Isolation and characterization of endophytic bacteria from the nickel hyperaccumulator plant Alyssum bertolonii

Microbial assisted alleviation of nickel toxicity in plants: A review

Nickel (Ni) is required in trace amounts (less than 500 µg kg-1) in plants to regulate metabolic processes, the immune system, and to act as an enzymatic catalytic cofactor. Conversely, when nickel is present in high concentration, it is considered as a toxic substance. Excessive human nickel exposure occurs through ingestion, inhalation, and skin contact, ultimately leading to respiratory, cardiovascular, and chronic kidney diseases. Due to anthropogenic activities, the nickel concentrations in various environmental scenarios have progressively risen to levels as high as 26,000 ppm in soil and 0.2 mg L-1 in water; surpassing the established safety threshold limits of 100 ppm for soil and 0.005 ppm for surface water. Nickel is required by various plant species for facilitating biological processes; in the range of 0.01-5 µg g-1 (dry weight). When present in excess, nickel toxicity in plants (10-1000 mg kg-1 dry weight mass) causes many disrupted metabolic processes; leading to lower growth, altered development, hindered seed germination, chlorosis, and necrosis. To tackle any metal-linked pollution issues, various remediation approaches are employed to remove heavy metals (especially nickel) and metalloids including physicochemical, and biological methods. Based on literature, the physicochemical methods are not commonly used due to their costly nature and the potential for producing secondary pollutants. Interestingly, bioremediation is considered by many practitioners as an easy-to-handle, efficient, and cost-effective approach, encompassing techniques such as phytoremediation, bioleaching, bioreactors, green landforming, and bio-augmentation. Operationally, phytoremediation is widely utilized for cleaning up contaminated sites. To support the phytoremediative processes, numerous nickel hyperaccumulating plants have been identified; these species can absorb from their surroundings and store high concentrations of nickel (through various mechanisms) in their biomass, thereby helping to detoxify nickel-contaminated soils via phytoextraction. The microbe-assisted phytoremediation further optimizes the nickel detoxification processes by fostering beneficial interactions between microbes and the nickel-hyperaccumulators; promoting enhanced metal uptake, transformation, and sequestration. Microbe-assisted phytoremediation can be categorized into four subtypes: bacterial-assisted phytoremediation, cyanoremediation, mycorrhizal-assisted remediation, and rhizoremediation. These diverse approaches are likely to offer more effective and sustainable remediative strategy to ecologically restore the nickel-contaminated environments.

Plant growth-promoting rhizobacterial secondary metabolites in augmenting heavy metal(loid) phytoremediation: An integrated green in situ ecorestorative technology

In recent times, increased geogenic and human-centric activities have caused significant heavy metal(loid) (HM) contamination of soil, adversely impacting environmental, plant, and human health. Phytoremediation is an evolving, cost-effective, environment-friendly, in situ technology that employs indigenous/exotic plant species as natural purifiers to remove toxic HM(s) from deteriorated ambient soil. Interestingly, the plant's rhizomicrobiome is pivotal in promoting overall plant nutrition, health, and phytoremediation. Certain secondary metabolites produced by plant growth-promoting rhizobacteria (PGPR) directly participate in HM bioremediation through chelation/mobilization/sequestration/bioadsorption/bioaccumulation, thus altering metal(loid) bioavailability for their uptake, accumulation, and translocation by plants. Moreover, the metallotolerance of the PGPR and the host plant is another critical factor for the successful phytoremediation of metal(loid)-polluted soil. Among the phytotechniques available for HM remediation, phytoextraction/phytoaccumulation (HM mobilization, uptake, and accumulation within the different plant tissues) and phytosequestration/phytostabilization (HM immobilization within the soil) have gained momentum in recent years. Natural metal(loid)-hyperaccumulating plants have the potential to assimilate increased levels of metal(loid)s, and several such species have already been identified as potential candidates for HM phytoremediation. Furthermore, the development of transgenic rhizobacterial and/or plant strains with enhanced environmental adaptability and metal(loid) uptake ability using genetic engineering might open new avenues in PGPR-assisted phytoremediation technologies. With the use of the Geographic Information System (GIS) for identifying metal(loid)-impacted lands and an appropriate combination of normal/transgenic (hyper)accumulator plant(s) and rhizobacterial inoculant(s), it is possible to develop efficient integrated phytobial remediation strategies in boosting the clean-up process over vast regions of HM-contaminated sites and eventually restore ecosystem health.

Perspectives of pteridophytes microbiome for bioremediation in agricultural applications

The microbiome is the synchronised congregation of millions of microbial cells in a particular ecosystem. The rhizospheric, phyllospheric, and endospheric microbial diversity of lower groups of plants like pteridophytes, which includes the Ferns and Fern Allies, have also given numerous alternative opportunities to achieve greener and sustainable agriculture. The broad-spectrum bioactivities of these microorganisms, including bioremediation of heavy metals (HMs) in contaminated soil, have been drawing the attention of agricultural researchers for the preparation of bioformulations for applications in climate-resilient and versatile agricultural production systems. Pteridophytes have an enormous capacity to absorb HMs from the soil. However, their direct application in the agricultural field for HM absorption seems infeasible. At the same time, utilisation of Pteridophyte-associated microbes having the capacity for bioremediation have been evaluated and can revolutionise agriculture in mining and mineral-rich areas. In spite of the great potential, this group of microbiomes has been less studied. Under these facts, this prospective review was carried out to summarise the basic and applied research on the potential of Pteridophyte microbiomes for soil bioremediation and other agricultural applications globally. Gaps have also been indicated to present scopes for future research programmes.

