Periodic Reporting for period 1 - SENSE (BioSensing and rhizospherE – eNdosphere geochemical microprofiling of polychlorinated byphenils degradation by Soil microbiota upon stimulation of root Exudates)
Reporting period: 2019-09-02 to 2021-09-01
Soil contamination by persistent organic pollutants (POPs) represents a severe threat for human health and causes land degradation, loss of soil fertility and biodiversity. Polychlorinated biphenyls (PCBs) are a family of 209 molecules featured by toxicity, recalcitrance and low chemical reactivity that cause severe ecological problems since they accumulate in the food chain, causing harmful effects in humans and animals, acting as endocrine disruptors. Therefore, PCBs still persist in sites where their production was carried out for decades, like the former Caffaro S.p.A. chemical factory in Brescia (an industrialized city of 200,000 inhabitants in North Italy) where about 100 hectars of soil show a contamination by a mixture of contaminants including PCBs often exceeding the legal thresholds for residential areas.
Phyto-rhizo-remediation is a promising technology for pollutant clean-up based on the ability of the plant holobiont, composed by the host plant and the associated microbiome, to uptake, transform and degrade chemicals. Plant roots indeed nurture a large diversity of soil microbes via exudation of chemical compounds and some of them have been demonstrated to be able to stimulate the microbial degradation of toxic compounds, like PCBs.
Despite the well documented role of the plant holobiont in ecosystem services, the complex interactions between the host plant and the microbiome are poorly understood, in particular in contaminated environments.
SENSE offers an innovative approach to sort out the temporal and spatial synergistic interplay within the plant holobiont components and the geochemistry of rhizosphere micro-niches supporting microbial degradation. The research has been approached from two complementary angles: i) set up and application of bacterial biosensors to examine root topography and dynamics of activation of the PCB degradation pathways upon stimulation by identified plant root exudates; ii) sensing the plant modulated chemical micro-habitats through microsensor/sensor devices during plant-microbe interaction under PCBs stress
Phyto-rhizo-remediation is a promising technology for pollutant clean-up based on the ability of the plant holobiont, composed by the host plant and the associated microbiome, to uptake, transform and degrade chemicals. Plant roots indeed nurture a large diversity of soil microbes via exudation of chemical compounds and some of them have been demonstrated to be able to stimulate the microbial degradation of toxic compounds, like PCBs.
Despite the well documented role of the plant holobiont in ecosystem services, the complex interactions between the host plant and the microbiome are poorly understood, in particular in contaminated environments.
SENSE offers an innovative approach to sort out the temporal and spatial synergistic interplay within the plant holobiont components and the geochemistry of rhizosphere micro-niches supporting microbial degradation. The research has been approached from two complementary angles: i) set up and application of bacterial biosensors to examine root topography and dynamics of activation of the PCB degradation pathways upon stimulation by identified plant root exudates; ii) sensing the plant modulated chemical micro-habitats through microsensor/sensor devices during plant-microbe interaction under PCBs stress
A first accomplishment of the project was the development of a methodology to simulate in vitro PCB stress in the model plant Arabidopsis thaliana. Metabolomics-based investigations in organic compounds released by the root (i.e. root exudates) showed a differential pattern of exudation under control conditions and in presence of PCB, representing the signature of root exudates potentially stimulating PCB degradation pathways in rhizosphere bacteria. Indeed, by modulating the exudation profile, the plant modifies the environmental niches of the root system to make them more prone to attract, recruit and affect the PCB degrading metabolism of soil bacteria, the so-called “cry for help” mechanism. Some root exudate molecules showed to be able to influence microbial motility, enhancing the chemotaxis toward the root system, while others are able to enhance microbial growth. All these aspects showed that root exudation is a key process in remodelling plant-associated microbiome to ensure key ecosystem services in contaminated soil.
A bacterial biosensor was generated, to investigate by fluorescence confocal microscopy the colonization profile of degrading bacteria on the root system and locate the active sites of the root where the expression of the reporter fluorescent label, responding to root exudates involved in enhancing the bacteria degradative metabolism, occurred. Importantly, PCB degrading bacteria showed a specific colonization profile, with preferential sites of adhesion being the root hairs or the root tip. Furthermore, a time-course of the fluorescent reporter activation lead to follow the dynamics and topography of the root exudates-driven stimulation of the bacterial PCB degradation pathway. The project contributed to develop a methodological approach to perform micro-profiling of the physico-chemical parameters in the root micro-habitats affected by the change in root exudation induced by PCB, through application of two different microsensor technologies. Complex plant-microbe interactions occur within a spatial area of few millimetres, therefore the knowledge of the specific physico-chemical conditions occurring are important to drive information on the influence that they can have on plant physiology and bacterial metabolism.
SENSE results were disseminated to an academic and scientific audience through participation to conferences and the publication of a manuscript that elaborate the evidence published so far to propose that ‘cry-for-help’ hypothesis, initially described in plant-pathogens challenge, may be part of the adaptation strategy to ensure the holobiont fitness in polluted environments. Outreach activities were performed to increase the awareness in general public of the fundamental role played by plant-associated microbiome in sustaining ecosystem services in contaminated environments.
A bacterial biosensor was generated, to investigate by fluorescence confocal microscopy the colonization profile of degrading bacteria on the root system and locate the active sites of the root where the expression of the reporter fluorescent label, responding to root exudates involved in enhancing the bacteria degradative metabolism, occurred. Importantly, PCB degrading bacteria showed a specific colonization profile, with preferential sites of adhesion being the root hairs or the root tip. Furthermore, a time-course of the fluorescent reporter activation lead to follow the dynamics and topography of the root exudates-driven stimulation of the bacterial PCB degradation pathway. The project contributed to develop a methodological approach to perform micro-profiling of the physico-chemical parameters in the root micro-habitats affected by the change in root exudation induced by PCB, through application of two different microsensor technologies. Complex plant-microbe interactions occur within a spatial area of few millimetres, therefore the knowledge of the specific physico-chemical conditions occurring are important to drive information on the influence that they can have on plant physiology and bacterial metabolism.
SENSE results were disseminated to an academic and scientific audience through participation to conferences and the publication of a manuscript that elaborate the evidence published so far to propose that ‘cry-for-help’ hypothesis, initially described in plant-pathogens challenge, may be part of the adaptation strategy to ensure the holobiont fitness in polluted environments. Outreach activities were performed to increase the awareness in general public of the fundamental role played by plant-associated microbiome in sustaining ecosystem services in contaminated environments.
The findings obtained so far will provide a proof of concept for the role of root chemistry as boost of soil microbiome degradative potential. SENSE outcomes will contribute to increase the understanding of the plant holobiont functioning, applied to environmental biotechnology. Rhizoremediation is a promising, cost-effective and green biotechnology and the knowledge of the complex interaction among the root chemistry and the degradative microbiome underpinning its success will be fundamental for tailoring effective strategies for the clean-up of contaminated sites.