Inoculated Seed Endophytes Modify the Poplar Responses to Trace Elements in Polluted Soil

Vannucchi, Francesca; Imperato, Valeria; Saran, Anabel; Staykov, Svetoslav; D’Haen, Jan; Sebastiani, L.; Vangronsveld, Jaco; Thijs, Sofie

doi:10.3390/agronomy11101987

Cited by 7 publications

(9 citation statements)

References 73 publications

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“…In addition, Kineococcus has a high level of metal tolerance (e.g., Zn, Cu, etc.) ( Vannucchi et al, 2021 ). The members of the genera Sphingomonas and Gemmatirosa were categorized as keystone taxa in native rhizosphere soils.…”

Section: Discussionmentioning

confidence: 99%

Changes in the structure and function of rhizosphere soil microbial communities induced by Amaranthus palmeri invasion

Zhang

Shi

et al. 2023

Front. Microbiol.

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IntroductionPlant invasion can profoundly alter ecosystem processes driven by microorganisms. The fundamental mechanisms linking microbial communities, functional genes, and edaphic characteristics in invaded ecosystems are, nevertheless, poorly understood.MethodsHere, soil microbial communities and functions were determined across 22 Amaranthus palmeri (A. palmeri) invaded patches by pairwise 22 native patches located in the Jing-Jin-Ji region of China using high-throughput amplicon sequencing and quantitative microbial element cycling technologies.ResultsAs a result, the composition and structure of rhizosphere soil bacterial communities differed significantly between invasive and native plants according to principal coordinate analysis. A. palmeri soils exhibited higher abundance of Bacteroidetes and Nitrospirae, and lower abundance of Actinobacteria than native soils. Additionally, compared to native rhizosphere soils, A. palmeri harbored a much more complex functional gene network with higher edge numbers, average degree, and average clustering coefficient, as well as lower network distance and diameter. Furthermore, the five keystone taxa identified in A. palmeri rhizosphere soils belonged to the orders of Longimicrobiales, Kineosporiales, Armatimonadales, Rhizobiales and Myxococcales, whereas Sphingomonadales and Gemmatimonadales predominated in the native rhizosphere soils. Moreover, random forest model revealed that keystone taxa were more important indicators of soil functional attributes than edaphic variables in both A. palmeri and native rhizosphere soils. For edaphic variables, only ammonium nitrogen was a significant predictor of soil functional potentials in A. palmeri invaded ecosystems. We also found keystone taxa in A. palmeri rhizosphere soils had strong and positive correlations with functional genes compared to native soils.DiscussionOur study highlighted the importance of keystone taxa as a driver of soil functioning in invaded ecosystem.

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Section: Discussionmentioning

confidence: 99%

Changes in the structure and function of rhizosphere soil microbial communities induced by Amaranthus palmeri invasion

Zhang

Shi

et al. 2023

Front. Microbiol.

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“…Kineococcus is a genus in the phylum of Actinobacteria and has been isolated in very diverse environments including desert soils [50], marine sediments [51], xylem sap and wood chips [52]. Several isolates are known for their tolerance against γ-radiation, strong oxidants and metals such as copper and zinc as well as their production of indole acetic acid, a plant hormone of the auxin class, inducing plant growth [53, 54].…”

Section: Discussionmentioning

confidence: 99%

From amplicons to strains: The limitations of metabarcoding as criterium in the selection process of biocontrol strains against the pome fruit pathogenNeonectria ditissima

Russ,

Elena Jimenez,

van den Beld

et al. 2023

Preprint

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European canker, caused by the fungal pathogenNeonectria ditissima, causes severe economic losses in apple production and conventional control measures are not sufficiently effective. Recently, parts of the endophyte community have been suggested to play a role in the response of the host to the pathogen, potentially leading to higher resistance of apple cultivars to disease outbreaks. In addition, advances on biologically controlling the disease have been booked by the application of fungi isolated at the boundary of cankered and healthy wood tissue. In this study we sought to evaluate if and how metabarcoding analysis can support decisions on selection of biological control agents in a two-steps process: first we profiled fungal and bacterial taxa using Illumina MiSeq sequencing on branches of potted apple trees that had been inoculated with either water or a suspension ofN. ditissimaspores. We combined the knowledge on the metataxonomic profile with quantitative data on theN. ditissimabranch colonisation (with relative abundances and absolute TaqMan qPCR concentrations) to identify taxa that show negative or positive correlations withN. ditissimaDNA concentration. Secondly, we compared our fungal metataxonomic profile to the ITS amplicons of fungal isolates that had been tested for biocontrol potential in bioassays in a previous study. The aim was to possibly link fungal taxa with proven efficacy against the pathogen to the microbiome composition. The only ASVs showing a consistent negative correlation to relative and absoluteN. ditissimaabundance belonged to the bacterial generaKineococcusandHymenobacter. For fungal taxa onlyN. ditissimaitself positively correlated to its increasing abundance, albeit only by rank and neither linearly nor beta binomially. Sequences belonging to the most promising antagonists from the study by Elena et al. (2022) could not be detected in the fungal microbiome profile at all. In addition, the combination of short reads length and high conservation within the chosen amplicon resulted in insufficient resolution to differentiate between a range of different efficacies of isolates belonging to the same genus (i.e.Aureobasidium).

