Effects of Secondary Plant Metabolites on Microbial Populations: Changes in Community Structure and Metabolic Activity in Contaminated Environments

Bioremediation of chlorophenol-contaminated sawmill soil using pilot-scale bioreactors under consecutive anaerobic-aerobic conditions

Chlorophenols (CPs), including pentachlorophenol (PCP), are chemicals of concern due to their toxicity and persistence. Here we describe a successful reactor-based remediation of CP-contaminated soil and assess changes in the toxicity patterns and bacterial communities during the remediation. The remediation consisted of separating half of the contaminated soil to be ground (samples M) in order to test whether the grinding expedited the remediation, the other half was left unground (samples P). Both soils were mixed with wastewater treatment sludge to increase their bacterial diversity and facilitate the degradation of CPs, and the resultant mixtures were placed in 2 bioreactors, M and P, operated for 16 months under anaerobic conditions to favor dehalogenation and for an additional 16 months under aerobic conditions to achieve complete mineralization. Samples were taken every 4 months for toxicity and microbial analyses. The results showed a 64% removal of total CPs (ΣCPs) in reactor P after just 18 months of remediation, whereas similar depletion in reactor M occurred after ∼25 months, indicating that the grinding decelerated the remediation. By the end of the experiment, both reactors achieved 93.5-95% removal. The toxicity tests showed a decrease in toxicity as the remediation progressed. The succession of bacterial communities over time was significantly associated with pH, anaerobic/aerobic phase and the concentration of the majority of CP congeners. Our data indicate that the supplementation of contaminated soil with sludge and further incubation in pilot-scale bioreactors under consecutive anaerobic-aerobic conditions proved to be effective at the remediation of CP-contaminated soil.

The stimulating role of syringic acid, a plant secondary metabolite, in the microbial degradation of structurally-related herbicide, MCPA

The ability of microorganisms to degrade xenobiotics can be exploited to develop cost-effective and eco-friendly bioremediation technologies. Microorganisms can degrade almost all organic pollutants, but this process might be very slow in some cases. A promising way to enhance removal of recalcitrant xenobiotics from the environment lies in the interactions between plant exudates such as plant secondary metabolites (PSMs) and microorganisms. Although there is a considerable body of evidence that PSMs can alter the microbial community composition and stimulate the microbial degradation of xenobiotics, their mechanisms of action remain poorly understood. With this in mind, our aim was to demonstrate that similarity between the chemical structures of PSMs and xenobiotics results in higher micropollutant degradation rates, and the occurrence of corresponding bacterial degradative genes. To verify this, the present study analyses the influence of syringic acid, a plant secondary metabolite, on the bacterial degradation of an herbicide, 4-chloro-2-methylphenoxyacetic acid (MCPA). In particular, the presence of appropriate MCPA degradative genes, MCPA removal efficiency and changes in samples phytotoxicity have been analyzed. Significant MCPA depletion was achieved in samples enriched with syringic acid. The results confirmed not only greater MCPA removal from the samples upon spiking with syringic acid, and thus decreased phytotoxicity, but also the presence of a greater number of genes responsible for MCPA biodegradation. 16S rRNA gene sequence analysis revealed ubiquitous enrichment of the β-proteobacteria Rhodoferax, Achromobacter, Burkholderia and Cupriavidus. The obtained results provide further confirmation that plant metabolites released into the rhizosphere can stimulate biodegradation of xenobiotics, including MCPA.

Phytoremediation of soil contaminated with PCBs using different plants and their associated microbial communities

