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Vitali F, Frascella A, Semenzato G, Del Duca S, Palumbo Piccionello A, Mocali S, Fani R, Emiliani G. Employing Genome Mining to Unveil a Potential Contribution of Endophytic Bacteria to Antimicrobial Compounds in the Origanum vulgare L. Essential Oil. Antibiotics (Basel) 2023; 12:1179. [PMID: 37508275 PMCID: PMC10376600 DOI: 10.3390/antibiotics12071179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Essential oils (EOs) from medicinal plants have long been used in traditional medicine for their widely known antimicrobial properties and represent a promising reservoir of bioactive compounds against multidrug-resistant pathogens. Endophytes may contribute to the yield and composition of EOs, representing a useful tool for biotechnological applications. In this work, we investigated the genomic basis of this potential contribution. The annotated genomes of four endophytic strains isolated from Origanum vulgare L. were used to obtain KEGG ortholog codes, which were used for the annotation of different pathways in KEGG, and to evaluate whether endophytes might harbor the (complete) gene sets for terpene and/or plant hormone biosynthesis. All strains possessed ortholog genes for the mevalonate-independent pathway (MEP/DOXP), allowing for the production of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) precursors. Ortholog genes for the next steps in terpenoid biosynthesis were scarce. All the strains possess potential plant growth promotion (PGP) ability, as shown by the presence of orthologous genes involved in the biosynthesis of indoleacetic acid. The main contribution of endophytes to the yield and composition of O. vulgare EO very likely resides in their PGP activities and in the biosynthesis of precursors of bioactive compounds.
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Affiliation(s)
- Francesco Vitali
- Research Centre for Agriculture and Environment, Council for Agricultural Research and Economics (CREA-AA), Via di Lanciola 12/A, 50125 Cascine del Riccio, Italy
| | - Arcangela Frascella
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy
| | - Giulia Semenzato
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
| | - Sara Del Duca
- Research Centre for Agriculture and Environment, Council for Agricultural Research and Economics (CREA-AA), Via di Lanciola 12/A, 50125 Cascine del Riccio, Italy
| | - Antonio Palumbo Piccionello
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Viale delle Scienze Ed.17, 90128 Palermo, Italy
| | - Stefano Mocali
- Research Centre for Agriculture and Environment, Council for Agricultural Research and Economics (CREA-AA), Via di Lanciola 12/A, 50125 Cascine del Riccio, Italy
| | - Renato Fani
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
| | - Giovanni Emiliani
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy
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Genomic, Molecular, and Phenotypic Characterization of Arthrobacter sp. OVS8, an Endophytic Bacterium Isolated from and Contributing to the Bioactive Compound Content of the Essential Oil of the Medicinal Plant Origanum vulgare L. Int J Mol Sci 2023; 24:ijms24054845. [PMID: 36902273 PMCID: PMC10002853 DOI: 10.3390/ijms24054845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/24/2023] [Accepted: 02/25/2023] [Indexed: 03/06/2023] Open
Abstract
Medicinal plants play an important role in the discovery of new bioactive compounds with antimicrobial activity, thanks to their pharmacological properties. However, members of their microbiota can also synthesize bioactive molecules. Among these, strains belonging to the genera Arthrobacter are commonly found associated with the plant's microenvironments, showing plant growth-promoting (PGP) activity and bioremediation properties. However, their role as antimicrobial secondary metabolite producers has not been fully explored. The aim of this work was to characterize the Arthrobacter sp. OVS8 endophytic strain, isolated from the medicinal plant Origanum vulgare L., from molecular and phenotypic viewpoints to evaluate its adaptation and influence on the plant internal microenvironments and its potential as a producer of antibacterial volatile molecules (VOCs). Results obtained from the phenotypic and genomic characterization highlight its ability to produce volatile antimicrobials effective against multidrug-resistant (MDR) human pathogens and its putative PGP role as a producer of siderophores and degrader of organic and inorganic pollutants. The outcomes presented in this work identify Arthrobacter sp. OVS8 as an excellent starting point toward the exploitation of bacterial endophytes as antibiotics sources.
