Bacillus amyloliquefaciens SAY09 Increases Cadmium Resistance in Plants by Activation of Auxin-Mediated Signaling Pathways

Rhizosphere microbial markers (micro-markers): A new physical examination indicator for traditional Chinese medicines

Rhizosphere microorganisms, as one of the most important components of the soil microbiota and plant holobiont, play a key role in the medicinal plant-soil ecosystem, which are closely related to the growth, adaptability, nutrient absorption, stress tolerance and pathogen resistance of host plants. In recent years, with the wide application of molecular biology and omics technologies, the outcomes of rhizosphere microorganisms on the health, biomass production and secondary metabolite biosynthesis of medicinal plants have received extensive attention. However, whether or to what extent rhizosphere microorganisms can contribute to the construction of the quality evaluation system of Chinese medicinal materials is still elusive. Based on the significant role of rhizosphere microbes in the survival and quality formation of medicinal plants, this paper proposed a new concept of rhizosphere microbial markers (micro-markers), expounded the relevant research methods and ideas of applying the new concept, highlighted the importance of micro-markers in the quality evaluation and control system of traditional Chinese medicines (TCMs), and introduced the potential value in soil environmental assessment, plant pest control and quality assessment of TCMs. It provides reference for developing ecological planting of TCMs and ensuring the production of high quality TCMs by regulating rhizosphere microbial communities.

Factors influencing cadmium accumulation in plants after inoculation with rhizobacteria: A meta-analysis

Rhizobacteria have the potential to enhance phytoremediation by generating substances that stimulate plant development and influence the effectiveness of cadmium (Cd) remediation by adjusting Cd availability via metal solubilization. Furthermore, rhizobacterial inoculation affects plants' metal tolerance and uptake by controlling the expression of several metal transporters, channels, and metal chelator genes. A meta-analysis was conducted to quantitatively assess the effects of rhizobacteria on Cd accumulation in plants using 207 individual observations from 47 articles. This meta-analysis showed an average Cd concentration increase of 8.09 % in plant cells under rhizobacteria treatment. The effects of different plant-microbial interactions on the bioaccumulation of Cd in plants varied. Selecting the proper rhizobacteria-plant association is essential to affect Cd buildup in plant roots and shoots. A more extended planting period (>30 days) and a suitable soil pH (<6, 7-8) would aid in the phytoextraction of Cd from the soil. This study comprehensively and quantitatively investigated the effects of plants, rhizobacteria, soil pH, planting period, experimental sites, and plant organs on plant Cd accumulation. According to the analysis of explanatory factors, plant species, planting period, soil pH, and rhizobacteria species have a more decisive influence on Cd accumulation than other factors. The results provide information for future research on the successful remediation of soils contaminated with Cd. More investigations are required to elucidate the intricate interactions between plant roots and microorganisms.

Epigenetic Control of Plant Response to Heavy Metals

Plants are sessile organisms that must adapt to environmental conditions, such as soil characteristics, by adjusting their development during their entire life cycle. In case of low-distance seed dispersal, the new generations are challenged with the same abiotic stress encountered by the parents. Epigenetic modification is an effective option that allows plants to face an environmental constraint and to share the same adaptative strategy with their progeny through transgenerational inheritance. This is the topic of the presented review that reports the scientific progress, up to date, gained in unravelling the epigenetic response of plants to soil contamination by heavy metals and metalloids, collectively known as potentially toxic elements. The effect of the microbial community inhabiting the rhizosphere is also considered, as the evidence of a transgenerational transfer of the epigenetic status that contributes to the activation in plants of response mechanisms to soil pollution.

Microbial volatile compounds (MVCs): an eco-friendly tool to manage abiotic stress in plants

Microbial volatile compounds (MVCs) are produced during the metabolism of microorganisms, are widely distributed in nature, and have significant applications in various fields. To date, several MVCs have been identified. Microbial groups such as bacteria and fungi release many organic and inorganic volatile compounds. They are typically small odorous compounds with low molecular masses, low boiling points, and lipophilic moieties with high vapor pressures. The physicochemical properties of MVCs help them to diffuse more readily in nature and allow dispersal to a more profound distance than other microbial non-volatile metabolites. In natural environments, plants communicate with several microorganisms and respond differently to MVCs. Here, we review the following points: (1) MVCs produced by various microbes including bacteria, fungi, viruses, yeasts, and algae; (2) How MVCs are effective, simple, efficient, and can modulate plant growth and developmental processes; and (3) how MVCs improve photosynthesis and increase plant resistance to various abiotic stressors.

Integrated biochemical and transcriptomic analysis reveals the effects of Burkholderia sp. SRB-1 on cadmium accumulating in Chrysopogon zizanioides L. under Cd stress

Application of plant growth-promoting rhizobacteria plays a vital role in enhancing phytoremediation efficiency. In this study, multiple approaches were employed to investigate the underlying mechanisms of Burkholderia sp. SRB-1 (SRB-1) on elevating Cd uptake and accumulation. Inoculation experiment indicated that SRB-1 could facilitate plant growth and Cd tolerance, as evidenced by the enhanced plant biomass and antioxidative enzymes activities. Cd content in plant shoots and roots increased about 36.56%-39.66% and 25.97%-130.47% assisted with SRB-1 when compared with control. Transcriptomics analysis revealed that SRB-1 upregulated expression of amiE, AAO1-2 and GA2-ox related to auxin and gibberellin biosynthesis in roots. Auxin and gibberellin, as hormone signals, regulated plant Cd tolerance and growth through activating hormone signal transduction pathways, which might also contribute to 67.94% increase of dry weight. The higher expression levels of ATP-binding cassette transporter subfamilies (ABCB, ABCC, ABCD and ABCG) in Chrysopogon zizanioides roots contributed to higher Cd uptake in Cd15 B (323.83 mg kg^-1) than Cd15 (136.28 mg kg^-1). Further, SRB-1 facilitated Cd migration from roots to shoots via upregulating the expression of Nramp, ZIP and HMA families. Our integrative analysis provided a molecular-scale perspective on Burkholderia sp. SRB-1 contributing to C. zizanioides performance.