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“…Zinc and cadmium are closely related transition metals that are frequent soil contaminants. Strain s3 probably has a high tolerance to cadmium and zinc because its genome encodes CadD, CzcD, and CzrB transporters that carry out Cd 2+ , Zn 2+ /Cd 2+ , and Zn 2+ efflux, respectively [6,62]. Strains s9, s12, and s17 also encode cadmium resistance transporters.…”

Section: Genes and Biochemical Pathways That Promote Plant Growth And...mentioning

confidence: 99%

“…Although Pseudomonas spp. strains do not contain cadmium resistance genes, they have great potential in soil remediation from zinc: each of the strains s2, s10, s15, and s20 contains the znuABC operon responsible for the transport of Zn 2+ ions inside the cell, as well as genes for the zinc transporter ZntB and the Cd(II)/Pb(II)-responsive transcriptional regulator CadR, which modulates the response to heavy metal exposure [6].…”

Section: Genes and Biochemical Pathways That Promote Plant Growth And...mentioning

confidence: 99%

“…The use of agrochemicals for these purposes may be limited both by legislation and from the position of possible impact on the environment, including soil and nearby water resources. Bioaugmentation of poplar trees using microorganisms can be used as an alternative and safe way of solving these problems [5,6]. This strategy, in turn, requires the study of the poplar microbiome and the characterization of its individual species, which, at present, are part of an intensively developing field in the study of plant-microbe interactions.…”

Section: Introductionmentioning

confidence: 99%

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Culturable Bacterial Endophytes of Wild White Poplar (Populus alba L.) Roots: A First Insight into Their Plant Growth-Stimulating and Bioaugmentation Potential

Gladysh,

Bogdanova,

Kovalev

et al. 2023

Biology

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The white poplar (Populus alba L.) has good potential for a green economy and phytoremediation. Bioaugmentation using endophytic bacteria can be considered as a safe strategy to increase poplar productivity and its resistance to toxic urban conditions. The aim of our work was to find the most promising strains of bacterial endophytes to enhance the growth of white poplar in unfavorable environmental conditions. To this end, for the first time, we performed whole-genome sequencing of 14 bacterial strains isolated from the tissues of the roots of white poplar in different geographical locations. We then performed a bioinformatics search to identify genes that may be useful for poplar growth and resistance to environmental pollutants and pathogens. Almost all endophytic bacteria obtained from white poplar roots are new strains of known species belonging to the genera Bacillus, Corynebacterium, Kocuria, Micrococcus, Peribacillus, Pseudomonas, and Staphylococcus. The genomes of the strains contain genes involved in the enhanced metabolism of nitrogen, phosphorus, and metals, the synthesis of valuable secondary metabolites, and the detoxification of heavy metals and organic pollutants. All the strains are able to grow on media without nitrogen sources, which indicates their ability to fix atmospheric nitrogen. It is concluded that the strains belonging to the genus Pseudomonas and bacteria of the species Kocuria rosea have the best poplar growth-stimulating and bioaugmentation potential, and the roots of white poplar are a valuable source for isolation of endophytic bacteria for possible application in ecobiotechnology.

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Inoculated Seed Endophytes Modify the Poplar Responses to Trace Elements in Polluted Soil

Cited by 7 publications

References 73 publications

Changes in the structure and function of rhizosphere soil microbial communities induced by Amaranthus palmeri invasion

Changes in the structure and function of rhizosphere soil microbial communities induced by Amaranthus palmeri invasion

From amplicons to strains: The limitations of metabarcoding as criterium in the selection process of biocontrol strains against the pome fruit pathogenNeonectria ditissima

Culturable Bacterial Endophytes of Wild White Poplar (Populus alba L.) Roots: A First Insight into Their Plant Growth-Stimulating and Bioaugmentation Potential

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