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Semenzato G, Faddetta T, Falsini S, Del Duca S, Esposito A, Padula A, Greco C, Mucci N, Zaccaroni M, Puglia AM, Papini A, Fani R. Endophytic Bacteria Associated with Origanum heracleoticum L. (Lamiaceae) Seeds. Microorganisms 2022; 10:microorganisms10102086. [PMID: 36296360 PMCID: PMC9612275 DOI: 10.3390/microorganisms10102086] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 11/16/2022] Open
Abstract
Seed-associated microbiota are believed to play a crucial role in seed germination, seedling establishment, and plant growth and fitness stimulation, due to the vertical transmission of a core microbiota from seeds to the next generations. It might be hypothesized that medicinal and aromatic plants could use the seeds as vectors to vertically transfer beneficial endophytes, providing plants with metabolic pathways that could influence phytochemicals production. Here, we investigated the localization, the structure and the composition of the bacterial endophytic population that resides in Origanum heracleoticum L. seeds. Endocellular bacteria, surrounded by a wall, were localized close to the aleurone layer when using light and transmission electron microscopy. From surface-sterilized seeds, cultivable endophytes were isolated and characterized through RAPD analysis and 16S RNA gene sequencing, which revealed the existence of a high degree of biodiversity at the strain level and the predominance of the genus Pseudomonas. Most of the isolates grew in the presence of six selected antibiotics and were able to inhibit the growth of clinical and environmental strains that belong to the Burkholderia cepacia complex. The endophytes production of antimicrobial compounds could suggest their involvement in plant secondary metabolites production and might pave the way to endophytes exploitation in the pharmaceutical field.
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Affiliation(s)
- Giulia Semenzato
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Teresa Faddetta
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies-STEBICEF, University of Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
| | - Sara Falsini
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Sara Del Duca
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Antonia Esposito
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Anna Padula
- Unit for Conservation Genetics (BIO-CGE), Institute for Environmental Protection and Research, Via Ca’ Fornacetta, 9, Ozzano dell’Emilia, 40064 Bologna, Italy
| | - Claudia Greco
- Unit for Conservation Genetics (BIO-CGE), Institute for Environmental Protection and Research, Via Ca’ Fornacetta, 9, Ozzano dell’Emilia, 40064 Bologna, Italy
| | - Nadia Mucci
- Unit for Conservation Genetics (BIO-CGE), Institute for Environmental Protection and Research, Via Ca’ Fornacetta, 9, Ozzano dell’Emilia, 40064 Bologna, Italy
| | - Marco Zaccaroni
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Anna Maria Puglia
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies-STEBICEF, University of Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
| | - Alessio Papini
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Renato Fani
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
- Correspondence:
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Semenzato G, Alonso-Vásquez T, Del Duca S, Vassallo A, Riccardi C, Zaccaroni M, Mucci N, Padula A, Emiliani G, Palumbo Piccionello A, Puglia AM, Fani R. Genomic Analysis of Endophytic Bacillus-Related Strains Isolated from the Medicinal Plant Origanum vulgare L. Revealed the Presence of Metabolic Pathways Involved in the Biosynthesis of Bioactive Compounds. Microorganisms 2022; 10:microorganisms10050919. [PMID: 35630363 PMCID: PMC9145963 DOI: 10.3390/microorganisms10050919] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/20/2022] [Accepted: 04/25/2022] [Indexed: 12/26/2022] Open
Abstract
Multidrug-resistant pathogens represent a serious threat to human health. The inefficacy of traditional antibiotic drugs could be surmounted through the exploitation of natural bioactive compounds of which medicinal plants are a great reservoir. The finding that bacteria living inside plant tissues, (i.e., the endophytic bacterial microbiome) can influence the synthesis of the aforementioned compounds leads to the necessity of unraveling the mechanisms involved in the determination of this symbiotic relationship. Here, we report the genome sequence of four endophytic bacterial strains isolated from the medicinal plant Origanum vulgare L. and able to antagonize the growth of opportunistic pathogens of cystic fibrosis patients. The in silico analysis revealed the presence of gene clusters involved in the production of antimicrobial compounds, such as paeninodin, paenilarvins, polymyxin, and paenicidin A. Endophytes’ adaptation to the plant microenvironment was evaluated through the analysis of the presence of antibiotic resistance genes in the four genomes. The diesel fuel degrading potential was also tested. Strains grew in minimum media supplemented with diesel fuel, but no n-alkanes degradation genes were found in their genomes, suggesting that diesel fuel degradation might occur through other steps involving enzymes catalyzing the oxidation of aromatic compounds.
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Affiliation(s)
- Giulia Semenzato
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy; (G.S.); (T.A.-V.); (S.D.D.); (A.V.); (C.R.); (M.Z.)
| | - Tania Alonso-Vásquez
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy; (G.S.); (T.A.-V.); (S.D.D.); (A.V.); (C.R.); (M.Z.)
| | - Sara Del Duca
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy; (G.S.); (T.A.-V.); (S.D.D.); (A.V.); (C.R.); (M.Z.)
| | - Alberto Vassallo
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy; (G.S.); (T.A.-V.); (S.D.D.); (A.V.); (C.R.); (M.Z.)
| | - Christopher Riccardi
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy; (G.S.); (T.A.-V.); (S.D.D.); (A.V.); (C.R.); (M.Z.)