Current Scenario and Future Prospects of Endophytic Microbes: Promising Candidates for Abiotic and Biotic Stress Management for Agricultural and Environmental Sustainability

Globally, substantial research into endophytic microbes is being conducted to increase agricultural and environmental sustainability. Endophytic microbes such as bacteria, actinomycetes, and fungi inhabit ubiquitously within the tissues of all plant species without causing any harm or disease. Endophytes form symbiotic relationships with diverse plant species and can regulate numerous host functions, including resistance to abiotic and biotic stresses, growth and development, and stimulating immune systems. Moreover, plant endophytes play a dominant role in nutrient cycling, biodegradation, and bioremediation, and are widely used in many industries. Endophytes have a stronger predisposition for enhancing mineral and metal solubility by cells through the secretion of organic acids with low molecular weight and metal-specific ligands (such as siderophores) that alter soil pH and boost binding activity. Finally, endophytes synthesize various bioactive compounds with high competence that are promising candidates for new drugs, antibiotics, and medicines. Bioprospecting of endophytic novel secondary metabolites has given momentum to sustainable agriculture for combating environmental stresses. Biotechnological interventions with the aid of endophytes played a pivotal role in crop improvement to mitigate biotic and abiotic stress conditions like drought, salinity, xenobiotic compounds, and heavy metals. Identification of putative genes from endophytes conferring resistance and tolerance to crop diseases, apart from those involved in the accumulation and degradation of contaminants, could open new avenues in agricultural research and development. Furthermore, a detailed molecular and biochemical understanding of endophyte entry and colonization strategy in the host would better help in manipulating crop productivity under changing climatic conditions. Therefore, the present review highlights current research trends based on the SCOPUS database, potential biotechnological interventions of endophytic microorganisms in combating environmental stresses influencing crop productivity, future opportunities of endophytes in improving plant stress tolerance, and their contribution to sustainable remediation of hazardous environmental contaminants.

Plant growth-promoting and heavy metal-resistant Priestia and Bacillus strains associated with pioneer plants from mine tailings

Open mine tailings dams are extreme artificial environments containing sizeable potentially toxic elements (PTEs), including heavy metals (HMs), transition metals, and metalloids. Furthermore, these tailings have nutritional deficiencies, including assimilable phosphorus sources, organic carbon, and combined nitrogen, preventing plant colonization. Bacteria, that colonize these environments, have mechanisms to tolerate the selective pressures of PTEs. In this work, several Priestia megaterium (formerly Bacillus megaterium), Bacillus mojavensis, and Bacillus subtilis strains were isolated from bulk tailings, anthills, rhizosphere, and endosphere of pioneer plants from abandoned mine tailings in Zacatecas, Mexico. Bacillus spp. tolerated moderate HMs concentrations, produced siderophores and indole-3-acetic acid (IAA), solubilized phosphates, and reduced acetylene in the presence of HMs. The strains harbored different PIB-type ATPase genes encoding for efflux pumps and Cation Diffusion Facilitator (CDF) genes. Moreover, nifH and nifD nitrogenase genes were detected in P. megaterium and B. mojavensis genomic DNA. They showed similarity with sequences of the beta-Proteobacteria species, which may represent likely horizontal transfer events. These Bacillus species precede the colonization of mine tailings by plants. Their phenotypic and genotypic features could be essential in the natural recovery of the sites by reducing the oxidative stress of HMs, fixing nitrogen, solubilizing phosphate, and accumulating organic carbon. These traits of the strains reflect the adaptations of Bacillus species to the mine tailings environment and could contribute to the success of phytoremediation efforts.

Rhizospheric bacteria: the key to sustainable heavy metal detoxification strategies

The increasing rate of industrialization, anthropogenic, and geological activities have expedited the release of heavy metals (HMs) at higher concentration in environment. HM contamination resulting due to its persistent nature, injudicious use poses a potential threat by causing metal toxicities in humans and animals as well as severe damage to aquatic organisms. Bioremediation is an emerging and reliable solution for mitigation of these contaminants using rhizospheric microorganisms in an environmentally safe manner. The strategies are based on exploiting microbial metabolism and various approaches developed by plant growth promoting bacteria (PGPB) to minimize the toxicity concentration of HM at optimum levels for the environmental clean-up. Rhizospheric bacteria are employed for significant growth of plants in soil contaminated with HM. Exploitation of bacteria possessing plant-beneficial traits as well as metal detoxifying property is an economical and promising approach for bioremediation of HM. Microbial cells exhibit different mechanisms of HM resistance such as active transport, extra cellular barrier, extracellular and intracellular sequestration, and reduction of HM. Tolerance of HM in microorganisms may be chromosomal or plasmid originated. Proteins such as MerT and MerA of mer operon and czcCBA, ArsR, ArsA, ArsD, ArsB, and ArsC genes are responsible for metal detoxification in bacterial cell. This review gives insights about the potential of rhizospheric bacteria in HM removal from various polluted areas. In addition, it also gives deep insights about different mechanism of action expressed by microorganisms for HM detoxification. The dual-purpose use of biological agent as plant growth enhancement and remediation of HM contaminated site is the most significant future prospect of this article.

