Phytoremediation is a promising technology to clean-up contaminated soils based on the synergistic actions of plants and microorganisms. However, to become a widely accepted, and predictable remediation alternative, a deeper understanding of the plant–microbe interactions is needed. A number of studies link the success of phytoremediation to the plant-associated microbiome functioning, though whether the microbiome can exist in alternative, functional states for soil remediation, is incompletely understood. Moreover, current approaches that target the plant host, and environment separately to improve phytoremediation, potentially overlook microbial functions and properties that are part of the multiscale complexity of the plant-environment wherein biodegradation takes place. In contrast, in situ studies of phytoremediation research at the metaorganism level (host and microbiome together) are lacking. Here, we discuss a competition-driven model, based on recent evidence from the metagenomics level, and hypotheses generated by microbial community ecology, to explain the establishment of a catabolic rhizosphere microbiome in a contaminated soil. There is evidence to ground that if the host provides the right level and mix of resources (exudates) over which the microbes can compete, then a competitive catabolic and plant-growth promoting (PGP) microbiome can be selected for as long as it provides a competitive superiority in the niche. The competition-driven model indicates four strategies to interfere with the microbiome. Specifically, the rhizosphere microbiome community can be shifted using treatments that alter the host, resources, environment, and that take advantage of prioritization in inoculation. Our model and suggestions, considering the metaorganism in its natural context, would allow to gain further knowledge on the plant–microbial functions, and facilitate translation to more effective, and predictable phytotechnologies.

Widespread pollution of terrestrial ecosystems with petroleum hydrocarbons (PHCs) has generated a need for remediation and, given that many PHCs are biodegradable, bio- and phyto-remediation are often viable approaches for active and passive remediation. This review focuses on phytoremediation with particular interest on the interactions between and use of plant-associated bacteria to restore PHC polluted sites. Plant-associated bacteria include endophytic, phyllospheric, and rhizospheric bacteria, and cooperation between these bacteria and their host plants allows for greater plant survivability and treatment outcomes in contaminated sites. Bacterially driven PHC bioremediation is attributed to the presence of diverse suites of metabolic genes for aliphatic and aromatic hydrocarbons, along with a broader suite of physiological properties including biosurfactant production, biofilm formation, chemotaxis to hydrocarbons, and flexibility in cell-surface hydrophobicity. In soils impacted by PHC contamination, microbial bioremediation generally relies on the addition of high-energy electron acceptors (e.g., oxygen) and fertilization to supply limiting nutrients (e.g., nitrogen, phosphorous, potassium) in the face of excess PHC carbon. As an alternative, the addition of plants can greatly improve bioremediation rates and outcomes as plants provide microbial habitats, improve soil porosity (thereby increasing mass transfer of substrates and electron acceptors), and exchange limiting nutrients with their microbial counterparts. In return, plant-associated microorganisms improve plant growth by reducing soil toxicity through contaminant removal, producing plant growth promoting metabolites, liberating sequestered plant nutrients from soil, fixing nitrogen, and more generally establishing the foundations of soil nutrient cycling. In a practical and applied sense, the collective action of plants and their associated microorganisms is advantageous for remediation of PHC contaminated soil in terms of overall cost and success rates for in situ implementation in a diversity of environments. Mechanistically, there remain biological unknowns that present challenges for applying bio- and phyto-remediation technologies without having a deep prior understanding of individual target sites. In this review, evidence from traditional and modern omics technologies is discussed to provide a framework for plant–microbe interactions during PHC remediation. The potential for integrating multiple molecular and computational techniques to evaluate linkages between microbial communities, plant communities and ecosystem processes is explored with an eye on improving phytoremediation of PHC contaminated sites.