Comprehensive mechanisms of heavy metal toxicity in plants, detoxification, and remediation

Natural and anthropogenic causes are continually growing sources of metals in the ecosystem; hence, heavy metal (HM) accumulation has become a primary environmental concern. HM contamination poses a serious threat to plants. A major focus of global research has been to develop cost-effective and proficient phytoremediation technologies to rehabilitate HM-contaminated soil. In this regard, there is a need for insights into the mechanisms associated with the accumulation and tolerance of HMs in plants. It has been recently suggested that plant root architecture has a critical role in the processes that determine sensitivity or tolerance to HMs stress. Several plant species, including those from aquatic habitats, are considered good hyperaccumulators for HM cleanup. Several transporters, such as the ABC transporter family, NRAMP, HMA, and metal tolerance proteins, are involved in the metal acquisition mechanisms. Omics tools have shown that HM stress regulates several genes, stress metabolites or small molecules, microRNAs, and phytohormones to promote tolerance to HM stress and for efficient regulation of metabolic pathways for survival. This review presents a mechanistic view of HM uptake, translocation, and detoxification. Sustainable plant-based solutions may provide essential and economical means of mitigating HM toxicity.

Microbial Volatile Organic Compounds: An Alternative for Chemical Fertilizers in Sustainable Agriculture Development

Microorganisms are exceptional at producing several volatile substances called microbial volatile organic compounds (mVOCs). The mVOCs allow the microorganism to communicate with other organisms via both inter and intracellular signaling pathways. Recent investigation has revealed that mVOCs are chemically very diverse and play vital roles in plant interactions and microbial communication. The mVOCs can also modify the plant's physiological and hormonal pathways to augment plant growth and production. Moreover, mVOCs have been affirmed for effective alleviation of stresses, and also act as an elicitor of plant immunity. Thus, mVOCs act as an effective alternative to various chemical fertilizers and pesticides. The present review summarizes the recent findings about mVOCs and their roles in inter and intra-kingdoms interactions. Prospects for improving soil fertility, food safety, and security are affirmed for mVOCs application for sustainable agriculture.

Do Volatiles Affect Bacteria and Plants in the Same Way? Growth and Biochemical Response of Non-Stressed and Cd-Stressed Arabidopsis thaliana and Rhizobium E20-8

Plant roots are colonized by rhizobacteria, and these soil microorganisms can not only stimulate plant growth but also increase tolerance to stress through the production of volatile organic compounds. However, little is known about the effect that these plant beneficial volatiles may have on bacteria. In this study, the effects on growth and oxidative status of different concentrations of three volatiles already reported to have a positive influence on plant growth (2-butanone, 3-methyl-1-butanol, and 2,3-butanediol) were determined in A. thaliana and Rhizobium sp. strain E20-8 via airborne exposure in the presence and absence of Cd. It was expected to ascertain if the plant and the bacterium are influenced in the same way by the volatiles, and if exposure to stress (Cd) shifts the effects of volatiles on plants and bacteria. Results showed the antioxidant activity of the volatiles protecting the plant cell metabolism from Cd toxicity and increasing plant tolerance to Cd. Effects on bacteria were less positive. The two alcohols (3-methyl-1-butanol and 2,3-butanediol) increased Cd toxicity, and the ketone (2-butanone) was able to protect Rhizobium from Cd stress, constituting an alternative way to protect soil bacterial communities from stress. The application of 2-butanone thus emerges as an alternative way to increase crop production and crop resilience to stress in a more sustainable way, either directly or through the enhancement of PGPR activity.

Biochar amendment reduces cadmium uptake by stimulating cadmium-resistant PGPR in tomato rhizosphere

Biochar amendment in the soil can exert a positive effect in reducing heavy metal toxicity in plants. However, it remains unclear the extent to which this effect is associated with the modulation of plant growth-promoting rhizobacteria (PGPR). Here, we initially conducted a pot experiment using tomato (Solanum lycopersicum L.) as a model plant grown in soil spiked with cadmium. First, we found biochar amendment to result in reduced cadmium uptake in tomato plants and trackable changes in the tomato rhizosphere microbiome. Then, a rhizosphere transplant experiment validated the importance of this microbiome modulation for cadmium-toxicity amelioration. Sequence-based analyses targeted the isolation of representative isolates of PGPR, including Bacillus and Flavisolibacter spp. that displayed in vitro cadmium tolerance and biosorption capabilities (in addition to abilities to solubilize phosphate and produce indole acetic acid). Last, we performed a soil inoculation experiment and confirmed the effectiveness of these isolates in reducing cadmium toxicity in tomato plants. Besides, we found the inoculation of these taxa as single inoculant and in combination to result in increased activities of specific antioxidant enzymes in tomato tissues. Taken together, this study revealed the ecological and physiological mechanisms by which biochar amendment indirectly alleviate cadmium toxicity in tomato plants, in this case, via the modulation and activity of specific PGPR populations. This study provides new insights into strategies able to promote beneficial PGPR in the rhizosphere with potential application to ameliorate heavy metal toxicity in plants.

The role of auxins and auxin-producing bacteria in the tolerance and accumulation of cadmium by plants

Cadmium (Cd) is one of the most toxic heavy metals for plant physiology and development. This review discusses Cd effects on auxin biosynthesis and homeostasis, and the strategies for restoring plant growth based on exogenous auxin application. First, the two well-characterized auxin biosynthesis pathways in plants are described, as well as the effect of exogenous auxin application on plant growth. Then, review describes the impacts of Cd on the content, biosynthesis, conjugation, and oxidation of endogenous auxins, which are related to a decrease in root development, photosynthesis, and biomass production. Finally, compelling evidence of the beneficial effects of auxin-producing rhizobacteria in plants exposed to Cd is showed, focusing on photosynthesis, oxidative stress, and production of antioxidant compounds and osmolytes that counteract Cd toxicity, favoring plant growth and improve phytoremediation efficiency. Expanding our understanding of the positive effects of exogenous auxins application and the interactions between bacteria and plants growing in Cd-polluted environments will allow us to propose phytoremediation strategies for restoring environments contaminated with this metal.