Regulation mechanism of plant response to heavy metal stress mediated by endophytic fungi

Endophytic fungi exist widely in plants and play an important role in the growth and adaptation of plants. They could be used in phytoremediation techniques against heavy metal contaminated soil since beneficial microbial symbionts can endow plants with resistance to external heavy metal stresses. This review summarized the regulation mechanism of plant response to heavy metal stress mediated by endophytic fungi. Potential endophytic fungi in enhancing plant's adaption to heavy metal stresses include arbuscular mycorrhizal fungi, dark septate endophytic fungi, plant growth promoting endophytic fungi. The mechanisms involve coevolution strategy, immune regulation and detoxification transport to improve the ability of plants to adapt to heavy metal stress. They can increase the synthesis of host hormones and maintaining the balance of endogenous hormones, strengthen osmotic regulation, regulate carbon and nitrogen metabolism, and increase immune activity, antioxidant enzyme and glutathione activity. They also help to improve the detoxification transport and heavy metal emission capacity of the host by significantly producing iron carrier, metallothionein and 1-aminocyclopropane-1-carboxylic acid deaminase. The combination of endophytic fungi and hyperaccumulation plants provides a promising technology for the ecological restoration of heavy metal contaminated soil. Endophytic fungi reserves further development on enhancing host plant's adaptability to heavy metal stresses.

Endophytic Pseudomonas sp. from Agave palmeri Participate in the Rhizophagy Cycle and Act as Biostimulants in Crop Plants

Plant growth-promoting bacteria are generating increasing interest in the agricultural industry as a promising alternative to traditional chemical fertilizers; however, much of the focus has been on rhizosphere bacteria. Bacterial endophytes are another promising source of plant growth-promoting bacteria, and though many plants have already been prospected for beneficial microbes, desert plants have been underrepresented in such studies. In this study, we show the growth-promoting potential of five strains of endophytic Pseudomonas sp. isolated from Agave palmeri, an agave from the Sonoran Desert. When inoculated onto Kentucky bluegrass, clover, carrot, coriander, and wheat, endophytic Pseudomonas sp. increased seedling root lengths in all hosts and seedling shoot lengths in Kentucky bluegrass, carrot, and wheat. Transformation of the Pseudomonas sp. strain P3AW to express the fluorescent protein mCherry revealed that Pseudomonas sp. becomes endophytic in non-native hosts and participates in parts of the rhizophagy cycle, a process by which endophytic bacteria cycle between the soil and roots, bringing in nutrients from the soil which are then extracted through reactive oxygen-mediated bacterial degradation in the roots. Tracking of the Pseudomonas sp. strain P3AW also provided evidence for a system of endophyte, or endophyte cell content, transport via the vascular bundle. These results provide further evidence of the rhizophagy cycle in plants and how it relates to growth promotion in plants by biostimulant bacteria.

Bioactive Compounds from Endophytic Bacteria Bacillus subtilis Strain EP1 with Their Antibacterial Activities

Endophytic bacteria boost host plant defense and growth by producing vital compounds. In the current study, a bacterial strain was isolated from the Boswellia sacra plant and identified as Bacillus subtilis strain EP1 (accession number: MT256301) through 16S RNA gene sequencing. From the identified bacteria, four compounds-1 (4-(4-cinnamoyloxy)phenyl)butanoic acid), 2 (cyclo-(L-Pro-D-Tyr)), 3 (cyclo-(L-Val-L-Phe)), and 4 (cyclo-(L-Pro-L-Val))-were isolated and characterized by 1D and 2D NMR and mass spectroscopy. Moreover, antibacterial activity and beta-lactam-producing gene inhibition (δ-(l-α-aminoadipyl)-l-cysteinyl-d-valine synthetase (ACVS) and aminoadipate aminotransferase (AADAT)) assays were performed. Significant antibacterial activity was observed against the human pathogenic bacterial strains (E. coli) by compound 4 with a 13 ± 0.7 mm zone of inhibition (ZOI), followed by compound 1 having an 11 ± 0.7 mm ZOI. In contrast, the least antibacterial activity among the tested samples was offered by compound 2 with a 10 ± 0.9 mm ZOI compared to the standard (26 ± 1.2 mm). Similarly, the molecular analysis of beta-lactam inhibition determined that compounds 3 and 4 inhibited the two genes (2- to 4-fold) in the beta-lactam biosynthesis (ACVS and AADAT) pathway. From these results, it can be concluded that future research on these compounds could lead to the inhibition of antibiotic-resistant pathogenic bacterial strains.

