<i>rpoB</i>, a promising marker for analyzing the diversity of bacterial communities by amplicon sequencing

Ogier, Jean-Claude; Pagès, Sylvie; Galan, Maxime; Barret, Mathieu; Gaudriault, Sophie

doi:10.1101/626119

Cited by 4 publications

(5 citation statements)

References 46 publications

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“…We found that plants (65% of genomes) and especially the phyllosphere compartment (41% of genomes) were the most prevalent source of Methylobacterium . From these genomes, we built a phylogenetic tree based on the complete nucleotide sequence of rpoB , a highly polymorphic marker that experienced no copy number variation in many bacteria taxa (44, 45), and that we confirmed to be single copy in Methylobacterium and related genera Microvirga and Enterovirga ( Figure 1, Supplementary dataset 1a ). In this phylogeny, we roughly identified main Methylobacterium groups (A, B, and C) previously defined based on the 16S gene (30) and found that phyllosphere-associated diversity was not randomly distributed in the Methylobacterium phylogenetic tree.…”

Section: Resultsmentioning

confidence: 99%

“…To assess Methylobacterium diversity at a finer evolutionary level, we thus developed a molecular marker targeting all members of the Methylobacteriaceae family, using the core gene rpoB ( Figure 1 (44, 45)). Based upon rpoB sequences available for Methylobacterium ( Supplementary dataset 1a) , as well as sequencing of rpoB partial sequences from 20 Methylobacterium isolates from a pilot survey in MSH in 2017 ( Figure 2d; Table S1; Supplementary dataset 1f,g ) we determined that this gene is polymorphic enough to explore diversity within the aforementioned Methylobacterium clades (See supplementary method ).…”

Section: Resultsmentioning

confidence: 99%

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Fine-Scale Adaptations to Environmental Variation and Growth Strategies Drive Phyllosphere Methylobacterium Diversity

Leducq

Seyer-Lamontagne

Condrain-Morel

et al. 2021

Preprint

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Methylobacterium is one of the most prevalent bacterial genera of the phyllosphere, present on the leaves of nearly every plant. Despite its ubiquity and its importance for host plant function, little is known about whether diversity over space and time within the genus reflects neutral processes like migration and drift, or environmental filtering of life history strategies and adaptations to temperature and host tree species. Here, we investigated how phylogenetic diversity within the genus Methylobacterium is structured by biogeography, seasonality, and growth strategies. Using deep, culture-independent barcoded marker gene sequencing coupled with culture-based approaches, we quantified seasonal shifts in Methylobacterium diversity over a year from early summer to fall in two temperate forests in Quebec, Canada. As an alternative to the 16S rRNA gene, we used rpoB, a highly polymorphic marker gene, which has not experienced detectable horizontal gene transfer nor copy number variation in Methylobacterium genomes. We cultured very different subsets of Methylobacterium diversity from the same leaf, depending upon the temperature of isolation and growth (20 C or 30 C). For instance, one the most abundant Methylobacterium lineages was almost exclusively isolated at 20 C, suggesting long-term adaptation to temperature. Both culture and barcoding approaches revealed that a considerable and previously underestimated diversity of Methylobacterium colonize the surface of leaves in temperate forests. This diversity was strongly structured according to both large (>100km; between forests) and small geographical scales (<1.2km within forests), and among host tree species, and was dynamic over seasonal time scales. To determine if these seasonal effects were driven by temperature, we measured growth of 79 isolates at different temperature treatments. Different lineages showed subtle and significant differences in growth performance when subject to temperature increase or decrease, but most have higher yield and slower growth rate at 20 than 30C, with strong lineage- and season-dependant variation in their overall growth strategies. We proposed that the homogenization of Methylobacterium community structure observed over a growing season resulted from the progressive replacement of isolates with high yield strategy typical of cooperative, structured communities, by isolates with rapid growth. Together our results show how Methylobacterium is phylogenetically structured into lineages with distinct growth strategies, which helps explain their differential abundance across regions, host tree species, and time. This works paves the way for further investigation of adaptive strategies and traits within a ubiquitous phyllosphere genus.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Fine-Scale Adaptations to Environmental Variation and Growth Strategies Drive Phyllosphere Methylobacterium Diversity

