Optimization of Molecular Methods for Detecting Duckweed-Associated Bacteria

The bacterial colonization dynamics of plants can differ between phylogenetically similar bacterial strains and in the context of complex bacterial communities. Quantitative methods that can resolve closely related bacteria within complex communities can lead to a better understanding of plant–micro...
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Autor*in:	Kenneth Acosta [verfasserIn] Shawn Sorrels [verfasserIn] William Chrisler [verfasserIn] Weijuan Huang [verfasserIn] Sarah Gilbert [verfasserIn] Thomas Brinkman [verfasserIn] Todd P. Michael [verfasserIn] Sarah L. Lebeis [verfasserIn] Eric Lam [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2023

Schlagwörter:	plant-microbe interactions plant-bacteria associations bacterial colonization duckweed duckweed-associated bacteria RISA

Übergeordnetes Werk:	In: Plants - MDPI AG, 2013, 12(2023), 4, p 872
Übergeordnetes Werk:	volume:12 ; year:2023 ; number:4, p 872

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.3390/plants12040872

Katalog-ID:	DOAJ079996361

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spelling	10.3390/plants12040872 doi (DE-627)DOAJ079996361 (DE-599)DOAJ5174dfbe52ab4dd9a0a6c95d57245535 DE-627 ger DE-627 rakwb eng QK1-989 Kenneth Acosta verfasserin aut Optimization of Molecular Methods for Detecting Duckweed-Associated Bacteria 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The bacterial colonization dynamics of plants can differ between phylogenetically similar bacterial strains and in the context of complex bacterial communities. Quantitative methods that can resolve closely related bacteria within complex communities can lead to a better understanding of plant–microbe interactions. However, current methods often lack the specificity to differentiate phylogenetically similar bacterial strains. In this study, we describe molecular strategies to study duckweed–associated bacteria. We first systematically optimized a bead-beating protocol to co-isolate nucleic acids simultaneously from duckweed and bacteria. We then developed a generic fingerprinting assay to detect bacteria present in duckweed samples. To detect specific duckweed–bacterium associations, we developed a genomics-based computational pipeline to generate bacterial strain-specific primers. These strain-specific primers differentiated bacterial strains from the same genus and enabled the detection of specific duckweed–bacterium associations present in a community context. Moreover, we used these strain-specific primers to quantify the bacterial colonization of duckweed by normalization to a plant reference gene and revealed differences in colonization levels between strains from the same genus. Lastly, confocal microscopy of inoculated duckweed further supported our PCR results and showed bacterial colonization of the duckweed root–frond interface and root interior. The molecular methods introduced in this work should enable the tracking and quantification of specific plant-microbe associations within plant-microbial communities. plant-microbe interactions plant-bacteria associations bacterial colonization duckweed duckweed-associated bacteria RISA Botany Shawn Sorrels verfasserin aut William Chrisler verfasserin aut Weijuan Huang verfasserin aut Sarah Gilbert verfasserin aut Thomas Brinkman verfasserin aut Todd P. Michael verfasserin aut Sarah L. Lebeis verfasserin aut Eric Lam verfasserin aut In Plants MDPI AG, 2013 12(2023), 4, p 872 (DE-627)737288345 (DE-600)2704341-1 22237747 nnns volume:12 year:2023 number:4, p 872 https://doi.org/10.3390/plants12040872 kostenfrei https://doaj.org/article/5174dfbe52ab4dd9a0a6c95d57245535 kostenfrei https://www.mdpi.com/2223-7747/12/4/872 kostenfrei https://doaj.org/toc/2223-7747 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 12 2023 4, p 872
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allfieldsSound	10.3390/plants12040872 doi (DE-627)DOAJ079996361 (DE-599)DOAJ5174dfbe52ab4dd9a0a6c95d57245535 DE-627 ger DE-627 rakwb eng QK1-989 Kenneth Acosta verfasserin aut Optimization of Molecular Methods for Detecting Duckweed-Associated Bacteria 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The bacterial colonization dynamics of plants can differ between phylogenetically similar bacterial strains and in the context of complex bacterial communities. Quantitative methods that can resolve closely related bacteria within complex communities can lead to a better understanding of plant–microbe interactions. However, current methods often lack the specificity to differentiate phylogenetically similar bacterial strains. In this study, we