In this work, we evaluate the abilities of the plants Brassica juncea, Avena sativa, Brachiaria decumbens, and Medicago sativa to uptake polychlorinated biphenyls (PCBs) and induce degradation of soil microorganisms from contaminated soil. Removal of PCBs 44, 66, 118, 153, 170, and 180 was evaluated in both rhizospheric and nonrhizospheric soils. Microbial and bphA1 gene quantifications were performed by real-time PCR. The PCB concentrations in plant tissues and soil were determined, and a fluorescein diacetate (FDA) hydrolysis assay was used to measure microbial activity in soil. The removal percentages for all PCB congeners in planted soil versus unplanted control soil were statistically significant and varied between 45% and 63%. PCBs 118, 153, 138, and 170 were detected in Brachiaria decumbens roots at different concentrations. In planted soil, an increase in the concentration of bacteria was observed compared to the initial concentration and the concentration in unplanted control soil; however, no significant differences were identified between plants. The number of copies of the bphA1 gene was higher in rhizospheric versus non- rhizospheric soil for all plants at the end of the experiment. However, alfalfa and oat rhizospheric soil showed significant differences in the copy number of the bphA1 gene. In general, the concentration of fluorescein in the rhizospheric soil was greater than that in the nonrhizospheric soil. Although the plants had a positive effect on PCB removal, this effect varied depending on the type of PCB, the plant, and the soil.

Plant Growth-Promoting Rhizobacteria: Context, Mechanisms of Action, and Roadmap to Commercialization of Biostimulants for Sustainable Agriculture

Microbes of the phytomicrobiome are associated with every plant tissue and, in combination with the plant form the holobiont. Plants regulate the composition and activity of their associated bacterial community carefully. These microbes provide a wide range of services and benefits to the plant; in return, the plant provides the microbial community with reduced carbon and other metabolites. Soils are generally a moist environment, rich in reduced carbon which supports extensive soil microbial communities. The rhizomicrobiome is of great importance to agriculture owing to the rich diversity of root exudates and plant cell debris that attract diverse and unique patterns of microbial colonization. Microbes of the rhizomicrobiome play key roles in nutrient acquisition and assimilation, improved soil texture, secreting, and modulating extracellular molecules such as hormones, secondary metabolites, antibiotics, and various signal compounds, all leading to enhancement of plant growth. The microbes and compounds they secrete constitute valuable biostimulants and play pivotal roles in modulating plant stress responses. Research has demonstrated that inoculating plants with plant-growth promoting rhizobacteria (PGPR) or treating plants with microbe-to-plant signal compounds can be an effective strategy to stimulate crop growth. Furthermore, these strategies can improve crop tolerance for the abiotic stresses (e.g., drought, heat, and salinity) likely to become more frequent as climate change conditions continue to develop. This discovery has resulted in multifunctional PGPR-based formulations for commercial agriculture, to minimize the use of synthetic fertilizers and agrochemicals. This review is an update about the role of PGPR in agriculture, from their collection to commercialization as low-cost commercial agricultural inputs. First, we introduce the concept and role of the phytomicrobiome and the agricultural context underlying food security in the 21st century. Next, mechanisms of plant growth promotion by PGPR are discussed, including signal exchange between plant roots and PGPR and how these relationships modulate plant abiotic stress responses via induced systemic resistance. On the application side, strategies are discussed to improve rhizosphere colonization by PGPR inoculants. The final sections of the paper describe the applications of PGPR in 21st century agriculture and the roadmap to commercialization of a PGPR-based technology.

Response of Plant Secondary Metabolites to Environmental Factors

Plant secondary metabolites (SMs) are not only a useful array of natural products but also an important part of plant defense system against pathogenic attacks and environmental stresses. With remarkable biological activities, plant SMs are increasingly used as medicine ingredients and food additives for therapeutic, aromatic and culinary purposes. Various genetic, ontogenic, morphogenetic and environmental factors can influence the biosynthesis and accumulation of SMs. According to the literature reports, for example, SMs accumulation is strongly dependent on a variety of environmental factors such as light, temperature, soil water, soil fertility and salinity, and for most plants, a change in an individual factor may alter the content of SMs even if other factors remain constant. Here, we review with emphasis how each of single factors to affect the accumulation of plant secondary metabolites, and conduct a comparative analysis of relevant natural products in the stressed and unstressed plants. Expectantly, this documentary review will outline a general picture of environmental factors responsible for fluctuation in plant SMs, provide a practical way to obtain consistent quality and high quantity of bioactive compounds in vegetation, and present some suggestions for future research and development.

