Composition, Seasonal Dynamics and Metabolic Potential of the Rhizosphere Microbiome Associated with Wild White Poplar
The white poplar (<i>Populus alba</i>) is a dioecious woody plant with significant potential for the phytoremediation of soils. To realize this potential, it is necessary to utilize growth-promoting microorganisms. One potential source of such beneficial microorganisms is the rhizosphere...
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2024-12-01
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| author | Mikhail I. Popchenko Dmitry S. Karpov Natalya S. Gladysh Maxim A. Kovalev Vsevolod V. Volodin George S. Krasnov Alina S. Bogdanova Nadezhda L. Bolsheva Maria S. Fedorova Anna V. Kudryavtseva |
| author_facet | Mikhail I. Popchenko Dmitry S. Karpov Natalya S. Gladysh Maxim A. Kovalev Vsevolod V. Volodin George S. Krasnov Alina S. Bogdanova Nadezhda L. Bolsheva Maria S. Fedorova Anna V. Kudryavtseva |
| author_sort | Mikhail I. Popchenko |
| collection | DOAJ |
| description | The white poplar (<i>Populus alba</i>) is a dioecious woody plant with significant potential for the phytoremediation of soils. To realize this potential, it is necessary to utilize growth-promoting microorganisms. One potential source of such beneficial microorganisms is the rhizosphere community of wild-growing trees. However, the structure, dynamics, and metabolism of the rhizosphere community of wild-growing white poplar remain poorly understood. To ascertain seasonal dynamics, species diversity, and metabolic potential, we sequenced 16S rRNA genes in metagenomes derived from 165 soil samples collected in spring and autumn from the root surfaces of 102 trees situated in disparate geographical locations. The three most prevalent phyla across all samples are Proteobacteria, Actinobacteriota, and Acidobacteriota. At the order level, the most prevalent orders are Sphingomonadales and Rhizobiales. Accordingly, the families Sphingomonadaceae and Rhizobiaceae were identified as dominant. The rhizospheric microbiome exhibited substantial inter-seasonal variation. Six families, including Caulobacteraceae, Xanthomonadaceae, Chitinophagaceae, Chthoniobacteraceae, Sphingomonadaceae, and Rhizobiaceae, exhibited alterations (spring-to-autumn) across all geographical locations under study. Members of the Rhizobiaceae family, which includes nitrogen-fixing bacteria, can provide poplar with plant-available forms of nitrogen such as nitrate and ammonium. The rhizosphere microbiome may facilitate the conversion of inorganic sulfur into sulfur-containing amino acids, cysteine and methionine, that are bioavailable to plants. Furthermore, the rhizosphere microbiome is capable of synthesizing amino acids, organic acids (including Krebs cycle acids), and some lipids and sugars. Consequently, the rhizosphere community can stimulate poplar growth by providing it with readily available forms of nitrogen and sulfur, as well as building blocks for the synthesis of proteins, nucleic acids, and other macromolecules. Many of these pathways, including nitrogen fixation, were subjected to seasonal changes. |
| format | Article |
| id | doaj-art-ca55223248394418b3842f60deea88b4 |
| institution | DOAJ |
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| publishDate | 2024-12-01 |
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| spelling | doaj-art-ca55223248394418b3842f60deea88b42025-08-20T02:55:39ZengMDPI AGBioTech2673-62842024-12-011345210.3390/biotech13040052Composition, Seasonal Dynamics and Metabolic Potential of the Rhizosphere Microbiome Associated with Wild White PoplarMikhail I. Popchenko0Dmitry S. Karpov1Natalya S. Gladysh2Maxim A. Kovalev3Vsevolod V. Volodin4George S. Krasnov5Alina S. Bogdanova6Nadezhda L. Bolsheva7Maria S. Fedorova8Anna V. Kudryavtseva9Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova, 119991 Moscow, RussiaEngelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova, 119991 Moscow, RussiaEngelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova, 119991 Moscow, RussiaEngelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova, 119991 Moscow, RussiaEngelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova, 