Flooding-induced rhizosphere Clostridium assemblage prevents root-to-shoot cadmium translocation in rice by promoting the formation of root apoplastic barriers

Water managements are the most effective agricultural practices for restraining cadmium (Cd) uptake and translocation in rice, which closely correlated with rhizosphere assembly of beneficial microbiome. However, the role of the assemblage of specific microbiota in controlling root-to-shoot Cd translocation in rice remains scarcely clear. The aim of this study was to ascertain how water managements shaped rhizosphere microbiome and mediated root-to-shoot Cd translocation. To disentangle the acting mechanisms of water managements, we performed an experiment monitoring Cd uptake and transport in rice and changes in soil microbial communities in response to continuously flooding and moistening irrigation. Continuously flooding changed rhizosphere microbial communities, leading to the increased abundance of anaerobic bacteria such as Clostridium populations. Weighted gene co-expression network analysis (WGCNA) showed that a dominant OTU163, corresponding to Clostridium sp. CSP1, exhibited a strong negative correlation with root-to-shoot Cd translocation. An integrated analysis of transcriptome and metabolome further indicated that the Clostridium-secreted butyric acid was involved in the regulation of phenylpropanoid pathway in rice roots. The formation of endodermal suberized barriers and lignified xylems was remarkably enhanced in the Clostridium-treated roots, which led to more Cd retained in root cell wall and less Cd in the xylem sap. Collectively, our results indicate that the development of root apoplastic barriers can be orchestrated by beneficial Clostridium strains that are assembled by host plants grown under flooding regime, thereby inhibiting root-to-shoot Cd translocation.

The Role of NO in the Amelioration of Heavy Metal Stress in Plants by Individual Application or in Combination with Phytohormones, Especially Auxin

Since the time of the Industrial Revolution, the accumulation of various heavy metals (HMs), such as cadmium (Cd), arsenic (As), lead (Pb), chromium (Cr), mercury (Hg), copper (Cu), zinc (Zn), nickel (Ni), etc., has increased substantially in the soil, causing a real risk to all kinds of consumers in the food chain. Moreover, excess HM accumulation is considered a major factor in decreasing plant growth and productivity. A number of recent studies have exhibited the astonishing impact of nitric oxide (NO), a multifunctional, gaseous signal molecule, on alleviating the destructive effects of HMs. Many reports revealed the noteworthy contribution of NO in reducing HM uptake and toxicity levels. In the present review, focus is given to the contribution of NO to decrease the toxicity levels of different HMs in a variety of plant species and their accumulation in those species. Simultaneously, this review also demonstrates the effects of NO on HM-stressed species, by its use both individually and along with auxin, a plant-growth-promoting phytohormone. Different perspectives about the reaction to the co-application of NO and auxin, as well as the differential role of NO to overcome HM stress, have been expanded.

Cadmium Phytotoxicity, Tolerance, and Advanced Remediation Approaches in Agricultural Soils; A Comprehensive Review

Cadmium (Cd) is a major environmental contaminant due to its widespread industrial use. Cd contamination of soil and water is rather classical but has emerged as a recent problem. Cd toxicity causes a range of damages to plants ranging from germination to yield suppression. Plant physiological functions, i.e., water interactions, essential mineral uptake, and photosynthesis, are also harmed by Cd. Plants have also shown metabolic changes because of Cd exposure either as direct impact on enzymes or other metabolites, or because of its propensity to produce reactive oxygen species, which can induce oxidative stress. In recent years, there has been increased interest in the potential of plants with ability to accumulate or stabilize Cd compounds for bioremediation of Cd pollution. Here, we critically review the chemistry of Cd and its dynamics in soil and the rhizosphere, toxic effects on plant growth, and yield formation. To conserve the environment and resources, chemical/biological remediation processes for Cd and their efficacy have been summarized in this review. Modulation of plant growth regulators such as cytokinins, ethylene, gibberellins, auxins, abscisic acid, polyamines, jasmonic acid, brassinosteroids, and nitric oxide has been highlighted. Development of plant genotypes with restricted Cd uptake and reduced accumulation in edible portions by conventional and marker-assisted breeding are also presented. In this regard, use of molecular techniques including identification of QTLs, CRISPR/Cas9, and functional genomics to enhance the adverse impacts of Cd in plants may be quite helpful. The review's results should aid in the development of novel and suitable solutions for limiting Cd bioavailability and toxicity, as well as the long-term management of Cd-polluted soils, therefore reducing environmental and human health hazards.

Belowground plant-microbe communications via volatile compounds

Volatile compounds play important roles in rhizosphere biological communications and interactions. The emission of plant and microbial volatiles is a dynamic phenomenon that is affected by several endogenous and exogenous signals. Diffusion of volatiles can be limited by their adsorption, degradation, and dissolution under specific environmental conditions. Therefore, rhizosphere volatiles need to be investigated on a micro and spatiotemporal scale. Plant and microbial volatiles can expand and specialize the rhizobacterial niche not only by improving the root system architecture such that it serves as a nutrient-rich shelter, but also by inhibiting or promoting the growth, chemotaxis, survival, and robustness of neighboring organisms. Root volatiles play an important role in engineering the belowground microbiome by shaping the microbial community structure and recruiting beneficial microbes. Microbial volatiles are appropriate candidates for improving plant growth and health during environmental challenges and climate change. However, some technical and experimental challenges limit the non-destructive monitoring of volatile emissions in the rhizosphere in real-time. In this review, we attempt to clarify the volatile-mediated intra- and inter-kingdom communications in the rhizosphere, and propose improvements in experimental design for future research.