describe molecular strategies to study duckweed–associated bacteria. We first systematically optimized a bead-beating protocol to co-isolate nucleic acids simultaneously from duckweed and bacteria. We then developed a generic fingerprinting assay to detect bacteria present in duckweed samples. To detect specific duckweed–bacterium associations, we developed a genomics-based computational pipeline to generate bacterial strain-specific primers. These strain-specific primers differentiated bacterial strains from the same genus and enabled the detection of specific duckweed–bacterium associations present in a community context. Moreover, we used these strain-specific primers to quantify the bacterial colonization of duckweed by normalization to a plant reference gene and revealed differences in colonization levels between strains from the same genus. Lastly, confocal microscopy of inoculated duckweed further supported our PCR results and showed bacterial colonization of the duckweed root–frond interface and root interior. The molecular methods introduced in this work should enable the tracking and quantification of specific plant-microbe associations within plant-microbial communities. plant-microbe interactions plant-bacteria associations bacterial colonization duckweed duckweed-associated bacteria RISA Botany Shawn Sorrels verfasserin aut William Chrisler verfasserin aut Weijuan Huang verfasserin aut Sarah Gilbert verfasserin aut Thomas Brinkman verfasserin aut Todd P. Michael verfasserin aut Sarah L. Lebeis verfasserin aut Eric Lam verfasserin aut In Plants MDPI AG, 2013 12(2023), 4, p 872 (DE-627)737288345 (DE-600)2704341-1 22237747 nnns volume:12 year:2023 number:4, p 872 https://doi.org/10.3390/plants12040872 kostenfrei https://doaj.org/article/5174dfbe52ab4dd9a0a6c95d57245535 kostenfrei https://www.mdpi.com/2223-7747/12/4/872 kostenfrei https://doaj.org/toc/2223-7747 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 12 2023 4, p 872
language	English
source	In Plants 12(2023), 4, p 872 volume:12 year:2023 number:4, p 872
sourceStr	In Plants 12(2023), 4, p 872 volume:12 year:2023 number:4, p 872
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topic_facet	plant-microbe interactions plant-bacteria associations bacterial colonization duckweed duckweed-associated bacteria RISA Botany
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container_title	Plants
authorswithroles_txt_mv	Kenneth Acosta @@aut@@ Shawn Sorrels @@aut@@ William Chrisler @@aut@@ Weijuan Huang @@aut@@ Sarah Gilbert @@aut@@ Thomas Brinkman @@aut@@ Todd P. Michael @@aut@@ Sarah L. Lebeis @@aut@@ Eric Lam @@aut@@
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callnumber-first	Q - Science
author	Kenneth Acosta
spellingShingle	Kenneth Acosta misc QK1-989 misc plant-microbe interactions misc plant-bacteria associations misc bacterial colonization misc duckweed misc duckweed-associated bacteria misc RISA misc Botany Optimization of Molecular Methods for Detecting Duckweed-Associated Bacteria
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topic_title	QK1-989 Optimization of Molecular Methods for Detecting Duckweed-Associated Bacteria plant-microbe interactions plant-bacteria associations bacterial colonization duckweed duckweed-associated bacteria RISA
topic	misc QK1-989 misc plant-microbe interactions misc plant-bacteria associations misc bacterial colonization misc duckweed misc duckweed-associated bacteria misc RISA misc Botany
topic_unstemmed	misc QK1-989 misc plant-microbe interactions misc plant-bacteria associations misc bacterial colonization misc duckweed misc duckweed-associated bacteria misc RISA misc Botany
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title	Optimization of Molecular Methods for Detecting Duckweed-Associated Bacteria
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title_full	Optimization of Molecular Methods for Detecting Duckweed-Associated Bacteria
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title_sort	optimization of molecular methods for detecting duckweed-associated bacteria
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title_auth	Optimization of Molecular Methods for Detecting Duckweed-Associated Bacteria