Soil microbial community structure and environmental effects of serpentine weathering under different vegetative covers in the serpentine mining area of Donghai County, China

The use of serpentine biological weathering to capture atmospheric CO₂ has attracted much attention. In the long-term mining activities in a serpentine mining area, a large amount of serpentine powder diffused into the surrounding forest and farmland soil. The study of the serpentine weathering in soils of different vegetative covers and the composition characteristics of soil carbonate has important implications for understanding the serpentine weathering and carbon sequestration under natural conditions. The microbial diversity on exposed rock serpentine surfaces and soil under different vegetative covers in the serpentine mining area in Donghai County, China was investigated by high-throughput sequencing technology, and the characteristics of serpentine weathering and soil carbonate in related area were also explored by XRF, XRD, SEM-EDS, and chemical analysis methods. The results showed that the richness and uniformity of the bacteria species community increased significantly with the increasing complexity of plant groups covering the rock surface, but the species richness and uniformity of fungi showed an overall declining trend. Furthermore, high‑magnesium calcite (HMC) is ubiquitous on the exposed rock surface and the soil under different vegetative covers in this area. Based on these results, combined with the verification test results of HMC fixed heavy metal ions, the model of serpentine weathering in serpentine mining soil to synthesize carbonate and fix heavy metal ions was developed. That is, with the increase in the degree of rock weathering and the colonization of plants, the soil and plants seem to shape jointly a relatively stable microbial community structure adapted to the environment of the serpentine mining area, which promotes the serpentine weathering coupled with the formation of HMC and immobilization of metal ions in the serpentine soil. This study provides a theoretical basis for the serpentine bio-weathering in the mine area to capture atmospheric CO₂.

Biosorption efficiency of nickel by various endophytic bacterial strains for removal of nickel from electroplating industry effluents: an operational study

Realising the hazardous effect of nickel on human health, microbes and plants are effectively used for bioremediation. The endophytic microorganisms have an important role in the phytoremediation of nickel using Vigna radiata. Therefore, in order to harness the potential of microbial strains, the present study was designed to examine the metal biosorption ability of endophytic bacterial strains isolated from plants growing in nickel-contaminated soil. A total of six endophytic nickel resistance bacteria were isolated from the plant Vigna radiata. The metal tolerant bacterial strains were identified following 16 S rRNA gene sequence analysis. Nickel biosorption estimation and plant growth-promoting (PGP) activities of isolated strains were performed and found high nickel biosorption efficiency of 91.3 ± 0.72% at 600 mg L^-1 using Bacillus safensis an isolated endophytic strain from Vigna radiata. Furthermore, high indole acetic acid (IAA) and exopolysaccharide (EPS) production were obtained in all the strains as compared to without nickel-containing medium used as control. Moreover, the production of high EPS suggests improved biosorption ability of isolated endophytic strains. In addition, a kinetic study was also performed to evaluate different adsorptions isotherms and support the nickel biosorption ability of endophytic strains. The treatment of nickel electroplating industrial effluent was also demonstrated by isolated endophytic strains. Among six (6) strains, B. cereus showed maximum 57.2 ± 0.62% biosorption efficiency of nickel which resulted in the removal of 1003.50 ± 0.90 mg L^-1 of nickel from the electroplating industry effluents containing initial 1791 ± 0.90 mg L^-1 of nickel. All other strains were also capable of significant nickel biosorption from electroplating industry effluents as well. Thus, isolated endophytic nickel tolerant strains can be further used at large-scale biosorption of nickel from electroplating industry effluent.

Surface sterilization for isolation of endophytes: Ensuring what (not) to grow

Endophytic microbiota opens a magnificent arena of metabolites that served as a potential source of medicines for treating a variety of ailments and having prospective uses in agriculture, food, cosmetics, and many more. There are umpteen reports of endophytes improving the growth and tolerance of plants. In addition, endophytes from lifesaving drug-producing plants such as Taxus, Nothapodytes, Catharanthus, and so forth have the ability to produce host mimicking compounds. To harness these benefits, it is imperative to isolate the true endophytes, not the surface microflora. The foremost step in endophyte isolation is the removal of epiphytic microbes from plant tissues, called as surface sterilization. The success of surface sterilization decides "what to grow" (the endophytes) and "what not to grow" (the epiphytes). It is very crucial to use an appropriate sterilant solution, concentration, and exposure time to ensure thorough surface disinfection with minimal damage to the endophytic diversity. Commonly used surface sterilants include sodium hypochlorite (2%-10%), ethanol (70%-90%), mercuric chloride (0.1%), formaldehyde (40%), and so forth. In addition, the efficiency could further be improved by pretreatment with surfactants such as Triton X-100, Tween 80, and Tween 20. This review comprehensively deals with the various sterilants and sterilization methods for the isolation of endophytic microbes. In addition, the mechanisms and rationale behind using specific surface sterilants have also been elaborated at length.

