Comparative Analysis of Bacterial Communities in a Potato Field as Determined by Pyrosequencing

Inceoglu, Oezguel; Al‐Soud, Waleed Abu; Salles, Joana Falcão; Semenov, A.; Elsas, Jan Dirk van

doi:10.1371/journal.pone.0023321

Cited by 212 publications

(132 citation statements)

References 54 publications

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“…Although these are interesting results, it should be noted that the abundance of seed transmitted bacteria we have observed in these juvenile rhizospheres may be exaggerated because they have not yet had a chance to be more heavily colonized during passage through soil as would older and larger root systems (Inceoglu et al 2011). As plants age, their rhizosecretions also change which can alter the microbial populations living around the root (Chaparro et al 2014).…”

Section: Discussionmentioning

confidence: 79%

Bacterial populations in juvenile maize rhizospheres originate from both seed and soil

Johnston‐Monje

Lundberg

Lazarovits³

et al. 2016

Plant Soil

205

130

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Background and aims To assess the impacts of soil microbes and plant genotype on the composition of maize associated bacterial communities. Methods Two genotypes of Brazilian maize were planted indoors on sterile sand, a deep underground subsoil, and a nutrient-rich topsoil from the Amazon jungle (terra preta). DNA was extracted from rhizospheres, phyllospheres, and surface sterilized roots for 16S rDNA fingerprinting and next generation sequencing.Results Neither plant genotype nor soil type appeared to influence bacterial diversity in phyllospheres or endospheres. Rhizospheres showed strikingly similar 16S rDNA ordination of both fingerprinting and sequencing data, with soil type driving grouping patterns and genotype having a significant impact only on sterile sand. Rhizospheres grown in non-sterile soils contained greater bacterial diversity than sterile-sand grown ones, however the dominant OTUs (species of Proteobacteria and Bacteroidetes) were found in all rhizospheres suggesting seeds as a common source of inoculum. Rhizospheres of the commercial hybrid appeared to contain less bacterial diversity than the landrace. Conclusions Maize rhizospheres receive diverse bacteria from soil, are influenced by the genotype or treatment of the seed, and are dominated by species of Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. As many dominant 16S rDNA sequences were observed in rhizospheres grown in both sterile and non-sterile substrate, we conclude that the most common bacterial cells in juvenile maize rhizospheres are seed transmitted.

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Section: Discussionmentioning

confidence: 79%

Bacterial populations in juvenile maize rhizospheres originate from both seed and soil

Johnston‐Monje

Lundberg

Lazarovits³

et al. 2016

Plant Soil

205

130

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“…This indicates that the DNA extraction procedure introduces significant bias, thereby influencing the interpretation of the microbial community observed. PCR-based metagenomic approaches such as DGGE Ramond et al, 2013), t-RFLP (Sessitsch et al, 2012;Ding et al, 2013) and next generation sequencing (Gottel et al, 2011;Lucero et al, 2011;Ìnceoğlu et al, 2011;Molina et al, 2012) are continuously used to elucidate the structure and ecological roles of plant-associated (and other) microbial communities. However, few, if any, of these studies share the same DNA extraction protocol and/or are preceded by an evaluation of DNA extraction procedures to select the most efficient.…”

Section: Discussionmentioning

confidence: 99%

Impact of metagenomic DNA extraction procedures on the identifiable endophytic bacterial diversity in Sorghum bicolor (L. Moench)