abstract	The bacterial colonization dynamics of plants can differ between phylogenetically similar bacterial strains and in the context of complex bacterial communities. Quantitative methods that can resolve closely related bacteria within complex communities can lead to a better understanding of plant–microbe interactions. However, current methods often lack the specificity to differentiate phylogenetically similar bacterial strains. In this study, we describe molecular strategies to study duckweed–associated bacteria. We first systematically optimized a bead-beating protocol to co-isolate nucleic acids simultaneously from duckweed and bacteria. We then developed a generic fingerprinting assay to detect bacteria present in duckweed samples. To detect specific duckweed–bacterium associations, we developed a genomics-based computational pipeline to generate bacterial strain-specific primers. These strain-specific primers differentiated bacterial strains from the same genus and enabled the detection of specific duckweed–bacterium associations present in a community context. Moreover, we used these strain-specific primers to quantify the bacterial colonization of duckweed by normalization to a plant reference gene and revealed differences in colonization levels between strains from the same genus. Lastly, confocal microscopy of inoculated duckweed further supported our PCR results and showed bacterial colonization of the duckweed root–frond interface and root interior. The molecular methods introduced in this work should enable the tracking and quantification of specific plant-microbe associations within plant-microbial communities.
abstractGer	The bacterial colonization dynamics of plants can differ between phylogenetically similar bacterial strains and in the context of complex bacterial communities. Quantitative methods that can resolve closely related bacteria within complex communities can lead to a better understanding of plant–microbe interactions. However, current methods often lack the specificity to differentiate phylogenetically similar bacterial strains. In this study, we describe molecular strategies to study duckweed–associated bacteria. We first systematically optimized a bead-beating protocol to co-isolate nucleic acids simultaneously from duckweed and bacteria. We then developed a generic fingerprinting assay to detect bacteria present in duckweed samples. To detect specific duckweed–bacterium associations, we developed a genomics-based computational pipeline to generate bacterial strain-specific primers. These strain-specific primers differentiated bacterial strains from the same genus and enabled the detection of specific duckweed–bacterium associations present in a community context. Moreover, we used these strain-specific primers to quantify the bacterial colonization of duckweed by normalization to a plant reference gene and revealed differences in colonization levels between strains from the same genus. Lastly, confocal microscopy of inoculated duckweed further supported our PCR results and showed bacterial colonization of the duckweed root–frond interface and root interior. The molecular methods introduced in this work should enable the tracking and quantification of specific plant-microbe associations within plant-microbial communities.
abstract_unstemmed	The bacterial colonization dynamics of plants can differ between phylogenetically similar bacterial strains and in the context of complex bacterial communities. Quantitative methods that can resolve closely related bacteria within complex communities can lead to a better understanding of plant–microbe interactions. However, current methods often lack the specificity to differentiate phylogenetically similar bacterial strains. In this study, we describe molecular strategies to study duckweed–associated bacteria. We first systematically optimized a bead-beating protocol to co-isolate nucleic acids simultaneously from duckweed and bacteria. We then developed a generic fingerprinting assay to detect bacteria present in duckweed samples. To detect specific duckweed–bacterium associations, we developed a genomics-based computational pipeline to generate bacterial strain-specific primers. These strain-specific primers differentiated bacterial strains from the same genus and enabled the detection of specific duckweed–bacterium associations present in a community context. Moreover, we used these strain-specific primers to quantify the bacterial colonization of duckweed by normalization to a plant reference gene and revealed differences in colonization levels between strains from the same genus. Lastly, confocal microscopy of inoculated duckweed further supported our PCR results and showed bacterial colonization of the duckweed root–frond interface and root interior. The molecular methods introduced in this work should enable the tracking and quantification of specific plant-microbe associations within plant-microbial communities.
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title_short	Optimization of Molecular Methods for Detecting Duckweed-Associated Bacteria
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