Coprinus comatus endophytic bacteria characteristics and mechanisms for the cadmium resistance

Characteristics and resistant mechanisms of macro-fungus endophytic bacteria to cadmium (Cd) have not been well defined. Strains L1 and L3 with Cd-resistant capacity were isolated from the fruiting body of Coprinus comatus, which were identified as Bacillus sp. Under the stress of Cd, the morphologies of both L1 and L3 changed to reduce the threat of Cd. The results of Fourier Transform Infrared Spectrometry indicated that functional groups such as -OH, -COOH, and -NH₂ participated in the Cd adsorption process. The contents of Cd adsorbed on the cell wall of L1 were 83.46-174.51% higher than that of L3. On the contrary, the contents of Cd accumulated in L1 cytoplasm were 38.77-74.77% lower than that of L3. As the level of Cd increased from 10 to 30 mg/L, the percentages of Cd distributed on the cell walls of L1 and L3 increased by 42.43% and 26.78%, respectively. The results also revealed that the contents of Cd absorbed by the sterilized strains L1 and L3 were 47.67-64.94% and 8.65-78.63% higher than that of living ones, respectively. In addition, the proline production of L1 was 23.75-109.68% higher than that of L3, while the malondialdehyde (MDA) production of L1 was 0.96-15.60% lower than that of L3. Thus, through the comparison of endophytic bacterial physiological responses, the possible characteristics and resistant mechanisms of macro-fungus endophytic bacteria under Cd stress were firstly reported.

Effects of ectomycorrhizal fungus bolete identity on the community assemblages of endofungal bacteria

Ectomycorrhiza-associated bacteria, especially endofungal bacterial microbiota (EBM) in the fruiting body, play important roles in driving the establishment and function of ectomycorrhizae. However, the influence of ectomycorrhizal fungus bolete identity on their EBM is still unclear. We analysed the EBM of three different bolete fruiting body species on Thousand Island Lake, including Tylopilus felleus, Tylopilus areolatus and Boletus queletii, and compared them with their corresponding mycosphere soil bacterial microbiota by high-throughput sequencing. The EBM was classified into Bacillus, Pseudomonas, Burkholderia and Stenotrophomonas genera. Proteobacteria, Bacteroidetes and Acidobacteria were predominant in the EBM of bolete fruiting bodies as well as their mycosphere soil, while Firmicutes was significantly higher in the EBM. Moreover, the core microbiome (342 operational taxonomic units) of the EBM was shared among the three bolete fungal species. The relative abundances of gene families related to cell cycle control and nucleotide, coenzyme and lipid metabolism were significantly higher in the EBM than in the corresponding mycosphere soil bacterial microbiota, but there was no difference among the three different boletes. The results suggested that the host identity of ectomycorrhizal fungus boletes could affect the EBM, which might be mainly due to the selection of host fungi for the different functional EBM needed.

Efficacy of rhizobacteria for degradation of profenofos and improvement in tomato growth

Pesticides are widely used for managing pathogens and pests for sustainable agricultural output to feed around seven billion people worldwide. After their targeted role, residues of these compounds may build up and persist in soils and in the food chain. This study evaluated the efficiency of bacterial strains capable of plant growth promotion and biodegradation of profenofos. To execute this, bacteria were isolated from an agricultural area with a history of repeated application of profenofos. The profenofos degrading bacterial strains with growth-promoting characteristics were identified based on biochemical and molecular approaches through partial 16S ribosomal rRNA gene sequencing. The results revealed that one strain, Enterobacter cloacae MUG75, degraded over 90% profenofos after 9 days of incubation. Similarly, plant growth was significantly increased in plants grown in profenofos (100 mg L^-1) contaminated soil inoculated with the same strain. The study demonstrated that inoculation of profenofos degrading bacterial strains increased plant growth and profenofos degradation. Novelty statementPesticides are extensively applied in the agriculture sector to overcome pest attacks and to increase food production to fulfill the needs of the growing world population. Residues of these pesticides can persist in the environment for long periods, may enter the groundwater reservoirs and cause harmful effects on living systems highlighting the need for bioremediation of pesticide-contaminated environments. Microbes can use pesticides as a source of carbon and energy and convert them into less toxic and non-toxic products. Application of profenofos degrading rhizobacteria in interaction with the plants in the rhizosphere can remediate the pesticide-contaminated soils and minimize their uptake into the food chain. Hence, this approach can improve soil health and food quality without compromising the environment.

Combination of Siderophore-Producing Bacteria and Piriformospora indica Provides an Efficient Approach to Improve Cadmium Tolerance in Alfalfa

Application of siderophore-producing microorganisms (SPMs), as an environmentally friendly approach, facilitates plant growth and survival under heavy metals toxicity. This study evaluated the effectiveness of SPMs, belonging to the bacterial genera Rhizobium and Pseudomonas and a root endophytic fungus (Piriformospora indica) to improve the fitness of alfalfa under cadmium (Cd) stress. A greenhouse experiment was performed as a randomized design with factorial arrangement of treatments. Treatments included microbial inoculations (Sinorhizobium meliloti, Pseudomonas fluorescence, and P. indica) and different Cd concentrations (0, 2, 5, 10 mg/kg) with three replications in potting media containing sand and sterile perlite (v/v, 2:1). The effect of Cd on plant growth and development, antioxidant enzymes activities, and accumulation of Cd and nutrients in alfalfa plant was investigated. Alfalfa inoculated with SPMs showed significantly higher biomass and nutrients uptake under both normal and Cd stress conditions than the controls. Under the highest Cd concentration (10 mg/kg), alfalfa plants inoculated with P. fluorescens and P. indica, either alone or in combination, showed the highest shoot dry weights. Cd-induced oxidative stress was mitigated by SPMs through enhanced antioxidant enzyme activities of catalase, ascorbate peroxidase, and guaiacol peroxidase. We showed that P. indica either alone or in combination with the siderophore producing bacteria (SPB) minimized the toxicity of Cd by enhanced growth rate and the lower Cd concentration in the shoots. In conclusion, metal-resistant SPMs could assist alfalfa to survive in Cd-contaminated soil by enhancing plant growth and development. Application of plant-associated microbes is an efficient, environmentally friendly approach to surmount the adverse effects of heavy metals toxicity on plants, animals, and humans. Graphical abstract.

