Root exudates mediated interactions belowground

Root exudates: from plant to rhizosphere and beyond

This article describes the composition of root exudates, how these metabolites are released to the rhizosphere and their importance in the recruitment of beneficial microbiota that alleviate plant stress. Metabolites secreted to the rhizosphere by roots are involved in several processes. By modulating the composition of the root exudates, plants can modify soil properties to adapt and ensure their survival under adverse conditions. They use several strategies such as (1) changing soil pH to solubilize nutrients into assimilable forms, (2) chelating toxic compounds, (3) attracting beneficial microbiota, or (4) releasing toxic substances for pathogens, etc. In this work, the composition of root exudates as well as the different mechanisms of root exudation have been reviewed. Existing methodologies to collect root exudates, indicating their advantages and disadvantages, are also described. Factors affecting root exudation have been exposed, including physical, chemical, and biological agents which can produce qualitative and quantitative changes in exudate composition. Finally, since root exudates play an important role in the recruitment of mycorrhizal fungi and plant growth-promoting rhizobacteria (PGPR), the mechanisms of interaction between plants and the beneficial microbiota have been highlighted.

Induced root-secreted D-galactose functions as a chemoattractant and enhances the biofilm formation of Bacillus velezensis SQR9 in an McpA-dependent manner

Chemotaxis towards root exudates and subsequent biofilm formation are very important for root colonization and for providing the beneficial functions of plant growth-promoting rhizobacteria (PGPRs). In this study, in comparison with other root-secreted compounds, D-galactose in the root exudates of cucumber was found to be a strong chemoattractant at the concentration of 1 μM for Bacillus velezensis SQR9. Chemotaxis assays with methyl-accepting chemotaxis proteins (MCPs) deletion strains demonstrated that McpA was solely responsible for chemotaxis towards D-galactose. Interestingly, D-galactose significantly enhanced the biofilm formation of SQR9 in an McpA-dependent manner. Further experiment showed that D-galactose also enhanced root colonization by SQR9. In addition, the secretion of D-galactose by cucumber roots could be induced by inoculation with SQR9, indicating that D-galactose may be an important signal in the interaction between plant and SQR9. These findings suggested that the root-secreted D-galactose was a signal, the secretion of which was induced by the beneficial bacteria, and which in turn induced colonization of the bacteria.

Oxalic Acid From Sesbania rostrata Seed Exudates Mediates the Chemotactic Response of Azorhizobium caulinodans ORS571 Using Multiple Strategies

Chemotaxis toward seed exudates is important in the establishment of microbe-plant associations. The objective of this work was to explore whether organic acids from the seed exudates of Sesbania rostrata play a role in recruiting Azorhizobium caulinodans ORS571 in the plant rhizosphere. High-performance liquid chromatography (HPLC) was used to analyze the organic acid content in seed exudates of S. rostrata and to further determine their roles in A. caulinodans growth and chemotactic response. Succinic, acetic, citric, oxalic, and lactic acids were the most abundant, and, except for oxalic acid, they could support A. caulinodans growth as the sole carbon source. TlpA1, a transmembrane chemoreceptor, was found to be involved in the chemotactic response to these organic acids. Oxalic acid played a direct role in the chemotactic response, but it also played an indirect role by promoting or inhibiting the chemotactic response toward other chemoeffectors. Furthermore, the indirect role of oxalic acid on other chemoeffectors was concentration-dependent. The effect of oxalic acid at different concentrations on host root colonization was also determined. By using different strategies, oxalic acid appears to play a major role in the early steps of the association of A. caulinodans and its host plant.

Phenotypic Heterogeneity of the Insect Pathogen Photorhabdus luminescens: Insights into the Fate of Secondary Cells

Photorhabdus luminescens is a Gram-negative bacterium that lives in symbiosis with soil nematodes and is simultaneously highly pathogenic toward insects. The bacteria exist in two phenotypically different forms, designated primary (1°) and secondary (2°) cells. Yet unknown environmental stimuli as well as global stress conditions induce phenotypic switching of up to 50% of 1° cells to 2° cells. An important difference between the two phenotypic forms is that 2° cells are unable to live in symbiosis with nematodes and are therefore believed to remain in the soil after a successful infection cycle. In this work, we performed a transcriptomic analysis to highlight and better understand the role of 2° cells and their putative ability to adapt to living in soil. We could confirm that the major phenotypic differences between the two cell forms are mediated at the transcriptional level as the corresponding genes were downregulated in 2° cells. Furthermore, 2° cells seem to be adapted to another environment as we found several differentially expressed genes involved in the cells' metabolism, motility, and chemotaxis as well as stress resistance, which are either up- or downregulated in 2° cells. As 2° cells, in contrast to 1° cells, chemotactically responded to different attractants, including plant root exudates, there is evidence for the rhizosphere being an alternative environment for the 2° cells. Since P. luminescens is biotechnologically used as a bio-insecticide, investigation of a putative interaction of 2° cells with plants is also of great interest for agriculture.IMPORTANCE The biological function and the fate of P. luminescens 2° cells were unclear. Here, we performed comparative transcriptomics of P. luminescens 1° and 2° cultures and found several genes, not only those coding for known phenotypic differences of the two cell forms, that are up- or downregulated in 2° cells compared to levels in 1° cells. Our results suggest that when 1° cells convert to 2° cells, they drastically change their way of life. Thus, 2° cells could easily adapt to an alternative environment such as the rhizosphere and live freely, independent of a host, putatively utilizing plant-derived compounds as nutrient sources. Since 2° cells are not able to reassociate with the nematodes, an alternative lifestyle in the rhizosphere would be conceivable.

Combined effects of rhizo-competitive rhizosphere and non-rhizosphere Bacillus in plant growth promotion and yield improvement of Eleusine coracana (Ragi)

This study emphasizes the beneficial role of rhizo-competitive Bacillus spp. isolated from rhizospheric and non-rhizospheric soil in plant growth promotion and yield improvement via nitrogen fixation and biocontrol of Sclerotium rolfsii causing foot rot disease in Eleusine coracana (Ragi). The selection of potent rhizobacteria was based on plant-growth-promoting attributes using Venn set diagram and Bonitur scale. Bacillus pumilus MSTA8 and Bacillus amyloliquefaciens MSTD26 were selected because they were effective in root colonization, rhizosphere competence, and biofilm formation using root exudates of E. coracana L. rich with carbohydrates, proteins, and amino acids. The relative chemotaxis index of the isolates expressed the invasive behavior of the rhizosphere. During pot and field trials, the consortium of the rhizobacteria in a vermiculite carrier increased the grain yield by 37.87%, with a significant harvest index of 16.45. Soil analysis after the field trial revealed soil reclamation potentials to manage soil nutrition and fertility. Both indexes ensured crop protection and production in eco-safe ways and herald commercialization of Bacillus bio-inoculant for improvement in crop production and disease management of E. coracana.

Autotoxicity Hinders the Natural Regeneration of Cinnamomum migao H. W. Li in Southwest China

Autotoxicity is a widespread phenomenon in nature and is considered to be the main factor affecting new natural recruitment of plant populations, which was proven in many natural populations. Cinnamomum migao H. W. Li is an endemic medicinal woody plant species mainly distributed in Southwestern China and is defined as an endangered species by the Red Paper of Endangered Plants in China. The lack of seedlings is considered a key reason for population degeneration; however, no studies were conducted to explain its causes. C. migao contains substances with high allelopathic potential, such as terpenoids, phenolics, and flavonoids, and has strong allelopathic effects on other species. Therefore, we speculate that one of the reasons for C. migao seedling scarcity in the wild is that it exhibits autotoxic allelopathy. In this study, which was performed from the perspective of autotoxicity, we collected leaves, pericarp, seeds, and branches of the same population; we simulated the effects of decomposition and release of litter from these different anatomical parts of C. migao in the field; and we conducted 210-day control experiments on seedling growth, with different concentration gradients, using associated aqueous extracts. The results showed that the leaf aqueous extract (leafAE) significantly inhibited growth indicators and increased damage of the lipid structure of the cell membrane of seedlings, suggesting that autotoxicity from C. migao is a factor restraining seedling growth. The results of the analyses of soil properties showed that, compared with the other treatments, leafAE treatment inhibited soil enzyme activity and also had an impact on soil fungi. Although leafAE could promote soil fertility to some extent, it did not change the effect of autotoxic substances on seedling growth. We conclude that autotoxicity is the main obstacle inhibiting seedling growth and the factor restraining the natural regeneration of C. migao.