Endophytic bacteria promote biomass production and mercury-bioaccumulation of Bermuda grass and Indian goosegrass

Plant growth-promoting endophytic bacteria can potentially improve the biomass production of Hg-accumulating grasses, resulting in improved Hg extraction from contaminated soils. This study aimed to analyze the effect of inoculation of Hg-resistant endophytic bacteria (i) Jeotgalicoccus huakuii (B1) and (ii) Bacillus amyloliquefaciens (B2), as single and consortium inoculant, on biomass production and Hg bioaccumulation of Bermuda grass (R1) and Indian goosegrass (R2) planted as monoculture and mixed cropping. The grass seeds were surface-sterilized before the inoculation. Both inoculated seeds with B1 and B2 (treatments) and uninoculated seeds were sown separately in sterilized sand. Grass seedlings of both treatments and control were replanted in the washed and sterilized sand medium, spiked with HgCl₂ (100 mg kg^-1). A subset of grass was harvested at 0, 4, 6, and 10 weeks after planting to measure biomass production and Hg bioaccumulation. The results showed that bacterial inoculation enhanced the grass biomass by 52.68% and Hg bioaccumulation by 47.76%. Mercury residue of Hg-spiked sand treated with the bacterial consortium was reduced by 80%. This suggests that endophytic bacteria can improve grass biomass production and enhance Hg bioaccumulation in grass biomass.

Plant Growth-Promoting Rhizobacteria as a Green Alternative for Sustainable Agriculture

Environmental stress is a major challenge for sustainable food production as it reduces yield by generating reactive oxygen species (ROS) which pose a threat to cell organelles and biomolecules such as proteins, DNA, enzymes, and others, leading to apoptosis. Plant growth-promoting rhizobacteria (PGPR) offers an eco-friendly and green alternative to synthetic agrochemicals and conventional agricultural practices in accomplishing sustainable agriculture by boosting growth and stress tolerance in plants. PGPR inhabit the rhizosphere of soil and exhibit positive interaction with plant roots. These organisms render multifaceted benefits to plants by several mechanisms such as the release of phytohormones, nitrogen fixation, solubilization of mineral phosphates, siderophore production for iron sequestration, protection against various pathogens, and stress. PGPR has the potential to curb the adverse effects of various stresses such as salinity, drought, heavy metals, floods, and other stresses on plants by inducing the production of antioxidant enzymes such as catalase, peroxidase, and superoxide dismutase. Genetically engineered PGPR strains play significant roles to alleviate the abiotic stress to improve crop productivity. Thus, the present review will focus on the impact of PGPR on stress resistance, plant growth promotion, and induction of antioxidant systems in plants.

An update on redox signals in plant responses to biotic and abiotic stress crosstalk: insights from cadmium and fungal pathogen interactions

Complex signalling pathways are involved in plant protection against single and combined stresses. Plants are able to coordinate genome-wide transcriptional reprogramming and display a unique programme of transcriptional responses to a combination of stresses that differs from the response to single stresses. However, a significant overlap between pathways and some defence genes in the form of shared and general stress-responsive genes appears to be commonly involved in responses to multiple biotic and abiotic stresses. Reactive oxygen and nitrogen species, as well as redox signals, are key molecules involved at the crossroads of the perception of different stress factors and the regulation of both specific and general plant responses to biotic and abiotic stresses. In this review, we focus on crosstalk between plant responses to biotic and abiotic stresses, in addition to possible plant protection against pathogens caused by previous abiotic stress. Bioinformatic analyses of transcriptome data from cadmium- and fungal pathogen-treated plants focusing on redox gene ontology categories were carried out to gain a better understanding of common plant responses to abiotic and biotic stresses. The role of reactive oxygen and nitrogen species in the complex network involved in plant responses to changes in their environment is also discussed.

Enhanced Iron Uptake in Plants by Volatile Emissions of Rahnella aquatilis JZ-GX1

Iron deficiency in soil has crucially restricted agricultural and forestry production. Volatile organic compounds (VOCs) produced by beneficial microorganisms have been proven to play an important role in inducing abiotic stress tolerance in plants. We investigated the effects of VOCs released by the rhizobacterium Rahnella aquatilis JZ-GX1 on the growth and root parameters of Arabidopsis thaliana under iron deficiency. The effect of the rhizobacterial VOCs on the gene expression in iron uptake and hormone signaling pathways were detected by RT-qPCR. Finally, the VOCs of the JZ-GX1 strain that could promote plant growth under iron deficiency stress were screened. The results showed that the JZ-GX1 strain could induce A. thaliana tolerance to iron deficiency stress by promoting the development of lateral roots and root hairs and increasing the activities of H⁺ ATPase and Fe³⁺ reductase. In addition, the AHA2, FRO2, and IRT1 genes of A. thaliana exposed to JZ-GX1-emitted VOCs were upregulated 25-, 1. 81-, and 1.35-fold, respectively, and expression of the abscisic acid (ABA) synthesis gene NCED3 was upregulated on both the 3rd and 5th days. Organic compounds were analyzed in the headspace of JZ-GX1 cultures, 2-undecanone and 3-methyl-1-butanol were found to promote Medicago sativa and A. thaliana growth under iron-limited conditions. These results demonstrated that the VOCs of R. aquatilis JZ-GX1 have good potential in promoting iron absorption in plants.

Efficacy of Indole Acetic Acid and Exopolysaccharides-Producing Bacillus safensis Strain FN13 for Inducing Cd-Stress Tolerance and Plant Growth Promotion in Brassica juncea (L.)

