Identification and Differentiation of Pseudomonas Species in Field Samples Using an
            <i>rpoD</i>
            Amplicon Sequencing Methodology

Lauritsen, Jonas Greve; Hansen, Morten Lindqvist; Bech, Pernille Kjersgaard; Jelsbak, Lars; Gram, Lone; Strube, Mikael Lenz

doi:10.1128/msystems.00704-21

Cited by 19 publications

(15 citation statements)

References 45 publications

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“…Researchers should consider these issues when evaluation metataxonomic data and we propose they consult RibDif before making conclusions on individual ASVs. Researchers being particularly interested in species differentiation should consider full-length V1V9 amplicons or primers tailored to individual genera as previously done for Pseudomonas ( Lauritsen et al , 2021 ) and Staphylococcus ( Strube et al , 2018 ).…”

Section: Discussionmentioning

confidence: 99%

“…To investigate this, we have developed RibDif, which allows users to easily and quickly answer if species within a given genus can be resolved using standard metataxonomic methods, hence letting users evaluate if ASVs are useful for their particular research question or if alternative methods are to be employed. As described previously, one solution is to develop primers not targeting the 16S region ( Lauritsen et al , 2021 ; Strube et al , 2018 ).…”

Section: Introductionmentioning

confidence: 99%

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RibDif: can individual species be differentiated by 16S sequencing?

Strube

2021

Bioinformatics Advances

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Metataxonomic analysis is now routinely used to profile the microbiome of virtually every ecological niche on planet Earth. The use of Amplicon Sequence Variants (ASVs), proposing to be the exact biological 16S rRNA amplicon sequences of a given biological system, is now considered the gold standard. However, the 16S rRNA genes, and in particular the amplicons derived from it, are not unique for most species nor are they necessarily unique within individual genomes. Despite these restrictions, individual ASVs are often used to make inferences on the state of a given ecosystem which may cause erroneous conclusions on the effects of a given species on a specific host phenotype or ecosystem. To support researchers working with metataxonomics, we have developed RibDif which easily and rapidly evaluates the feasibility of using metataxonomics to profile individual species. We use RibDif to demonstrate that the genus Pseudoalteromonas contain species that are impossible to distinguish with 16S amplicons and that this is a common motif in bacterial genera. We propose that researchers consult RibDif when making conclusions on individual species from metataxonomic data. Availability Ribdif is freely available along with source code and detailed documentation at https://github.com/mikaells/RibDif

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

RibDif: can individual species be differentiated by 16S sequencing?

Strube

2021

Bioinformatics Advances

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“…Pseudomonas is one of the most diversified and successful bacterial groups yet described (41). The 16S rRNA gene amplicon sequencing has become the standard for culture -independent, taxonomic profiling of environmental microbial populations (42). Nevertheless, the 16S rRNA genes of closely related Pseudomonas species are remarkably similar, with less than 1 % nucleotide dissimilarity among several species (43).…”

Section: Discussionmentioning

confidence: 99%

Effect of some Pseudomonas strains and Agave americana L. on wheat germination under salt stress

Mokrani

Nabti

2022

Plant Sci. Today

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Currently, several efforts focus remedying the problem of agricultural soil salinity using eco-friendly strategies. This study aimed particularly the study of Triticum durum (durum wheat) seeds germination in the presence of Pseudomonas strains and hydro-alcoholic extract of Agave americana L. under saline stress conditions. The preliminary phytochemical screening of A. americana, phylogenetic identification and production of indole-3-acetic acid (IAA) by Pseudomonas strains, in vitro impact of hydro-alcoholic extract and Pseudomonas strains combination on salt stress resistance, preliminary effects of A. americana on Triticum durum germination and phytopathogenic fungi inhibition under salt stress were carried out using corresponding protocols. In in vitro trials, phytochemical screening revealed the richness of A. americana in polyphenols (1014.062±161.017 mM GA equivalent/g FW) and flavonoids (51.065±27.391 mg quercetin equivalent/g FW). The ability of Pseudomonas strains to produce the phytohormone indole-3-acetic acid (IAA) varied from 116.67±8.25 µg/ml to 857.14±80.50 µg/ml. The leaf extract of A. americana is an effective osmoprotectant that improves the resistance of the strain P1 Pseudomonas plecoglissicida to saline stress. In in vivo experiments, the extract of A. americana did not show any effect on the germination of wheat seeds. However, it effectively inhibited the contamination of seeds by phytopathogenic fungi during germination and saline conditions. Findings of the study revealed that Pseudomonas plecoglissicida and A. americana extract are very promising for the inhibition of phytopathogenic fungi and the alleviation of salt stress.

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“…S8 at https://doi.org/10.48804/KKFWS9 ). Profiling based on the rpoD gene, encoding the sigma 70 factor of RNA polymerase, is suitable for species-level differentiation in Pseudomonas , which cannot be achieved with 16S rRNA sequence analysis ( 25 , 26 ). LP producers are absent from the Pseudomonas aeruginosa and Pseudomonas pertucinogena lineages.…”

Section: Resultsmentioning

confidence: 99%

Charting the Lipopeptidome of Nonpathogenic Pseudomonas

et al. 2023

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Pseudomonas species are prominent producers of lipopeptides that support proliferation in a multitude of environments and foster varied lifestyles. By genome mining of biosynthetic gene clusters (BGCs) with lipopeptide-specific organization, we mapped the global Pseudomonas lipopeptidome and linked its staggering diversity to taxonomy of the producers, belonging to different groups within the major Pseudomonas fluorescens lineage.

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Identification and Differentiation of Pseudomonas Species in Field Samples Using an rpoD Amplicon Sequencing Methodology

Cited by 19 publications

References 45 publications

RibDif: can individual species be differentiated by 16S sequencing?

RibDif: can individual species be differentiated by 16S sequencing?

Effect of some Pseudomonas strains and Agave americana L. on wheat germination under salt stress

Charting the Lipopeptidome of Nonpathogenic Pseudomonas

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