| | - Marco Zaccaroni
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy; (G.S.); (T.A.-V.); (S.D.D.); (A.V.); (C.R.); (M.Z.)
| | - Nadia Mucci
- Institute for Environmental Protection and Research, Via Ca’ Fornacetta 9, Ozzano dell’Emilia, 40064 Bologna, Italy; (N.M.); (A.P.)
| | - Anna Padula
- Institute for Environmental Protection and Research, Via Ca’ Fornacetta 9, Ozzano dell’Emilia, 40064 Bologna, Italy; (N.M.); (A.P.)
| | - Giovanni Emiliani
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), Via Madonna del Piano 10, Sesto Fiorentino, 50019 Florence, Italy;
| | - Antonio Palumbo Piccionello
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies-STEBICEF, University of Palermo, Viale delle Scienze Ed.17, 90128 Palermo, Italy; (A.P.P.); (A.M.P.)
| | - Anna Maria Puglia
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies-STEBICEF, University of Palermo, Viale delle Scienze Ed.17, 90128 Palermo, Italy; (A.P.P.); (A.M.P.)
| | - Renato Fani
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy; (G.S.); (T.A.-V.); (S.D.D.); (A.V.); (C.R.); (M.Z.)
- Correspondence: ; Tel.: +39-0554574742
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Delfino V, Calonico C, Nostro AL, Castronovo LM, Duca SD, Chioccioli S, Coppini E, Fibbi D, Vassallo A, Fani R. Antibacterial activity of bacteria isolated from Phragmites australis against multidrug-resistant human pathogens. Future Microbiol 2021; 16:291-303. [PMID: 33709774 DOI: 10.2217/fmb-2020-0244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background: Rising number of multidrug-resistant human pathogens demands novel antibiotics: to this aim, unexplored natural sources are investigated to find new compounds. In this context, bacteria associated to medicinal plants, including Phragmites australis, might represent an important source of antimicrobial compounds. Materials & methods: In the present work, 21 bacterial endophytes isolated from P. australis roots were tested, by cross-streaking, for their inhibitory activity against 36 multidrug-resistant pathogens isolated from food, clinical patients and hospitals. Results & conclusion: Seven endophytes, belonging to Pseudomonas and Stenotrophomonas, were able to inhibit the growth of most of the target strains. In conclusion, this preliminary work could pave the way for the discovery of new antibiotics against superbugs.
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Affiliation(s)
- Vania Delfino
- Department of Health Sciences, University of Florence, Viale Pieraccini 6, Florence, 50139, Italy
| | - Carmela Calonico
- Department of Health Sciences, University of Florence, Viale Pieraccini 6, Florence, 50139, Italy
| | - Antonella Lo Nostro
- Department of Health Sciences, University of Florence, Viale Pieraccini 6, Florence, 50139, Italy
| | - Lara Mitia Castronovo
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019, Italy
| | - Sara Del Duca
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019, Italy
| | - Sofia Chioccioli
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019, Italy
| | - Ester Coppini
- G.I.D.A. SpA, Via Baciacavallo 36, Prato, 59100, Italy
| | | | - Alberto Vassallo
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019, Italy
| | - Renato Fani
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019, Italy
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Li J, Wang Y, Dong Y, Zhang W, Wang D, Bai H, Li K, Li H, Shi L. The chromosome-based lavender genome provides new insights into Lamiaceae evolution and terpenoid biosynthesis. HORTICULTURE RESEARCH 2021; 8:53. [PMID: 33642593 PMCID: PMC7917091 DOI: 10.1038/s41438-021-00490-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/23/2020] [Accepted: 12/29/2020] [Indexed: 05/05/2023]
Abstract
The aromatic shrub Lavandula angustifolia produces various volatile terpenoids that serve as resources for essential oils and function in plant-insect communication. To better understand the genetic basis of the terpenoid diversity in lavender, we present a high-quality reference genome for the Chinese lavender cultivar "Jingxun 2" using PacBio and Hi-C technologies to anchor the 894.50 Mb genome assembly into 27 pseudochromosomes. In addition to the γ triplication event, lavender underwent two rounds of whole-genome duplication (WGD) during the Eocene-Oligocene (29.6 MYA) and Miocene-Pliocene (6.9 MYA) transitions. As a result of tandem duplications and lineage-specific WGDs, gene families related to terpenoid biosynthesis in lavender are substantially expanded compared to those of five other species in Lamiaceae. Many terpenoid biosynthesis transcripts are abundant in glandular trichomes. We further integrated the contents of ecologically functional terpenoids and coexpressed terpenoid biosynthetic genes to construct terpenoid-gene networks. Typical gene clusters, including TPS-TPS, TPS-CYP450, and TPS-BAHD, linked with compounds that primarily function as attractants or repellents, were identified by their similar patterns of change during flower development or in response to methyl jasmonate. Comprehensive analysis of the genetic basis of the production of volatiles in lavender could serve as a foundation for future research into lavender evolution, phytochemistry, and ecology.