Untreated wastewater used for irrigating crops is the major source of toxic heavy metals and other pollutants in soils. These heavy metals affect plant growth and deteriorate the quality of edible parts of growing plants. Phytohormone (IAA) and exopolysaccharides (EPS) producing plant growth-promoting rhizobacteria can reduce the toxicity of metals by stabilizing them in soil. The present experiment was conducted to evaluate the IAA and EPS-producing rhizobacterial strains for improving growth, physiology, and antioxidant activity of Brassica juncea (L.) under Cd-stress. Results showed that Cd-stress significantly decreased the growth and physiological parameters of mustard plants. Inoculation with Cd-tolerant, IAA and EPS-producing rhizobacterial strains, however, significantly retrieved the inhibitory effects of Cd-stress on mustard growth, and physiology by up regulating antioxidant enzyme activities. Higher Cd accumulation and proline content was observed in the roots and shoot tissues upon Cd-stress in mustard plants while reduced proline and Cd accumulation was recorded upon rhizobacterial strains inoculation. Maximum decrease in proline contents (12.4%) and Cd concentration in root (26.9%) and shoot (29%) in comparison to control plants was observed due to inoculation with Bacillus safensis strain FN13. The activity of antioxidant enzymes was increased due to Cd-stress; however, the inoculation with Cd-tolerant, IAA-producing rhizobacterial strains showed a non-significant impact in the case of the activity of superoxide dismutase (SOD), peroxidase (POX) and catalase (CAT) in Brassica juncea (L.) plants under Cd-stress. Overall, Bacillus safensis strain FN13 was the most effective strain in improving the Brassica juncea (L.) growth and physiology under Cd-stress. It can be concluded, as the strain FN13 is a potential phytostabilizing biofertilizer for heavy metal contaminated soils, that it can be recommended to induce Cd-stress tolerance in crop plants.

Garbage enzymes effectively regulated the succession of enzymatic activities and the bacterial community during sewage sludge composting

This study evaluated nitrogen transformation, enzymatic activities and bacterial succession during sewage sludge composting with and without garbage enzymes (GE and CK, respectively). The results showed that GE addition significantly increased fluorescein diacetate hydrolase (FDA), cellulase, and nitrogenase activities during the composting process. GE addition reduced the cumulative NH₃ emissions by 66.5%, increased the peak NH₄-N content by 26.3% and increased the total nitrogen (TN) content of the end compost by 39.2% compared to CK. Microbiological analysis revealed that GE addition significantly increased the relative abundance of Firmicutes during the thermophilic and cooling phases relative to CK. The selected factors affected the bacterial community composition in the following order: NH₄-N > TOC > FDA > TN > C/N. Network analysis also showed that the enzymes were secreted mainly by Bacillus and norank_f_Caldilineaceae in GE, while they were secreted primarily by norank_f_Methylococcaceae in CK during the composting process.

Priming Strategies for Benefiting Plant Performance under Toxic Trace Metal Exposure

Combating environmental stress related to the presence of toxic elements is one of the most important challenges in plant production. The majority of plant species suffer from developmental abnormalities caused by an exposure to toxic concentrations of metals and metalloids, mainly Al, As, Cd, Cu, Hg, Ni, Pb, and Zn. However, defense mechanisms are activated with diverse intensity and efficiency. Enhancement of defense potential can be achieved though exogenously applied treatments, resulting in a higher capability of surviving and developing under stress and become, at least temporarily, tolerant to stress factors. In this review, I present several already recognized as well as novel methods of the priming process called priming, resulting in the so-called “primed state” of the plant organism. Primed plants have a higher capability of surviving and developing under stress, and become, at least temporarily, tolerant to stress factors. In this review, several already recognized as well as novel methods of priming plants towards tolerance to metallic stress are discussed, with attention paid to similarities in priming mechanisms activated by the most versatile priming agents. This knowledge could contribute to the development of priming mixtures to counteract negative effects of multi-metallic and multi-abiotic stresses. Presentation of mechanisms is complemented with information on the genes regulated by priming towards metallic stress tolerance. Novel compounds and techniques that can be exploited in priming experiments are also summarized.

Cadmium-tolerant endophytic Pseudomonas rhodesiae strains isolated from Typha latifolia modify the root architecture of Arabidopsis thaliana Col-0 in presence and absence of Cd

In this work, we isolated four Cd-tolerant endophytic bacteria from Typha latifolia roots that grow at a Cd-contaminated site. Bacterial isolates GRC065, GRC066, GRC093, and GRC140 were identified as Pseudomonas rhodesiae. These bacterial isolates tolerate cadmium and have abilities for phosphate solubilization, siderophore production, indole acetic acid (IAA) synthesis, and ACC deaminase activity, suggesting that they are plant growth-promoting rhizobacteria. Bacterial inoculation in Arabidopsis thaliana seedlings showed that P. rhodesiae strains increase total fresh weight and number of lateral roots concerning non-inoculated plants. These results indicated that P. rhodesiae strains promote A. thaliana seedlings growth by modifying the root system. On the other hand, in A. thaliana seedlings exposed to 2.5 mg/l of Cd, P. rhodesiae strains increased the number and density of lateral roots concerning non-inoculated plants, indicating that they modify the root architecture of A. thaliana seedlings exposed to cadmium. The results showed that P. rhodesiae strains promote the development of lateral roots in A. thaliana seedlings cultivated in both conditions, with and without cadmium. These results suggest that P. rhodesiae strains could exert a similar role inside the roots of T. latifolia that grow in the Cd-contaminated environment.

Current advances in plant-microbe communication via volatile organic compounds as an innovative strategy to improve plant growth

Volatile organic compounds (VOCs) emitted by microorganisms have demonstrated an important role to improve growth and tolerance against abiotic stress on plants. Most studies have used Arabidopsis thaliana as a model plant, extending to other plants of commercial interest in the last years. Interestingly, the microbial VOCs are characterized by its biodegradable structure, quick action, absence of toxic substances, and acts at lower concentration to regulate plant physiological changes. These compounds modulate plant physiological processes such as phytohormone pathways, photosynthesis, nutrient acquisition, and metabolisms. Besides, the regulation of gene expression associated with cell components, biological processes, and molecular function are triggered by microbial VOCs. Otherwise, few studies have reported the important role of VOCs for confer plant tolerance to abiotic stress, such as drought and salinity. Although VOCs have shown an efficient action to enhance the plant growth under controlled conditions, there are still great challenges for their greenhouse or field application. Therefore, in this review, we summarize the current knowledge about the technical procedures, study cases, and physiological mechanisms triggered by microbial VOCs to finally discuss the challenges of its application in agriculture.

