Understanding the development of roots exposed to contaminants and the potential of plant-associated bacteria for optimization of growth

Ecotoxicological bioassays with terrestrial plants: a holistic view of standards, guidelines, and protocols

Terrestrial and aquatic ecosystems face various chemicals that might induce acute and/or long-term harm. To assess these impacts, ecotoxicological bioassays are essential. However, bioassays using animals, particularly mammals, are costly, time-consuming, and raise ethical concerns. In this context, terrestrial plants emerge as a viable alternative to conventional assays. Thus, the aim of this review was to address the history and evolution of plant bioassays, highlighting the main regulations, guidelines, and protocols governing the use of terrestrial plants in ecotoxicological tests. Initially, plant bioassays were employed to assess the cytogenotoxic effects of chemicals, gaining prominence with the GENE-TOX program in the 80s. Subsequently, plants were used in allelopathy bioassays and in studies aimed to examine the ecotoxicity of pesticides in soil. Currently, ecotoxicological bioassays with plants are regulated by specific standards, such as ASTM E1963-22, EPA 600/3-88/029, EPS 1/RM/45, ISO 11269-1, ISO 11269-2, ISO 17126, ISO 18763, ISO 29200, ISO 22030, OECD-208, OECD-227, OCSPP 850.4100, OCSPP 850.4230, OCSPP 850.4800 and OPPTS 850.4200. The existing protocols standardize bioassays in greenhouse and lab environments, and the duration of the tests varies from hours to months. The main ecotoxicological parameters to be analyzed after exposure include germination percentage, survival rate, root length, aerial part length, fresh mass of exposed plants, and phytotoxicity symptoms. In addition, the absorption rate of substances and genotoxic and mutagenic effects might also be assessed. Therefore, data in this review demonstrate that terrestrial plants represent an important tool in the analysis of environmental risks associated with chemicals and might serve as crucial allies in modern ecotoxicology.

A systematic review on endophytic fungi and its role in the commercial applications

MAIN CONCLUSION

EF have been explored for its beneficial impact on environment and for its commercial applications. It has proved its worth in these sectors and showed an impact on biological properties of plants by producing various bioactive molecules and enzymes. Endophytes are plant mutualists that live asymptomatically within plant tissues and exist in almost every plant species. Endophytic fungi benefit from the host plant nutrition, and the host plant gains improved competitive abilities and tolerance against pathogens, herbivores, and various abiotic stresses. Endophytic fungi are one of the most inventive classes which produce secondary metabolites and play a crucial role in human health and other biotic aspects. This review is focused on systematic study on the biodiversity of endophytic fungi in plants, and their role in enhancing various properties of plants such as antimicrobial, antimycobacterial, antioxidant, cytotoxic, anticancer, and biological activity of secondary metabolites produced by various fungal endophytes in host plants reported from 1994 to 2021. This review emphasizes the endophytic fungal population shaped by host genotype, environment, and endophytic fungi genotype affecting host plant. The impact of endophytic fungi has been discussed in detail which influences the commercial properties of plants. Endophytes also have an influence on plant productivity by increasing parameters such as nutrient recycling and phytostimulation. Studies focusing on mechanisms that regulate attenuation of secondary metabolite production in EF would provide much needed impetus on ensuring continued production of bioactive molecules from a indubitable source. If this knowledge is further extensively explored regarding fungal endophytes in plants for production of potential phytochemicals, then it will help in exploring a keen area of interest for pharmacognosy.

Genetic Circuit Design in Rhizobacteria

Genetically engineered plants hold enormous promise for tackling global food security and agricultural sustainability challenges. However, construction of plant-based genetic circuitry is constrained by a lack of well-characterized genetic parts and circuit design rules. In contrast, advances in bacterial synthetic biology have yielded a wealth of sensors, actuators, and other tools that can be used to build bacterial circuitry. As root-colonizing bacteria (rhizobacteria) exert substantial influence over plant health and growth, genetic circuit design in these microorganisms can be used to indirectly engineer plants and accelerate the design-build-test-learn cycle. Here, we outline genetic parts and best practices for designing rhizobacterial circuits, with an emphasis on sensors, actuators, and chassis species that can be used to monitor/control rhizosphere and plant processes.

Plant growth-promoting actinobacterial inoculant assisted phytoremediation increases cadmium uptake in Sorghum bicolor under drought and heat stresses

In this study, two proficient Cadmium (Cd) resistant and plant growth-promoting actinobacterial strains were isolated from metal-polluted soils and identified as Streptomyces sp. strain RA04 and Nocardiopsis sp. strain RA07. Multiple abiotic stress tolerances were found in these two actinobacterial strains, including Cd stress (CdS), drought stress (DS) and high-temperature stress (HTS). Both actinobacterial strains exhibited multifarious plant growth-promoting (PGP) traits such as phosphate solubilization, and production of indole-3-acetic acid, siderophores and 1-aminocyclopropane-1-carboxylate deaminase under CdS, DS and HTS conditions. The inoculation of strains RA04 and RA07 significantly increased Sorghum bicolor growth and photosynthetic pigments under CdS, DS, HTS, CdS + DS and CdS + HTS conditions as compared to their respective uninoculated plants. The actinobacterial inoculants reduced malondialdehyde concentration and enhanced antioxidant enzymes in plants cultivated under various abiotic stress conditions, indicating that actinobacterial inoculants reduced oxidative damage. Furthermore, strains RA04 and RA07 enhanced the accumulation of Cd in plant tissues and the translocation of Cd from root to shoot under CdS, CdS + DS and CdS + HTS treatments as compared to their respective uninoculated plants. These findings suggest that RA04 and RA07 strains could be effective bio-inoculants to accelerate phytoremediation of Cd polluted soil even in DS and HTS conditions.

The role of roots and rhizosphere in providing tolerance to toxic metals and metalloids

Human activity and natural processes have led to the widespread dissemination of metals and metalloids, many of which are toxic and have a negative impact on plant growth and development. Roots, as the first point of contact, are essential in endowing plants with tolerance to excess metal(loid) in the soil. The most important root processes that contribute to tolerance are: adaptation of transport processes that affect uptake efflux and long-distance transport of metal(loid)s; metal(loid) detoxification within root cells via conjugation to thiol rich compounds and subsequent sequestration in the vacuole; plasticity in root architecture; the presence of bacteria and fungi in the rhizosphere that impact on metal(loid) bioavailability; the role of root exudates. In this review, we provide details on these processes and assess their relevance on the detoxification of arsenic, cadmium, mercury and zinc in crops. Furthermore, we assess which of these strategies have been tested in field conditions and whether they are effective in terms of improving crop metal(loid) tolerance.