24-Epibrassinolide alleviates organic pollutants-retarded root elongation by promoting redox homeostasis and secondary metabolism in Cucumis sativus L

Environmental pollution by organic pollutants (OPs) has become a global concern due to its detrimental effects on the environment and human health. As plants are used to remediate contaminated sites, understanding the responses of plants to various OPs and fortification of plant tolerance are of great significance. In this work, we studied the biochemical and molecular responses of cucumber plants to three well-known OPs, 2,4,6-trichlorophenol, chlorpyrifos and oxytetracycline in the absence or presence of 24-epibrassinolide (EBR), a potent regulator of plant growth and stress tolerance. The results showed that the selected three OPs retarded root elongation; however, the phytotoxic effects of OPs were attenuated by exogenous EBR. OPs induced accumulations of both hydrogen peroxide (H₂O₂) and nitric oxide (NO) in root tips and resulted in an increased malondialdehyde (MDA) content, an indicator of membrane lipid peroxidation. Exogenous EBR reduced accumulations of H₂O₂, NO and MDA in the roots by increasing the expression of antioxidant and detoxification genes and the activities of the corresponding enzymes. Intriguingly, EBR not only promoted the activities of glutathione S-transferase and glutathione reductase, but also increased the content of reduced glutathione without altering the content of oxidized glutathione, which resulted in a reduced redox state under OPs stress. Furthermore, EBR increased the free radical scavenging capacity, flavonoid content and the activity and transcription of secondary metabolism related enzymes. Our results suggest that EBR treatment may fortify secondary metabolism to enhance antioxidant capacity in response to OPs treatment, which might have potential implication in phytoremediation of OPs.

Secondary compound hypothesis revisited: Selected plant secondary metabolites promote bacterial degradation of cis-1,2-dichloroethylene (cDCE)

Cis-1,2-dichloroethylene (cDCE), which is a common hazardous compound, often accumulates during incomplete reductive dechlorination of higher chlorinated ethenes (CEs) at contaminated sites. Simple monoaromatics, such as toluene and phenol, have been proven to induce biotransformation of cDCE in microbial communities incapable of cDCE degradation in the absence of other carbon sources. The goal of this microcosm-based laboratory study was to discover non-toxic natural monoaromatic secondary plant metabolites (SPMEs) that could enhance cDCE degradation in a similar manner to toluene and phenol. Eight SPMEs were selected on the basis of their monoaromatic molecular structure and widespread occurrence in nature. The suitability of the SPMEs chosen to support bacterial growth and to promote cDCE degradation was evaluated in aerobic microbial cultures enriched from cDCE-contaminated soil in the presence of each SPME tested and cDCE. Significant cDCE depletions were achieved in cultures enriched on acetophenone, phenethyl alcohol, p-hydroxybenzoic acid and trans-cinnamic acid. 16S rRNA gene sequence analysis of each microbial community revealed ubiquitous enrichment of bacteria affiliated with the genera Cupriavidus, Rhodococcus, Burkholderia, Acinetobacter and Pseudomonas. Our results provide further confirmation of the previously stated secondary compound hypothesis that plant metabolites released into the rhizosphere can trigger biodegradation of environmental pollutants, including cDCE.

Efficient phytoremediation of organic contaminants in soils using plant-endophyte partnerships

Soil pollution with organic contaminants is one of the most intractable environmental problems today, posing serious threats to humans and the environment. Innovative strategies for remediating organic-contaminated soils are critically needed. Phytoremediation, based on the synergistic actions of plants and their associated microorganisms, has been recognized as a powerful in situ approach to soil remediation. Suitable combinations of plants and their associated endophytes can improve plant growth and enhance the biodegradation of organic contaminants in the rhizosphere and/or endosphere, dramatically expediting the removal of organic pollutants from soils. However, for phytoremediation to become a more widely accepted and predictable alternative, a thorough understanding of plant-endophyte interactions is needed. Many studies have recently been conducted on the mechanisms of endophyte-assisted phytoremediation of organic contaminants in soils. In this review, we highlight the superiority of organic pollutant-degrading endophytes for practical applications in phytoremediation, summarize alternative strategies for improving phytoremediation, discuss the fundamental mechanisms of endophyte-assisted phytoremediation, and present updated information regarding the advances, challenges, and new directions in the field of endophyte-assisted phytoremediation technology.