Genome-Wide Identification and Characterization of Calcium Metabolism Related Gene Families in Arabidopsis thaliana and Their Regulation by Bacillus amyloliquefaciens Under High Calcium Stress

Several gene families involved in calcium signaling have been detected in plants, including calmodulin (CaM), calcium dependent protein kinases (CDPK), calcineurin B-like (CBL) and cyclic nucleotide-gated channels (CNGCs). In our previous study, we demonstrated that Bacillus amyloliquefaciens LZ04 (B. amyloliquefaciens LZ04) regulate genes involved in calcium stress in Arabidopsis thaliana (A. thaliana). Here, we aimed to explore the potential involvement of calcium-related gene families in the response of A. thaliana to calcium stress and the potential regulatory effects of B. amyloliquefaciens LZ04 on these genes. The structure, duplication, synteny, and expression profiles of 102 genes in calcium-related gene families in A. thaliana were investigated. Hidden Markov Models (HMMs) and BLASTP were used to predict candidate genes and conserved domains of the candidate genes were confirmed in SMART and NCBI CDD databases. Gene duplications and synteny were uncovered by BLASTP and phylogenetic analysis. The transcriptome expression profiles of candidate genes were investigated by strand-specific sequencing. Cluster analysis was used to find the expression profiles of calcium-related genes families under different treatment conditions. A total of 102 genes in calcium-related gene families were detected in A. thaliana genome, including 34 CDPK genes, 20 CNGC genes, 18 CIPK genes, 22 IQD genes, and 10 CBP genes. Additionally, of the 102 genes, 33 duplications (32.35%) and 26 gene pairs including 48 genes (47.06%) were detected. Treatment with B. amyloliquefaciens LZ04 enhanced the resistance of A. thaliana under high calcium stress by regulating some of the genes in the calcium-related gene families. Functional enrichment analysis revealed that the genes clustered in the 42nd expression profile which may be B. amyloliquefaciens-responsive genes under calcium stress were enriched in protein phosphorylation and protein modification process. Transcriptome data was validated by RT-PCR and the results generally corroborated the transcriptome sequencing results. These results may be useful for agricultural improvement in high calcium stress regions.

Alleviation of Cd phytotoxicity and enhancement of rape seedling growth by plant growth-promoting bacterium Enterobacter sp. Zm-123

The present study aims to investigate the impact of a metal-tolerant bacterium on metal detoxification and rape seedling growth promotion under Cd stress. The results showed that the isolated bacterium Enterobacter sp. Zm-123 has capability to resist Cd (200 mg/L), produce IAA (26.67 mg/L) and siderophores (82.34%), and solubilize phosphate (137.5 mg/L), etc. Zm-123 inoculation significantly enhanced the fresh weight of rape seedlings from 9.47 to 19.98% and the root length from 10.42 to 57.05% compared with non-inoculation group under different concentrations of Cd (0, 0.5, 1, 3, 5 mg/L) (p < 0.05). It also significantly increased the content of chlorophyll, soluble sugar, soluble protein, and proline (p < 0.05) in rape seedlings. Moreover, a significant elevation in catalase (CAT) and peroxidase (POD) activities and a significant reduction in malondialdehyde (MDA), electrolyte leakage (EL), and Cd content in rape seedlings were detected owing to Zm-123 inoculation (p < 0.05). The combined results imply that strain Zm-123 can alleviate the Cd phytotoxicity and promote the rape seedling growth by improving the physiological activity and antioxidant level, which can be potentially applied to protect plants from Cd toxicity.

Microbial inoculant and garbage enzyme reduced cadmium (Cd) uptake in Salvia miltiorrhiza (Bge.) under Cd stress

The uptake and accumulation of cadmium (Cd) in Salvia miltiorrhiza (Bge.) negatively affects the quality of its harvested roots, and seriously threatens human health. This study investigates the effect of a microbial inoculant (MI) and garbage enzyme (GE) on Cd uptake, the accumulation of bioactive compounds, and the community composition of microbes in the rhizosphere soil of S. miltiorrhiza under Cd stress. S. miltiorrhiza seedlings were transplanted to Cd-contaminated pots and irrigated with an MI, GE, a combination of an MI and GE (MIGE) or water (control). The results indicated that treatments with an MI, GE or MIGE can reduce Cd uptake in S. miltiorrhiza. The MIGE treatment had greater efficiency in reducing Cd uptake than the control (reduction by 37.90%), followed by the GE (25.31%) and MI (5.84%) treatments. Treatments with an MI, GE and MIGE had no significant impact on fresh and dry root biomass. Relative to the control, the MI treatment had the highest efficiency in increasing the accumulation of total tanshinones (an increase of 40.45%), followed by the GE treatment (40.08%), with the MIGE treatment (9.90%) treatment not having a more favorable effect than the separate application of an MI or GE. The salvianolic acid content for all groups was higher than the standard prescribed by Chinese pharmacopoeia, notwithstanding a slightly lower level in the treated groups relative to the control. In addition, metagenomic analysis indicated changes in the relative abundance of soil microbes associated with the bioremediation of heavy metals. The relative abundances of Brevundimonas, Microbacterium, Cupriavidus and Aspergillus were significantly greater in the treated groups than in the Control. These results suggest that using MI and GE, either separately or together, may not only improve the quality of S. miltiorrhiza but may also facilitate the microbial remediation of soil contaminated with Cd.

