Carbon deposition in soil rhizosphere following amendments with compost and its soluble fractions, as evaluated by combined soil-plant rhizobox and reporter gene systems

Humic substances increase tomato tolerance to osmotic stress while modulating vertically transmitted endophytic bacterial communities

While humic substances (HS) are recognized for their role in enhancing plant growth under abiotic stress by modulating hormonal and redox metabolisms, a key question remains: how do HS influence the microbiota associated with plants? This study hypothesizes that the effects of HS extend beyond plant physiology, impacting the plant-associated bacterial community. To explore this, we investigated the combined and individual impacts of HS and osmotic stress on tomato plant physiology and root endophytic communities. Tomatoes were grown within a sterile hydroponic system, which allowed the experiment to focus on seed-transmitted endophytic bacteria. Moreover, sequencing the 16S-ITS-23S region of the rrn operon (~4,500 bp) in a metabarcoding assay using the PNA-chr11 clamp nearly eliminated the reads assigned to Solanum lycopersicum and allowed the species-level identification of these communities. Our findings revealed that HS, osmotic stress, and their combined application induce changes in bacterial endophytic communities. Osmotic stress led to reduced plant growth and a decrease in Bradyrhizobium sp., while the application of HS under osmotic stress resulted in increased tomato growth, accompanied by an increase in Frigoribacterium sp., Roseateles sp., and Hymenobacter sp., along with a decrease in Sphingomonas sp. Finally, HS application under non-stress conditions did not affect plant growth but did alter the endophytic community, increasing Hymenobacter sp. and decreasing Sphingomonas sp. This study enhances the understanding of plant-endophyte interactions under stress and HS application, highlighting the significance of the vertically transmitted core microbiome in tomato roots and suggesting new insights into the mode of action of HS that was used as a biostimulant.

Maximizing trace metal phytoextraction through planting methods: Role of rhizosphere fertility and microbial activities

Brownfields are a widespread problem in the world. The poor quality of these soils and the potential presence of contaminants can pose a significant threat to plant establishment and growth. However, it may be possible to improve their establishment with an appropriate agricultural practice. In this paper, the effects of two common planting strategies, seeding and transplanting, on the establishment and growth of the hyperaccumulator species Noccaea caerulescens and on its phytoextraction capacity were investigated. A field experiment was conducted by direct sowing of N. caerulescens seeds on a plot of contaminated Technosols in Jeandelaincourt, France. At the same time, seeds were sown on potting soil under controlled conditions. One month later, the seedlings were transplanted to the field. One year later, the results showed that transplanting improved the establishment and growth of N. caerulescens. This was due to a decrease in soil pH in the rhizosphere, which subsequently increased nutrient availability. This change in rhizosphere properties also appeared to be the key that improved microbial activities in the rhizosphere soil of transplanted plants. The observed improvement in both rhizosphere nutrient availability and microbial activities, in turn, increased auxin concentrations in the rhizosphere and consequently a more developed root system was observed in the transplanted plants. Furthermore, the Cd and Zn phytoextraction yield of transplanted plants is 2.5 and 5 times higher, respectively, than that of sown plants. In conclusion, N. caerulescens transplantation on contaminated sites seems to be an adequate strategy to improve plant growth and enhance trace metal phytoextraction.

Humic Substances in Combination With Plant Growth-Promoting Bacteria as an Alternative for Sustainable Agriculture

Plant growth-promoting bacteria (PGPB) and humic substances (HSs) are promising options for reducing the use of pesticides and mineral fertilizers. Although many studies have shown the effects of PGPB and HSs separately, little information is available on plant responses to the combined application of these biostimulants despite the great potential for the simultaneous action of these biological inputs. Thus, the objective of this review is to present an overview of scientific studies that addressed the application of PGPB and HSs to different crops. First, we discuss the effect of these biostimulants on biological nitrogen fixation, the various effects of the inoculation of beneficial bacteria combined with the application of HSs on promoting the growth of nonleguminous plants and how this combination can increase bacterial colonization of plant hosts. We also address the effect of PGPB and HSs on plant responses to abiotic stresses, in addition to discussing the role of HSs in protecting plants against pathogens. There is a lack of studies that address the role of PGPB + HSs in biocontrol. Understanding the factors involved in the promotion of plant growth through the application of PGPB and HSs can assist in the development of efficient biostimulants for agricultural management. This approach has the potential to accelerate the transition from conventional cultivation to sustainable agrosystems.