Effect of aridity and dune type on rhizosphere soil bacterial communities of Caragana microphylla in desert regions of northern China

Understanding the response of soil properties and bacterial communities in rhizosphere soil to aridity and dune types is fundamental to desertification control. This study investigated soil properties and bacterial communities of both rhizosphere and bulk soils of Caragana microphylla from four sites with different aridity indices, and one site with three different types of dunes. All sites were located in the desert regions of northern China. The results indicated that compared with the bulk soil, the soil nutrient content of rhizosphere, especially the content of total phosphorus, was generally significantly improved in different desertification environments. The bacterial richness and diversity were also higher than those of bulk soil, especially in arid regions and fixed dunes. Firmicutes, Actinobacteria, Proteobacteria, and Acidobacteria were the most dominant phyla in all samples. The regression analyses showed that at different sites, soil total organic C, total N, Na⁺, and total P played key roles in determining the bacterial community structure while total organic carbon, electronic conductivity, pH and total phosphorus were the dominant factors at the different dunes. The results further revealed that the dominant phyla strongly affected by environmental factors at different sites were Acidobacteria, Gemmatimonadetes, and Actinobacteria among which, Acidobacteria and Gemmatimonadetes were negatively correlated with Na⁺ content. At different types of dunes, Actinobacteria, Planctomycetes, and Gemmatimonadetes were particularly affected by environmental factors. The increased abundance of Actinobacteria in the rhizosphere soil was mainly caused by the decreased soil pH.

Characterization and variation of the rhizosphere fungal community structure of cultivated tetraploid cotton

Rhizosphere fungal communities exert important influencing forces on plant growth and health. However, information on the dynamics of the rhizosphere fungal community structure of the worldwide economic crop cotton (Gossypium spp.) is limited. In the present study, next-generation sequencing of nuclear ribosomal internal transcribed spacer-1 (ITS1) was performed to characterize the rhizosphere fungal communities of G. hirsutum cv. TM-1 (upland cotton) and G. barbadense cv. Hai 7124 (island cotton). The plants were grown in field soil (FS) that had been continuously cropped with cotton and nutrient-rich soil (NS) that had not been cropped. The fungal species richness, diversity, and community composition were analyzed and compared among the soil resources, cotton genotypes, and developmental stages. We found that the fungal community structures were different between the rhizosphere and bulk soil and the difference were significantly varied between FS and NS. Our results suggested that cotton rhizosphere fungal community structure variation may have been primarily influenced by the interaction of cotton roots with different soil resources. We also found that the community composition of the cotton rhizosphere fungi varied significantly during different developmental stages. In addition, we observed fungi that was enriched or depleted at certain developmental stages and genotypes in FS and NS, and these insights can lay a foundation for deep research into the dynamics of pathogenic fungi and nutrient absorption of cotton roots. This research illustrates the characteristics of the cotton rhizosphere fungal communities and provides important information for understanding the potential influences of rhizosphere fungal communities on cotton growth and health.

Constructed wetland for wastewater reuse: Role and efficiency in removing enteric pathogens

Water stress has become a perennial concern in most of the developing countries due to rapid urbanization and population growth. As the growing population requires more fresh water and better ways for wastewater disposal, the demand for wastewater reclamation has increased drastically in recent years. Wastewater, either raw or treated, is being widely used for agricultural irrigation in developing countries, which cause a serious threat to human health mainly because of its pathogenic content. One of the alternative methods to treat wastewater and make it reusable for agricultural irrigation is to implement constructed wetland (CW); a sustainable and cost-effective technology that is applicable for the elimination of both pollutants and pathogens from wastewater. Despite its wide application, the role of macrophytes that form an integral part of CW and specific mechanisms involved in pathogen removal by them is still barely understood due to complexities involved and influencing factors. This has, therefore, attracted various scientific studies to reveal further functional mechanisms involved in vegetated CW to increase its proficiencies. This review paper illustrates the comparative studies of different CW and their pathogen removal efficiencies with major emphasis on macrophytes involved and factors influencing related mechanism. Further, the paper also covers detailed information on the enteric pathogens present in wastewater and the associated health risks involved in its reuse. The ultimate objective is to further clarify the role of CW in enteric pathogen removal and its efficiency for wastewater purification in perspective with safe reuse in agriculture.

Restrictive water condition modifies the root exudates composition during peanut-PGPR interaction and conditions early events, reversing the negative effects on plant growth

Water deficit is one of the most serious environmental factors that affect the productivity of crops in the world. Arachis hypogaea is a legume with a high nutritional value and 70% is cultivated in semi-arid regions. This research aimed to study the effect of water deficit on peanut root exudates composition, analyzing the importance of exudates on peanut-PGPR interaction under restrictive water condition. Peanut seedlings were subjected to six treatments: 0 and 15 mM PEG, in combination with non-inoculated, Bradyrhizobium sp. and Bradyrhizobium-Azospirillum brasilense inoculated treatments. We analyzed the 7-day peanut root exudate in response to a water restrictive condition and the presence of bacterial inocula. Molecular analysis was performed by HPLC, UPLC and GC. Bacteria motility, chemotaxis, bacterial adhesion to peanut roots and peanut growth parameters were analyzed. Restrictive water condition modified the pattern of molecules exuded by roots, increasing the exudation of Naringenin, oleic FA, citric and lactic acid, and stimulation the release of terpenes of known antioxidant and antimicrobial activity. The presence of microorganisms modified the composition of root exudates. Water deficit affected the first events of peanut-PGPR interaction and the root exudates favored bacterial mobility, the chemotaxis and attachment of bacteria to peanut roots. Changes in the profile of molecules exuded by roots allowed A. hypogaea-Bradyrhizobium and A.hypogaea-Bradyrhizobium-Azospirillum interaction thus reversing the negative effects of restrictive water condition on peanut growth. These findings have a future potential application to improve plant-PGPR interactions under water deficit by formulating inoculants containing key molecules exuded during stress.

Allelochemicals and Signaling Chemicals in Plants

Plants abound with active ingredients. Among these natural constituents, allelochemicals and signaling chemicals that are released into the environments play important roles in regulating the interactions between plants and other organisms. Allelochemicals participate in the defense of plants against microbial attack, herbivore predation, and/or competition with other plants, most notably in allelopathy, which affects the establishment of competing plants. Allelochemicals could be leads for new pesticide discovery efforts. Signaling chemicals are involved in plant neighbor detection or pest identification, and they induce the production and release of plant defensive metabolites. Through the signaling chemicals, plants can either detect or identify competitors, herbivores, or pathogens, and respond by increasing defensive metabolites levels, providing an advantage for their own growth. The plant-organism interactions that are mediated by allelochemicals and signaling chemicals take place both aboveground and belowground. In the case of aboveground interactions, mediated air-borne chemicals are well established. Belowground interactions, particularly in the context of soil-borne chemicals driving signaling interactions, are largely unknown, due to the complexity of plant-soil interactions. The lack of effective and reliable methods of identification and clarification their mode of actions is one of the greatest challenges with soil-borne allelochemicals and signaling chemicals. Recent developments in methodological strategies aim at the quality, quantity, and spatiotemporal dynamics of soil-borne chemicals. This review outlines recent research regarding plant-derived allelochemicals and signaling chemicals, as well as their roles in agricultural pest management. The effort represents a mechanistically exhaustive view of plant-organism interactions that are mediated by allelochemicals and signaling chemicals and provides more realistic insights into potential implications and applications in sustainable agriculture.

Tomato plants rather than fertilizers drive microbial community structure in horticultural growing media

Synthetic fertilizer production is associated with a high environmental footprint, as compounds typically dissolve rapidly leaching emissions to the atmosphere or surface waters. We tested two recovered nutrients with slower release patterns, as promising alternatives for synthetic fertilizers: struvite and a commercially available organic fertilizer. Using these fertilizers as nitrogen source, we conducted a rhizotron experiment to test their effect on plant performance and nutrient recovery in juvenile tomato plants. Plant performance was significantly improved when organic fertilizer was provided, promoting higher shoot biomass. Since the microbial community influences plant nitrogen availability, we characterized the root-associated microbial community structure and functionality. Analyses revealed distinct root microbial community structure when different fertilizers were supplied. However, plant presence significantly increased the similarity of the microbial community over time, regardless of fertilization. Additionally, the presence of the plant significantly reduced the potential ammonia oxidation rates, implying a possible role of the rhizosheath microbiome or nitrification inhibition by the plant. Our results indicate that nitrifying community members are impacted by the type of fertilizer used, while tomato plants influenced the potential ammonia-oxidizing activity of nitrogen-related rhizospheric microbial communities. These novel insights on interactions between recovered fertilizers, plant and associated microbes can contribute to develop sustainable crop production systems.