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Affiliation(s)
- Jingrui Li
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Xiangshan, 100093, Beijing, China
- University of Chinese Academy of Sciences, 100015, Beijing, China
| | - Yiming Wang
- Novogene Bioinformatics Institute, 100083, Beijing, China
| | - Yanmei Dong
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Xiangshan, 100093, Beijing, China
- University of Chinese Academy of Sciences, 100015, Beijing, China
| | - Wenying Zhang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Xiangshan, 100093, Beijing, China
- University of Chinese Academy of Sciences, 100015, Beijing, China
| | - Di Wang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Xiangshan, 100093, Beijing, China
| | - Hongtong Bai
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Xiangshan, 100093, Beijing, China
| | - Kui Li
- Novogene Bioinformatics Institute, 100083, Beijing, China.
| | - Hui Li
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Xiangshan, 100093, Beijing, China.
| | - Lei Shi
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Xiangshan, 100093, Beijing, China.
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Castronovo LM, Vassallo A, Mengoni A, Miceli E, Bogani P, Firenzuoli F, Fani R, Maggini V. Medicinal Plants and Their Bacterial Microbiota: A Review on Antimicrobial Compounds Production for Plant and Human Health. Pathogens 2021; 10:pathogens10020106. [PMID: 33498987 PMCID: PMC7911374 DOI: 10.3390/pathogens10020106] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 12/15/2022] Open
Abstract
Medicinal plants (MPs) have been used since antiquity in traditional and popular medicine, and they represent a very important source of bioactive molecules, including antibiotic, antiviral, and antifungal molecules. Such compounds are often of plant origin, but in some cases, an origin or a modification from plant microbiota has been shown. Actually, the research continues to report the production of bioactive molecules by plants, but the role of plant–endophytic interaction is emerging. Classic examples are mainly concerned with fungal endophytes; however, it has been recently shown that bacterial endophytes can also play an important role in influencing the plant metabolism related to the synthesis of bioactive compounds. In spite of this, a deep investigation on the power of MP bacterial endophytes is lacking. Here, an overview of the studies on MP bacterial microbiota and its role in the production of plant antimicrobial compounds contributing to prime host defense system and representing a huge resource for biotech and therapeutic applications is provided.
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Affiliation(s)
- Lara Mitia Castronovo
- Department of Biology, University of Florence, 50019 Florence, Italy; (L.M.C.); (A.V.); (A.M.); (E.M.); (P.B.)
| | - Alberto Vassallo
- Department of Biology, University of Florence, 50019 Florence, Italy; (L.M.C.); (A.V.); (A.M.); (E.M.); (P.B.)
| | - Alessio Mengoni
- Department of Biology, University of Florence, 50019 Florence, Italy; (L.M.C.); (A.V.); (A.M.); (E.M.); (P.B.)
| | - Elisangela Miceli
- Department of Biology, University of Florence, 50019 Florence, Italy; (L.M.C.); (A.V.); (A.M.); (E.M.); (P.B.)
| | - Patrizia Bogani
- Department of Biology, University of Florence, 50019 Florence, Italy; (L.M.C.); (A.V.); (A.M.); (E.M.); (P.B.)
| | - Fabio Firenzuoli
- CERFIT, Research and Innovation Center in Phytotherapy and Integrated Medicine, Tuscany Region, Careggi University Hospital, 50141 Florence, Italy;
| | - Renato Fani
- Department of Biology, University of Florence, 50019 Florence, Italy; (L.M.C.); (A.V.); (A.M.); (E.M.); (P.B.)
- Correspondence: (R.F.); (V.M.); Tel.: +39-0554574742 (R.F.); +39-0554574731 (V.M.)
| | - Valentina Maggini
- Department of Biology, University of Florence, 50019 Florence, Italy; (L.M.C.); (A.V.); (A.M.); (E.M.); (P.B.)
- CERFIT, Research and Innovation Center in Phytotherapy and Integrated Medicine, Tuscany Region, Careggi University Hospital, 50141 Florence, Italy;
- Correspondence: (R.F.); (V.M.); Tel.: +39-0554574742 (R.F.); +39-0554574731 (V.M.)