The interaction between particulate organic matter and copper, zinc in paddy soil

Particulate organic matter (POM) acts as a metals sink in soil, but only a few studies focused on the interaction of POM and heavy metals in paddy soil. The aim of this study is to investigate the interaction between POM and Copper (Cu)/Zinc (Zn). Two levels of Cu (100, 400 mg kg^-1) and Zn (250, 500 mg kg^-1) were used in a soil culture experiment. Our results showed that POM was porous structure and varied in size. Hydroxyl and carboxyl involved in POM adsorption of Cu and Zn. Rhizosphere effects roughen the surface of POM and enhanced the capacity of POM on heavy metals absorption. Cu-humic (26.2-33.9%) and Cu-citrate (38.5-42.4%) were dominated in POM, and Cu-goethite (41.7-57.7%), Cu-sulphide (6.6-27.6%) was dominated in soil. Rhizosphere effects decreased the proportion of organic-bond Cu along with the increasing the proportion of Cu-sulphide in POM. Addition of Cu and Zn inhibited the degradation of POM but rhizosphere effects promoted. Carbon content was increased in POM by heavy metal and rhizosphere effects. Our findings indicated that POM tended to retain the heavy metals in soil and heavy metals inhibited the degradation of POM, however, rhizosphere effects decreased the stability of POM-metals interactions.

Interactions of two novel stabilizing amendments with sunflower plants grown in a contaminated soil

Several efficient stabilizing amendments have been recently proposed for the remediation of metal(loid)-contaminated soils. However, information on their interactions with plants, which is a crucial factor in soil environments, are still scarce. An amorphous manganese oxide (AMO) synthesized from organic compounds and nano zerovalent iron (nZVI) have been previously tested as promising stabilizing agents usable both for the stabilization of metals and As. Experiments with rhizoboxes were performed in order to evaluate their influence on the mobility of metal(loid)s in the bulk soil and rhizosphere of sunflower (Helianthus annuus L.) together with their impact on metal uptake and biomass yield. Generally, AMO proved more efficient than nZVI in all stages of experiment. Furthermore, the AMO effectively reduced water- and 0.01 M CaCl₂-extractable fractions of Cd, Pb and Zn. The decreased bioavailability of contaminating metal(loid)s resulted in significant increase of microbial activity in AMO-amended soil. Together with metal(loid) extractability, the AMO was also able to significantly reduce the uptake of metals and ameliorate plant growth, especially in the case of Zn, since this metal was taken up in excessive amounts from the control soil causing strong phytotoxicity and even death of young seedlings. On the other hand, AMO application lead to significant release of Mn that was readily taken up by plants. Resulting Mn concentrations in biomass exceeded toxicity thresholds while plants were showing emergent Mn phytotoxicity symptoms. We highlight the need of such complex studies involving plants and soil biota when evaluating the efficiency of stabilizing amendments in contaminated soils.

