Root colonization ability of herbicide-resistant PGP bacteria evaluated by 16S rRNA metabarcoding
Аутори
Bez, CristinaGalić, Ivana
Bertani, Iris
Stanković, Nada
Venturi, Vittorio
Остала ауторства
Morić, IvanaĐorđević, Valentina
Конференцијски прилог (Објављена верзија)
,
© 2023 Institute of Molecular Genetics and Genetic Engineering, University of Belgrade
Метаподаци
Приказ свих података о документуАпстракт
In terms of agricultural sustainability, herbicide-resistant, plant growth promoting (PGP)
bacteria that can improve crop yield are valuable resource. To exhibit PGP traits, the
bacteria must be able to colonize and survive in the rhizosphere.
Upon screening the herbicide-resistant bacterial collection, candidates with the highest
PGP potential were grouped into three consortia to evaluate their ability to colonize roots
and persist in the natural/local plant microbiome in the pot. Experiments were conducted
with seeds of commercial maize hybrids under controlled conditions, with and without
herbicide. Colonization ability was evaluated by examining multiple plants from each
treatment at two-time points during the experiment. 16S rRNA amplicon community
profiling was performed to precisely target the bacterial strains used in the three
consortia and investigate how the local microbiome might be altered by the application of
the consortia. Bioinformatic analysis was performed... using qiime2, clustering of reads into
amplicon sequence variants ASVs using the DADA2 plugin, and the taxonomic assignment
was based on a customized dataset formed from the 16S rRNA gene sequences of the
ten isolates used in this study or by using the Silva rRNA database. For clustering and
comparison of ASVs based on sequence similarity, the program cd-hit was used, with
the sequence similarity parameter set to 98% to be considered part of the same cluster.
The obtained dataset was imported into R using the package qiime2R, and subsequent
analyzes and graphs were generated using either the R packages phyloseq, microbiome,
or reshape2. We identified seven out of ten inoculated strains in both time points tested
and with comparable abundance, indicating that most of the bacterial isolates tested have
the ability to colonize the root system of maize. Furthermore, the natural/local microbiome
of maize plants is not disturbed by the three consortia used in this study, implying that
they are good candidates for future biotechnological applications.
Кључне речи:
metabarcoding / 16S / consortium / bacteria / PGPИзвор:
4th Belgrade Bioinformatics Conference, 2023, 4, 71-71Издавач:
- Belgrade : Institute of molecular genetics and genetic engineering
Финансирање / пројекти:
- FEMS Research and Training Grant ID: 1818
- Министарство науке, технолошког развоја и иновација Републике Србије, институционално финансирање - 200042 (Универзитет у Београду, Институт за молекуларну генетику и генетичко инжењерство) (RS-MESTD-inst-2020-200042)
Напомена:
- Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 2023
Колекције
Институција/група
Institut za molekularnu genetiku i genetičko inženjerstvoTY - CONF AU - Bez, Cristina AU - Galić, Ivana AU - Bertani, Iris AU - Stanković, Nada AU - Venturi, Vittorio PY - 2023 UR - https://belbi.bg.ac.rs/ UR - https://imagine.imgge.bg.ac.rs/handle/123456789/2012 AB - In terms of agricultural sustainability, herbicide-resistant, plant growth promoting (PGP) bacteria that can improve crop yield are valuable resource. To exhibit PGP traits, the bacteria must be able to colonize and survive in the rhizosphere. Upon screening the herbicide-resistant bacterial collection, candidates with the highest PGP potential were grouped into three consortia to evaluate their ability to colonize roots and persist in the natural/local plant microbiome in the pot. Experiments were conducted with seeds of commercial maize hybrids under controlled conditions, with and without herbicide. Colonization ability was evaluated by examining multiple plants from each treatment at two-time points during the experiment. 