Regulatory hubs and strategies for improving heavy metal tolerance in plants: Chemical messengers, omics and genetic engineering

Heavy metal (HM) accumulation in the agricultural soil and its toxicity is a major threat for plant growth and development. HMs disrupt functional integrity of the plants, induces altered phenological and physiological responses and slashes down qualitative crop yield. Chemical messengers such as phytohormones, plant growth regulators and gasotransmitters play a crucial role in regulating plant growth and development under metal toxicity in plants. Understanding the intricate network of these chemical messengers as well as interactions of genes/metabolites/proteins associated with HM toxicity in plants is necessary for deciphering insights into the regulatory circuit involved in HM tolerance. The present review describes (a) the role of chemical messengers in HM-induced toxicity mitigation, (b) possible crosstalk between phytohormones and other signaling cascades involved in plants HM tolerance and (c) the recent advancements in biotechnological interventions including genetic engineering, genome editing and omics approaches to provide a step ahead in making of improved plant against HM toxicities.

Evaluation of temperature, pH and nutrient conditions in bacterial growth and extracellular hydrolytic activities of two Alicyclobacillus spp. strains

Extremophile bacteria have developed the metabolic machinery for living in extreme temperatures, pH, and high-salt content. Two novel bacterium strains Alicyclobacillus sp. PA1 and Alicyclobacillus sp. PA2, were isolated from crater lake El Chichon in Chiapas, Mexico. Phylogenetic tree analysis based on the 16SrRNA gene sequence revealed that the strain Alicyclobacillus sp. PA1 and Alicyclobacillus sp. PA2 were closely related to Alicyclobacillus species (98% identity and 94.73% identity, respectively). Both strains were Gram variable, and colonies were circular, smooth and creamy. Electron microscopy showed than Alicyclobacillus sp. PA1 has a daisy-like form and Alicyclobacillus sp. PA2 is a regular rod. Both strains can use diverse carbohydrates and triglycerides as carbon source and they also can use organic and inorganic nitrogen source. But, the two strains can grow without any carbon or nitrogen sources in the culture medium. Temperature, pH and nutrition condition affect bacterial growth. Maximum growth was produced at 65 °C for Alicyclobacillus sp. PA1 (0.732 DO₆₀₀) at pH 3 and Alicyclobacillus sp. PA2 (0.725 DO₆₀₀) at pH 5. Inducible extracellular extremozyme activities were determined for β-galactosidase (Alicyclobacillus sp. PA1: 88.07 ± 0.252 U/mg, Alicyclobacillus sp. PA2: 51.57 ± 0.308 U/mg), cellulose (Alicyclobacillus sp. PA1: 141.20 ± 0.585 U/mg, Alicyclobacillus sp. PA2: 51.57 ± 0.308 U/mg), lipase (Alicyclobacillus sp. PA1: 138.25 ± 0.600 U/mg, Alicyclobacillus sp. PA2: 175.75 ± 1.387 U/mg), xylanase (Alicyclobacillus sp. PA1: 174.72 ± 1.746 U/mg, Alicyclobacillus sp. PA2: 172.69 ± 0.855U/mg), and protease (Alicyclobacillus sp. PA1: 15.12 ± 0.121 U/mg, Alicyclobacillus sp. PA2: 15.33 ± 0.284 U/mg). These results provide new insights on extreme enzymatic production on Alicyclobacillus species.

Endophyte roles in nutrient acquisition, root system architecture development and oxidative stress tolerance

Plants associate with communities of microbes (bacteria and fungi) that play critical roles in plant development, nutrient acquisition and oxidative stress tolerance. The major share of plant microbiota is endophytes which inhabit plant tissues and help them in various capacities. In this article, we have reviewed what is presently known with regard to how endophytic microbes interact with plants to modulate root development, branching, root hair formation and their implications in overall plant development. Endophytic microbes link the interactions of plants, rhizospheric microbes and soil to promote nutrient solubilization and further vectoring these nutrients to the plant roots making the soil-plant-microbe continuum. Further, plant roots internalize microbes and oxidatively extract nutrients from microbes in the rhizophagy cycle. The oxidative interactions between endophytes and plants result in the acquisition of nutrients by plants and are also instrumental in oxidative stress tolerance of plants. It is evident that plants actively cultivate microbes internally, on surfaces and in soils to acquire nutrients, modulate development and improve health. Understanding this continuum could be of greater significance in connecting endophytes with the hidden half of the plant that can also be harnessed in applied terms to enhance nutrient acquisition through the development of favourable root system architecture for sustainable production under stress conditions.

Changes induced by lead in root system architecture of Arabidopsis seedlings are mediated by PDR2-LPR1/2 phosphate dependent way

As sessile organisms, plants respond to changing environments modulating their genetic expression, metabolism and postembryonic developmental program (PDP) to adapt. Among environmental stressor, lead (Pb) is one of the most hazardous pollutants which limits crop productivity. Here, we describe in detail the effects of a wide range of concentrations of Pb on growth and development and a possible convergence with phosphate (Pi) starvation response. We found that the response to Pb presents a biphasic curve dose response in biomass accumulation: below 400 µM show a stimulatory effect meanwhile at Pb doses up to 600 µM effects are inhibitory. We found that +Pb (800 µM) modifies root system architecture (RSA) and induces acidification media, according to in silico ion interaction, in the growing medium Pb and Pi coprecipitate and plants grow in both Pi deficiency and Pb stress at the same time, however in spite of seedlings are under Pi starvation AtPT2 expression are Pb downregulated indicating that in addition to Pi starvation stress, Pb regulates physiological responses in root system. Using the mutants stop1, lpr1/2 and lpi3, which are affected in Pi starvation response, we found that changes in RSA by +Pb is genetically regulated and there are shared pathways with Pi starvation response mediated by PDR2-LPR1/2 and LPI3 pathways since lpr1/2 and lpi3 mutants are insensitive to +Pb and Pi starvation. Taking together, these results indicate that similar changes in RSA induced by independent environmental stimuli +Pb and Pi starvation are due to similar mediated response by PDR2-LPR1/2 pathway.