Giant reed growth and effects on soil biological fertility in assisted phytoremediation of an industrial polluted soil

Phytoremediation is a cost-effective "green technology" that uses plants to improve the soil properties of polluted sites, preventing the dispersion of pollutants and reducing the mobility of potentially toxic elements (PTEs) through their adsorption and accumulation by roots or precipitation within the root zone. Being highly tolerant to pollutants and other abiotic stresses, giant reed (Arundo donax L.) is a suitable biomass crop for phytoremediation of contaminated soils. We report the results of a two-year open-air lysimeter study aimed at assessing the adaptability of giant reed to grow on industrial substrates polluted by Pb and Zn and at testing commercial humic acids from leonardite as improvers of plant performance. We evaluated giant reed potential for: 1) biomass production for energy or biomaterial recovery; 2) PTE phytoextraction and 3) soil fertility restoration. Chemical fertility was monitored by measuring soil C while soil biological fertility was estimated by quantifying the abundance of bacterial functional genes regulating nitrogen fixation (nifH) and nitrification (amoA). Giant reed above-ground growth on the polluted soils was slightly lower (-16%) than on a non-polluted soil, with a preferential storage of biomass in the rhizome acting as a survival strategy in limiting growing conditions. Humic acids improved plant stress tolerance and production levels. As aerial biomass (shoots) did not accumulate PTEs, the plant in question can be used for bioenergy or biopolymer production. In contrast, below-ground biomass (rhizomes) accumulated PTEs, and can thus be harvested and removed from soil to improve phytoremediation protocols and also used as industrial biofuel. Giant reed growth increased the abundance of N-cycling bacteria and soil C in the rhizospheric soil, as well as reduced soil Pb and Zn EDTA extractable fraction.

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

Secondary plant metabolites (SPMEs) play an important role in plant survival in the environment and serve to establish ecological relationships between plants and other organisms. Communication between plants and microorganisms via SPMEs contained in root exudates or derived from litter decomposition is an example of this phenomenon. In this review, the general aspects of rhizodeposition together with the significance of terpenes and phenolic compounds are discussed in detail. We focus specifically on the effect of SPMEs on microbial community structure and metabolic activity in environments contaminated by polychlorinated biphenyls (PCBs) and polyaromatic hydrocarbons (PAHs). Furthermore, a section is devoted to a complex effect of plants and/or their metabolites contained in litter on bioremediation of contaminated sites. New insights are introduced from a study evaluating the effects of SPMEs derived during decomposition of grapefruit peel, lemon peel, and pears on bacterial communities and their ability to degrade PCBs in a long-term contaminated soil. The presented review supports the "secondary compound hypothesis" and demonstrates the potential of SPMEs for increasing the effectiveness of bioremediation processes.

Biochar and biosolids increase tree growth and improve soil quality for urban landscapes

Urban soil quality is often degraded and a challenging substrate for trees. This study was conducted to assess the impacts of biochar (BC), biosolids (BS), wood chips (WC), compost (COM), aerated compost tea (ACT), and a nitrogen plus potassium fertilizer (NK) for improving three typical urban soils and tree sapling growth. Across the three soil types, the most significant changes in soil properties were observed with BS and BC. Biosolids decreased soil pH and increased available N, N mineralization, and microbial respiration. Biochar increased total organic C. Increases in microbial respiration were also observed with NK, COM, and WC in only the sand soil. Leachate concentrations of dissolved organic C were greater with BS and COM, but nitrate in leachates did not differ among the treatments. The greatest and most significant increases in and growth were found with BS and BC. Tree growth was modeled from plant-available N and microbial respiration. The N content in the treatments appeared to be a strong determinant of tree growth for all treatments except BC. Nitrogen fertilizer, COM, and WC are the most common urban soil amendments and mulches in use today. This study provides evidence that BS and BC are acceptable, and possibly preferred, alternatives for improving urban soil quality and tree growth.