Bacterial and fungal communities in boreal forest soil are insensitive to changes in snow cover conditions

The northern regions are experiencing considerable changes in winter climate leading to more frequent warm periods, rain-on-snow events and reduced snow pack diminishing the insulation properties of snow cover and increasing soil frost and freeze-thaw cycles. In this study, we investigated how the lack of snow cover, formation of ice encasement and snow compaction affect the size, structure and activities of soil bacterial and fungal communities. Contrary to our hypotheses, snow manipulation treatments over one winter had limited influence on microbial community structure, bacterial or fungal copy numbers or enzyme activities. However, microbial community structure and activities shifted seasonally among soils sampled before snow melt, in early and late growing season and seemed driven by substrate availability. Bacterial and fungal communities were dominated by stress-resistant taxa such as the orders Acidobacteriales, Chaetothyriales and Helotiales that are likely adapted to adverse winter conditions. This study indicated that microbial communities in acidic northern boreal forest soil may be insensitive to direct effects of changing snow cover. However, in long term, the detrimental effects of increased ice and frost to plant roots may alter plant derived carbon and nutrient pools to the soil likely leading to stronger microbial responses.

A Holistic View of Soils in Delivering Ecosystem Services in Forests: A Case Study in South Korea

In 1955, after the Korean War, only 35% of the national land area in South Korea was covered by forests. In the 1960s, the Korean Government implemented the national forestation program in order to increase the extent of the forest surface and thereby counteract the negative ecological consequences from deforestation, such as erosion and ground instability. According to previous studies, this led to an increase in carbon (C) accumulated in the forest biomass of 1.48 Gt CO2 (0.40 Gt C) in the period 1954–2012. However, these studies did not take into account the amount of soil organic carbon (SOC) that was accumulated during that period and the influence of management practices on soil ecosystem services. Currently, South Korean authorities are considering the idea of implementing some forest management practices in order to increase timber extraction (e.g., by reducing the cutting age of the trees or by applying thinning and tending measures). In this study, we assess the influence of these management regimes on SOC dynamics and propose a theoretical framework to assess the influence of forest management practices on three ecosystem services, namely, C sequestration, water supply, and biomass production, while considering soil functioning, and especially SOC, as a group of supporting services underpinning the three named ecosystem services. We find that, in terms of SOC sequestration, reducing the cutting age from 80 to 40 years would be suitable only in the case of high biomass production forests, whereas in the case of lower biomass production forests reducing the cutting age would achieve very low SOC levels. However, we propose that increasing tree species diversity, even though it would not lead to a direct increase in the SOC content, could help to lessen the negative effects of reducing the cutting age by improving other soil properties, which in turn positively affect soil functioning (e.g., soil biodiversity, nutrient availability) and the resilience of the forest ecosystem. Finally, we discuss potential policy approaches to incentivize sustainable management practices in South Korean forests from a soil protection perspective.

Efficient assembly and long-term stability of defensive microbiomes via private resources and community bistability

Understanding the mechanisms that promote the assembly and maintenance of host-beneficial microbiomes is an open problem. Empirical evidence supports the idea that animal and plant hosts can combine 'private resources' with the ecological phenomenon known as 'community bistability' to favour some microbial strains over others. We briefly review evidence showing that hosts can: (i) protect the growth of beneficial strains in an isolated habitat, (ii) use antibiotics to suppress non-beneficial, competitor strains, and (iii) provide resources that only beneficial strains are able to translate into an increased rate of growth, reproduction, or antibiotic production. We then demonstrate in a spatially explicit, individual-based model that these three mechanisms act similarly by selectively promoting the initial proliferation of preferred strains, that is, by acting as a private resource. The faster early growth of preferred strains, combined with the phenomenon of 'community bistability,' allows those strains to continue to dominate the microbiome even after the private resource is withdrawn or made public. This is because after a beneficial colony reaches a sufficiently large size, it can resist invasion by parasites without further private support from the host. We further explicitly model localized microbial interactions and diffusion dynamics, and we show that an intermediate level of antibiotic diffusion is the most efficient mechanism in promoting preferred strains and that there is a wide range of parameters under which hosts can promote the assembly of a self-sustaining defensive microbiome. This in turn supports the idea that hosts readily evolve to promote host-beneficial defensive microbiomes.

Effect of plants and their root exudate on bacterial activities during rhizobacterium-plant remediation of phenol from water

We investigated remediation of phenol from water using microbe-plant partnerships. Co-introduction of maize seedlings, Pseudomonas fluorescens rifampicin-resistant P13 and P. stutzeri P7 carrying self-transmissible TOL-like plasmids reduced phenol content in water at lower phenol concentrations (25, 50, and 75 mg/L), similar to individual introduction of the bacteria. Co-introduction of plants and bacteria significantly reduced phenol content in water at higher phenol concentrations (100, 125, and 150 mg/L) compared to using individual introduction of the bacteria. Moreover, TOL-like plasmids were transferred from P7 to P13. Addition of plants promoted the growth of both strains, leading to increased plasmid transfer. At higher phenol concentrations, addition of plants resulted in increases of catechol 2, 3-dioxygenase (C23O) activity and reduction in level of reactive oxygen species (ROS) of bacteria in the degradation experiments. Increased plasmid transfer and C23O activity and reduction in ROS level might be the major reasons why plants promote bacterial degradation of phenol at higher phenol concentrations. Furthermore, root exudate of maize seedlings and artificial root exudate (ARE) constructed using major components of the root exudate had the same effects on bacterial activities. Unlike the ARE, deletion of glucose, arabinose, or fructose or all the monosaccharides from ARE resulted in no increase in numbers of both strains and in plasmid transfer. At the higher phenol concentrations, deletion of glutamic acid, aspartic acid, alanine, or glycine or all the amino acids did not stimulate bacterial C23O activity. Deletion of fumaric, oxaloacetic or citric acids still reduced bacterial ROS level as ARE did, but, deletion of all the organic acids or DIMBOA, a hydroxamic acid, did not reduce bacterial ROS level as ARE did. The data showed that each monosaccharide might be important for sufficient numbers of plant-associated bacteria and increased plasmid transfer while each amino acid might be important for maintaining bacterial C23O activity and that DIMBOA might be responsible for the decrease in ROS levels. These results are the basis for efficient remediation of phenol from water by microbe-plant partnerships and further studies on the mechanism of rhizobacterium-plant interaction.

Nanoparticle Size and Coating Chemistry Control Foliar Uptake Pathways, Translocation, and Leaf-to-Rhizosphere Transport in Wheat

Nanoenabled foliar-applied agrochemicals can potentially be safer and more efficient than conventional products. However, limited understanding about how nanoparticle properties influence their interactions with plant leaves, uptake, translocation through the mesophyll to the vasculature, and transport to the rest of the plant prevents rational design. This study used a combination of Au quantification and spatial analysis to investigate how size (3, 10, or 50 nm) and coating chemistry (PVP versus citrate) of gold nanoparticles (AuNPs) influence these processes. Following wheat foliar exposure to AuNPs suspensions (∼280 ng per plant), adhesion on the leaf surface was increased for smaller sizes, and PVP-AuNPs compared to citrate-AuNPs. After 2 weeks, there was incomplete uptake of citrate-AuNPs with some AuNPs remaining on the outside of the cuticle layer. However, the fraction of citrate-AuNPs that had entered the leaf was translocated efficiently to the plant vasculature. In contrast, for similar sizes, virtually all of the PVP-AuNPs crossed the cuticle layer after 2 weeks, but its transport through the mesophyll cells was lower. As a consequence of PVP-AuNP accumulation in the leaf mesophyll, wheat photosynthesis was impaired. Regardless of their coating and sizes, the majority of the transported AuNPs accumulated in younger shoots (10-30%) and in roots (10-25%), and 5-15% of the NPs <50 nm were exuded into the rhizosphere soil. A greater fraction of larger sizes AuNPs (presenting lower ζ potentials) was transported to the roots. The key hypotheses about the NPs physical-chemical and plant physiology parameters that may matter to predict leaf-to-rhizosphere transport are also discussed.