Nicotiana tabacum-associated bioengineered Pseudomonas putida can enhance rhizoremediation of soil containing 2,4-dinitrotoluene

Rhizoremediation processes are based on plant-bacteria interactions and can be effectively used for cleaning many pollutants from the environment to overcome the constraints of individual phytoremediation. Here, 1 mM and 1.5 mM concentrations of 2,4-dinitrotoluene (2,4-DNT) degrading Pseudomonas putida (P. putida) strain KT.DNT and various growth stages of Nicotiana tabacum (N. tabacum) were initially assayed in in vitro tissue culture system and the best conditions for the association of plant-rhizobacterium were ascertained to remediation of the soil contaminated with 2,4-DNT. 5-days old N. tabacum plants inoculated with 2 × 106 cfu/mL bacterial inoculum for 3 weeks were preferred for rhizoremediation experiments as they showed a nearly threefold increase in the fresh and dry biomass in comparison to noninoculated ones. When these seedlings were planted either alone or together with P. putida KT2440 or P. putida KT.DNT in soils contaminated with 1 mM and 1.5 mM of 2,4-DNT, the maximum degradation rate of 98% and ~ 93% were determined at the end of 14 days by KT.DNT inoculated tobacco plants. Our results indicate that it would be advantageous to use the 2,4-DNT-degrading bacterium inoculated with N. tabacum plants to accelerate and enhance the cleanup of soil contaminated with 2,4-DNT.

Acute toxicity evaluation of nanoparticles mixtures using luminescent bacteria

As the application of nanoparticles (NPs) and their release to the environment has increased, it is important to verify their toxicity, with a special emphasis on particle solubilization and the interaction of NP mixtures. In the current study, a model luminescent bacteria, Vibrio fischeri, was employed to test the acute toxicity of individual NPs and their binary mixtures, including metal NPs (ZnNPs, CuNPs) and metal oxide NPs (ZnONPs, CuONPs). The independent action model was used to reflect the synergistic, additive, or antagonistic interactions of binary mixtures of these NPs. The results showed that the median effective concentration (EC₅₀) inhibited the luminescence of V. fischeri were 20.5, 4.1, 11.6, and 118.7 mg L^-1 for ZnNPs, CuNPs, ZnONPs, and CuONPs, respectively, suggesting that the toxicity of these NPs to V. fischeri were as the following order: CuNPs > ZnONPs > ZnNPs > CuONPs. The combined effect of NPs were found to be antagonistic for CuNPs-ZnONPs and CuNPs-CuONPs, synergistic for CuONPs-ZnNPs, CuNPs-ZnNPs, and ZnONPs-CuONPs, and additive for ZnNPs-ZnONPs, revealing a complex pattern of possible interactions. The differences of dissolved metal ions partly accounted for the different combined toxicity of binary mixtures of NPs. The findings have important implications for better understanding the true environmental risk of NP mixtures.

Biotransformation of 2,4-dinitrotoluene by the beneficial association of engineered Pseudomonas putida with Arabidopsis thaliana

2,4-dinitrotoluene (2,4-DNT) is a priority environmental xenobiotic pollutant which has toxic, mutagenic, and carcinogenic properties. Thus, its biodegradation by applying recent approaches such as taking advantage of plant-bacteria interactions is crucial. In this work, the genes from Burkholderia sp. R34, necessary for 2,4-DNT degradation, were integrated into wild-type Pseudomonas putida (P. putida) KT2440 genome, and this strain, named KT.DNT, was inoculated to soil in in vitro conditions. To estimate the disappearance of 2,4-DNT in contaminated soil, samples were taken from different time intervals, extracted and analyzed using high-performance liquid chromatography (HPLC). Biotransformation of 2,4-DNT increased gradually and the degradation in soil after 14-days of treatment with the bacterium was found to be the 97.1%, indicating that the engineered strain could be a remarkable candidate for in situ bioremediation of 2,4-DNT-contaminated sites. In addition, in vitro interaction of this bacterium with a model plant, Arabidopsis thaliana (A. thaliana), enhanced lateral root and root hair formation together with dry root weight. Moreover, the initial 2,4-DNT concentration was decreased to 68% within 2 h with the plant-associated KT.DNT in liquid culture. Hence, the usage of this bacterium with plants could also be a promising application for the 2,4-DNT biotransformation.

Root-associated microorganisms reprogram plant life history along the growth-stress resistance tradeoff

Growth-defense tradeoffs are a major constraint on plant evolution. While the genetics of resource allocation is well established, the regulatory role of plant-associated microorganisms is still unclear. Here, we demonstrate that plant-associated microorganisms can reposition the plant phenotype along the same growth-defense tradeoff that determines phenotypic effects of plant mutations. We grew plants with microorganisms altering ethylene balance, a key hormone regulating plant investment into growth and stress tolerance. Microbial ethylene reduction had a similar effect to mutations disrupting ethylene signaling: both increased plant growth but at the cost of a strong stress hypersensitivity. We conclude that microbial impact on phenotype can offset the effects of mutations and that apparent plant growth promotion has strong pleiotropic effects. This study confirms that plant life history should be addressed as a joint product of plant genotype and its associated microbiota.

Cadmium and Plant Development: An Agony from Seed to Seed

Anthropogenic pollution of agricultural soils with cadmium (Cd) should receive adequate attention as Cd accumulation in crops endangers human health. When Cd is present in the soil, plants are exposed to it throughout their entire life cycle. As it is a non-essential element, no specific Cd uptake mechanisms are present. Therefore, Cd enters the plant through transporters for essential elements and consequently disturbs plant growth and development. In this review, we will focus on the effects of Cd on the most important events of a plant's life cycle covering seed germination, the vegetative phase and the reproduction phase. Within the vegetative phase, the disturbance of the cell cycle by Cd is highlighted with special emphasis on endoreduplication, DNA damage and its relation to cell death. Furthermore, we will discuss the cell wall as an important structure in retaining Cd and the ability of plants to actively modify the cell wall to increase Cd tolerance. As Cd is known to affect concentrations of reactive oxygen species (ROS) and phytohormones, special emphasis is put on the involvement of these compounds in plant developmental processes. Lastly, possible future research areas are put forward and a general conclusion is drawn, revealing that Cd is agonizing for all stages of plant development.

