Plant age and genotype affect the bacterial community composition in the tuber rhizosphere of field-grown sweet potato plants

Marques, Joana Montezano; Silva, Thais F. da; Vollú, Renata Estebanez; Blank, Arie Fitzgerald; Ding, Guo-Chun; Seldin, Lucy; Smalla, Kornelia

doi:10.1111/1574-6941.12313

Cited by 142 publications

(97 citation statements)

References 53 publications

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“…A recent experiment with the establishment of rhizosphere communities in three cultivars of potato (Solanum tuberosum) grown in two distinct field sites revealed that only 4% of operational taxonomic units were dependent on the host genotype by 40% soil-specific abundance (Weinert et al, 2011). Interestingly, potato cultivars showed differences in microbes belonging to the families of bacteria that have been studied extensively for their ability to control plant pathogens (Weinert et al, 2011), and in another study, it was shown that plant age and genotype of sweet potato (Ipomoea batatas) also influenced the root microbiome (Marques et al, 2014). Similarly, the structure and function of the rhizospheric bacterial community associated with Arabidopsis at four different plant development stages (seedling, vegetative, bolting, and flowering) were analyzed and showed that there were no significant differences in bacterial community structure .…”

Section: Determination Of Microbiome By Host Host Genotypementioning

confidence: 99%

Functional Soil Microbiome: Belowground Solutions to an Aboveground Problem

2014

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There is considerable evidence in the literature that beneficial rhizospheric microbes can alter plant morphology, enhance plant growth, and increase mineral content. Of late, there is a surge to understand the impact of the microbiome on plant health. Recent research shows the utilization of novel sequencing techniques to identify the microbiome in model systems such as Arabidopsis (Arabidopsis thaliana) and maize (Zea mays). However, it is not known how the community of microbes identified may play a role to improve plant health and fitness. There are very few detailed studies with isolated beneficial microbes showing the importance of the functional microbiome in plant fitness and disease protection. Some recent work on the cultivated microbiome in rice (Oryza sativa) shows that a wide diversity of bacterial species is associated with the roots of field-grown rice plants. However, the biological significance and potential effects of the microbiome on the host plants are completely unknown. Work performed with isolated strains showed various genetic pathways that are involved in the recognition of host-specific factors that play roles in beneficial host-microbe interactions. The composition of the microbiome in plants is dynamic and controlled by multiple factors. In the case of the rhizosphere, temperature, pH, and the presence of chemical signals from bacteria, plants, and nematodes all shape the environment and influence which organisms will flourish. This provides a basis for plants and their microbiomes to selectively associate with one another. This Update addresses the importance of the functional microbiome to identify phenotypes that may provide a sustainable and effective strategy to increase crop yield and food security.

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Section: Determination Of Microbiome By Host Host Genotypementioning

confidence: 99%

Functional Soil Microbiome: Belowground Solutions to an Aboveground Problem

2014

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“…The community composition of the rhizosphere microbiome is affected by many factors, such as ambient conditions, physical and chemical properties of soil, background microbial composition of soil, the stage of plant development and plant genotype 23–27 . Marques et al .…”

Section: Introductionmentioning

confidence: 99%

The Variation in the Rhizosphere Microbiome of Cotton with Soil Type, Genotype and Developmental Stage

Qiao

Wang

Zhang

et al. 2017

Sci Rep

197

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Plant roots and soil microorganisms interact with each other mainly in the rhizosphere. Changes in the community structure of the rhizosphere microbiome are influenced by many factors. In this study, we determined the community structure of rhizosphere bacteria in cotton, and studied the variation of rhizosphere bacterial community structure in different soil types and developmental stages using TM-1, an upland cotton cultivar (Gossypium hirsutum L.) and Hai 7124, a sea island cotton cultivar (G. barbadense L.) by high-throughput sequencing technology. Six bacterial phyla were found dominantly in cotton rhizosphere bacterial community including Acidobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Proteobacteria, and Verrucomicrobia. The abundance of Acidobacteria, Cyanobacteria, Firmicutes, Planctomycetes and Proteobacteria were largely influenced by cotton root. Bacterial α-diversity in rhizosphere was lower than that of bulk soil in nutrient-rich soil, but higher in cotton continuous cropping field soil. The β-diversity in nutrient-rich soil was greater than that in continuous cropping field soil. The community structure of the rhizosphere bacteria varied significantly during different developmental stages. Our results provided insights into the dynamics of cotton rhizosphere bacterial community and would facilitate to improve cotton growth and development through adjusting soil bacterial community structure artificially.

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“…In recent years amplicon sequencing technology became an important tool in rhizosphere microbiology and revolutionized the field. With increasing read length and sequencing depth this technology now allows analyzing multiple replicates as previously done by DGGE to determine the effect of various biotic and abiotic factors on the microbial community composition in the rhizosphere (Marques et al 2014;Schreiter et al 2014a). The community composition analysis done by pyro-or illumina sequencing at a much higher resolution level largely confirmed data obtained by DGGE.…”

Section: Bacterial and Fungal Community Composition In The Rhizospherementioning

confidence: 83%

“…Whereas in the tuber rhizosphere of sweet potato in particular the relative abundance of Firmicutes (Bacillus and Paenibacillus) was enriched compared to bulk soil (Marques et al 2014). …”

Section: Main Findings Obtained By Molecular Analysis Of Rhizosphere mentioning

confidence: 95%

“…Therefore it is highly recommended for comparison of data from different studies to carefully read the sampling protocols described, as the fractions of the rhizosphere microbial communities analyzed differed-depending on the protocols applied-in the proportion of rhizoplane and bulk soil microorganisms present. Rhizosphere total community (TC-) DNA was extracted from the soil brushed off from the root (Marques et al 2014). This technique is typically used when long-distance transport of samples is needed and microbes residing on the rhizoplane or in soil particles glued to the roots or from fine roots were likely missing.…”

Section: Experimental Design and Samplingmentioning

confidence: 99%

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Microbial Communities in the Rhizosphere Analyzed by Cultivation-Independent DNA-Based Methods

Schreiter

Eltlbany

Smalla

2014

Principles of Plant-Microbe Interactions

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The development of methods to extract nucleic acids directly from the rhizosphere or from microbial cells detached by a mechanical treatment from roots opened new dimensions to study the rhizosphere microbiome and to overcome limitations of cultivation-dependent methods. This chapter summarizes the potentials and limitations of cultivation-independent methods used by our group in the last 15 years to investigate microbial communities in the rhizosphere and their response to changing environmental conditions. We showed that rhizosphere microbial communities are highly dynamic, and that their composition is mainly shaped by the plant and the soil type and factors influencing these drivers of microbial diversity in the rhizosphere.

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Plant age and genotype affect the bacterial community composition in the tuber rhizosphere of field-grown sweet potato plants

Cited by 142 publications

References 53 publications

Functional Soil Microbiome: Belowground Solutions to an Aboveground Problem

Functional Soil Microbiome: Belowground Solutions to an Aboveground Problem

The Variation in the Rhizosphere Microbiome of Cotton with Soil Type, Genotype and Developmental Stage

Microbial Communities in the Rhizosphere Analyzed by Cultivation-Independent DNA-Based Methods

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