Plant evenness modulates the effect of plant richness on soil bacterial diversity

Understanding the relationships between aboveground and belowground biodiversity will help to expand our knowledge on how ecological communities and processes are interactively determined, and thus provide new perspectives for the conservation of biodiversity. Despite the theoretical analyses generally predicting a positive relationship between plant richness and soil microbial diversity, the results from empirical studies have been mixed, probably due to the effect of plant evenness. To investigate this relationship, we conducted field experiments in two geographically distinct sites (Linhai and Shenmu, >1400km apart), by simultaneously manipulating plant richness (2, 4, and 8 species) and evenness (homogeneous versus non-homogeneous). After one year, the bacterial response to plant richness with different plant evenness levels was evaluated using terminal restriction fragment length polymorphism (T-RFLP) analysis. Our results showed that plant evenness modulated plant richness effects on bacterial community, as reflected by the more pronounced positive correlations between bacterial richness and plant richness in homogeneous plant community than in the non-homogeneous treatment. Additionally, plant community structure significantly affected bacterial communities only in the homogeneous treatment in Shenmu, but not in the non-homogeneous treatments. Our results demonstrate that plant evenness could regulate plant richness effects on bacterial alpha- and beta-diversity and thus provide valuable insights into the association between aboveground and belowground biodiversity.

Identification of Populus Small RNAs Responsive to Mutualistic Interactions With Mycorrhizal Fungi, Laccaria bicolor and Rhizophagus irregularis

Ecto- and endo-mycorrhizal colonization of Populus roots have a positive impact on the overall tree health and growth. A complete molecular understanding of these interactions will have important implications for increasing agricultural or forestry sustainability using plant:microbe-based strategies. These beneficial associations entail extensive morphological changes orchestrated by the genetic reprogramming in both organisms. In this study, we performed a comparative analysis of two Populus species (Populus deltoides and P. trichocarpa) that were colonized by either an arbuscular mycorrhizal fungus (AmF), Rhizophagus irregularis or an ectomycorrhizal fungus (EmF), Laccaria bicolor, to describe the small RNA (sRNA) landscape including small open reading frames (sORFs) and micro RNAs (miRNAs) involved in these mutualistic interactions. We identified differential expression of sRNAs that were, to a large extent, (1) within the genomic regions lacking annotated genes in the Populus genome and (2) distinct for each fungal interaction. These sRNAs may be a source of novel sORFs within a genome, and in this regard, we identified potential sORFs encoded by the sRNAs. We predicted a higher number of differentially-expressed miRNAs in P. trichocarpa (4 times more) than in P. deltoides (conserved and novel). In addition, 44 miRNAs were common in P. trichocarpa between the EmF and AmF treatments, and only 4 miRNAs were common in P. deltoides between the treatments. Root colonization by either fungus was more effective in P. trichocarpa than in P. deltoides, thus the relatively few differentially-expressed miRNAs predicted in P. deltoides might reflect the extent of the symbiosis. Finally, we predicted several genes targets for the plant miRNAs identified here, including potential fungal gene targets. Our findings shed light on additional molecular tiers with a role in Populus-fungal mutualistic associations and provides a set of potential molecular targets for future enhancement.

Impacting Microbial Communities and Absorbing Pollutants by Canna Indica and Cyperus Alternifolius in a Full-Scale Constructed Wetland System

Wetland plants that cover the wetlands play an important role in reducing pollutants. The aim of this study was to investigate the effect of two plant species on microbial communities and nitrogen-removal genes and to evaluate the contributions of absorbing pollutants by Canna indica (CI) and Cyperus alternifolius (CA) to the removal performance in both a vertical subsurface flow constructed wetland and a horizontal subsurface flow constructed wetland, which were part of a full-scale hybrid constructed wetland system. The microbial assemblages were determined using 16S rRNA high-throughput sequencing. Results showed that the presence of CI and CA positively affected microbial abundance and community in general and which was positive for the total bacteria and ammonia nitrogen removal in the CWs. The higher abundance of Nitrospirae appeared in the non-rhizosphere sediment (NRS) than that in the rhizosphere sediment (RS). More denitrification genes were found in NRS than in RS. The copy numbers of narG, nirS and nosZ genes for CA were higher than those for CI. Wetland plant species can significantly (P < 0.05) affect the distribution of microbial communities in RS. Plant selection is important to promote the development of microbial communities with a more active and diverse catabolic capability and the contribution of plant absorption to the overall removal rate of wetland system can be neglected.

Insight into effects of citric acid on adsorption of phthalic acid esters (PAEs) in mangrove sediments

The adsorption of phthalate esters (PAEs) in mangrove sediment greatly influences their availability to aquatic organisms, however, the adsorption processes of PAEs in mangrove sediment, as well as the effects of root exudates, are poorly understood. In this study, dimethyl phthalate (DMP), diethyl phthalate (DEP) and dibutyl phthalate (DBP) was used as model PAEs to determine the effects and mechanism of citric acid on the adsorption kinetics and isotherms of PAEs in the mangrove sediments. The adsorption kinetics followed pseudo-second order model, describing the characteristics of heterogeneous chemisorption of PAEs in mangrove sediments. The adsorption isotherms of DMP and DEP followed Freundlich model, implying the characteristics of surface multilayer heterogeneous adsorption; while the Henry model better described the adsorption isotherms of DBP, suggesting that hydrophobic partition accounted for DBP adsorption in the mangrove sediments. Inter-chemical variability was observed in adsorption capacity (q_e) with the sequence of DBP > DEP > DMP. Surface polarity index ((C-O + COOH + C˭O)%) of particulate organic matter (POM) regulated the adsorption capacity of DMP and DEP in mangrove sediments, while different POM content among mangrove sediments explained the difference in the sorption strength for DBP. The presence of citric acid enhanced the q_e of the three PAEs by 6.4-12.6%. These findings are of great significance to reveal that the root exudates play a crucial role in the PAEs adsorption in mangrove sediments, and provide valuable information for availability of PAEs in mangrove ecosystem.

Utilization of Mentha aquatica L. for removal of fecal pathogens and heavy metals from water of Bosna river, Bosnia and Herzegovina

The aim of the present study was to investigate the potential of Mentha aquatica L. for phytoremediation of water contaminated with heavy metals and fecal pathogens from Bosna river. The water was treated with M. aquatica for 5, 10, and 15 days consecutively after which it was analyzed for the various physicochemical and microbiological parameters. The initial concentration of cadmium (Cd) ranged from 3.644 to 6.108 µg/l, while lead (Pb) varied between 0.1 and 1.386 µg/l. After treatment, M. aquatica accumulated significant amounts of cadmium (Cd) and lead (Pb) with the highest removal rates of 96.49% for Cd and 45.72% for Pb. Values of several physicochemical parameters were decreased after 15 days treatment period. All water samples were analyzed for enumeration of aerobic heterotrophic bacteria, total coliforms, and fecal coliforms by the membrane filtration. Removal efficiency was greater than 80% for microbiological parameters. The concentration of heavy metals was determined in different plant parts and subsequently, the translocation factor was determined. In M. aquatica plant parts, concentrations of Pb and Cd were increased after 15 days of treatment. Our results demonstrated that M. aquatica could be good candidates for the removal of fecal pathogens and heavy metals present in surface water.

A review on removal of organophosphorus pesticides in constructed wetland: Performance, mechanism and influencing factors

The residues of organophosphorus pesticides (OPPs) have been widely detected in rivers, the gulf, and even groundwater and drinking water, which may pose a serious threat to aquatic ecosystems and human health. Compared to other treatments, constructed wetlands (CWs) have been demonstrated to be a cost-effective alternative risk mitigation strategy for non-point-source pesticide pollution. This review summarizes 32 studies related to the remediation of OPPs in 117 CWs during 2001-2017 worldwide. The performances, mechanisms and influencing factors in the studies are comprehensively and critically reviewed in this paper. Overall, the OPPs were efficiently removed with an efficiency up to 87.22 ± 16.61%. The removal efficiency, differences and related reasons among different types of CWs in developed and developing countries and the different types of OPPs in CWs are well-evaluated in detail. In addition, the main processes for OPPs removal in CWs involve phytoremediation (plant uptake, phytoaccumulation, phytovolatilization and phytodegradation), substrate adsorption or sedimentation, and biodegradation. Based on the quantitative analysis by mass balance, for water-soluble pesticides, the dominant removal process was via microbiological degradation. This result was in contrast to findings obtained with hydrophobic OPPs, for which the dominant processes were biodegradation and sorption by substrate. Therefore, the behavior of microbial transformation prevails. Additionally, the presence of plants can facilitate the elimination of OPPs in CWs, promoting the process by an average percentage of approximately 6.19 ± 9.46%. Statistical analysis shows that loading of inlet OPPs is the largest limiting factor and that the HRT and T are the most significant parameters that influence the efficiency of trapping OPPs in CWs. Simultaneously, we can also obtain suitable parameters for the design and operation of CWs. This review promotes further research on plant-microbe joint combined remediation and examines the different behaviors of water-soluble and hydrophobic OPPs in CWs.

