Culture-Dependent and Metabarcoding Characterization of the Sugar Beet (<i>Beta vulgaris</i> L.) Microbiome for High-Yield Isolation of Bacteria with Plant Growth-Promoting Traits
The diversity of plant-associated bacteria is vast and can be determined by 16S rRNA gene metabarcoding. Fewer of them have plant-beneficial properties. To harness their benefits for plants, we must isolate them. This study aimed to check whether 16S rRNA gene metabarcoding has predictive power in i...
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| Format: | Article |
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MDPI AG
2023-06-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/11/6/1538 |
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| author | Tamara Krstić Tomić Iva Atanasković Ivan Nikolić Nataša Joković Tatjana Stević Slaviša Stanković Tanja Berić Jelena Lozo |
| author_facet | Tamara Krstić Tomić Iva Atanasković Ivan Nikolić Nataša Joković Tatjana Stević Slaviša Stanković Tanja Berić Jelena Lozo |
| author_sort | Tamara Krstić Tomić |
| collection | DOAJ |
| description | The diversity of plant-associated bacteria is vast and can be determined by 16S rRNA gene metabarcoding. Fewer of them have plant-beneficial properties. To harness their benefits for plants, we must isolate them. This study aimed to check whether 16S rRNA gene metabarcoding has predictive power in identifying the majority of known bacteria with plant-beneficial traits that can be isolated from the sugar beet (<i>Beta vulgaris</i> L.) microbiome. Rhizosphere and phyllosphere samples collected during one season at different stages of plant development were analyzed. Bacteria were isolated on rich unselective media and plant-based media enriched with sugar beet leaves or rhizosphere extracts. The isolates were identified by sequencing the 16S rRNA gene and tested in vitro for their plant-beneficial properties (stimulation of germination; exopolysaccharide, siderophore, and HCN production; phosphate solubilization; and activity against sugar beet pathogens). The highest number of co-occurring beneficial traits was eight, found in isolates of five species: <i>Acinetobacter calcoaceticus</i>, <i>Bacillus australimaris</i>, <i>B. pumilus</i>, <i>Enterobacter ludwiigi</i>, and <i>Pantoea ananatis</i>. These species were not detected by metabarcoding and have not previously been described as plant-beneficial inhabitants of sugar beets. Thus, our findings point out the necessity of a culture-dependent microbiome analysis and advocate for low-nutrient plant-based media for high-yield isolation of plant-beneficial taxa with multiple beneficial traits. A culture-dependent and -independent approach is required for community diversity assessment. Still, isolation on plant-based media is the best approach to select isolates for potential use as biofertilizers and biopesticides in sugar beet cultivation. |
| first_indexed | 2024-03-11T02:08:09Z |
| format | Article |
| id | doaj.art-48039544c79e4454b8507c6b1bc3bec5 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-11T02:08:09Z |
| publishDate | 2023-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-48039544c79e4454b8507c6b1bc3bec52023-11-18T11:43:16ZengMDPI AGMicroorganisms2076-26072023-06-01116153810.3390/microorganisms11061538Culture-Dependent and Metabarcoding Characterization of the Sugar Beet (<i>Beta vulgaris</i> L.) Microbiome for High-Yield Isolation of Bacteria with Plant Growth-Promoting TraitsTamara Krstić Tomić0Iva Atanasković1Ivan Nikolić2Nataša Joković3Tatjana Stević4Slaviša Stanković5Tanja Berić6Jelena Lozo7University of Belgrade, Faculty of Biology, 11000 Belgrade, SerbiaUniversity of Belgrade, Faculty of Biology, 11000 Belgrade, SerbiaUniversity of Belgrade, Faculty of Biology, 11000 Belgrade, SerbiaFaculty of Sciences and Mathematics, University of Niš, 18000 Niš, SerbiaInstitute for Medicinal Plants Research “Dr. Josif Pančić”, 11000 