Understanding the molecular mechanisms for the enhanced phytoremediation of heavy metals through plant growth promoting rhizobacteria: A review

Rapid industrialization, modern agricultural practices and other anthropogenic activities add a significant quantity of toxic heavy metals into the environment, which induces severe toxic effects on all form of living organisms, alter the soil properties and its biological activity. Remediation of heavy metal contaminated sites has become an urgent necessity. Among the existing strategies, phytoremediation is an eco-friendly and much convincing tool for the remediation of heavy metals. However, the applicability of phytoremediation in contaminated sites is restricted by two prime factors such as i) slow growth rate at higher metal contaminated sites and ii) metal bioavailability. This circumstance could be minimized and accelerate the phytoremediation efficiency by incorporating the potential plant growth promoting rhizobacterial (PGPR) as a combined approach. PGPR inoculation might improve the plant growth through the production of plant growth promoting substances and improve the heavy metal remediation efficiency by the secretion of chelating agents, acidification and redox changes. Moreover, rhizobacterial inoculation consolidates the metal tolerance and uptake by regulating the expression of various metal transporters, tolerant and metal chelator genes. However, the exact underlying molecular mechanism of PGPR mediated plant growth promotion and phytoremediation of heavy metals is poorly understood. Thus, the present review provides clear information about the molecular mechanisms excreted by PGPR strains in plant growth promotion and phytoremediation of heavy metals.

Enterobacter asburiae Reduces Cadmium Toxicity in Maize Plants by Repressing Iron Uptake-Associated Pathways

Soil microbes have recently been utilized to improve cadmium (Cd) tolerance and lower its accumulation in plants. Nevertheless, whether rhizobacteria can prevent Cd uptake by graminaceous plants and the underlying mechanisms remain elusive. In this study, inoculation with Enterobacter asburiae NC16 reduced transpiration rates and the expression of some iron (Fe) uptake-related genes including ZmFer, ZmYS1, ZmZIP, and ZmNAS2 in maize (Zea mays) plants, which contributed to mitigation of Cd toxicity. However, the inoculation with NC16 failed to suppress the transpiration rates and transcription of these Fe uptake-related genes in plants treated with fluridone, an abscisic acid (ABA) biosynthetic inhibitor, indicating that the impacts of NC16-inoculation observed were dependent on the actions of ABA. We found that NC16 increased the host ABA levels by mediating the metabolism of ABA rather than its synthesis. Moreover, the capacity of NC16 to inhibit plant uptake of Cd was greatly weakened in plants overexpressing ZmZIP, encoding a zinc/iron transporter. Collectively, our findings indicated that E. asburiae NC16 reduced Cd toxicity in maize plants at least partially by hampering the Fe uptake-associated pathways.

Role of nitric oxide in plant responses to heavy metal stress: exogenous application versus endogenous production

Anthropogenic activities, such as industrial processes, mining, and agriculture, lead to an increase in heavy metal concentrations in soil, water, and air. Given their stability in the environment, heavy metals are difficult to eliminate and can constitute a human health risk by entering the food chain through uptake by crop plants. An excess of heavy metals is toxic for plants, which have various mechanisms to prevent their accumulation. However, once metals enter the plant, oxidative damage sometimes occurs, which can lead to plant death. Initial production of nitric oxide (NO), which may play a role in plant perception, signalling, and stress acclimation, has been shown to protect against heavy metals. Very little is known about NO-dependent mechanisms downstream from signalling pathways in plant responses to heavy metal stress. In this review, using bioinformatic techniques, we analyse studies of the involvement of NO in plant responses to heavy metal stress, its possible role as a cytoprotective molecule, and its relationship with reactive oxygen species. Some conclusions are drawn and future research perspectives are outlined to further elucidate the signalling mechanisms underlying the role of NO in plant responses to heavy metal stress.

Induced Systemic Resistance (ISR) and Fe Deficiency Responses in Dicot Plants

Plants develop responses to abiotic stresses, like Fe deficiency. Similarly, plants also develop responses to cope with biotic stresses provoked by biological agents, like pathogens and insects. Some of these responses are limited to the infested damaged organ, but other responses systemically spread far from the infested organ and affect the whole plant. These latter responses include the Systemic Acquired Resistance (SAR) and the Induced Systemic Resistance (ISR). SAR is induced by pathogens and insects while ISR is mediated by beneficial microbes living in the rhizosphere, like bacteria and fungi. These root-associated mutualistic microbes, besides impacting on plant nutrition and growth, can further boost plant defenses, rendering the entire plant more resistant to pathogens and pests. In the last years, it has been found that ISR-eliciting microbes can induce both physiological and morphological responses to Fe deficiency in dicot plants. These results suggest that the regulation of both ISR and Fe deficiency responses overlap, at least partially. Indeed, several hormones and signaling molecules, like ethylene (ET), auxin, and nitric oxide (NO), and the transcription factor MYB72, emerged as key regulators of both processes. This convergence between ISR and Fe deficiency responses opens the way to the use of ISR-eliciting microbes as Fe biofertilizers as well as biopesticides. This review summarizes the progress in the understanding of the molecular overlap in the regulation of ISR and Fe deficiency responses in dicot plants. Root-associated mutualistic microbes, rhizobacteria and rhizofungi species, known for their ability to induce morphological and/or physiological responses to Fe deficiency in dicot plant species are also reviewed herein.

Bacillus subtilis STU6 Ameliorates Iron Deficiency in Tomato by Enhancement of Polyamine-Mediated Iron Remobilization

Iron (Fe) deficiency often triggers arginine overproduction in plants. However, it remains elusive whether Fe deficiency-induced increases of arginine levels are involved in beneficial rhizobacteria recruitment and that the mechanism underlying rhizobacteria induced plant Fe deficiency tolerance. Here, Bacillus subtilis STU6 increased soluble Fe content in tomato, thereby alleviating Fe deficiency-induced chlorosis. In a split-root system, STU6 significantly induced arginine exudation by Fe-deficient roots, and increased arginine levels promoted spermidine (Spd) production by STU6 and bacterial colonization. Deletion of the STU6 speB gene inhibited Spd synthesis and abrogated STU6-induced increments of soluble Fe content in the Fe-deficient plants. Increased host Spd levels by STU6 greatly stimulated the NO accumulation in the Fe-deficient roots. Furthermore, disruption of NO signaling markedly repressed STU6-mediated cell wall Fe remobilization. Collectively, our data provide important evidence that chemical dialogues between tomato and STU6 contribute to enhancement of microbe-mediated plant adaptation to Fe deficiency.