Response of denitrification in paddy soils with different nitrification rates to soil moisture and glucose addition

Denitrification is one of the most important N loss pathways in paddy soil. The nitrification rate is a key natural feature for controlling denitrification N loss in paddy soil. However, the relationship between nitrification and denitrification under different conditions in paddy soil remains unknown. By using ¹⁵N tracing, we investigated the response of denitrification loss to soil moisture and glucose addition in six paddy soils, whose net nitrification rates ranged from 0.36 mg N kg^-1 day^-1 to 5.72 mg N kg^-1 day^-1. The soils were amended with or without glucose to simulate root exudates at rates of 100 mg kg^-1 of soil and incubated under either 60% water holding capacity (WHC) or flooded (2 cm depth) at 25 °C for 15 days. Denitrification loss was calculated by the unrecovered ¹⁵NH₄⁺. The results showed that the soil nitrification rate significantly affected the N recovery form and denitrification loss of the applied ¹⁵N. NH₄⁺ was the main recovered N form of the applied ¹⁵N in soil with a low nitrification rates. Denitrification losses were higher in the high nitrification rate soil than soil with low nitrification rate in all treatments. The correlation between denitrification and nitrification rates was well fit by Michaelis-Menten kinetics during the incubation, irrespective of soil moisture and glucose addition, and the R² ranged from 0.801 to 0.977 (P < 0.05). Glucose addition did not stimulate denitrification under either 60% WHC or flooded conditions. The results showed that nitrification rate, rather than labile organic supply, controlled denitrification in paddy soil.

Distinct rhizosphere effect on active and total bacterial communities in paddy soils

Rhizosphere microbes are critical for plant health and biogeochemical cycles. Understanding the diversity of active microorganisms in the rhizosphere is key to enhancing plant growth and productivity. We examined rhizosphere bacterial communities of rice by comparison of the 16S ribosomal subunit amplicons generated from both the total (DNA-based, 16S rRNA gene) and the active (RNA-based, 16S rRNA) soil microbiota. Analysis based on the 16S rRNA gene showed a higher microbial diversity, but with little change in bacterial populations across the growth stages of the plant. Analysis of 16S rRNA recovered much less diversity, demonstrating that much of the 16S signal was derived from free DNA, dead or inactive cells. The rRNA analysis showed a stable microbial population present in the rhizosphere, and this was distinct from that in the bulk soil, which was also stable across the growth period. Root exudates (e.g., acetate, lactate, oxalate and succinate), which are major components contributing to the rhizosphere effect, appeared to shape the bacterial community, with some taxa (e.g., Oxobacter, Lachnospiraceae, Coprococcus and α-Proteobacteria) being enhanced in the rhizosphere. Soil compartments (rhizosphere vs. bulk) had a greater effect on the bacterial communities than did the plant phenological stages, especially at the rRNA level. These results suggest that the rhizosphere effect plays a key role in structuring the bacterial communities in rhizosphere soils with a distinct effect on active and total bacterial communities.

Diversity analysis of the rhizospheric and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range

Increasing evidence has confirmed the importance of plant-associated bacteria for plant growth and productivity, and thus it is hypothesized that interactions between bacteria and alien plants might play an important role in plant invasions. However, the diversity of the bacterial communities associated with invasive plants is poorly understood. We therefore investigated the diversity of rhizospheric and endophytic bacteria associated with the invasive annual plant Senecio vulgaris L. (Asteraceae) based on 16S rRNA gene data obtained from 57 samples of four Senecio vulgaris populations in a subtropical mountainous area in central China. Significant differences in diversity were observed between plant compartments. Specifically, the rhizosphere harbored many more bacterial operational taxonomic units and showed higher alpha diversity than the leaf and root endospheres. The relative abundance profiles of the bacterial community composition differed substantially between the compartments and populations, especially at the phylum and family levels. However, the top five phyla (Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Acidobacteria) accounted for more than 90% of all the bacterial communities. Moreover, similar endophytic communities with a shared core set of bacteria were observed from different Senecio vulgaris populations. Heavy-metal-resistant, phosphate-solubilizing bacteria (Brevundimonas diminuta), nitrogen-fixing bacteria (Rhizobium leguminosarum), and cold-resistant bacteria (Exiguobacterium sibiricum) were present in the endosphere at relatively high abundance. This study, which reveals the structure of bacterial communities and their putative function in invasive Senecio vulgaris plants, is the first step in investigating the role of plant-bacteria interactions in the invasion of this species in China.

Inoculation of Rhizoglomus irregulare or Trichoderma atroviride differentially modulates metabolite profiling of wheat root exudates

Root exudation patterns are linked to, among other things, plant growth, plant-microbe interaction and the priming effect. In this work, two complementary metabolomic approaches (both liquid and gas chromatography coupled to mass spectrometry) were applied to investigate the modulation of root exudation imposed by two beneficial fungi (substrate treatment of Trichoderma atroviride AT10, substrate application of Rhizoglomus irregulare BEG72 and seed treatment with T. atroviride AT10) on wheat (Triticum aestivum L.). The inoculation with R. irregulare elicited significant increases (by 18%, 39% and 20%) in the shoot, root dry biomass and root-to-shoot ratio compared to untreated plants, whereas inoculation with T. atroviride, as a substrate drench or as a seed coating, exhibited intermediate values for these parameters. The metabolomic approach demonstrated a broad chemical diversity, with more than 2900 compounds annotated in the root exudates. Overall, the Orthogonal Projections to Latent Structures Discriminant Analysis (OPLS-DA) supervised modelling highlighted a distinctive modulation of the metabolic profile in the root exudates as a function of both fungal inoculation and means of application. Most of the differences could be ascribed to lipids (sterols and membrane lipids), phenolic compounds and terpenoids, siderophores and chelating acids, derivatives of amino acids and phytohormones, and as such, the interaction between the wheat roots and beneficial fungi resulted in a complex response in terms of root exudates, likely involving a cascade of processes. Nonetheless, the changes imposed by plant-microbe interactions can contribute to the support of the biostimulant effects of both T. atroviride and R. irregulare.

Stable Isotope Probing of Microbiota Structure and Function in the Plant Rhizosphere

Stable isotope probing of microbial nucleic acids applied in the rhizosphere enables (a) the identification of the active microbial community involved in root exudate assimilation and those involved in soil organic matter degradation, and (b) the study of the impact of plants via root exudates on the in situ expression of microbial functions. By incubating plants under ¹³CO₂, fresh carbon exuded by the plant will be labeled and hence the microbial community assimilating ¹³C-root exudates will incorporate ¹³C into their cellular macromolecules. Labeled DNA, RNA, and proteins can be used to identify microorganisms that assimilated the root exudates. We provide a step-by-step protocol on how to apply stable isotope probing of DNA and RNA in the plant rhizosphere to identify the active microbial communities and analyze their gene expression.

In situ phytoremediation of copper and cadmium in a co-contaminated soil and its biological and physical effects

Phytoremediation is a potential cost-effective technology for remediating heavy metal-contaminated soils.

Root Exudation of Primary Metabolites: Mechanisms and Their Roles in Plant Responses to Environmental Stimuli

Root exudation is an important process determining plant interactions with the soil environment. Many studies have linked this process to soil nutrient mobilization. Yet, it remains unresolved how exudation is controlled and how exactly and under what circumstances plants benefit from exudation. The majority of root exudates including primary metabolites (sugars, amino acids, and organic acids) are believed to be passively lost from the root and used by rhizosphere-dwelling microbes. In this review, we synthetize recent advances in ecology and plant biology to explain and propose mechanisms by which root exudation of primary metabolites is controlled, and what role their exudation plays in plant nutrient acquisition strategies. Specifically, we propose a novel conceptual framework for root exudates. This framework is built upon two main concepts: (1) root exudation of primary metabolites is driven by diffusion, with plants and microbes both modulating concentration gradients and therefore diffusion rates to soil depending on their nutritional status; (2) exuded metabolite concentrations can be sensed at the root tip and signals are translated to modify root architecture. The flux of primary metabolites through root exudation is mostly located at the root tip, where the lack of cell differentiation favors diffusion of metabolites to the soil. We show examples of how the root tip senses concentration changes of exuded metabolites and translates that into signals to modify root growth. Plants can modify the concentration of metabolites either by controlling source/sink processes or by expressing and regulating efflux carriers, therefore challenging the idea of root exudation as a purely unregulated passive process. Through root exudate flux, plants can locally enhance concentrations of many common metabolites, which can serve as sensors and integrators of the plant nutritional status and of the nutrient availability in the surrounding environment. Plant-associated micro-organisms also constitute a strong sink for plant carbon, thereby increasing concentration gradients of metabolites and affecting root exudation. Understanding the mechanisms of and the effects that environmental stimuli have on the magnitude and type of root exudation will ultimately improve our knowledge of processes determining soil CO₂ emissions, ecosystem functioning, and how to improve the sustainability of agricultural production.