Leducq

Seyer-Lamontagne

Condrain-Morel

et al. 2021

Preprint

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“…This marker is reported to be suitable for phylogenetic analyses as it provides a better resolution at the species level (Ogier et al . 2019). The phylogenetic tree included 29 representative Aeromonas sp.…”

Section: Methodsmentioning

confidence: 99%

Antimicrobial resistance in Aeromonas species isolated from aquatic environments in Brazil

Conte

Palmeiro

Bavaroski

et al. 2020

J. Appl. Microbiol.

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Aim The current study was conducted to determine the antimicrobial resistance profile and genetic relatedness of Aeromonas sp. isolated from healthcare and urban effluents, wastewater treatment plant (WWTP) and river water. Methods and Results We detected the presence of genes conferring resistance to β‐lactam, quinolone and aminoglycoside. Multilocus sequence typing was carried out to differentiate the strains, and multilocus phylogenetic analysis was used to identify the species. A total of 28 cefotaxime‐resistant Aeromonas sp. strains were identified, harbouring uncommon Guiana‐extended‐spectrum (GES)‐type β‐lactamases (GES‐1, GES‐5, GES‐7 and GES‐16). Multidrug‐resistant Aeromonas sp. were found in hospital wastewater, WWTP and sanitary effluent, and A. caviae was identified as the most prevalent species (85·7%). Conclusion The release of untreated healthcare effluents, presence of antimicrobials in the environment, in addition to multidrug‐resistant Aeromonas sp., are all potential factors for the spread of resistance. Significance and Impact of the Study We identified a vast repertoire of antimicrobial resistance genes (ARG) in Aeromonas sp. from diverse aquatic ecosystems, including those that encode enzymes degrading broad‐spectrum antimicrobials widely used to treat healthcare‐associated infections. Hospital and sanitary effluents serve as potential sources of bacteria harbouring ARG and are a threat to public health.

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“…Here, we have demonstrated that direct linking of near-16S genomic sequences to those of the V1-V2 16S rRNA region gives a number of significant methodological advancements to microbiome characterization. Although alternative approaches to interrogate microbiomes have been suggested [50,51], the amount of 16S rRNA sequences in the databases greatly exceeds those of other bacterial genes and whole genomes, favouring the use of 16S rRNA as a phylogenetic marker. Considerable effort has been devoted to improving its taxonomic resolution [13,14], but because of limited diversity of within-gene sequences and hardly predictable gene copy numbers [52] unequivocal characterization of microbiomes was barely possible.…”

Section: Discussionmentioning

confidence: 99%

High-resolution microbiome analysis enabled by linking of 16S rRNA gene sequences with adjacent genomic contexts

et al. 2021

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Sequence-based characterization of bacterial communities has long been a hostage of limitations of both 16S rRNA gene and whole metagenome sequencing. Neither approach is universally applicable, and the main efforts to resolve constraints have been devoted to improvement of computational prediction tools. Here, we present semi-targeted 16S rRNA sequencing (st16S-seq), a method designed for sequencing V1–V2 regions of the 16S rRNA gene along with the genomic locus upstream of the gene. By in silico analysis of 13 570 bacterial genome assemblies, we show that genome-linked 16S rRNA sequencing is superior to individual hypervariable regions or full-length gene sequences in terms of classification accuracy and identification of gene copy numbers. Using mock communities and soil samples we experimentally validate st16S-seq and benchmark it against the established microbial classification techniques. We show that st16S-seq delivers accurate estimation of 16S rRNA gene copy numbers, enables taxonomic resolution at the species level and closely approximates community structures obtainable by whole metagenome sequencing.

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rpoB, a promising marker for analyzing the diversity of bacterial communities by amplicon sequencing

Abstract: 1 9

Cited by 4 publications

References 46 publications

Fine-Scale Adaptations to Environmental Variation and Growth Strategies Drive Phyllosphere Methylobacterium Diversity

Fine-Scale Adaptations to Environmental Variation and Growth Strategies Drive Phyllosphere Methylobacterium Diversity

Antimicrobial resistance in Aeromonas species isolated from aquatic environments in Brazil

High-resolution microbiome analysis enabled by linking of 16S rRNA gene sequences with adjacent genomic contexts

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