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8
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Castronovo LM, Calonico C, Ascrizzi R, Del Duca S, Delfino V, Chioccioli S, Vassallo A, Strozza I, De Leo M, Biffi S, Bacci G, Bogani P, Maggini V, Mengoni A, Pistelli L, Lo Nostro A, Firenzuoli F, Fani R. The Cultivable Bacterial Microbiota Associated to the Medicinal Plant Origanum vulgare L.: From Antibiotic Resistance to Growth-Inhibitory Properties. Front Microbiol 2020; 11:862. [PMID: 32457726 PMCID: PMC7226918 DOI: 10.3389/fmicb.2020.00862] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 04/09/2020] [Indexed: 12/14/2022] Open
Abstract
The insurgence of antibiotic resistance and emergence of multidrug-resistant (MDR) pathogens prioritize research to discover new antimicrobials. In this context, medicinal plants produce bioactive compounds of pharmacological interest: some extracts have antimicrobial properties that can contrast different pathogens. For such a purpose, Origanum vulgare L. (Lamiaceae family) is a medicinal aromatic plant, whose essential oil (EO) is recognized for its antiseptic, antimicrobial and antiviral activities. The cultivable bacteria from different compartments (i.e., flower, leaf, stem and soil) were isolated in order to: (i) characterize the bacterial microbiota associated to the plant, determining the forces responsible for the structuring of its composition (by evaluation of cross inhibition); (ii) investigate if bacterial endophytes demonstrate antimicrobial activities against human pathogens. A pool of plants belonging to O. vulgare species was collected and the specimen chemotype was defined by hydrodistillation of its essential oil. The isolation of plant associated bacteria was performed from the four compartments. Microbiota was further characterized through a culture-independent approach and next-generation sequencing analysis, as well. Isolates were molecularly typed by Random Amplified Polymorphic DNA (RAPD) profiling and taxonomically assigned by 16S rRNA gene sequencing. Antibiotic resistance profiles of isolates and pairwise cross-inhibition of isolates on agar plates (i.e., antagonistic interactions) were also assessed. High level of diversity of bacterial isolates was detected at both genus and strain level in all different compartments. Most strains were tolerant against common antibiotics; moreover, they produced antagonistic patterns of interactions mainly with strains from different compartments with respect to that of original isolation. Strains that exhibited high inhibitory properties were further tested against human pathogens, revealing a strong capacity to inhibit the growth of strains resistant to several antibiotics. In conclusion, this study regarded the characterization of O. vulgare L. chemotype and of the bacterial communities associated to this medicinal plant, also allowing the evaluation of antibiotic resistance and antagonistic interactions. This study provided the bases for further analyses on the possible involvement of endophytic bacteria in the production of antimicrobial molecules that could have an important role in clinical and therapeutic applications.
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Affiliation(s)
| | - Carmela Calonico
- Department of Health Sciences, University of Florence, Florence, Italy
| | | | - Sara Del Duca
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Vania Delfino
- Department of Health Sciences, University of Florence, Florence, Italy
| | - Sofia Chioccioli
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Alberto Vassallo
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Iolanda Strozza
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | | | | | - Giovanni Bacci
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Patrizia Bogani
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Valentina Maggini
- Department of Biology, University of Florence, Sesto Fiorentino, Italy.,Research and Innovation Center in Phytotherapy and Integrated Medicine - CERFIT Careggi University Hospital, Florence, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | | | | | - Fabio Firenzuoli
- Research and Innovation Center in Phytotherapy and Integrated Medicine - CERFIT Careggi University Hospital, Florence, Italy
| | - Renato Fani
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
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Endophytic Bacteria Associated with Medicinal Plant Vernonia anthelmintica: Diversity and Characterization. Curr Microbiol 2020; 77:1457-1465. [PMID: 32211943 DOI: 10.1007/s00284-020-01924-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 02/14/2020] [Indexed: 12/11/2022]
Abstract
Increasing evidence shows that endophytic bacteria living inside plant tissue may possess similar biological activity and produce similar metabolites to their hosts. This study aimed to determine the diversity of endophytic bacteria associated with Vernonia anthelmintica and to evaluate their biological activity. The bacteria were isolated from the plant tissue using culture-dependent techniques. Comparison of the 16S rRNA gene sequences of endophytic bacteria isolated from V. anthelmintica showed that isolates belong to the species Micrococcus endophyticus VERA1, Bacillus megaterium VERA2, Pseudomonas chlororaphis VERA3, P. kilonensis VERA4, Stenotrophomonas pavanii VERA5, B. endophyticus VERA6, S. maltophilia VERA7, Pantoea ananatis VERA8, B. atrophaeus VERA9 and M. flavus VERA10. Activity studies showed that the endophytic bacteria share several similar biological properties with their host plant including antimicrobial, anti-vitiligo and antidiabetic activities. These findings indicate that plant phytochemical compounds and activity play an important role in the physiological properties of their endophytes.