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Background: Conventional agriculture relies on chemical pesticides and fertilizers, which can degrade ecosystems. A reduction of these harmful practices is required, replacing (or integrating) them with more eco-friendly approaches, such as microbial inoculation. Tomato is an important agricultural product, with a high content of bioactive compounds (folate, ascorbate, polyphenols, and carotenoids). The focus of this research was to investigate the plant growth-promoting (PGP) abilities of bacterial strains isolated from different tomato cultivars, with the aim to develop systems to improve plant health and crop productivity based on microbial inoculation. Methods:A pool of different tomato cultivars already available on the market and new tomato hybrids were selected based on their nutritional quality (high content of biologically active compounds). A total of 23 strains were isolated from tomato roots (11 rhizospheric strains and 12 root endophytes). The cultivable isolates were analyzed for a number of different PGP traits: organic acids (OA), indole acetic acid (IAA), ACC deaminase, and siderophore production. The effects of microbial inoculation on root growth of Arabidopsis thaliana were also evaluated using a Vertical Agar Plate assay. Results:A high percentage of the isolated strains tested positive for the following PGP traits: 73 % were able to produce OA, 89 % IAA, 83 % ACC deaminase, and 87 % siderophores. The most striking result were remarkable increases in the formation of root hairs for most of the inoculated plants. This effect was obvious for all A. thaliana seedlings inoculated with the isolated endophytes, and for the 50 % of the seedlings inoculated with the rhizospheric strains.

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Phytoremediation is increasingly adopted as a more sustainable approach for soil remediation. However, significant advances in efficiency are still necessary to attain higher levels of environmental and economic sustainability. Current interventions do not always give the expected outcomes in field settings due to an incomplete understanding of the multicomponent biological interactions. New advances in -omics are gradually implemented for studying microbial communities of polluted land in situ. This opens new perspectives for the discovery of biodegradative strains and provides us new ways of interfering with microbial communities to enhance bioremediation rates. This review presents retrospectives and future perspectives for plant microbiome studies relevant to phytoremediation, as well as some knowledge gaps in this promising research field. The implementation of phytoremediation in soil clean-up management systems is discussed, and an overview of the promoting factors that determine the growth of the phytoremediation market is given. Continuous growth is expected since elimination of contaminants from the environment is demanded. The evolution of scientific thought from a reductionist view to a more holistic approach will boost phytoremediation as an efficient and reliable phytotechnology. It is anticipated that phytoremediation will prove the most promising for organic contaminant degradation and bioenergy crop production on marginal land.

The potential use of biochar from olive mill waste for in situ remediation of metal contaminated soils was evaluated. Biochar was mixed with metal contaminated soil originating from the vicinity of an old zinc smelter. Soil-biochar mixtures were equilibrated for 30 and 90 days. At these time points, Ca(NO3)2 exchangeable metals were determined, and effects of the biochar amendment on soil toxicity were investigated using plants, bacteria, and earthworms. Bean (Phaseolus vulgaris) growth, metal content, antioxidative enzymes activities, and soluble protein contents were determined. Furthermore, effects on soil microbial communities (activity, diversity, richness) were examined using Biolog ECOplates. After 120 days of soil-biochar equilibration, effects on weight and reproduction of Eisenia foetida were evaluated. With increasing biochar application rate and equilibration period, Ca(NO3)2 exchangeable metals decreased, and growth of bean plants improved; leaf metal contents reduced, the activities of antioxidative stress enzymes decreased, and soluble protein contents increased. Soil microbial activity, richness, and diversity were augmented. Earthworm mortality lowered, and their growth and reproduction showed increasing trends.

Abstract. Elevated atmospheric CO 2 levels and increasing nitrogen deposition both stimulate plant production in terrestrial ecosystems. Moreover, nitrogen deposition could alleviate an increasing nitrogen limitation experienced by plants exposed to elevated CO 2 concentrations. However, an increased rate of C flux through the soil compartment as a consequence of elevated CO 2 concentrations has been suggested to limit C sequestration in terrestrial ecosystems, questioning the potential for terrestrial C uptake to mitigate increasing atmospheric CO 2 concentrations. Our study used data from 77 published studies applying elevated CO 2 and/or N fertilization treatment to monitor carbon storage potential in grasslands, and considered the influence of management practices involving biomass removal or irrigation on the elevated CO 2 effects. Our results confirmed a positive effect of elevated CO 2 levels and nitrogen fertilization on plant growth, but revealed that N availability is essential for the increased C influx under elevated CO 2 to propagate into belowground C pools. However, moderate nutrient additions also promoted decomposition processes in elevated CO 2 , reducing the potential for increased soil C storage. An important role was attributed to the CO 2 response of root biomass in soil carbon responses to elevated CO 2 , since there was a lower potential for increases in soil C content when root biomass increased. Future elevated CO 2 concentrations and increasing N deposition might thus increase C storage in plant biomass, but the potential for increased soil C storage is limited.