Cadmium and zinc bioaccumulation by Phytolacca americana from hydroponic media and contaminated soils

Hydroponic, greenhouse and field experiments were conducted to explore the potential of pokeweed (Phytolacca americana L.) to accumulate Zn and Cd from nutrient solutions and contaminated soils. The hydroponic results confirmed that this native species is a strong Zn and Cd bioaccumulator that does not experience severe phytotoxicity until quite high root and shoot concentrations, approaching 4000 and 1600 mg kg^-1 of Zn, and 1500 and 500 mg kg^-1 of Cd, respectively. These high Zn and Cd concentrations were accompanied by increased sulfur and lower manganese in both shoots and roots. However, in field and greenhouse trials with soils historically contaminated by a number of heavy metals including Zn and Cd, concentrations of Zn and Cd in shoots of P. americana reached concentrations less than 30% and 10%, respectively, of those achieved with hydroponics. The main constraint to phytoremediation of soils by P. americana was the low concentrations of Zn and Cd in soil solution. Pretreatment of the metal-contaminated soil by oxalic acid increased soluble Cd and Zn but failed to increase plant uptake of either metal, a possible result of higher solubility of competing metal ions (Cu, Mn) or low bioavailability of Cd and Zn-oxalate complexes.

Improved arsenic phytoextraction by combined use of mobilizing chemicals and autochthonous soil bacteria

Proper plant selection and application of suitable strategies are key factors to ensure the effectiveness of a reclamation via phytoremediation approach. In this study, micro- and meso-cosm scale experimentation has been realized to address a persistent contamination by arsenic on a disused industrial site through an assisted phytoremediation intervention. Three crop species, namely Brassica juncea, Helianthus annuus and Zea mays, have been considered and the addition of K₂HPO₄, a common mobilizing agent for As, or (NH₄)S₂O₃, a promising additive for As mobilization in case of mercury co-presence, evaluated. The use of these additives significantly enhanced the bioavailability of the target contaminant and therefore its phytoextraction up to 80%. Furthermore, in order to maximize the extraction efficiency of the plants, the influence of five indigenous Plant Growth Promoting Bacteria (PGPB), in combination with the mobilizing agents, was measured. The addition of the microbial consortium led to a further increase in the total uptake of arsenic, especially in B. juncea (up to 140%). The combined strategy supports and enhances the arsenic phytoextraction together with an improvement of the soil quality, as shown by phytotoxicity tests.

Inoculation of plant growth-promoting bacteria Bacillus sp. YM-1 alleviates the toxicity of Pb to pakchoi

Heavy metal accumulation in plants may imperil human health. Inoculation of plant growth-promoting bacteria can alleviate the toxicity of heavy metal and promote plant growth. In this study, Bacillus sp. YM-1, a heavy metal resistant and plant growth-promoting bacterium, was immobilized with spent substrate of mushroom and applied to alleviate the toxicity of Pb to pakchoi. The results indicated that the biomass of pakchoi in inoculation group was increased by 17.45 to 27.05% compared with that in non-inoculated group (p < 0.05). The root and shoot were lengthened by 13.45% to 39.17% and 20.23% to 42.36%, respectively. The content of Pb in root and shoot obviously reduced and that in edible part (shoot) was less than 0.2 mg kg^-1 in the low concentration of Pb. Other indicators such as superoxide dismutase (SOD), peroxidase (POD), chlorophyll, and protein all testified that YM-1 inoculation was conducive to the alleviation of Pb toxicity to pakchoi.

Microbial modulation of plant ethylene signaling: ecological and evolutionary consequences

The plant hormone ethylene is one of the central regulators of plant development and stress resistance. Optimal ethylene signaling is essential for plant fitness and is under strong selection pressure. Plants upregulate ethylene production in response to stress, and this hormone triggers defense mechanisms. Due to the pleiotropic effects of ethylene, adjusting stress responses to maximize resistance, while minimizing costs, is a central determinant of plant fitness. Ethylene signaling is influenced by the plant-associated microbiome. We therefore argue that the regulation, physiology, and evolution of the ethylene signaling can best be viewed as the interactive result of plant genotype and associated microbiota. In this article, we summarize the current knowledge on ethylene signaling and recapitulate the multiple ways microorganisms interfere with it. We present ethylene signaling as a model system for holobiont-level evolution of plant phenotype: this cascade is tractable, extremely well studied from both a plant and a microbial perspective, and regulates fundamental components of plant life history. We finally discuss the potential impacts of ethylene modulation microorganisms on plant ecology and evolution. We assert that ethylene signaling cannot be fully appreciated without considering microbiota as integral regulatory actors, and we more generally suggest that plant ecophysiology and evolution can only be fully understood in the light of plant-microbiome interactions.

Modeling of Cd adsorption to goethite-bacteria composites

The accurate modeling of heavy metal adsorption in complex systems is fundamental for risk assessments in soils and associated environments. Bacteria-iron (hydr)oxide associations in soils and sediments play a critical role in heavy metal immobilization. The reduced adsorption of heavy metals on these composites have been widely reported using the component additivity (CA) method. However, there is a lack of a mechanism model to account for these deviations. In this study, we established models for Cd adsorption on goethite-Pseudomonas putida composites at 1:1 and 5:1 mass ratios. Cadmium adsorption on the 5:1 composite was consistent with the additivity method. However, the CA method over predicted Cd adsorption by approximately 8% on the 1:1 composite at high Cd concentration. The deviation was corrected by adding the site blockage reactions between P. putida and goethite. Both CA and "CA-site masking" models for Cd adsorption onto the composites were in line with the ITC data. These results indicate that CA method in simulating Cd adsorption on bacteria-iron oxides composites is limited to low bacterial and Cd concentrations. Therefore the interfacial complexation reactions that occur between iron (hydr)oxides and bacteria should be taken into account when high concentrations of bacteria and heavy metals are present.

