Hydrocarbon substrate richness impacts microbial abundance, microbiome composition, and hydrocarbon loss

Bell, Terrence H.; Camillone, Nina; Abram, Katrina; Bruns, Maryann Victoria; Yergeau, Étienne; St‐Arnaud, Marc

doi:10.1016/j.apsoil.2021.104015

Cited by 6 publications

(4 citation statements)

References 61 publications

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“…However, the total bacterial abundance was not significantly impacted over the PHE contamination gradient. This is consistent with the literature, where hydrocarbon contamination usually impacts bacterial diversity but not necessarily abundance (Bell et al 2021;Cébron et al 2022).…”

Section: Bacterial Communities Positively Impacted By the Phe Gradientsupporting

confidence: 93%

Taxonomic and functional responses of soil and root bacterial communities associated with poplar exposed to a contamination gradient of phenanthrene

Gréau

Blaudez

Cordier

et al. 2023

FEMS Microbiology Ecology

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Polycyclic aromatic hydrocarbon (PAH) contamination of industrial wasteland soils affects microbial diversity, but little is known about the dose-response effects of such contaminants on taxonomic and functional diversities of rhizospheric and plant endophytic bacteria. This study focused on the response of soil and root bacterial communities associated to poplar grown in a contamination gradient of phenanthrene (PHE). It was hypothesized that the increase in contamination would modify gradually the bacterial diversity and functions. The effects of the PHE contamination were limited to soil communities and did not affect the poplar root endophytome where Streptomyces and Cutibacterium were the most abundant genera. Along the PHE gradient, alpha-diversity indices decreased and the community structure of soil bacteria at the taxonomic level shifted. The abundance of genes involved in PAH-degradation pathways and the relative proportion of certain microbial taxa such as Polaromonas, Sphingopyxis, Peredibacter, Phenylobacterium, Ramlibacter, Sphingomonas, Pseudomonas, often described as potential PAH biodegraders, increased with the PHE concentration in the soil community. Conversely, the contamination negatively impacted other taxa like Nocardioides, Streptomyces, Gaiella, Solirubrobacter, Bradyrhizobium and Nitrospira. Functional inference and enzymatic activity measurements revealed that some bacterial functions related to carbon, nitrogen and phosphorus cycles were modified in soil throughout the PHE gradient. This study allowed a deeper understanding of the complex plant-bacteria interactions in the case of soil PAH contamination and the potential impact on soil functioning.

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Section: Bacterial Communities Positively Impacted By the Phe Gradientsupporting

confidence: 93%

Taxonomic and functional responses of soil and root bacterial communities associated with poplar exposed to a contamination gradient of phenanthrene

Gréau

Blaudez

Cordier

et al. 2023

FEMS Microbiology Ecology

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“…Resource abundance and diversity can be important factors influencing microbial diversity and composition (Bell et al, 2021; Langenheder & Prosser, 2008; She et al, 2018). We detected differences between absorptive and transportive fine roots for the root metabolome, which were primarily linked to a greater relative abundance of the sugars sorbitol, trehalose and mannitol in the absorptive fine roots and inositol in the transportive fine roots, amino acids isoleucine, cysteine and valine in the absorptive fine roots, and ornithine and asparagine in the transportive fine roots, and the fatty acids oleic acid and palmitic acid in the absorptive fine roots.…”

Section: Discussionmentioning

confidence: 99%

Functionally discrete fine roots differ in microbial assembly, microbial functional potential, and produced metabolites

King,

Yates,

Cao

et al. 2023

Plant Cell & Environment

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Traditionally, fine roots were grouped using arbitrary size categories, rarely capturing the heterogeneity in physiology, morphology and functionality among different fine root orders. Fine roots with different functional roles are rarely separated in microbiome‐focused studies and may result in confounding microbial signals and host‐filtering across different root microbiome compartments. Using a 26‐year‐old common garden, we sampled fine roots from four temperate tree species that varied in root morphology and sorted them into absorptive and transportive fine roots. The rhizoplane and rhizosphere were characterized using 16S rRNA gene and internal transcribed spacer region amplicon sequencing and shotgun metagenomics for the rhizoplane to identify potential microbial functions. Fine roots were subject to metabolomics to spatially characterize resource availability. Both fungi and bacteria differed according to root functional type. We observed additional differences between the bacterial rhizoplane and rhizosphere compartments for absorptive but not transportive fine roots. Rhizoplane bacteria, as well as the root metabolome and potential microbial functions, differed between absorptive and transportive fine roots, but not the rhizosphere bacteria. Functional differences were driven by sugar transport, peptidases and urea transport. Our data highlights the importance of root function when examining root‐microbial relationships, emphasizing different host selective pressures imparted on different root microbiome compartments.

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“…Although the community compositions of each kingdom were found to be significantly different between both cultivars in each biotope, their alpha diversity remained statistically similar, which could reflect the differential abundances of some taxa. Increasing microbial diversity in roots and rhizosphere often leads to greater functional trait diversity, redundancy and complementarity, which would improve ecological services, as well as plant resistance to environmental changes and pathogen invasion [1,71,72]. In a contaminated environment, higher diversification of the soil microbiome have been found to be more effective for the biodegradation of some crude oil fractions [73].…”

Section: Beta and Alpha Diversitiesmentioning

confidence: 99%

Ectomycorrhizal Fungi Dominated the Root and Rhizosphere Microbial Communities of Two Willow Cultivars Grown for Six-Years in a Mixed-Contaminated Environment

Faubert

Labrecque

Hijri

2022

JoF

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There is a growing interest in plant microbiome’s engineering to optimize desired functions such as improved phytoremediation. This study is aimed at examining the microbial communities inhabiting the roots and rhizospheres of two Salix miyabeana cultivars that had been grown in a short-rotation intensive culture (SRIC) system for six years in a soil contaminated with the discharge from a petrochemical factory. DNA was extracted from roots and rhizospheric soils, and fungal ITS and bacterial and archaeal 16S rDNA regions were amplified and sequenced using Illumina MiSeq technology. Cultivars ‘SX61’ and ‘SX64’ were found to harbor a similar diversity of fungal, bacterial, and archaeal amplicon sequence variants (ASVs). As expected, a greater microbial diversity was found in the rhizosphere biotope than in the roots of both cultivars, except for cultivar ‘SX64’, where a similar fungal diversity was observed in both biotopes. However, we found that microbial community structures were cultivar- and biotope-specific. Although the implication of some identified taxa for plant adaptability and biomass production capacity remains to be explored, this study provides valuable and useful information regarding microbes that could potentially favor the implantation and phytoremediation efficiency of Salix miyabeana in mixed contamination sites in similar climatic environments.

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Hydrocarbon substrate richness impacts microbial abundance, microbiome composition, and hydrocarbon loss

Cited by 6 publications

References 61 publications

Taxonomic and functional responses of soil and root bacterial communities associated with poplar exposed to a contamination gradient of phenanthrene

Taxonomic and functional responses of soil and root bacterial communities associated with poplar exposed to a contamination gradient of phenanthrene

Functionally discrete fine roots differ in microbial assembly, microbial functional potential, and produced metabolites

Ectomycorrhizal Fungi Dominated the Root and Rhizosphere Microbial Communities of Two Willow Cultivars Grown for Six-Years in a Mixed-Contaminated Environment

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