Belgrade, SerbiaUniversity of Belgrade, Faculty of Biology, 11000 Belgrade, SerbiaUniversity of Belgrade, Faculty of Biology, 11000 Belgrade, SerbiaUniversity of Belgrade, Faculty of Biology, 11000 Belgrade, SerbiaThe diversity of plant-associated bacteria is vast and can be determined by 16S rRNA gene metabarcoding. Fewer of them have plant-beneficial properties. To harness their benefits for plants, we must isolate them. This study aimed to check whether 16S rRNA gene metabarcoding has predictive power in identifying the majority of known bacteria with plant-beneficial traits that can be isolated from the sugar beet (<i>Beta vulgaris</i> L.) microbiome. Rhizosphere and phyllosphere samples collected during one season at different stages of plant development were analyzed. Bacteria were isolated on rich unselective media and plant-based media enriched with sugar beet leaves or rhizosphere extracts. The isolates were identified by sequencing the 16S rRNA gene and tested in vitro for their plant-beneficial properties (stimulation of germination; exopolysaccharide, siderophore, and HCN production; phosphate solubilization; and activity against sugar beet pathogens). The highest number of co-occurring beneficial traits was eight, found in isolates of five species: <i>Acinetobacter calcoaceticus</i>, <i>Bacillus australimaris</i>, <i>B. pumilus</i>, <i>Enterobacter ludwiigi</i>, and <i>Pantoea ananatis</i>. These species were not detected by metabarcoding and have not previously been described as plant-beneficial inhabitants of sugar beets. Thus, our findings point out the necessity of a culture-dependent microbiome analysis and advocate for low-nutrient plant-based media for high-yield isolation of plant-beneficial taxa with multiple beneficial traits. A culture-dependent and -independent approach is required for community diversity assessment. Still, isolation on plant-based media is the best approach to select isolates for potential use as biofertilizers and biopesticides in sugar beet cultivation.https://www.mdpi.com/2076-2607/11/6/1538sugar beetplant microbiome16S rRNA metabarcodingplant-based mediaseasonal changes |
| spellingShingle | Tamara Krstić Tomić Iva Atanasković Ivan Nikolić Nataša Joković Tatjana Stević Slaviša Stanković Tanja Berić Jelena Lozo Culture-Dependent and Metabarcoding Characterization of the Sugar Beet (<i>Beta vulgaris</i> L.) Microbiome for High-Yield Isolation of Bacteria with Plant Growth-Promoting Traits Microorganisms sugar beet plant microbiome 16S rRNA metabarcoding plant-based media seasonal changes |
| title | Culture-Dependent and Metabarcoding Characterization of the Sugar Beet (<i>Beta vulgaris</i> L.) Microbiome for High-Yield Isolation of Bacteria with Plant Growth-Promoting Traits |
| title_full | Culture-Dependent and Metabarcoding Characterization of the Sugar Beet (<i>Beta vulgaris</i> L.) Microbiome for High-Yield Isolation of Bacteria with Plant Growth-Promoting Traits |
| title_fullStr | Culture-Dependent and Metabarcoding Characterization of the Sugar Beet (<i>Beta vulgaris</i> L.) Microbiome for High-Yield Isolation of Bacteria with Plant Growth-Promoting Traits |
| title_full_unstemmed | Culture-Dependent and Metabarcoding Characterization of the Sugar Beet (<i>Beta vulgaris</i> L.) Microbiome for High-Yield Isolation of Bacteria with Plant Growth-Promoting Traits |
| title_short | Culture-Dependent and Metabarcoding Characterization of the Sugar Beet (<i>Beta vulgaris</i> L.) Microbiome for High-Yield Isolation of Bacteria with Plant Growth-Promoting Traits |
| title_sort | culture dependent and metabarcoding characterization of the sugar beet i beta vulgaris i l microbiome for high yield isolation of bacteria with plant growth promoting traits |
| topic | sugar beet plant microbiome 16S rRNA metabarcoding plant-based media seasonal changes |
| url | https://www.mdpi.com/2076-2607/11/6/1538 |
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