Cadmium and zinc activate adaptive mechanisms in Nicotiana tabacum similar to those observed in metal tolerant plants

MAIN CONCLUSION

Tobacco germinated and grew in the presence of high concentrations of cadmium and zinc without toxic symptoms. Evidence suggests that these ions are sequestered into the vacuole by heavy metal/H + exchanger mechanisms. Heavy metal hyperaccumulation and hypertolerance are traits shared by a small set of plants which show specialized physiological and molecular adaptations allowing them to accumulate and sequester toxic metal ions. Nicotiana tabacum was used to test its potential as a metal-accumulator in a glass house experiment. Seed germination was not affected in the presence of increasing concentrations of zinc and cadmium. Juvenile and adult plants could concentrate CdCl2 and ZnSO4 to levels exceeding those in the hydroponic growth medium and maintained or increased their leaf dry weight when treated with 0.5- or 1-mM CdCl2 or 1-mM ZnSO4 for 5 days. Accumulation of heavy metals did not affect the chlorophyll and carotenoid levels, while variable effects were observed in cell sap osmolarity. Heavy metal-dependent H+ transport across the vacuole membrane was monitored using quinacrine fluorescence quenching. Cadmium- or zinc-dependent fluorescence recovery revealed that increasing concentrations of heavy metals stimulated the activities of the tonoplast Cd2+ or Zn2+/H+ exchangers. Immunodetection of the V-ATPase subunits showed that the increased proton transport by zinc was not due to changes in protein amount. MTP1 and MTP4 immunodetection and semiquantitative RT-PCR of NtMTP1, NtNRAMP1, and NtZIP1 helped to identify the genes that are likely involved in sequestration of cadmium and zinc in the leaf and root tissue. Finally, we demonstrated that cadmium and zinc treatments induced an accumulation of zinc in leaf tissues. This study shows that N. tabacum possesses a hyperaccumulation response, and thus could be used for phytoremediation purposes.

Concentration-dependent alterations in gene expression induced by cadmium in Solanum lycopersicum

Cadmium (Cd) toxicity in agricultural soil has received significant attention because of its higher transformation in the food chain and toxicity to humans. The aim of the present study was to develop sensitive and specific biomarkers for Cd stress. Therefore, transcriptional analyses were performed to investigate concentration-response characteristics of Cd responsive genes identified from a Solanum lycopersicum microarray. The results showed that the lowest observable adverse effect concentrations (LOAECs) of Cd to S. lycopersicum were 1 mg/kg for seed germination, 8 mg/kg for root dry weight, 8 mg/kg for root elongation, and 8 mg/kg for root morphology. Furthermore, the genes were differentially expressed even at the lowest Cd concentrations (0.5 mg/kg), indicating that the detection of Cd in soil at the molecular level is a highly sensitive method. Cd in soil was positively correlated with the expression of the F-box protein PP2-B15 (r = 0.809, p < 0.01) and zinc transporter 4 (r = 0.643, p < 0.01), indicating that these two genes could be selected as indicators of soil Cd contamination.

Root avoidance of toxic metals requires the GeBP-LIKE 4 transcription factor in Arabidopsis thaliana

Plants reorganize their root architecture to avoid growth into unfavorable regions of the rhizosphere. In a screen based on chimeric repressor gene-silencing technology, we identified the Arabidopsis thaliana GeBP-LIKE 4 (GPL4) transcription factor as an inhibitor of root growth that is induced rapidly in root tips in response to cadmium (Cd). We tested the hypothesis that GPL4 functions in the root avoidance of Cd by analyzing root proliferation in split medium, in which only half of the medium contained toxic concentrations of Cd. The wild-type (WT) plants exhibited root avoidance by inhibiting root growth in the Cd side but increasing root biomass in the control side. By contrast, GPL4-suppression lines exhibited nearly comparable root growth in the Cd and control sides and accumulated more Cd in the shoots than did the WT. GPL4 suppression also altered the root avoidance of toxic concentrations of other essential metals, modulated the expression of many genes related to oxidative stress, and consistently decreased reactive oxygen species concentrations. We suggest that GPL4 inhibits the growth of roots exposed to toxic metals by modulating reactive oxygen species concentrations, thereby allowing roots to colonize noncontaminated regions of the rhizosphere.

Characterization of bacterial communities associated with Brassica napus L. growing on a Zn-contaminated soil and their effects on root growth

The interaction between plant growth-promoting bacteria (PGPB) and plants can enhance biomass production and metal tolerance of the host plants. This work aimed at isolating and characterizing the cultivable bacterial community associated with Brassica napus growing on a Zn-contaminated site, for selecting cultivable PGPB that might enhance biomass production and metal tolerance of energy crops. The effects of some of these bacterial strains on root growth of B. napus exposed to increasing Zn and Cd concentrations were assessed. A total of 426 morphologically different bacterial strains were isolated from the soil, the rhizosphere, and the roots and stems of B. napus. The diversity of the isolated bacterial populations was similar in rhizosphere and roots, but lower in soil and stem compartments. Burkoholderia, Alcaligenes, Agrococcus, Polaromonas, Stenotrophomonas, Serratia, Microbacterium, and Caulobacter were found as root endophytes exclusively. The inoculation of seeds with Pseudomonas sp. strains 228 and 256, and Serratia sp. strain 246 facilitated the root development of B. napus at 1,000 µM Zn. Arthrobacter sp. strain 222, Serratia sp. strain 246, and Pseudomonas sp. 228 and 262 increased the root length at 300 µM Cd.

Toxicity responses of Cu and Cd: the involvement of miRNAs and the transcription factor SPL7

BACKGROUND

MicroRNAs are important posttranscriptional regulators of gene expression playing a role in developmental processes as well as in stress responses, including metal stress responses. Despite the identification of several metal-responsive miRNAs, the regulation and the role of these miRNAs and their targets remain to be explored. In this study, miRNAs involved in the response to Cd and Cu excess in Arabidopsis thaliana are identified. In addition, the involvement of the transcription factor SPL7, namely the key regulator of Cu homeostasis, in these metal stress responses is demonstrated by the use of an spl7 knockout mutant. Furthermore, more insight is given in the Cd-induced Cu deficiency response through determining the effects of adding supplemental Cu to Cd-exposed plants.

RESULTS

Thirteen miRNAs were identified in response to Cu and Cd excess in A. thaliana. Several of these miRNAs (miR397a, miR398b/c and miR857) were oppositely affected under Cu and Cd exposure. The induced expression of these miRNAs after Cd exposure was totally abolished in the spl7 mutant (SQUAMOSA promoter binding protein like7), indicating a major role for SPL7 in the Cd response. Plants exposed to Cd showed a higher Cu content in the roots, whereas the Cu content in the leaves of the spl7 mutant was reduced. Furthermore, the Cd-induced Cu deficiency response disappeared when supplemental Cu was added.

CONCLUSIONS

Copper- and Cd-responsive miRNAs were identified and several of them are SPL7-dependently regulated. SPL7 seems to be a shared component between both the Cu toxicity and the Cd toxicity response, yet oppositely regulated, that is inactivated after Cu exposure and activated after Cd exposure. Since SPL7 is the key regulator of Cu homeostasis, and Cd affects the Cu homeostasis, we hypothesize that SPL7 is activated in response to Cd possibly due to a Cd-induced Cu deficiency. Since adding additional Cu to Cd-exposed plants resulted in the disappearance of the Cu deficiency response, Cd possibly provokes Cu deficiency, thereby activating SPL7 and inducing subsequently the Cu deficiency response.