Bioaugmentation with copper tolerant endophyte Pseudomonas lurida strain EOO26 for improved plant growth and copper phytoremediation by Helianthus annuus

Organic fertilizers became a better alternative to chemical fertilizers in modern agricultural practices however, contamination of copper (Cu) from organic fertilizer is still a major concern for the globe. Plant growth promoting (PGP) microorganisms showed their efficiency to combat with this problem and thus Cu tolerant PGP endophytes from roots of Odontarrhena obovata (Alyssum obovatum) growing on Cu smelter contaminated serpentine soil were explored in present study. Out of twenty-four isolates, Pseudomonas lurida strain EOO26 identified by 16s rRNA gene sequencing was selected to check its efficacy for Cu-remediation. The strain EOO26 showed multi-metal tolerance, drought resistance and exhibited PGP attributes such as 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, siderophore and ammonia production. Significant production of indole-3-acetic acid and phosphate-solubilization under different Cu concentration (0-100 mg L^-1) at varying pH (5.0-8.0) suggests potentiality of this strain to work effectively under wide range of abiotic stress conditions. Plant growth experiment (pH 6.8 ± 0.3) in copper spiked soil suggested a significant increase in length and dry weight of root and shoot of sunflower (Helianthus annuus) after inoculation with strain EOO26. Plants inoculated with strain EOO26 resulted in increase in Cu uptake by 8.6-fold for roots and 1.9-fold for leaves than uninoculated plants. The total plant uptake in inoculated Cu treatment was 2.6-fold higher than uninoculated one, which is much higher than the previously reported Cu accumulating plants. The excellent adaptation abilities and promising metal removal efficiency strongly indicate superiority of strain EOO26 for phytoremediation of Cu-contamination and may work effectively for Cu removal from contaminated soils.

Processing of Metals and Metalloids by Actinobacteria: Cell Resistance Mechanisms and Synthesis of Metal(loid)-Based Nanostructures

Metal(loid)s have a dual biological role as micronutrients and stress agents. A few geochemical and natural processes can cause their release in the environment, although most metal-contaminated sites derive from anthropogenic activities. Actinobacteria include high GC bacteria that inhabit a wide range of terrestrial and aquatic ecological niches, where they play essential roles in recycling or transforming organic and inorganic substances. The metal(loid) tolerance and/or resistance of several members of this phylum rely on mechanisms such as biosorption and extracellular sequestration by siderophores and extracellular polymeric substances (EPS), bioaccumulation, biotransformation, and metal efflux processes, which overall contribute to maintaining metal homeostasis. Considering the bioprocessing potential of metal(loid)s by Actinobacteria, the development of bioremediation strategies to reclaim metal-contaminated environments has gained scientific and economic interests. Moreover, the ability of Actinobacteria to produce nanoscale materials with intriguing physical-chemical and biological properties emphasizes the technological value of these biotic approaches. Given these premises, this review summarizes the strategies used by Actinobacteria to cope with metal(loid) toxicity and their undoubted role in bioremediation and bionanotechnology fields.

Zinc- and cadmium-tolerant endophytic bacteria from Murdannia spectabilis (Kurz) Faden. studied for plant growth-promoting properties, in vitro inoculation, and antagonism

This research aims to isolate and identify Zn- and Cd-tolerant endophytic bacteria from Murdannia spectabilis, identify their properties with and without Zn and Cd stress, and to investigate the effect of bacterial inoculation in an in vitro system. Twenty-four isolates could survive on trypticase soya agar (TSA) supplemented with Zn (250-500 mg L^-1) and/or Cd (20-50 mg L^-1) that belonged to the genera Bacillus, Pantoea, Microbacterium, Curtobacterium, Chryseobacterium, Cupriavidus, Siphonobacter, and Pseudomonas. Each strain had different indole-3-acetic acid (IAA), 1-aminocyclopropane-1-carboxylate (ACC) deaminase and siderophore production, nitrogen fixation, phosphate solubilization, and lignocellulosic enzyme characteristics. Cupriavidus plantarum MDR5 and Chryseobacterium sp. MDR7 were selected for inoculation into plantlets that were already occupied by Curtobacterium sp. TMIL due to them have a high tolerance for Zn and Cd while showing no pathogenicity. As determined via an in vitro system, Cupriavidus plantarum MDR5 remained in the plants to a greater extent than Chryseobacterium sp. MDR7, while Curtobacterium sp. TMIL was the dominant species. The Zn plus Cd treatment supported the persistence of Cupriavidus plantarum MDR5. Dual and mixed cultivation showed no antagonistic effects between the endophytes. Although the plant growth and Zn/Cd accumulation were not significantly affected by the Zn-/Cd-tolerant endophytes, the inoculation did not weaken the plants. Therefore, Cupriavidus plantarum MDR5 could be applied in a bioaugmentation process.