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Kushwaha P, Kashyap PL, Bhardwaj AK, Kuppusamy P, Srivastava AK, Tiwari RK. Bacterial endophyte mediated plant tolerance to salinity: growth responses and mechanisms of action. World J Microbiol Biotechnol 2020; 36:26. [PMID: 31997078 DOI: 10.1007/s11274-020-2804-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 01/22/2020] [Indexed: 12/18/2022]
Abstract
Salinity stress is one of the key constraints for sustainable crop production. It has gained immense importance in the backdrop of climate change induced imbalanced terrestrial water budgets. The traditional agronomic approaches and breeding salt-tolerant genotypes have often proved insufficient to alleviate salinity stress. Newer approaches like the use of bacterial endophytes associated with agricultural crops have occupied center place recently, owing to their advantageous role in improving crop growth, health and yield. Research evidences have revealed that bacterial endophytes can promote plant growth by accelerating availability of mineral nutrients, helping in production of phytohormones, siderophores, and enzymes, and also by activating systemic resistance against insect pest and pathogens in plants. These research developments have opened an innovative boulevard in agriculture for capitalizing bacterial endophytes, single species or consortium, to enhance plant salt tolerance capabilities, and ultimately lead to translational refinement of crop-production business under salty environments. This article reviews the latest research progress on the identification and functional characterization of salt tolerant endophytic bacteria and illustrates various mechanisms triggered by them for plant growth promotion under saline environment.
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Affiliation(s)
- Prity Kushwaha
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Uttar Pradesh, Mau, 275103, India
| | - Prem Lal Kashyap
- ICAR-Indian Institute of Wheat and Barley Research (IIWBR), Karnal, 132001, India.
| | - Ajay Kumar Bhardwaj
- ICAR-Central Soil Salinity Research Institute (CSSRI), Karnal, 132001, India.
| | - Pandiyan Kuppusamy
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Uttar Pradesh, Mau, 275103, India
| | - Alok Kumar Srivastava
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Uttar Pradesh, Mau, 275103, India
| | - Rajesh Kumar Tiwari
- AMITY University, Uttar Pradesh Lucknow Campus, Malhaur, Gomti Nagar Extension, Lucknow, 227105, India
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11
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Maggini V, Miceli E, Fagorzi C, Maida I, Fondi M, Perrin E, Mengoni A, Bogani P, Chiellini C, Mocali S, Fabiani A, Decorosi F, Giovannetti L, Firenzuoli F, Fani R. Antagonism and antibiotic resistance drive a species-specific plant microbiota differentiation in Echinacea spp. FEMS Microbiol Ecol 2019; 94:5037916. [PMID: 29912319 DOI: 10.1093/femsec/fiy118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 06/06/2018] [Indexed: 12/19/2022] Open
Abstract
A key factor in the study of plant-microbes interactions is the composition of plant microbiota, but little is known about the factors determining its functional and taxonomic organization. Here we investigated the possible forces driving the assemblage of bacterial endophytic and rhizospheric communities, isolated from two congeneric medicinal plants, Echinacea purpurea (L.) Moench and Echinacea angustifolia (DC) Heller, grown in the same soil, by analysing bacterial strains (isolated from three different compartments, i.e. rhizospheric soil, roots and stem/leaves) for phenotypic features such as antibiotic resistance, extracellular enzymatic activity, siderophore and indole 3-acetic acid production, as well as cross-antagonistic activities. Data obtained highlighted that bacteria from different plant compartments were characterized by specific antibiotic resistance phenotypes and antibiotic production, suggesting that the bacterial communities themselves could be responsible for structuring their own communities by the production of antimicrobial molecules selecting bacterial-adaptive phenotypes for plant tissue colonization.