An automated, cost-effective and scalable, flood-and-drain based root phenotyping system for cereals

BACKGROUND

Genetic studies on the molecular mechanisms of the regulation of root growth require the characterisation of a specific root phenotype to be linked with a certain genotype. Such studies using classical labour-intensive methods are severely hindered due to the technical limitations that are associated with the impeded observation of the root system of a plant during its growth. The aim of the research presented here was to develop a reliable, cost-effective method for the analysis of a plant root phenotype that would enable the precise characterisation of the root system architecture of cereals.

RESULTS

The presented method describes a complete system for automatic supplementation and continuous sensing of culture solution supplied to plants that are grown in transparent tubes containing a solid substrate. The presented system comprises the comprehensive pipeline consisting of a modular-based and remotely-controlled plant growth system and customized imaging setup for root and shoot phenotyping. The system enables an easy extension of the experimental capacity in order to form a combined platform that is comprised of parallel modules, each holding up to 48 plants. The conducted experiments focused on the selection of the most suitable conditions for phenotyping studies in barley: an optimal size of the glass beads, diameters of the acrylic tubes, composition of a medium, and a rate of the medium flow.

CONCLUSIONS

The developed system enables an efficient, accurate and highly repeatable analysis of the morphological features of the root system of cereals. Because a simple and fully-automated control system is used, the experimental conditions can easily be normalised for different species of cereals. The scalability of the module-based system allows its capacity to be adjusted in order to meet the requirements of a particular experiment.

Evaluating the Combined Toxicity of Cu and ZnO Nanoparticles: Utility of the Concept of Additivity and a Nested Experimental Design

Little is understood regarding the effects of mixtures of different metal-based nanoparticles (NPs). Using concentration-addition (CA) and independent-action (IA) models, we evaluated the combined toxicity of Cu and ZnO NPs based on five nested combinations, i.e., Cu(NO3)2-CuNPs, Zn(NO3)2-ZnONPs, Cu(NO3)2-ZnONPs, Zn(NO3)2-CuNPs, and CuNPs-ZnONPs on root elongation of Lactuca sativa L. The CA and IA models performed equally well in estimating the toxicity of mixtures of Cu(NO3)2-CuNPs, Zn(NO3)2-ZnONPs, and Zn(NO3)2-CuNPs, whereas the IA model was significantly better for fitting the data of Cu(NO3)2-ZnONPs and CuNPs-ZnONPs mixtures. Dissolved Cu proved to be the most toxic metal species to lettuce roots in the tests, followed by Cu NPs, dissolved Zn, and ZnO NPs, respectively. An antagonistic effect was observed for ZnO NPs on the toxicity of Cu NPs. This antagonistic effect is expected to be the result of interactions between dissolved Cu and dissolved Zn, particulate Zn and dissolved Zn, particulate Cu and dissolved Zn, and between particulate Zn and dissolved Cu. In general terms, assuming additivity gives a first indication of the combined toxicity with soluble and insoluble metal particles, both being important in driving the toxicity of metal-based NPs to higher plants.

Nutrient removal by up-scaling a hybrid floating treatment bed (HFTB) using plant and periphyton: From laboratory tank to polluted river

Planted floating treatment bed (FTB) is an innovative technique of removing nutrients from polluted water but limited in deep water and cold seasons. Periphyton was integrated into FTB for a hybrid floating treatment bed (HFTB) to improve its nutrient removal capacity. To assess its potential for treating nutrient-polluted rivers, HFTB was up-scaled from 5L laboratory tanks to 350L outdoor tanks and then to a commercial-scale 900m section of polluted river. Plants and periphyton interacted in HFTB with periphyton limiting plant root growth and plants having shading effects on periphyton. Non-overlapping distribution of plants and periphyton can minimize the negative interactions in HFTB. HFTB successfully kept TN and TP of the river at less than 2.0 and 0.02mgL(-1), respectively. This study indicates that HFTB can be easily up-scaled for nutrients removal from polluted rivers in different seasons providing a long-term, environmentally-friendly method to remediate polluted ecosystems.

Hydrogen Peroxide, Signaling in Disguise during Metal Phytotoxicity

Plants exposed to excess metals are challenged by an increased generation of reactive oxygen species (ROS) such as superoxide ([Formula: see text]), hydrogen peroxide (H2O2) and the hydroxyl radical ((•)OH). The mechanisms underlying this oxidative challenge are often dependent on metal-specific properties and might play a role in stress perception, signaling and acclimation. Although ROS were initially considered as toxic compounds causing damage to various cellular structures, their role as signaling molecules became a topic of intense research over the last decade. Hydrogen peroxide in particular is important in signaling because of its relatively low toxicity, long lifespan and its ability to cross cellular membranes. The delicate balance between its production and scavenging by a plethora of enzymatic and metabolic antioxidants is crucial in the onset of diverse signaling cascades that finally lead to plant acclimation to metal stress. In this review, our current knowledge on the dual role of ROS in metal-exposed plants is presented. Evidence for a relationship between H2O2 and plant metal tolerance is provided. Furthermore, emphasis is put on recent advances in understanding cellular damage and downstream signaling responses as a result of metal-induced H2O2 production. Finally, special attention is paid to the interaction between H2O2 and other signaling components such as transcription factors, mitogen-activated protein kinases, phytohormones and regulating systems (e.g. microRNAs). These responses potentially underlie metal-induced senescence in plants. Elucidating the signaling network activated during metal stress is a pivotal step to make progress in applied technologies like phytoremediation of polluted soils.

