompass the entirety of the citrus microbiome and the chemistries associated with that microbial community. We describe the spatial niche diversity of bacteria and fungi associated with citrus roots, stems, and leaves using traditional microbial culturing integrated with culture-independent methods. Using the culturable sector of the citrus microbiome, we created a microbial repository using a high-throughput bulk culturing and microbial identification pipeline. We integrated an in vitro agar diffusion inhibition bioassay into our culturing pipeline that queried the repository for antimicrobial activity against Liberibacter crescens, a culturable surrogate for the nonculturable "Candidatus Liberibacter asiaticus" bacterium associated with HLB. We identified microbes with robust inhibitory activity against L. crescens that include the fungi Cladosporium cladosporioides and Epicoccum nigrum and bacterial species of Pantoea, Bacillus, and Curtobacterium Purified bioactive natural products with anti-"Ca. Liberibacter asiaticus" activity were identified from the fungus C. cladosporioides Bioassay-guided fractionation of an organic extract of C. cladosporioides yielded the natural products cladosporols A, C, and D as the active agents against L. crescens This work serves as a foundation for unraveling the complex chemistries associated with the citrus microbiome to begin to understand the functional roles of members of the microbiome, with the long-term goal of developing anti-"Ca Liberibacter asiaticus" bioinoculants that thrive in the citrus holosystem.IMPORTANCE Globally, citrus is threatened by huanglongbing (HLB), and the lack of effective control measures is a major concern of farmers, markets, and consumers. There is compelling evidence that plant health is a function of the activities of the plant's associated microbiome. Using Liberibacter crescens, a culturable surrogate for the unculturable HLB-associated bacterium "Candidatus Liberibacter asiaticus," we tested the hypothesis that members of the citrus microbiome produce potential anti-"Ca Liberibacter asiaticus" natural products with potential anti-"Ca Liberibacter asiaticus" activity. A subset of isolates obtained from the microbiome inhibited L. crescens growth in an agar diffusion inhibition assay. Further fractionation experiments linked the inhibitory activity of the fungus Cladosporium cladosporioides to the fungus-produced natural products cladosporols A, C, and D, demonstrating dose-dependent antagonism to L. crescens.
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Affiliation(s)
- Alex Blacutt
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Nichole Ginnan
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Tyler Dang
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Sohrab Bodaghi
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Georgios Vidalakis
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Paul Ruegger
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Beth Peacock
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Polrit Viravathana
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Flavia Campos Vieira
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Christopher Drozd
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Barbara Jablonska
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - James Borneman
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Greg McCollum
- U.S. Department of Agriculture, Agricultural Research Service, Fort Pierce, Florida, USA
| | | | | | - Victoria Berry
- Point Loma Nazarene University, San Diego, California, USA
| | | | | | - Philippe E Rolshausen
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, California, USA
| | - M Caroline Roper
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
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Su Y, Ashworth VETM, Geitner NK, Wiesner MR, Ginnan N, Rolshausen P, Roper C, Jassby D. Delivery, Fate, and Mobility of Silver Nanoparticles in Citrus Trees. ACS Nano 2020; 14:2966-2981. [PMID: 32141736 DOI: 10.1021/acsnano.9b07733] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Crop disease control is crucial for the sustainable development of agriculture, with recent advances in nanotechnology offering a promising solution to this pressing problem. However, the efficacy of nanoparticle (NP) delivery methods has not been fully explored, and knowledge regarding the fate and mobility of NPs within trees is still largely unknown. In this study, we evaluate the efficiency of NP delivery methods and investigate the mobility and distribution of NPs with different surface coatings (citrate (Ct), polyvinylpyrrolidone (PVP), and gum Arabic (GA)) within Mexican lime citrus trees. In contrast to the limited delivery efficiency reported for foliar and root delivery methods, petiole feeding and trunk injection are able to deliver a large amount of NPs into trees, although petiole feeding takes much longer time than trunk injection (7 days vs 2 h in citrus trees). Once NPs enter plants, steric repulsive interactions between NPs and conducting tube surfaces are predicted to facilitate NP transport throughout the plant. Compared to PVP and Ct, GA is highly effective in inhibiting the aggregation of NPs in synthetic sap and enhancing the mobility of NPs in trees. Over a 7 day experimental period, the majority of the Ag recovered from trees (10 mL, 10 ppm GA-AgNP suspension) remain throughout the trunk (81.0% on average), with a considerable amount in the roots (11.7% on average), some in branches (4.4% on average), and a limited amount in leaves (2.9% on average). Furthermore, NP concentrations during injection and tree incubation time postinjection are found to impact the distribution of Ag in tree. We also present evidence for a transport pathway that allows NPs to move from the xylem to the phloem, which disperses the NPs throughout the plant architecture, including to the roots.
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Affiliation(s)
- Yiming Su
- Department of Civil and Environmental Engineering, University of California, Los Angeles, California 90095, United States
| | - Vanessa E T M Ashworth
- Department of Botany and Plant Sciences, University of California, Riverside, California 92521, United States
| | - Nicholas K Geitner
- Department of Civil and Environmental Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Mark R Wiesner
- Department of Civil and Environmental Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Nichole Ginnan
- Department of Plant Pathology, University of California, Riverside, California 92521, United States
| | - Philippe Rolshausen
- Department of Botany and Plant Sciences, University of California, Riverside, California 92521, United States
| | - Caroline Roper
- Department of Plant Pathology, University of California, Riverside, California 92521, United States
| | - David Jassby
- Department of Civil and Environmental Engineering, University of California, Los Angeles, California 90095, United States
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