Role of organic amendments on enhanced bioremediation of heavy metal(loid) contaminated soils

As land application becomes one of the important waste utilization and disposal practices, soil is increasingly being seen as a major source of metal(loid)s reaching food chain, mainly through plant uptake and animal transfer. With greater public awareness of the implications of contaminated soils on human and animal health there has been increasing interest in developing technologies to remediate contaminated sites. Bioremediation is a natural process which relies on soil microorganisms and higher plants to alter metal(loid) bioavailability and can be enhanced by addition of organic amendments to soils. Large quantities of organic amendments, such as manure compost, biosolid and municipal solid wastes are used as a source of nutrients and also as a conditioner to improve the physical properties and fertility of soils. These organic amendments that are low in metal(loid)s can be used as a sink for reducing the bioavailability of metal(loid)s in contaminated soils and sediments through their effect on the adsorption, complexation, reduction and volatilization of metal(loid)s. This review examines the mechanisms for the enhanced bioremediation of metal(loid)s by organic amendments and discusses the practical implications in relation to sequestration and bioavailability of metal(loid)s in soils.

Chemical composition and bioactivity properties of size-fractions separated from a vermicompost humic acid

Preparative high performance size-exclusion chromatography (HPSEC) was applied to humic acids (HA) extracted from vermicompost in order to separate humic matter of different molecular dimension and evaluate the relationship between chemical properties of size-fractions (SF) and their effects on plant root growth. Molecular dimensions of components in humic SF was further achieved by diffusion-ordered nuclear magnetic resonance spectroscopy (DOSY-NMR) based on diffusion coefficients (D), while carbon distribution was evaluated by solid state (CP/MAS) (13)C NMR. Seedlings of maize and Arabidopsis were treated with different concentrations of SF to evaluate root growth. Six different SF were obtained and their carbohydrate-like content and alkyl chain length decreased with decreasing molecular size. Progressive reduction of aromatic carbon was also observed with decreasing molecular size of separated fractions. Diffusion-ordered spectroscopy (DOSY) spectra showed that SF were composed of complex mixtures of aliphatic, aromatic and carbohydrates constituents that could be separated on the basis of their diffusion. All SF promoted root growth in Arabidopsis and maize seedlings but the effects differed according to molecular size and plant species. In Arabidopsis seedlings, the bulk HA and its SF revealed a classical large auxin-like exogenous response, i.e.: shortened the principal root axis and induced lateral roots, while the effects in maize corresponded to low auxin-like levels, as suggested by enhanced principal axis length and induction of lateral roots. The reduction of humic heterogeneity obtained in HPSEC separated size-fractions suggested that their physiological influence on root growth and architecture was less an effect of their size than their content of specific bioactive molecules. However, these molecules may be dynamically released from humic superstructures and exert their bioactivity when weaker is the humic conformational stability as that obtained in the separated size-fractions.

Effects of a humic acid and its size-fractions on the bacterial community of soil rhizosphere under maize (Zea mays L.)

The effects of a humic acid (HA) and its size-fractions on plants carbon deposition and the structure of microbial communities in the rhizosphere soil of maize (Zea mays L.) plants were studied. Experiments were conducted in rhizobox systems that separate an upper soil-plant compartment from a lower compartment, where roots are excluded from the rhizosphere soil by a nylon membrane. The upper rhizobox compartment received the humic additions, whereas, after roots development, the rhizosphere soil in the lower compartment was sampled and sliced into thin layers. The lux-marked biosensor Pseudomonas fluorescens 10586 pUCD607 biosensor showed a significant increase in the deposition of bioavailable sources of carbon in the rhizosphere of soils when treated with bulk HA, but no response was found for treatments with the separated size-fractions. PCR-DGGE molecular fingerprintings revealed that the structure of rhizosphere microbial communities was changed by all humic treatments and that the smaller and more bioavailable size-fractions were more easily degraded by microbial activity than the bulk HA. On the other hand, highly hydrophobic and strongly associated humic molecules in the bulk HA required additional plant rhizodeposition before their bio-transformation could occur. This work highlights the importance of applying advanced biological and biotechnological methods to notice changes occurring in plant rhizodeposition and rhizosphere microbial activity. Moreover, it suggests correlations between the molecular properties of humic matter and their effects on microbial communities in the rhizosphere as mediated by root exudation.