Sniffing bacterial volatile compounds for healthier plants

Bacterial volatile compounds (BVCs) are not waste or by-products of primary metabolism but rather have critical roles in the biology and ecological competence of bacteria. BVCs are exploited as a source of nutrients and information in plant-bacteria interactions. They target key points in plant physiology, activating downstream metabolic pathways by a domino effect. BVCs are an ancient signal and are involved in plant-bacteria communication, which was shaped during evolutionary history and established before the development of higher plants. This type of communication is not exclusive to mutualistic interactions, because pathogens also use volatiles to alter plant physiology. Here, fragmented information is drawn together to provide a clearer view of how BVCs affect such interactions.

Arabidopsis Transcription Factor MYB102 Increases Plant Susceptibility to Aphids by Substantial Activation of Ethylene Biosynthesis

Induction of ethylene biosynthesis by aphids increases the susceptibility of several plant species to aphids. Recent studies have indicated that some MYB transcription factors regulate the phloem-based defense against aphid infestation by modulating ethylene (ET) signaling. Arabidopsis MYB102 has previously been shown to be induced by wound signaling and regulate defense response against chewing insects. However, it remains unclear whether ArabidopsisMYB102 takes part in the defense response of plants to aphids. Here, we investigated the function of MYB102 in the response of Arabidopsis to aphid infestation. ArabidopsisMYB102 was primarily expressed in vascular tissues, and its transcription was remarkably induced by green peach aphids (GPA; Myzus persicae). The results of RNA-Sequencing revealed that overexpression of MYB102 in Arabidopsis promoted ET biosynthesis by upregulation of some 1-aminocyclopropane-1-carboxylate synthase (ACS) genes, which are rate-limiting enzymes of the ET-synthetic pathway. Enhanced ET levels led to reduced Arabidopsis resistance to GPA. Furthermore, dominant suppression of MYB102 inhibited aphid-induced increase of ET levels in Arabidopsis. In agreement with a negative regulatory role for ET in aphid defense responses, the MYB102-overexpressing lines were more susceptible to GPA than wild-type (WT) plants. Overexpression of MYB102 in Arabidopsis obviously repressed aphid-induced callose deposition. Conversely, overexpression of MYB102 failed to increase aphid susceptibility in both the ET-insensitive mutants and plants treated with inhibitors of ET signaling pathways, demonstrating that the ET was critical for promoting aphid performance conferred by overexpression of MYB102. Collectively, our findings indicate that the Arabidopsis MYB102 increases host susceptibility to GPA through the ET-dependent signaling pathways.

From Petri Dishes to Model Ecosystems

Model ecosystems could provide significant insight into the evolution and behavior of real ecosystems. We discuss the advantages and limitations of common approaches like mesocosms. In this context, we highlight recent breakthroughs that allow for the creation of networks of organisms with independently controlled environments and rates of chemical exchange.

Microbial volatiles as plant growth inducers

Agricultural practices require novel products that allow sustainable development and commercial production according to the needs of farmers and consumers. Therefore, in the last decade, eco-friendly alternatives have been studied, so volatile organic compounds (VOCs) emitted by microorganisms have emerged as a cheaper, effective, efficient, and an eco-friendly alternative. VOCs are lipophilic compounds derived from microbial metabolic pathways with low molecular weight (<300 g mol-1), low boiling point, and high vapor pressure that allow them to act as signal molecules over short and long distances. Main case studies provide evidence that VOCs released from diverse microorganisms (i.e. Bacillus, Pseudomonas, Arthrobacter, Fusarium, and Alternaria) can stimulate growth on a specific "target" seedling, such as Arabidopsis and tobacco. Some identified compounds, such as 3-hydroxy-2-butanone (acetoin), 2,3-butanediol, 2-pentylfuran, or dimethylhexadecylmine have shown their ability to elicit growth at root or leaf level. Few studies indicate that VOCs act in the regulation at phytohormone, metabolic pathways and nutrition levels according to genetic, proteomic, and metabolic analyses; but action mechanisms associated with growth-inducing activity are poorly understood. In this work, we reviewed case studies regarding identified compounds and action mechanisms for a better understanding of the information collected so far. Additionally, a brief description about the effects of VOCs for induction of resistance and tolerance in plants are presented, where compounds such as acetoin, dimethyl disulfide, 3-pentanol and 6-pentyl-α-pyrone have been reported. Furthermore, we summarized the knowledge to direct future studies that propose microbial VOCs as a technological innovation in agriculture and horticulture.

Involvement of abscisic acid in microbe-induced saline-alkaline resistance in plants

Soil salinity-alkalinity is one of abiotic stresses that lead to plant growth inhibition and yield loss. It has recently been indicated that plant growth promoting rhizobacteria (PGPR) can enhance the capacity of plants to counteract negative effects caused by adverse environments. However, whether PGPR confers increased saline-alkaline resistance of plants and the underlying mechanisms remain unclear. We thus investigated the effects of Bacillus licheniformis (strain SA03) on Chrysanthemum plants grown under saline-alkaline conditions. Soil inoculation with SA03 significantly mitigated saline-alkaline stress in plants with augmented photosynthesis, biomass and survival rates. Moreover, the inoculated plants accumulated more Fe and less Na⁺ content than the non-inoculated plants under the stress. However, the inoculation with SA03 failed to trigger a series of saline-alkaline stress responses in abscisic acid (ABA)- and nitric oxide (NO)-deficient plants. Furthermore, NO acted as a secondary messenger of ABA to regulate the stress responses and tolerance in Chrysanthemum plants. Therefore, these findings indicated that B. licheniformis SA03 could be employed to improve saline-alkaline tolerance of plants by mediating cellular ABA levels.