Symbiotic and Nonsymbiotic Members of the Genus Ensifer (syn. Sinorhizobium) Are Separated into Two Clades Based on Comparative Genomics and High-Throughput Phenotyping

Rhizobium–legume symbioses serve as paradigmatic examples for the study of mutualism evolution. The genus Ensifer (syn. Sinorhizobium) contains diverse plant-associated bacteria, a subset of which can fix nitrogen in symbiosis with legumes. To gain insights into the evolution of symbiotic nitrogen fixation (SNF), and interkingdom mutualisms more generally, we performed extensive phenotypic, genomic, and phylogenetic analyses of the genus Ensifer. The data suggest that SNF likely emerged several times within the genus Ensifer through independent horizontal gene transfer events. Yet, the majority (105 of 106) of the Ensifer strains with the nodABC and nifHDK nodulation and nitrogen fixation genes were found within a single, monophyletic clade. Comparative genomics highlighted several differences between the “symbiotic” and “nonsymbiotic” clades, including divergences in their pangenome content. Additionally, strains of the symbiotic clade carried 325 fewer genes, on average, and appeared to have fewer rRNA operons than strains of the nonsymbiotic clade. Initial characterization of a subset of ten Ensifer strains identified several putative phenotypic differences between the clades. Tested strains of the nonsymbiotic clade could catabolize 25% more carbon sources, on average, than strains of the symbiotic clade, and they were better able to grow in LB medium and tolerate alkaline conditions. On the other hand, the tested strains of the symbiotic clade were better able to tolerate heat stress and acidic conditions. We suggest that these data support the division of the genus Ensifer into two main subgroups, as well as the hypothesis that pre-existing genetic features are required to facilitate the evolution of SNF in bacteria.

A high Mn(II)-tolerance strain, Bacillus thuringiensis HM7, isolated from manganese ore and its biosorption characteristics

Microorganisms play a significant part in detoxifying and immobilizing excessive metals. The present research isolated a strain (HM7) with high Mn(II) tolerance from Mn(II)-contaminated soil samples. The 16S rDNA sequence analysis showed that HM7 had a 99% similarity to Bacillus thuringiensis, which can survive under a high concentration 4,000 mg/L of Mn(II), and the highest removal rate was up to 95.04% at the concentration of 400 mg/L. The highest Mn(II) removal rate was detected at the contact time 72 h, temperature 30 °C, and pH 5.0, while the differences in strain growth and Mn(II) removal rate among different inoculation doses were insignificant. Scanning electron microscopy indicated B. thuringiensis HM7 cells appeared irregular and cracked under Mn(II) stress. Fourier transform infrared exhibited that functional groups like carboxyl, hydroxyl, amino, sulfhydryl groups, and amide bands might take part in the complexation of Mn(II). In addition, HM7 suggested the ability of indoleacetic acid production, siderophore production, and P’ solubilization potential. Therefore, HM7 might have a potential to promote metal absorption by changing the form of heavy metals, and the experiments supported the application of B. thuringiensis HM7 as a biological adsorbent in Mn(II) contaminated environment remediation.

A multifunctional rhizobacterial strain with wide application in different ferns facilitates arsenic phytoremediation

Pteris vittata and Pteris multifida are widely studied As hyperaccumulators that absorb As mainly via roots. Hence, rhizobacteria exhibit promising potential in phytoextraction owing to their immense microbial diversity and interactions with plants. Pseudomonas vancouverensis strain m318 that contains aioA-like genes was screened from P. multifida's rhizosphere through the high As resistance (minimum inhibitory concentrations (MICs) against As(III): 16 mM; MICs against As(V): 320 mM), rapid As oxidation (98% oxidation by bacterial cultures (OD_600nm = 1) from 200 μL of 0.1 mM As(III) within 24 h), predominant secretion of IAA (12.45 mg L^-1) and siderophores (siderophore unit: 88%). Strain m318 showed significant chemotactic response and high colonization efficiency to P. vittata roots, which suggested its wide host affinity. Interestingly, inoculation with strain m318 enhanced the proportion of aioA-like genes in the rhizosphere. And in field trials, inoculation with strain m318 increased As accumulation in P. vittata by 48-146% and in P. multifida by 42-233%. Post-transplantation inoculations also increased As accumulation in both ferns. The abilities of the isolated multifunctional strain m318 and the increase in the rhizosphere microbial aioA-like genes are thus speculated to be involved in As transformation in the rhizospheres and roots of P. vittata and P. multifida.