16S rRNA amplicon community profiling was performed to precisely target the bacterial strains used in the three consortia and investigate how the local microbiome might be altered by the application of the consortia. Bioinformatic analysis was performed using qiime2, clustering of reads into amplicon sequence variants ASVs using the DADA2 plugin, and the taxonomic assignment was based on a customized dataset formed from the 16S rRNA gene sequences of the ten isolates used in this study or by using the Silva rRNA database. For clustering and comparison of ASVs based on sequence similarity, the program cd-hit was used, with the sequence similarity parameter set to 98% to be considered part of the same cluster. The obtained dataset was imported into R using the package qiime2R, and subsequent analyzes and graphs were generated using either the R packages phyloseq, microbiome, or reshape2. We identified seven out of ten inoculated strains in both time points tested and with comparable abundance, indicating that most of the bacterial isolates tested have the ability to colonize the root system of maize. Furthermore, the natural/local microbiome of maize plants is not disturbed by the three consortia used in this study, implying that they are good candidates for future biotechnological applications. PB - Belgrade : Institute of molecular genetics and genetic engineering C3 - 4th Belgrade Bioinformatics Conference T1 - Root colonization ability of herbicide-resistant PGP bacteria evaluated by 16S rRNA metabarcoding EP - 71 SP - 71 VL - 4 UR - https://hdl.handle.net/21.15107/rcub_imagine_2012 ER -
@conference{ author = "Bez, Cristina and Galić, Ivana and Bertani, Iris and Stanković, Nada and Venturi, Vittorio", year = "2023", abstract = "In terms of agricultural sustainability, herbicide-resistant, plant growth promoting (PGP) bacteria that can improve crop yield are valuable resource. To exhibit PGP traits, the bacteria must be able to colonize and survive in the rhizosphere. Upon screening the herbicide-resistant bacterial collection, candidates with the highest PGP potential were grouped into three consortia to evaluate their ability to colonize roots and persist in the natural/local plant microbiome in the pot. Experiments were conducted with seeds of commercial maize hybrids under controlled conditions, with and without herbicide. Colonization ability was evaluated by examining multiple plants from each treatment at two-time points during the experiment. 16S rRNA amplicon community profiling was performed to precisely target the bacterial strains used in the three consortia and investigate how the local microbiome might be altered by the application of the consortia. Bioinformatic analysis was performed using qiime2, clustering of reads into amplicon sequence variants ASVs using the DADA2 plugin, and the taxonomic assignment was based on a customized dataset formed from the 16S rRNA gene sequences of the ten isolates used in this study or by using the Silva rRNA database. For clustering and comparison of ASVs based on sequence similarity, the program cd-hit was used, with the sequence similarity parameter set to 98% to be considered part of the same cluster. The obtained dataset was imported into R using the package qiime2R, and subsequent analyzes and graphs were generated using either the R packages phyloseq, microbiome, or reshape2. We identified seven out of ten inoculated strains in both time points tested and with comparable abundance, indicating that most of the bacterial isolates tested have the ability to colonize the root system of maize. Furthermore, the natural/local microbiome of maize plants is not disturbed by the three consortia used in this study, implying that they are good candidates for future biotechnological applications.", publisher = "Belgrade : Institute of molecular genetics and genetic engineering", journal = "4th Belgrade Bioinformatics Conference", title = "Root colonization ability of herbicide-resistant PGP bacteria evaluated by 16S rRNA metabarcoding", pages = "71-71", volume = "4", url = "https://hdl.handle.net/21.15107/rcub_imagine_2012" }
Bez, C., Galić, I., Bertani, I., Stanković, N.,& Venturi, V.. (2023). Root colonization ability of herbicide-resistant PGP bacteria evaluated by 16S rRNA metabarcoding. in 4th Belgrade Bioinformatics Conference Belgrade : Institute of molecular genetics and genetic engineering., 4, 71-71. https://hdl.handle.net/21.15107/rcub_imagine_2012
Bez C, Galić I, Bertani I, Stanković N, Venturi V. Root colonization ability of herbicide-resistant PGP bacteria evaluated by 16S rRNA metabarcoding. in 4th Belgrade Bioinformatics Conference. 2023;4:71-71. https://hdl.handle.net/21.15107/rcub_imagine_2012 .
Bez, Cristina, Galić, Ivana, Bertani, Iris, Stanković, Nada, Venturi, Vittorio, "Root colonization ability of herbicide-resistant PGP bacteria evaluated by 16S rRNA metabarcoding" in 4th Belgrade Bioinformatics Conference, 4 (2023):71-71, https://hdl.handle.net/21.15107/rcub_imagine_2012 .