Exploring the Roles of Aquaporins in Plant⁻Microbe Interactions

Aquaporins (AQPs) are membrane channel proteins regulating the flux of water and other various small solutes across membranes. Significant progress has been made in understanding the roles of AQPs in plants' physiological processes, and now their activities in various plant⁻microbe interactions are receiving more attention. This review summarizes the various roles of different AQPs during interactions with microbes which have positive and negative consequences on the host plants. In positive plant⁻microbe interactions involving rhizobia, arbuscular mycorrhizae (AM), and plant growth-promoting rhizobacteria (PGPR), AQPs play important roles in nitrogen fixation, nutrient transport, improving water status, and increasing abiotic stress tolerance. For negative interactions resulting in pathogenesis, AQPs help plants resist infections by preventing pathogen ingress by influencing stomata opening and influencing defensive signaling pathways, especially through regulating systemic acquired resistance. Interactions with bacterial or viral pathogens can be directly perturbed through direct interaction of AQPs with harpins or replicase. However, whilst these observations indicate the importance of AQPs, further work is needed to develop a fuller mechanistic understanding of their functions.

Diversity of NC10 bacteria associated with sediments of submerged Potamogeton crispus (Alismatales: Potmogetonaceae)

Background

The nitrite-dependent anaerobic methane oxidation (N-DAMO) pathway, which plays an important role in carbon and nitrogen cycling in aquatic ecosystems, is mediated by “Candidatus Methylomirabilis oxyfera” (M. oxyfera) of the NC10 phylum. M. oxyfera-like bacteria are widespread in nature, however, the presence, spatial heterogeneity and genetic diversity of M. oxyfera in the rhizosphere of aquatic plants has not been widely reported.

Method

In order to simulate the rhizosphere microenvironment of submerged plants, Potamogeton crispus was cultivated using the rhizobox approach. Sediments from three compartments of the rhizobox: root (R), near-rhizosphere (including five sub-compartments of one mm width, N1–N5) and non-rhizosphere (>5 mm, Non), were sampled. The 16S rRNA gene library was used to investigate the diversity of M. oxyfera-like bacteria in these sediments.

Results

Methylomirabilis oxyfera-like bacteria were found in all three sections, with all 16S rRNA gene sequences belonging to 16 operational taxonomic units (OTUs). A maximum of six OTUs was found in the N1 sub-compartment of the near-rhizosphere compartment and a minimum of four in the root compartment (R) and N5 near-rhizosphere sub-compartment. Indices of bacterial community diversity (Shannon) and richness (Chao1) were 0.73–1.16 and 4–9, respectively. Phylogenetic analysis showed that OTU1-11 were classified into group b, while OTU12 was in a new cluster of NC10.

Discussion

Our results confirmed the existence of M. oxyfera-like bacteria in the rhizosphere microenvironment of the submerged plant P. crispus. Group b of M. oxyfera-like bacteria was the dominant group in this study as opposed to previous findings that both group a and b coexist in most other environments. Our results indicate that understanding the ecophysiology of M. oxyfera-like bacteria group b may help to explain their existence in the rhizosphere sediment of aquatic plant.

Plant Nutrient Resource Use Strategies Shape Active Rhizosphere Microbiota Through Root Exudation

Plant strategies for soil nutrient uptake have the potential to strongly influence plant-microbiota interactions, due to the competition between plants and microorganisms for soil nutrient acquisition and/or conservation. In the present study, we investigate whether these plant strategies could influence rhizosphere microbial activities via root exudation, and contribute to the microbiota diversification of active bacterial communities colonizing the root-adhering soil (RAS) and inhabiting the root tissues. We applied a DNA-based stable isotope probing (DNA-SIP) approach to six grass species distributed along a gradient of plant nutrient resource strategies, from conservative species, characterized by low nitrogen (N) uptake, a long lifespans and low root exudation level, to exploitative species, characterized by high rates of photosynthesis, rapid rates of N uptake and high root exudation level. We analyzed their (i) associated microbiota composition involved in root exudate assimilation and soil organic matter (SOM) degradation by 16S-rRNA-based metabarcoding. (ii) We determine the impact of root exudation level on microbial activities (denitrification and respiration) by gas chromatography. Measurement of microbial activities revealed an increase in denitrification and respiration activities for microbial communities colonizing the RAS of exploitative species. This increase of microbial activities results probably from a higher exudation rate and more diverse metabolites by exploitative plant species. Furthermore, our results demonstrate that plant nutrient resource strategies have a role in shaping active microbiota. We present evidence demonstrating that plant nutrient use strategies shape active microbiota involved in root exudate assimilation and SOM degradation via root exudation.

Phosphorus Solubilization by Bacillus Species

Microbial solubilization applies the natural ability of a microorganism to liberate phosphorus from unavailable structures. The main mechanism recognized to be responsible for the solubilization of phosphorus is the production of different types of organic acids. Three kinds of Bacillus species and three types of raw materials (poultry bones, fish bones, and ash) were tested for solubilization. The following parameters were compared for all discussed cases: pH, specific growth rate, solubilization factor, released phosphorus concentration, and total and individual concentration of organic acids. Utilization of ash brought about the highest specific and maximum specific growth rates. A decrease in pH was observed in most of the discussed cases with the exception of fish bones. At the same time, fish bones had the highest concentration of released P₂O₅ and the highest total concentration of produced organic acids (gluconic, lactic, acetic, succinic, and propionic) in all discussed cases. The tested Bacillus species produced the mentioned acids with the exception of B. megaterium, where propionic acid was not present. The lactic and acetic acids were those produced in the highest amount. The kind of raw materials and type of Bacillus species used in solubilization had a strong influence on the kind of organic acids that were detected in the broth culture and its total concentration, which had a direct influence on the amount of released phosphorus. The combination of Bacillus megaterium with the fish bones at 5 g/L is proposed as the pair that gives the highest concentration of released phosphorus (483 ± 5 mg/L).

Processes that determine the interplay of root exudation, methane emission and yield in rice agriculture

Rice is the most important staple food for half of the world's population, but also accounts for about 10% of all anthropogenic CH₄ emissions. In spite of a wealth of information on the mechanistic basis and the importance of the rice plant in mediating these emissions, the significance of root exudation for CH₄ emissions and the processes that determine root exudation are not well understood. Root exudates derive from photosynthate allocated to the root and subjected to root anabolic and catabolic processes. Key processes in roots that determine the extent of root exudation and, hence, CH₄ emission from rice agriculture, include (i) deviation of metabolites from root anabolic and catabolic pathways facilitating root exudation, but also (ii) xylem loading and transport of potential root exudates for reallocation to the leaves, and (iii) xylem loading of sucrose in roots for its transport into reproductive organs, both suppressing root exudation. These processes are modulated by plant development and metabolic requirements resulting from different functions of root exudation. In the present report the interplay of root exudation, CH₄ emission and yield are discussed.

Acid Neutralization by Mining Waste Dissolution under Conditions Relevant for Agricultural Applications

The acidification of agricultural soils in high rainfall regions is usually countered by the application of finely ground calcite or dolomite. As this carbonate dissolves, soil pH is raised, but CO2 is released. Mining activities often produce large quantities of very fine silicate rock-derived powders that are commonly deposited in stockpiles. However, the dissolution of such powders can also result in an increase in pH, without any direct release of CO2. Of particular interest are those silicate powders that have a high reactivity and higher capacity for raising pH. In this contribution, we report experimental work addressing the dissolution of various silicate rock-derived powders that were produced during mining activities in Norway under conditions that were representative of weathering in agricultural soils. Three different powders—derived from Åheim dunite, Stjernøya nepheline syenite, or Tellnes ilmenite norite—were exposed to different acids at pH 4 in unstirred flow cells, and dissolution or leaching kinetics were determined from the changes in the fluid composition. Based on these kinetics, pH neutralization rates were determined for the individual powders and compared to expected values for carbonates. Based on this comparison, it is concluded that the application of silicate rock-derived powder dissolution to replace carbonate-based liming may not be feasible due to slower reaction rates, unless larger quantities of a finer particle size than normal are used. The application of larger volumes of slower-reacting silicates may have the additional benefit of reducing the required frequency of liming.