Survival Strategies of the Plant-Associated Bacterium Enterobacter sp. Strain EG16 under Cadmium Stress

Plant-associated bacteria are of great interest because of their potential use in phytoremediation. However, their ability to survive and promote plant growth in metal-polluted soils remains unclear. In this study, a soilborne Cd-resistant bacterium was isolated and identified as Enterobacter sp. strain EG16. It tolerates high external Cd concentrations (Cd(2+) MIC, >250 mg liter(-1)) and is able to produce siderophores and the plant hormone indole-3-acetic acid (IAA), both of which contribute to plant growth promotion. Surface biosorption in this strain accounted for 31% of the total Cd accumulated. The potential presence of cadmium sulfide, shown by energy-dispersive X-ray (EDX) analysis, suggested intracellular Cd binding as a Cd response mechanism of the isolate. Cd exposure resulted in global regulation at the transcriptomic level, with the bacterium switching to an energy-conserving mode by inhibiting energy-consuming processes while increasing the production of stress-related proteins. The stress response system included increased import of sulfur and iron, which become deficient under Cd stress, and the redirection of sulfur metabolism to the maintenance of intracellular glutathione levels in response to Cd toxicity. Increased production of siderophores, responding to Cd-induced Fe deficiency, not only is involved in the Cd stress response systems of EG16 but may also play an important role in promoting plant growth as well as alleviating the Cd-induced inhibition of IAA production. The newly isolated strain EG16 may be a suitable candidate for microbially assisted phytoremediation due to its high resistance to Cd and its Cd-induced siderophore production, which is likely to contribute to plant growth promotion.

Ethylene and Metal Stress: Small Molecule, Big Impact

The phytohormone ethylene is known to mediate a diverse array of signaling processes during abiotic stress in plants. Whereas many reports have demonstrated enhanced ethylene production in metal-exposed plants, the underlying molecular mechanisms are only recently investigated. Increasing evidence supports a role for ethylene in the regulation of plant metal stress responses. Moreover, crosstalk appears to exist between ethylene and the cellular redox balance, nutrients and other phytohormones. This review highlights our current understanding of the key role ethylene plays during responses to metal exposure. Moreover, particular attention is paid to the integration of ethylene within the broad network of plant responses to metal stress.

In Vitro Morphogenesis of Arabidopsis to Search for Novel Endophytic Fungi Modulating Plant Growth

Fungal endophytes have shown to affect plant growth and to confer stress tolerance to the host; however, effects of endophytes isolated from water plants have been poorly investigated. In this study, fungi isolated from stems (stem-E) and roots (root-E) of Mentha aquatica L. (water mint) were identified, and their morphogenetic properties analysed on in vitro cultured Arabidopsis (L.) Heynh., 14 and 21 days after inoculation (DAI). Nineteen fungi were analysed and, based on ITS analysis, 17 isolates showed to be genetically distinct. The overall effect of water mint endophytes on Arabidopsis fresh (FW) and dry weight (DW) was neutral and positive, respectively, and the increased DW, mainly occurring 14 DAI, was possibly related to plant defence mechanism. Only three fungi increased both FW and DW of Arabidopsis at 14 and 21 DAI, thus behaving as plant growth promoting (PGP) fungi. E-treatment caused a reduction of root depth and primary root length in most cases and inhibition-to-promotion of root area and lateral root length, from 14 DAI. Only Phoma macrostoma, among the water mint PGP fungi, increased both root area and depth, 21 DAI. Root depth and area 14 DAI were shown to influence DWs, indicating that the extension of the root system, and thus nutrient uptake, was an important determinant of plant dry biomass. Reduction of Arabidopsis root depth occurred to a great extent when plants where treated with stem-E while root area decreased or increased under the effects of stem-E and root-E, respectively, pointing to an influence of the endophyte origin on root extension. M. aquatica and many other perennial hydrophytes have growing worldwide application in water pollution remediation. The present study provided a model for directed screening of endophytes able to modulate plant growth in the perspective of future field applications of these fungi.

Gene Networks Involved in Hormonal Control of Root Development in Arabidopsis thaliana: A Framework for Studying Its Disturbance by Metal Stress

Plant survival under abiotic stress conditions requires morphological and physiological adaptations. Adverse soil conditions directly affect root development, although the underlying mechanisms remain largely to be discovered. Plant hormones regulate normal root growth and mediate root morphological responses to abiotic stress. Hormone synthesis, signal transduction, perception and cross-talk create a complex network in which metal stress can interfere, resulting in root growth alterations. We focus on Arabidopsis thaliana, for which gene networks in root development have been intensively studied, and supply essential terminology of anatomy and growth of roots. Knowledge of gene networks, mechanisms and interactions related to the role of plant hormones is reviewed. Most knowledge has been generated for auxin, the best-studied hormone with a pronounced primary role in root development. Furthermore, cytokinins, gibberellins, abscisic acid, ethylene, jasmonic acid, strigolactones, brassinosteroids and salicylic acid are discussed. Interactions between hormones that are of potential importance for root growth are described. This creates a framework that can be used for investigating the impact of abiotic stress factors on molecular mechanisms related to plant hormones, with the limited knowledge of the effects of the metals cadmium, copper and zinc on plant hormones and root development included as case example.

Sequencing, assembly, annotation, and gene expression: novel insights into the hormonal control of carrot root development revealed by a high-throughput transcriptome

Previous studies have indicated that hormonal control is essential for plant root growth. The root of the carrot is an edible vegetable with a high nutritional value. However, molecular mechanisms underlying hormone-mediated root growth of carrot have not been illustrated. Therefore, the present study collected carrot root samples from four developmental stages, and performed transcriptome sequencing to understand the molecular functions of plant hormones in carrot root growth. A total of 160,227 transcripts were generated from our transcriptome, which were assembled into 32,716 unigenes with an average length of 1,453 bp. A total of 4,818 unigenes were found to be differentially expressed between the four developmental stages. In total, 87 hormone-related differentially expressed genes were identified, and the roles of the hormones are extensively discussed. Our results suggest that plant hormones may regulate carrot root growth in a phase-dependent manner, and these findings will provide valuable resources for future research on carrot root development.

Toxic effects of copper-based nanoparticles or compounds to lettuce (Lactuca sativa) and alfalfa (Medicago sativa)

The increased production and use of nanoparticles (NPs) has generated concerns about their impact on living organisms. In this study, nCu, bulk Cu, nCuO, bulk CuO, Cu(OH)2 (CuPRO 2005, Kocide 3000), and CuCl2 were exposed for 15 days to 10 days-old hydroponically grown lettuce (Lactuca sativa) and alfalfa (Medicago sativa). Each compound was applied at 0, 5, 10, and 20 mg L(-1). At harvest, we measured the size of the plants and determined the concentration of Cu, macro and microelements by using ICP-OES. Catalase and ascorbate peroxidase activity was also determined. Results showed that all Cu NPs/compounds reduced the root length by 49% in both plant species. All Cu NPs/compounds increased Cu, P, and S (>100%, >50%, and >20%, respectively) in alfalfa shoots and decreased P and Fe in lettuce shoot (>50% and >50%, respectively, excluding Fe in CuCl2 treatment). Biochemical assays showed reduced catalase activity in alfalfa (root and shoot) and increased ascorbate peroxidase activity in roots of both plant species. Results suggest that Cu NPs/compounds not only reduced the size of the plants but altered nutrient content and enzyme activity in both plant species.