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Affiliation(s)
- Valentina Maggini
- Dept. of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino (Florence), Italy.,Center for Integrative Medicine, Careggi University Hospital, Dept. of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Elisangela Miceli
- Dept. of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino (Florence), Italy
| | - Camilla Fagorzi
- Dept. of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino (Florence), Italy
| | - Isabel Maida
- Dept. of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino (Florence), Italy
| | - Marco Fondi
- Dept. of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino (Florence), Italy
| | - Elena Perrin
- Dept. of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino (Florence), Italy
| | - Alessio Mengoni
- Dept. of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino (Florence), Italy
| | - Patrizia Bogani
- Dept. of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino (Florence), Italy
| | - Carolina Chiellini
- Dept. of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino (Florence), Italy
| | - Stefano Mocali
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di ricerca Agricoltura e Ambiente (CREA-AA), via di Lanciola 12/A, 50125 Cascine del Riccio (Florence), Italy
| | - Arturo Fabiani
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di ricerca Agricoltura e Ambiente (CREA-AA), via di Lanciola 12/A, 50125 Cascine del Riccio (Florence), Italy
| | - Francesca Decorosi
- Department of Agri-food Production and Environmental Science, University of Florence, Florence, Italy
| | - Luciana Giovannetti
- Department of Agri-food Production and Environmental Science, University of Florence, Florence, Italy
| | - Fabio Firenzuoli
- Center for Integrative Medicine, Careggi University Hospital, Dept. of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Renato Fani
- Dept. of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino (Florence), Italy
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12
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Chiellini C, Maida I, Maggini V, Bosi E, Mocali S, Emiliani G, Perrin E, Firenzuoli F, Mengoni A, Fani R. Preliminary data on antibacterial activity of Echinacea purpurea-associated bacterial communities against Burkholderia cepacia complex strains, opportunistic pathogens of Cystic Fibrosis patients. Microbiol Res 2016; 196:34-43. [PMID: 28164789 DOI: 10.1016/j.micres.2016.12.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 11/17/2016] [Accepted: 12/03/2016] [Indexed: 12/22/2022]
Abstract
Burkholderia cepacia complex bacteria (Bcc) represent a serious threat for immune-compromised patient affected by Cystic Fibrosis (CF) since they are resistant to many substances and to most antibiotics. For this reason, the research of new natural compounds able to inhibit the growth of Bcc strains has raised new interest during the last years. A source of such natural compounds is represented by medicinal plants and, in particular, by bacterial communities associated with these plants able to produce molecules with antimicrobial activity. In this work, a panel of 151 (endophytic) bacteria isolated from three different compartments (rhizospheric soil, roots, and stem/leaves) of the medicinal plant Echinacea purpurea were tested (using the cross-streak method) for their ability to inhibit the growth of 10 Bcc strains. Data obtained revealed that bacteria isolated from the roots of E. purpurea are the most active in the inhibition of Bcc strains, followed by bacteria isolated from the rhizospheric soil, and endophytes from stem/leaf compartment. At the same time, Bcc strains of environmental origin showed a higher resistance toward inhibition than the Bcc strains with clinical (i.e. CF patients) origin. Differences in the inhibition activity of E. purpurea-associated bacteria are mainly linked to the environment -the plant compartment- rather than to their taxonomical position.
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Affiliation(s)
- Carolina Chiellini
- Department of Biology, University of Florence, Via Madonna del Piano, 6 I-50019 Sesto Fiorentino, Florence, Italy.
| | - Isabel Maida
- Department of Biology, University of Florence, Via Madonna del Piano, 6 I-50019 Sesto Fiorentino, Florence, Italy.
| | - Valentina Maggini
- Department of Biology, University of Florence, Via Madonna del Piano, 6 I-50019 Sesto Fiorentino, Florence, Italy; Center for Integrative Medicine, Careggi University Hospital, University of Florence, Florence, Italy.
| | - Emanuele Bosi
- Department of Biology, University of Florence, Via Madonna del Piano, 6 I-50019 Sesto Fiorentino, Florence, Italy.
| | - Stefano Mocali
- CREA-ABP Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, centro di ricerca per l'Agrobiologia e la Pedologia, Via di Lanciola 12A, Cascine del Riccio, 50125 Florence (FI), Italy.
| | - Giovanni Emiliani
- Tree and Timber Institute National Research Council, Via Madonna del Piano, 10 I-50019 Sesto Fiorentino, Florence, Italy.
| | - Elena Perrin
- Department of Biology, University of Florence, Via Madonna del Piano, 6 I-50019 Sesto Fiorentino, Florence, Italy.
| | - Fabio Firenzuoli
- Center for Integrative Medicine, Careggi University Hospital, University of Florence, Florence, Italy.
| | - Alessio Mengoni
- Department of Biology, University of Florence, Via Madonna del Piano, 6 I-50019 Sesto Fiorentino, Florence, Italy.
| | - Renato Fani
- Department of Biology, University of Florence, Via Madonna del Piano, 6 I-50019 Sesto Fiorentino, Florence, Italy.
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13
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Phenotypic and genomic characterization of the antimicrobial producer Rheinheimera sp. EpRS3 isolated from the medicinal plant Echinacea purpurea: insights into its biotechnological relevance. Res Microbiol 2016; 168:293-305. [PMID: 27884784 DOI: 10.1016/j.resmic.2016.11.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 11/11/2016] [Accepted: 11/14/2016] [Indexed: 12/23/2022]
Abstract
In recent years, there has been increasing interest in plant microbiota; however, despite medicinal plant relevance, very little is known about their highly complex endophytic communities. In this work, we report on the genomic and phenotypic characterization of the antimicrobial compound producer Rheinheimera sp. EpRS3, a bacterial strain isolated from the rhizospheric soil of the medicinal plant Echinacea purpurea. In particular, EpRS3 is able to inhibit growth of different bacterial pathogens (Bcc, Acinetobacter baumannii, and Klebsiella pneumoniae) which might be related to the presence of gene clusters involved in the biosynthesis of different types of secondary metabolites. The outcomes presented in this work highlight the fact that the strain possesses huge biotechnological potential; indeed, it also shows antimicrobial effects upon well-described multidrug-resistant (MDR) human pathogens, and it affects plant root elongation and morphology, mimicking indole acetic acid (IAA) action.