Exploiting rhizosphere microbial cooperation for developing sustainable agriculture strategies

The rhizosphere hosts a considerable microbial community. Among that community, bacteria called plant growth-promoting rhizobacteria (PGPR) can promote plant growth and defense against diseases using diverse distinct plant-beneficial functions. Crop inoculation with PGPR could allow to reduce the use of pesticides and fertilizers in agrosystems. However, microbial crop protection and growth stimulation would be more efficient if cooperation between rhizosphere bacterial populations was taken into account when developing biocontrol agents and biostimulants. Rhizospheric bacteria live in multi-species biofilms formed all along the root surface or sometimes inside the plants (i.e., endophyte). PGPR cooperate with their host plants and also with other microbial populations inside biofilms. These interactions are mediated by a large diversity of microbial metabolites and physical signals that trigger cell-cell communication and appropriate responses. A better understanding of bacterial behavior and microbial cooperation in the rhizosphere could allow for a more successful use of bacteria in sustainable agriculture. This review presents an ecological view of microbial cooperation in agrosystems and lays the emphasis on the main microbial metabolites involved in microbial cooperation, plant health protection, and plant growth stimulation. Eco-friendly inoculant consortia that will foster microbe-microbe and microbe-plant cooperation can be developed to promote crop growth and restore biodiversity and functions lost in agrosystems.

High PAH degradation and activity of degrading bacteria during alfalfa growth where a contrasted active community developed in comparison to unplanted soil

PAH biodegradation in plant rhizosphere has been investigated in many studies, but the timescale of degradation and degrading bacteria activity was rarely considered. We explored the impact of plants on the temporal variability of PAH degradation, microbial abundance, activity, and bacterial community structure in a rhizotron experiment. A historically contaminated soil was spiked with PAHs, planted or not with alfalfa, over 22 days with sampling once a week. In both conditions, most of the spiked PAHs were dissipated during the first week, conducting to polar polycyclic aromatic compound production and to decreased richness and diversity of bacterial communities. We showed a rapid impact of the rhizosphere on PAH degradation via the increased activity of PAH-degrading bacteria. After 12 days, PAH degradation was significantly higher in the planted (100% degradation) than in unplanted (70%) soil. Gram-negative (Proteobacteria) PAH-dioxygenase genes and transcripts were higher in planted than unplanted soil and were correlated to the spiked PAH degradation. Conversely, Gram-positive (Actinobacteria) PAH-dioxygenase gene transcription was constant over time in both conditions. At 12 days, plant growth favored the activity of many Gammaproteobacteria (Pseudomonadaceae, Stenotrophomonas, and Acinetobacter) while in unplanted soil Alphaproteobacteria (Sphingomonadaceae, Sphingobium, and Magnetospirillum) and Actinobacteria (Iamia, Geodermatophilaceae, and Solirubrobacterales) were more active.

Plant host habitat and root exudates shape fungal diversity

The rhizospheric microbiome is clearly affected by plant species and certain of their functional traits. These functional traits allow plants to adapt to their environmental conditions by acquiring or conserving nutrients, thus defining different ecological resource-use plant strategies. In the present study, we investigated whether plants with one of the two nutrient-use strategies (conservative versus exploitative) could influence fungal communities involved in soil organic matter degradation and root exudate assimilation, as well as those colonizing root tissues. We applied a DNA-based, stable-isotope probing (DNA-SIP) approach to four grass species distributed along a gradient of plant nutrient resource strategies, ranging from conservative to exploitative species, and analyzed their associated mycobiota composition using a fungal internal transcribed spacer (ITS) and Glomeromycotina 18S rRNA gene metabarcoding approach. Our results demonstrated that fungal taxa associated with exploitative and conservative plants could be separated into two general categories according to their location: generalists, which are broadly distributed among plants from each strategy and represent the core mycobiota of soil organic matter degraders, root exudate consumers in the root-adhering soil, and root colonizers; and specialists, which are locally abundant in one species and more specifically involved in soil organic matter degradation or root exudate assimilation on the root-adhering soil and the root tissues. Interestingly, for arbuscular mycorrhizal fungi analysis, all plant roots were mainly colonized by Glomus species, whereas an increased diversity of Glomeromycotina genera was observed for the exploitative plant species Dactylis glomerata.

Root exudation rate as functional trait involved in plant nutrient-use strategy classification

Plants adopt a variety of life history strategies to succeed in the Earth's diverse environments. Using functional traits which are defined as "morphological, biochemical, physiological, or phonological" characteristics measurable at the individual level, plants are classified according to their species' adaptative strategies, more than their taxonomy, from fast growing plant species to slower-growing conservative species. These different strategies probably influence the input and output of carbon (C)-resources, from the assimilation of carbon by photosynthesis to its release in the rhizosphere soil via root exudation. However, while root exudation was known to mediate plant-microbe interactions in the rhizosphere, it was not used as functional trait until recently. Here, we assess whether root exudate levels are useful plant functional traits in the classification of plant nutrient-use strategies and classical trait syndromes? For this purpose, we conducted an experiment with six grass species representing along a gradient of plant resource-use strategies, from conservative species, characterized by low biomass nitrogen (N) concentrations and a long lifespans, to exploitative species, characterized by high rates of photosynthesis and rapid rates of N acquisition. Leaf and root traits were measured for each grass and root exudate rate for each planted soil sample. Classical trait syndromes in plant ecology were found for leaf and root traits, with negative relationships observed between specific leaf area and leaf dry matter content or between specific root length and root dry matter content. However, a new root trait syndrome was also found with root exudation levels correlating with plant resource-use strategy patterns, specifically, between root exudation rate and root dry matter content. We therefore propose root exudation rate can be used as a key functional trait in plant ecology studies and plant strategy classification.

Below-ground-above-ground Plant-microbial Interactions: Focusing on Soybean, Rhizobacteria and Mycorrhizal Fungi

INTRODUCTION

Organisms seldom exist in isolation and are usually involved in interactions with several hosts and these interactions in conjunction with the physicochemical parameters of the soil affect plant growth and development. Researches into below and aboveground microbial community are unveiling a myriad of intriguing interactions within the rhizosphere, and many of the interactions are facilitated by exudates that are secreted by plants roots. These interactions can be harnessed for beneficial use in agriculture to enhance crop productivity especially in semi-arid and arid environments.

THE RHIZOSPHERE

The rhizosphere is the region of soil close to plants roots that contain large number of diverse organisms. Examples of microbial candidates that are found in the rhizosphere include the Arbuscular Mycorrhizal Fungi (AMF) and rhizobacteria. These rhizosphere microorganisms use plant root secretions such as mucilage and flavonoids which are able to influence their diversity and function and also enhance their potential to colonize plants root.

NATURAL INTERACTIONS BETWEEN MICROORGANISMS AND PLANT

In the natural environments, plants live in interactions with different microorganisms, which thrive belowground in the rhizosphere and aboveground in the phyllosphere. Some of the plant-microbial interactions (which can be in the form of antagonism, amensalism, parasitism and symbiosis) protect the host plants against detrimental microbial and non-microbial invaders and provide nutrients for plants while others negatively affect plants. These interactions can influence below-ground-above-ground plants' biomass development thereby playing significant role in sustaining plants. Therefore, understanding microbial interactions within the rhizosphere and phyllosphere is urgent towards farming practices that are less dependent on conventional chemical fertilizers, which have known negative impacts on the environments.

BELOW GROUND RHIZOBACTERIA INTERACTIONS ALLEVIATE DROUGHT STRESS

Drought stress is one of the major factors militating against agricultural productivity globally and is likely to further increase. Belowground rhizobacteria interactions could play important role in alleviating drought stress in plants. These beneficial rhizobacterial colonize the rhizosphere of plants and impart drought tolerance by up regulation or down regulation of drought responsive genes such as ascorbate peroxidase, S-adenosyl-methionine synthetase, and heat shock protein.