Phyto-rhizoremediation of polychlorinated biphenyl contaminated soils: An outlook on plant-microbe beneficial interactions

Polychlorinated biphenyls (PCBs) are toxic chemicals, recalcitrant to degradation, bioaccumulative and persistent in the environment, causing adverse effects on ecosystems and human health. For this reason, the remediation of PCB-contaminated soils is a primary issue to be addressed. Phytoremediation represents a promising tool for in situ soil remediation, since the available physico-chemical technologies have strong environmental and economic impacts. Plants can extract and metabolize several xenobiotics present in the soil, but their ability to uptake and mineralize PCBs is limited due to the recalcitrance and low bioavailability of these molecules that in turn impedes an efficient remediation of PCB-contaminated soils. Besides plant degradation ability, rhizoremediation takes into account the capability of soil microbes to uptake, attack and degrade pollutants, so it can be seen as the most suitable strategy to clean-up PCB-contaminated soils. Microbes are in fact the key players of PCB degradation, performed under both aerobic and anaerobic conditions. In the rhizosphere, microbes and plants positively interact. Microorganisms can promote plant growth under stressed conditions typical of polluted soils. Moreover, in this specific niche, root exudates play a pivotal role by promoting the biphenyl catabolic pathway, responsible for microbial oxidative PCB metabolism, and by improving the overall PCB degradation performance. Besides rhizospheric microbial community, also the endophytic bacteria are involved in pollutant degradation and represent a reservoir of microbial resources to be exploited for bioremediation purposes. Here, focusing on plant-microbe beneficial interactions, we propose a review of the available results on PCB removal from soil obtained combining different plant and microbial species, mainly under simplified conditions like greenhouse experiments. Furthermore, we discuss the potentiality of "omics" approaches to identify PCB-degrading microbes, an aspect of paramount importance to design rhizoremediation strategies working efficiently under different environmental conditions, pointing out the urgency to expand research investigations to field scale.

Native Phytoremediation Potential of Urtica dioica for Removal of PCBs and Heavy Metals Can Be Improved by Genetic Manipulations Using Constitutive CaMV 35S Promoter

Although stinging nettle (Urtica dioica) has been shown to reduce HM (heavy metal) content in soil, its wider phytoremediation potential has been neglected. Urtica dioica was cultivated in soils contaminated with HMs or polychlorinated biphenyls (PCBs). After four months, up to 33% of the less chlorinated biphenyls and 8% of HMs (Zn, Pb, Cd) had been removed. Bacteria were isolated from the plant tissue, with the endophytic bacteria Bacillus shackletonii and Streptomyces badius shown to have the most significant effect. These bacteria demonstrated not only benefits for plant growth, but also extreme tolerance to As, Zn and Pb. Despite these results, the native phytoremediation potential of nettles could be improved by biotechnologies. Transient expression was used to investigate the functionality of the most common constitutive promoter, CaMV 35S in Urtica dioica. This showed the expression of the CUP and bphC transgenes. Collectively, our findings suggest that remediation by stinging nettle could have a much wider range of applications than previously thought.

Plant-assisted bioremediation of a historically PCB and heavy metal-contaminated area in Southern Italy

A plant-assisted bioremediation strategy was applied in an area located in Southern Italy, close to the city of Taranto, historically contaminated by polychlorinated biphenyls (PCBs) and heavy metals. A specific poplar clone (Monviso) was selected for its ability to promote organic pollutant degradation in the rhizosphere, as demonstrated elsewhere. Chemical and microbiological analyses were performed at the time of poplar planting in selected plots at different distances from the trunk (0.25-1m) and at different soil depths (0-20 and 20-40cm), at day 420. A significant decrease in PCB congeners and a reduction in all heavy metals was observed where the poplar trees were present. No evidence of PCB and heavy metal reduction was observed in the non poplar-vegetated soil. Microbial analyses (dehydrogenase activity, cell viability, microbial abundance) of the autochthonous microbial community showed an improvement in soil quality. In particular, microbial activity generally increased in the poplar-rhizosphere and a positive effect was observed in some cases at up to 1m distance from the trunk and up to 40cm depth. The Monviso clone was effective in promoting both a general decrease in contaminant occurrence and an increase in microbial activity in the chronically polluted area a little more than one year after planting.