119991 Moscow, RussiaEngelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova, 119991 Moscow, RussiaEngelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova, 119991 Moscow, RussiaEngelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova, 119991 Moscow, RussiaEngelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova, 119991 Moscow, RussiaEngelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova, 119991 Moscow, RussiaThe white poplar (<i>Populus alba</i>) is a dioecious woody plant with significant potential for the phytoremediation of soils. To realize this potential, it is necessary to utilize growth-promoting microorganisms. One potential source of such beneficial microorganisms is the rhizosphere community of wild-growing trees. However, the structure, dynamics, and metabolism of the rhizosphere community of wild-growing white poplar remain poorly understood. To ascertain seasonal dynamics, species diversity, and metabolic potential, we sequenced 16S rRNA genes in metagenomes derived from 165 soil samples collected in spring and autumn from the root surfaces of 102 trees situated in disparate geographical locations. The three most prevalent phyla across all samples are Proteobacteria, Actinobacteriota, and Acidobacteriota. At the order level, the most prevalent orders are Sphingomonadales and Rhizobiales. Accordingly, the families Sphingomonadaceae and Rhizobiaceae were identified as dominant. The rhizospheric microbiome exhibited substantial inter-seasonal variation. Six families, including Caulobacteraceae, Xanthomonadaceae, Chitinophagaceae, Chthoniobacteraceae, Sphingomonadaceae, and Rhizobiaceae, exhibited alterations (spring-to-autumn) across all geographical locations under study. Members of the Rhizobiaceae family, which includes nitrogen-fixing bacteria, can provide poplar with plant-available forms of nitrogen such as nitrate and ammonium. The rhizosphere microbiome may facilitate the conversion of inorganic sulfur into sulfur-containing amino acids, cysteine and methionine, that are bioavailable to plants. Furthermore, the rhizosphere microbiome is capable of synthesizing amino acids, organic acids (including Krebs cycle acids), and some lipids and sugars. Consequently, the rhizosphere community can stimulate poplar growth by providing it with readily available forms of nitrogen and sulfur, as well as building blocks for the synthesis of proteins, nucleic acids, and other macromolecules. Many of these pathways, including nitrogen fixation, were subjected to seasonal changes.https://www.mdpi.com/2673-6284/13/4/52<i>Populus alba</i>rhizospheresoil metagenomicsmicrobial diversityamplicon sequence data16S rDNA |
| spellingShingle | Mikhail I. Popchenko Dmitry S. Karpov Natalya S. Gladysh Maxim A. Kovalev Vsevolod V. Volodin George S. Krasnov Alina S. Bogdanova Nadezhda L. Bolsheva Maria S. Fedorova Anna V. Kudryavtseva Composition, Seasonal Dynamics and Metabolic Potential of the Rhizosphere Microbiome Associated with Wild White Poplar BioTech <i>Populus alba</i> rhizosphere soil metagenomics microbial diversity amplicon sequence data 16S rDNA |
| title | Composition, Seasonal Dynamics and Metabolic Potential of the Rhizosphere Microbiome Associated with Wild White Poplar |
| title_full | Composition, Seasonal Dynamics and Metabolic Potential of the Rhizosphere Microbiome Associated with Wild White Poplar |
| title_fullStr | Composition, Seasonal Dynamics and Metabolic Potential of the Rhizosphere Microbiome Associated with Wild White Poplar |
| title_full_unstemmed | Composition, Seasonal Dynamics and Metabolic Potential of the Rhizosphere Microbiome Associated with Wild White Poplar |
| title_short | Composition, Seasonal Dynamics and Metabolic Potential of the Rhizosphere Microbiome Associated with Wild White Poplar |
| title_sort | composition seasonal dynamics and metabolic potential of the rhizosphere microbiome associated with wild white poplar |
| topic | <i>Populus alba</i> rhizosphere soil metagenomics microbial diversity amplicon sequence data 16S rDNA |
| url | https://www.mdpi.com/2673-6284/13/4/52 |
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