INSIGHTS INTO BELOW AND ABOVE THE GROUND MICROBIAL INTERACTIONS VIA OMIC STUDIES

Investigating complex microbial community in the environment is a big challenge. Therefore, omic studies of microorganisms that inhabit the rhizosphere are important since this is where most plant-microbial interactions occur. One of the aims of this review is not to give detailed account of all the present omic techniques, but instead to highlight the current omic techniques that can possibly lead to detection of novel genes and their respective proteins within the rhizosphere which may be of significance in enhancing crop plants (such as soybean) productivity especially in semi-arid and arid environments.

FUTURE PROSPECTS AND CONCLUSIONS

Plant-microbial interactions are not totally understood, and there is, therefore, the need for further studies on these interactions in order to get more insights that may be useful in sustainable agricultural development. With the emergence of omic techniques, it is now possible to effectively monitor transformations in rhizosphere microbial community together with their effects on plant development. This may pave way for scientists to discover new microbial species that will interact effectively with plants. Such microbial species can be used as biofertilizers and/or bio-pesticides to increase crop yield and enhance global food security.

Effect of Burkholderia tropica and Herbaspirillum frisingense strains on sorghum growth is plant genotype dependent

Sorghum is a multipurpose crop that is cultivated worldwide. Plant growth-promoting bacteria (PGPB) have important roles in enhancing sorghum biomass and nutrient uptake and suppressing plant pathogens. The aim of this research was to test the effects of the endophytic bacterial species Kosakonia radicincitans strain IAC/BECa 99, Enterobacter asburiae strain IAC/BECa 128, Pseudomonas fluorescens strain IAC/BECa 141, Burkholderia tropica strain IAC/BECa 135 and Herbaspirillum frisingense strain IAC/BECa 152 on the growth and root architecture of four sorghum cultivars (SRN-39, Shanqui-Red, BRS330, BRS509), with different uses and strigolactone profiles. We hypothesized that the different bacterial species would trigger different growth plant responses in different sorghum cultivars. Burkholderia tropica and H. frisingense significantly increased the plant biomass of cultivars SRN-39 and BRS330. Moreover, cultivar BRS330 inoculated with either strain displayed isolates significant decrease in average root diameter. This study shows that Burkholderia tropica strain IAC/BECa 135 and H. frisingense strain IAC/BECa 152 are promising PGPB strains for use as inocula for sustainable sorghum cultivation.

Personalized Medicine for Crops? Opportunities for the Application of Molecular Recognition in Agriculture

This perspective examines the detection of rhizosphere biomarkers, namely, root exudates and microbial metabolites, using molecular recognition elements, such as molecularly imprinted polymers, antibodies, and aptamers. Tracking these compounds in the rhizosphere could provide valuable insight into the status of the crop and soil in a highly localized way. The outlook and potential impact of the combination of molecular recognition and other innovations, such as nanotechnology and precision agriculture, and the comparison to advances in personalized medicine are considered.

Effect of nicotine from tobacco root exudates on chemotaxis, growth, biocontrol efficiency, and colonization by Pseudomonas aeruginosa NXHG29

Accumulated evidence suggests that root exudates have a major role in mediating plant-microbe interactions in the rhizosphere. Here, we characterized tobacco root exudates (TREs) by GC-MS and nicotine, scopoletin, and octadecane were identified as three main components of TREs. Qualitative and quantitative chemotaxis assays revealed that Pseudomonas aeruginosa NXHG29 with antagonistic activity displayed positive chemotactic responses towards TREs and their three main components (nicotine, scopoletin, octadecane) and its enhanced chemotaxis were induced by these substances in a concentration-dependent manner. Furthermore, following GC-MS and chemotaxis analysis, nicotine was selected as the target for evaluation of the effect on NXHG29 regarding antagonism, growth, root colonization and biocontrol efficiency. Results of in vitro studies showed that nicotine as a sole carbon source could enhance growth of NXHG29 and significantly increased the antagonism of NXHG29. We also demonstrated that nicotine exerted enhancing effects on the colonization ability of NXHG29 on tobacco roots by combining CLSM observations with investigation of population level dynamics by selective dilution plating method. Results from greenhouse experiments suggested nicotine exhibited stimulatory effects on the biocontrol efficiency of NXHG29 against bacterial wilt and black shank on tobacco. The stimulatory effect of nicotine was affected by the concentration and timing of nicotine application and further supported by the results of population level of NXHG29 on tobacco roots. This is the first report on the enhancement effect of nicotine from TREs on an antagonistic bacterium for its root colonization, control of soil-borne pathogens, regarding the chemotaxis and in vitro antagonism and growth.

Rhizosphere Microbiomes Modulated by Pre-crops Assisted Plants in Defense Against Plant-Parasitic Nematodes

Plant-parasitic nematodes cause considerable damage to crop plants. The rhizosphere microbiome can affect invasion and reproductive success of plant-parasitic nematodes, thus affecting plant damage. In this study, we investigated how the transplanted rhizosphere microbiome from different crops affect plant-parasitic nematodes on soybean or tomato, and whether the plant’s own microbiome from the rhizosphere protects it better than the microbiome from fallow soil. Soybean plants growing in sterilized substrate were inoculated with the microbiome extracted from the rhizosphere of soybean, maize, or tomato. Controls were inoculated with extracts from bulk soil, or not inoculated. After the microbiome was established, the root lesion nematode Pratylenchus penetrans was added. Root invasion of P. penetrans was significantly reduced on soybean plants inoculated with the microbiome from maize or soybean compared to tomato or bulk soil, or the uninoculated control. In the analogous experiment with tomato plants inoculated with either P. penetrans or the root knot nematode Meloidogyne incognita, the rhizosphere microbiomes of maize and tomato reduced root invasion by P. penetrans and M. incognita compared to microbiomes from soybean or bulk soil. Reproduction of M. incognita on tomato followed the same trend, and it was best suppressed by the tomato rhizosphere microbiome. In split-root experiments with soybean and tomato plants, a systemic effect of the inoculated rhizosphere microbiomes on root invasion of P. penetrans was shown. Furthermore, some transplanted microbiomes slightly enhanced plant growth compared to uninoculated plants. The microbiomes from maize rhizosphere and bulk soil increased the fresh weights of roots and shoots of soybean plants, and microbiomes from soybean rhizosphere and bulk soil increased the fresh weights of roots and shoots of tomato plants. Nematode invasion did not affect plant growth in these short-term experiments. In conclusion, this study highlights the importance of the rhizosphere microbiome in protecting crops against plant-parasitic nematodes. An effect of pre-crops on the rhizosphere microbiome might be harnessed to enhance the resistance of crops towards plant-parasitic nematodes. However, nematode-suppressive effects of a particular microbiome may not necessarily coincide with improvement of plant growth in the absence of plant-parasitic nematodes.

Comparison of Iris pseudacorus wetland systems with unplanted systems on pollutant removal and microbial community under nanosilver exposure

Rapidly developing industry raises concerns about the environmental risks of silver nanoparticles (AgNPs), but the effects of AgNPs on the performance and microbial community in the constructed wetlands remain unclear. In this study, long-term exposure of AgNPs in two VFCWs was conducted to determine the effects of AgNPs on the pollutant removal and microbial community structure. Before exposing AgNPs, the water quality of effluent was better in planted wetland (CW2), compared with unplanted wetland (CW1). After continuous exposure of 100μg/L AgNPs, the COD (chemical oxygen demand) removal of two CWs had no difference. However, addition of AgNPs reduced the nitrogen and phosphorus removal in two CWs, with decreasing average removal efficiencies of ammonia nitrogen from 46.31% to 32.09% and 59.66% to 51.06%, total nitrogen from 57.76% to 43.78% and 67.35 to 60.58%, total phosphorus from 71.29% to 59.31% and 67.35% to 60.58%, respectively. The vegetable wetlands showed higher resistances to AgNPs loading than unplanted wetlands. In addition, AgNPs accumulated in the wetland substrate, especially in the soil layer with the silver concentration of approximately 4.32μg/g. The small portion of silver was found in plant tissues, and plants played a minor role to remove the AgNPs from wastewater. Moreover, the constructed wetlands could effectively remove the AgNPs from the synthetic wastewater. The illumine high-throughput sequencing results demonstrated the variations of the bacterial community structure at the exposure of AgNPs. The results showed that the dominant phyla were Proteobacteria, Acidobacteria and Bacteroidetes. Compared with unplanted wetlands, the contents of several nitrifying bacteria such as Candidatus Nitrososphaera (AOA) and Nitrospira (NOB) at genus level increased, leading to the higher nitrogen removal in the planted wetlands.