Specific amplification of bacterial DNA by optimized so-called universal bacterial primers in samples rich of plant DNA

Dorn‐In, Samart; Bassitta, Rupert; Schwaiger, Karin; Bauer, Johann; Hölzel, Christina

doi:10.1016/j.mimet.2015.04.001

Cited by 68 publications

(54 citation statements)

References 50 publications

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“…As preliminary data indicated a huge co-amplification of plastids when DNA was used as a target, we used RNA in this study, as plastid content in rRNA is low (Supplementary Figure S1). To compare the resident and active community, we also performed DNA amplification using the primer 338F/789R, which was reported to exclude chloroplast amplification (Dorn-In et al, 2015). Our data indicated a higher number of genera in 16S rRNA sequences when primer pair S-D-Bact-0008-a-S-16 and S-D-Bact-0343-a-A-15 was used to amplify the obtained cDNA compared to DNA amplification using 338F/789R.…”

Section: Methodsmentioning

confidence: 99%

Dominant Groups of Potentially Active Bacteria Shared by Barley Seeds become Less Abundant in Root Associated Microbiome

et al. 2017

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Endophytes are microorganisms colonizing plant internal tissues. They are ubiquitously associated with plants and play an important role in plant growth and health. In this work, we grew five modern cultivars of barley in axenic systems using sterile sand mixture as well as in greenhouse with natural soil. We characterized the potentially active microbial communities associated with seeds and roots using rRNA based amplicon sequencing. The seeds of the different cultivars share a great part of their microbiome, as we observed a predominance of a few bacterial OTUs assigned to Phyllobacterium, Paenibacillus, and Trabusiella. Seed endophytes, particularly members of the Enterobacteriacea and Paenibacillaceae, were important members of root endophytes in axenic systems, where there were no external microbes. However, when plants were grown in soil, seed endophytes became less abundant in root associated microbiome. We observed a clear enrichment of Actinobacteriacea and Rhizobiaceae, indicating a strong influence of the soil bacterial communities on the composition of the root microbiome. Two OTUs assigned to Phyllobacteriaceae were found in all seeds and root samples growing in soil, indicating a relationship between seed-borne and root associated microbiome in barley. Even though the role of endophytic bacteria remains to be clarified, it is known that many members of the genera detected in our study produce phytohormones, shape seedling exudate profile and may play an important role in germination and establishment of the seedlings.

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Section: Methodsmentioning

confidence: 99%

Dominant Groups of Potentially Active Bacteria Shared by Barley Seeds become Less Abundant in Root Associated Microbiome

et al. 2017

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“…Library preparation was accomplished according to the “16S Metagenomic Sequencing Library Preparation” protocol proposed by Illumina Inc., San Diego, CA, United States. Briefly, polymerase chain reaction (PCR) of the 16S rRNA region was performed in triplicates using the primers 335Fc (5′-CADACTCCTACGGGAGGC-3′) and 769Rc (5′-ATCCTGTTTGMTMCCCVCRC-3′) published by Dorn-In et al (2015) with Illumina adapter sequences. The reaction mix contained of 12.5 μl NEB Next High Fidelity Master Mix (Illumina Inc., United States), 0.5 μl of each primer (10 pmol/μl), 2.5 μl of 3% BSA, 100–200 ng of template DNA and ad DEPC water 25 μl.…”

Section: Methodsmentioning

confidence: 99%

The Influence of Land Use Intensity on the Plant-Associated Microbiome of Dactylis glomerata L.

et al. 2017

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In this study, we investigated the impact of different land use intensities (LUI) on the root-associated microbiome of Dactylis glomerata (orchardgrass). For this purpose, eight sampling sites with different land use intensity levels but comparable soil properties were selected in the southwest of Germany. Experimental plots covered land use levels from natural grassland up to intensively managed meadows. We used 16S rRNA gene based barcoding to assess the plant-associated community structure in the endosphere, rhizosphere and bulk soil of D. glomerata. Samples were taken at the reproductive stage of the plant in early summer. Our data indicated that roots harbor a distinct bacterial community, which clearly differed from the microbiome of the rhizosphere and bulk soil. Our results revealed Pseudomonadaceae, Enterobacteriaceae and Comamonadaceae as the most abundant endophytes independently of land use intensity. Rhizosphere and bulk soil were dominated also by Proteobacteria, but the most abundant families differed from those obtained from root samples. In the soil, the effect of land use intensity was more pronounced compared to root endophytes leading to a clearly distinct pattern of bacterial communities under different LUI from rhizosphere and bulk soil vs. endophytes. Overall, a change of community structure on the plant–soil interface was observed, as the number of shared OTUs between all three compartments investigated increased with decreasing land use intensity. Thus, our findings suggest a stronger interaction of the plant with its surrounding soil under low land use intensity. Furthermore, the amount and quality of available nitrogen was identified as a major driver for shifts in the microbiome structure in all compartments.

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“…The selection of genes was not intended to be exhaustive, rather they provided key ‘biomarkers’ that have been routinely measured previously (e.g., Graham et al 2011; Knapp et al 2010; Knapp et al 2011; Pei et al 2006; Pruden et al 2006). 16S ribosomal ribonucleic acid (16S rRNA) genes were also measured to determine relative abundances of ARG as a surrogate measure of ‘total bacteria’, using the 338F-805R primer pair (5′-3′; with 515F probe) that should minimise non-target binding to plant, animal and fungal DNA (Dorn-In et al 2015). …”

Section: Methodsmentioning

confidence: 99%

Relationship between antibiotic resistance genes and metals in residential soil samples from Western Australia

Knapp

Callan

Aitken

et al. 2016

Environ Sci Pollut Res

146

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Increasing drug-resistant infections have drawn research interest towards examining environmental bacteria and the discovery that many factors, including elevated metal conditions, contribute to proliferation of antibiotic resistance (AR). This study examined 90 garden soils from Western Australia to evaluate predictions of antibiotic resistance genes from total metal conditions by comparing the concentrations of 12 metals and 13 genes related to tetracycline, beta-lactam and sulphonamide resistance. Relationships existed between metals and genes, but trends varied. All metals, except Se and Co, were related to at least one AR gene in terms of absolute gene numbers, but only Al, Mn and Pb were associated with a higher percentage of soil bacteria exhibiting resistance, which is a possible indicator of population selection. Correlations improved when multiple factors were considered simultaneously in a multiple linear regression model, suggesting the possibility of additive effects occurring. Soil-metal concentrations must be considered when determining risks of AR in the environment and the proliferation of resistance.

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Specific amplification of bacterial DNA by optimized so-called universal bacterial primers in samples rich of plant DNA

Cited by 68 publications

References 50 publications

Dominant Groups of Potentially Active Bacteria Shared by Barley Seeds become Less Abundant in Root Associated Microbiome

Dominant Groups of Potentially Active Bacteria Shared by Barley Seeds become Less Abundant in Root Associated Microbiome

The Influence of Land Use Intensity on the Plant-Associated Microbiome of Dactylis glomerata L.

Relationship between antibiotic resistance genes and metals in residential soil samples from Western Australia

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