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14
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Checcucci A, Maida I, Bacci G, Ninno C, Bilia AR, Biffi S, Firenzuoli F, Flamini G, Fani R, Mengoni A. Is the plant-associated microbiota of Thymus spp. adapted to plant essential oil? Res Microbiol 2016; 168:276-282. [PMID: 27884782 DOI: 10.1016/j.resmic.2016.11.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 11/09/2016] [Accepted: 11/11/2016] [Indexed: 10/20/2022]
Abstract
We examined whether the microbiota of two related aromatic thyme species, Thymus vulgaris and Thymus citriodorus, differs in relation to the composition of the respective essential oil (EO). A total of 576 bacterial isolates were obtained from three districts (leaves, roots and rhizospheric soil). They were taxonomically characterized and inspected for tolerance to the EO from the two thyme species. A district-related taxonomic pattern was found. In particular, high taxonomic diversity among the isolates from leaves was detected. Moreover, data obtained revealed a differential pattern of resistance of the isolates to EOs extracted from T. vulgaris and T. citriodorus, which was interpreted in terms of differing chemical composition of the EO of their respective host plants. In conclusion, we suggest that bacterial colonization of leaves in Thymus spp. is influenced by the EO present in leaf glandular tissue as one of the selective forces shaping endophytic community composition.
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Affiliation(s)
- Alice Checcucci
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Florence 50019, Italy
| | - Isabel Maida
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Florence 50019, Italy
| | - Giovanni Bacci
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Florence 50019, Italy
| | - Cristina Ninno
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Florence 50019, Italy
| | - Anna Rita Bilia
- Department of Chemistry Ugo Schiff, University of Florence, Via Ugo Schiff 6, I-50019 Sesto Fiorentino, Florence 50019, Italy
| | - Sauro Biffi
- Il giardino delle Erbe, "Augusto Rinaldi Ceroni", Casola Valsenio, Ravenna, Italy
| | - Fabio Firenzuoli
- Centre for Integrative Medicine, Careggi University Hospital, University of Florence, Florence, Italy
| | - Guido Flamini
- Department of Pharmacy, University of Pisa, Via Bonanno Pisano 6, I-56126 Pisa, Italy
| | - Renato Fani
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Florence 50019, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Florence 50019, Italy.
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15
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Mora-Ruiz MDR, Font-Verdera F, Orfila A, Rita J, Rosselló-Móra R. Endophytic microbial diversity of the halophyteArthrocnemum macrostachyumacross plant compartments. FEMS Microbiol Ecol 2016; 92:fiw145. [DOI: 10.1093/femsec/fiw145] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2016] [Indexed: 11/13/2022] Open
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16
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Maida I, Chiellini C, Mengoni A, Bosi E, Firenzuoli F, Fondi M, Fani R. Antagonistic interactions between endophytic cultivable bacterial communities isolated from the medicinal plantEchinacea purpurea. Environ Microbiol 2015; 18:2357-65. [DOI: 10.1111/1462-2920.12911] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 05/15/2015] [Accepted: 05/16/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Isabel Maida
- Department of Biology; University of Florence; Via Madonna del Piano 6 Sesto Fiorentino Florence I-50019 Italy
| | - Carolina Chiellini
- Department of Biology; University of Florence; Via Madonna del Piano 6 Sesto Fiorentino Florence I-50019 Italy
- CRA-ABP Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria; Centro di ricerca per l'Agrobiologia e la Pedologia; Piazza M. D'Azeglio 30 Firenze FI 50121 Italy
| | - Alessio Mengoni
- Department of Biology; University of Florence; Via Madonna del Piano 6 Sesto Fiorentino Florence I-50019 Italy
| | - Emanuele Bosi
- Department of Biology; University of Florence; Via Madonna del Piano 6 Sesto Fiorentino Florence I-50019 Italy
| | - Fabio Firenzuoli
- Center for Integrative Medicine; Careggi University Hospital; University of Florence; Florence Italy
| | - Marco Fondi
- Department of Biology; University of Florence; Via Madonna del Piano 6 Sesto Fiorentino Florence I-50019 Italy
| | - Renato Fani
- Department of Biology; University of Florence; Via Madonna del Piano 6 Sesto Fiorentino Florence I-50019 Italy
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