Problems inherent to a meta-analysis of proteomics data: a case study on the plants' response to Cd in different cultivation conditions

This meta-analysis focuses on plant-proteome responses to cadmium (Cd) stress. Initially, some general topics related to a proteomics meta-analysis are discussed: (1) obstacles encountered during data analysis, (2) a consensus in proteomic research, (3) validation and good reporting practices for protein identification and (4) guidelines for statistical analysis of differentially abundant proteins. In a second part, the Cd responses in leaves and roots obtained from a proteomics meta-analysis are discussed in (1) a time comparison (short versus long term exposure), and (2) a culture comparison (hydroponics versus soil cultivation). Data of the meta-analysis confirmed the existence of an initial alarm phase upon Cd exposure. Whereas no metabolic equilibrium is established in hydroponically exposed plants, an equilibrium seems to be manifested in roots of plants grown in Cd-contaminated soil after long term exposure. In leaves, the carbohydrate metabolism is primarily affected independent of the exposure time and the cultivation method. In addition, a metabolic shift from CO2-fixation towards respiration is manifested, independent of the cultivation system. Finally, some ideas for the improvement of proteomics setups and for comparisons between studies are discussed.

BIOLOGICAL SIGNIFICANCE

This meta-analysis focuses on the plant responses to Cd stress in leaves and roots at the proteome level. This meta-analysis points out the encountered obstacles when performing a proteomics meta-analysis related to inherent technologies, but also related to experimental setups. Furthermore, the question is addressed whether an extrapolation of results obtained in hydroponic cultivation towards soil-grown plants is possible.

Auxin and the integration of environmental signals into plant root development

BACKGROUND

Auxin is a versatile plant hormone with important roles in many essential physiological processes. In recent years, significant progress has been made towards understanding the roles of this hormone in plant growth and development. Recent evidence also points to a less well-known but equally important role for auxin as a mediator of environmental adaptation in plants.

SCOPE

This review briefly discusses recent findings on how plants utilize auxin signalling and transport to modify their root system architecture when responding to diverse biotic and abiotic rhizosphere signals, including macro- and micro-nutrient starvation, cold and water stress, soil acidity, pathogenic and beneficial microbes, nematodes and neighbouring plants. Stress-responsive transcription factors and microRNAs that modulate auxin- and environment-mediated root development are also briefly highlighted.

CONCLUSIONS

The auxin pathway constitutes an essential component of the plant's biotic and abiotic stress tolerance mechanisms. Further understanding of the specific roles that auxin plays in environmental adaptation can ultimately lead to the development of crops better adapted to stressful environments.

Endophytic Burkholderia fungorum DBT1 can improve phytoremediation efficiency of polycyclic aromatic hydrocarbons

Burkholderia fungorum DBT1 is a bacterial strain isolated from an oil refinery discharge and capable of transforming dibenzothiophene, phenanthrene, naphthalene, and fluorene. In order to evaluate the influence of a policyclic aromatic hydrocarbon (PAH)-transforming bacterial strain on the phytoremediation of organic contaminants, B. fungorum DBT1 was inoculated into hybrid poplar (Populus deltoides×Populus nigra). The poplar plants were grown for 18-wk with or without naphthalene, phenanthrene, fluorene and dibenzothiophene (488mgkg(-1) soil each) in non-sterile sand-peat substrate. Evidences were gained that B. fungorum DBT1 was present in high concentration in poplar root tissues (2.9-9.5×10(3)CFUg(-1)), while the strain was not detected in stem, leaves and rhizosphere. When poplar was planted in uncontaminated substrate, the infection caused negative effects on biomass index, leaves and stem dry weight, without showing however any disease symptoms. On the other hand, plants inoculated with the strain DBT1 resulted in better tolerance against the toxic effects of PAHs, in terms of root dry weight. Although the presence of plants acted as the main effective treatment for PAH dissipation (82-87%), the inoculum with DBT1 strain lead to the highest PAH abatement (up to 99%). In the present study, an environmental isolate with proper metabolic features was demonstrated to be possibly suitable as a poplar endophyte for improving microbe-assisted phytoremediation in PAH contaminated matrices.

Cultivar variation in morphological response of peanut roots to cadmium stress and its relation to cadmium accumulation

This study aimed to test the hypothesis that root morphology may play a crucial role in the variation in Cd accumulation among peanut (Arachis hypogaea L.) cultivars. The biomass, Cd accumulation and root morphology of five peanut cultivars were determined under 2 and 20μM CdCl2 in a hydroponic experiment. Excess Cd considerably decreased the root lengths (RL), surface area (SA), specific root length (SRL) and number of root tips, but increased the root diameters (RD). Cd-induced decreases in RL and SA were significant in the 0-0.2 and 0.2-0.4mm diameter classes. Peanut cultivars differ in Cd accumulation and root morphological parameters. A positive correlation was observed between RL and Cd amount in shoots. RD negatively correlated to Cd concentrations in roots and shoots. Positive correlations were also found between RL vs. shoot Cd concentration, SA vs. Cd amount in shoots, SRL vs. root Cd concentration, SRL vs. shoot Cd concentration, and SRL vs. Cd amount in shoots. The fine roots play a crucial role in determining Cd accumulation in peanut plants. Cultivars with more fine roots in their root system (i.e. Haihua 1 and Zhenghong 3) have high capability of Cd accumulation.

Plant root research: the past, the present and the future

This special issue is dedicated to root biologists past and present who have been exploring all aspects of root structure and function with an extensive publication record going over 100 years. The content of the Special Issue on Root Biology covers a wide scale of contributions, spanning interactions of roots with microorganisms in the rhizosphere, the anatomy of root cells and tissues, the subcellular components of root cells, and aspects of metal accumulation and stresses on root function and structure. We have organized the papers into three topic categories: (1) root ecology, interactions with microbes, root architecture and the rhizosphere; (2) experimental root biology, root structure and physiology; and (3) applications of new technology to study root biology. Finally, we will speculate on root research for the future.