Maropola

Ramond

Trindade

2015

Journal of Microbiological Methods

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Keywords:Metagenomic DNA extraction Endophytic bacteria Sorghum root and stem t-RFLP Pyrosequencing Culture-independent studies rely on the quantity and quality of the extracted environmental metagenomic DNA (mDNA). To fully access the plant tissue microbiome, the extracted plant mDNA should allow optimal PCR applications and the genetic content must be representative of the total microbial diversity. In this study, we evaluated the endophytic bacterial diversity retrieved using different mDNA extraction procedures. Metagenomic DNA from sorghum (Sorghum bicolor L. Moench) stem and root tissues were extracted using two classical DNA extraction protocols (CTAB-and SDS-based) and five commercial kits. The mDNA yields and quality as well as the reproducibility were compared. 16S rRNA gene terminal restriction fragment length polymorphism (t-RFLP) was used to assess the impact on endophytic bacterial community structures observed. Generally, the classical protocols obtained high mDNA yields from sorghum tissues; however, they were less reproducible than the commercial kits. Commercial kits retrieved higher quality mDNA, but with lower endophytic bacterial diversities compared to classical protocols. The SDS-based protocol enabled access to the highest sorghum endophytic diversities. Therefore, "SDS-extracted" sorghum root and stem microbiome diversities were analysed via 454 pyrosequencing, and this revealed that the two tissues harbour significantly different endophytic communities. Nevertheless, both communities are dominated by agriculturally important genera such as Microbacterium, Agrobacterium, Sphingobacterium, Herbaspirillum, Erwinia, Pseudomonas and Stenotrophomonas; which have previously been shown to play a role in plant growth promotion. This study shows that DNA extraction protocols introduce biases in culture-independent studies of environmental microbial communities by influencing the mDNA quality, which impacts the microbial diversity analyses and evaluation. Using the broad-spectrum SDSbased DNA extraction protocol allows the recovery of the most diverse endophytic communities associated with sorghum tissues and, as such, establishes a reliable basis for future study of endophytic communities.

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“…For example, Micallef et al (2009a) through denaturing gradient gel electrophoresis analysis observed that Arabidopsis rhizosphere microbial communities varied with plant development and that microbial communities in early plant development were more distinct to the bulk soil and that this difference decreased with plant age. Similarly, an assessment of the potato rhizosphere demonstrated that young potato plants showed cultivar-dependent rhizosphere microbial communities but these differences in the microbiomes disappeared as the plants aged (Inceoglu et al, 2011). Soybean rhizosphere microbial communities were also influenced by plant development; early reproductive growth stages of the soybean plant produced more complex microbial communities than late stage soybean plants (Xu et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

Rhizosphere microbiome assemblage is affected by plant development

2013

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There is a concerted understanding of the ability of root exudates to influence the structure of rhizosphere microbial communities. However, our knowledge of the connection between plant development, root exudation and microbiome assemblage is limited. Here, we analyzed the structure of the rhizospheric bacterial community associated with Arabidopsis at four time points corresponding to distinct stages of plant development: seedling, vegetative, bolting and flowering. Overall, there were no significant differences in bacterial community structure, but we observed that the microbial community at the seedling stage was distinct from the other developmental time points. At a closer level, phylum such as Acidobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria and specific genera within those phyla followed distinct patterns associated with plant development and root exudation. These results suggested that the plant can select a subset of microbes at different stages of development, presumably for specific functions. Accordingly, metatranscriptomics analysis of the rhizosphere microbiome revealed that 81 unique transcripts were significantly (Po0.05) expressed at different stages of plant development. For instance, genes involved in streptomycin synthesis were significantly induced at bolting and flowering stages, presumably for disease suppression. We surmise that plants secrete blends of compounds and specific phytochemicals in the root exudates that are differentially produced at distinct stages of development to help orchestrate rhizosphere microbiome assemblage.

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Comparative Analysis of Bacterial Communities in a Potato Field as Determined by Pyrosequencing

Cited by 212 publications

References 54 publications

Bacterial populations in juvenile maize rhizospheres originate from both seed and soil

Bacterial populations in juvenile maize rhizospheres originate from both seed and soil

Impact of metagenomic DNA extraction procedures on the identifiable endophytic bacterial diversity in Sorghum bicolor (L. Moench)

Rhizosphere microbiome assemblage is affected by plant development

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