Assessment of endophytic bacterial diversity in rose by high-throughput sequencing analysis

The endophytic bacterial diversity of rose was analyzed by high-throughput sequencing of 16S rDNA and functional prediction of the bacterial community. The number of bacterial sequence reads obtained from 18 rose samples ranged from 63,951 to 114,833, and reads were allocated to 1982 OTUs based on sequences of the V3-V4 region. The highest Shannon Index was found in Luogang rose (1.93), while the lowest was found in Grasse rose (0.35). The bacterial sequence reads were grouped into three different phyla: Firmicutes, Proteobacteria, and Actinobacteria. At the genus level, Bacillus and Staphylococcus had the highest abundance across all 18 samples; Bacillus was particularly abundant in Daguo rose (99.09%), Rosa damascena (99.65%), and Fenghua rose (99.58%). Unclassified OTUs were also found in all samples. PICRUSt gene prediction revealed that each endophyte sample contained multiple KEGG functional modules related to human metabolism and health. A high abundance of functional genes were involved in (1) Amino Acid Metabolism, (2) Carbohydrate Metabolism, (3) Cellular Processes and Signaling, (4) Energy Metabolism, and (5) Membrane Transport, indicating that the endophytic community comprised a wide variety of microorganisms and genes that could be used for further studies. The rose endophytic bacterial community is rich in diversity; community composition varies among roses and contains functional information related to human health.

Co-cropping with three phytoremediation crops influences rhizosphere microbiome community in contaminated soil

Human industrial activities have left millions of hectares of land polluted with trace element metals and persistent organic pollutants (POPs) around the world. Although contaminated sites are environmentally damaging, high economic costs often discourage soil remediation efforts. Phytoremediation is a potential green technology solution but can be challenging due to the diversity of anthropogenic contaminants. Co-cropping could provide improved tolerance to diverse soil challenges by taking advantage of distinct crop capabilities. Co-cropping of three species with potentially complementary functions, Festuca arundinacea, Salix miyabeana and Medicago sativa, perform well on diversely contaminated soils. Here, rhizosphere microbiomes of each crop in monoculture and in all co-cropping combinations were compared using 16S rRNA gene amplification, sequencing and differential abundance analysis. The hyperaccumulating F. arundinacea rhizosphere microbiome included putative plant growth promoting bacteria (PGPB) and metal tolerance species, such as Rhizorhapis suberifaciens, Cellvibrio fibrivorans and Pseudomonas lini. The rhizosphere microbiome of the fast-growing tree S. miyabeana included diverse taxa involved in POP degradation, including the species Phenylobacterium panacis. The well-characterised nitrogen-fixing M. sativa microbiome species, Sinorhizobium meliloti, was identified alongside others involved in nutrient acquisition and putative yet-to-be-cultured Candidatus saccharibacteria (TM7-1 group). The majority of differentially abundant rhizosphere-associated bacterial species were maintained in co-cropping pairs, with pairs having higher numbers of differentially abundant taxa than monocultures in all cases. This was not the case when all three crops were co-cropped, where most host-specific bacterial species were not detected as differentially abundant, indicating the potential for reduced rhizosphere functionality. The crops cultivated in pairs here retained rhizosphere microbiome bacteria involved in these monoculture ecosystem services of plant growth promotion, POP tolerance and degradation, and improved nutrient acquisition. These findings provide a promising outlook of the potential for complementary co-cropping strategies for phytoremediation of the multifaceted anthropogenic pollution which can disastrously affect soils around the world.

Comprehensive Genome Analysis on the Novel Species Sphingomonas panacis DCY99T Reveals Insights into Iron Tolerance of Ginseng

Plant growth-promoting rhizobacteria play vital roles not only in plant growth, but also in reducing biotic/abiotic stress. Sphingomonas panacis DCY99T is isolated from soil and root of Panax ginseng with rusty root disease, characterized by raised reddish-brown root and this is seriously affects ginseng cultivation. To investigate the relationship between 159 sequenced Sphingomonas strains, pan-genome analysis was carried out, which suggested genomic diversity of the Sphingomonas genus. Comparative analysis of S. panacis DCY99T with Sphingomonas sp. LK11 revealed plant growth-promoting potential of S. panacis DCY99T through indole acetic acid production, phosphate solubilizing, and antifungal abilities. Detailed genomic analysis has shown that S. panacis DCY99T contain various heavy metals resistance genes in its genome and the plasmid. Functional analysis with Sphingomonas paucimobilis EPA505 predicted that S. panacis DCY99T possess genes for degradation of polyaromatic hydrocarbon and phenolic compounds in rusty-ginseng root. Interestingly, when primed ginseng with S. panacis DCY99T during high concentration of iron exposure, iron stress of ginseng was suppressed. In order to detect S. panacis DCY99T in soil, biomarker was designed using spt gene. This study brings new insights into the role of S. panacis DCY99T as a microbial inoculant to protect ginseng plants against rusty root disease.

Zinc solubilizing bacteria (Bacillus megaterium) with multifarious plant growth promoting activities alleviates growth in Capsicum annuum L

The present study was designed to isolate an array of zinc solubilizing bacteria (ZSB) and to characterize them for plant growth promotion (PGP) attributes with respect to Capsicum annuum L. For this purpose, seventy bacteria were procured from cow dung and screened for zinc solubilization (ZnO and ZnCO₃). Where, isolate CDK25 was found to be the most potent owing to its maximum zinc solubilization (ZnO) ability (5.0 cm). For quantitative assay, atomic absorption spectroscopy (AAS) was used, where CDK25 showed markedly higher solubilization of ZnO (20.33 ppm). It was investigated that CDK25 also endowed with multiple PGP attributes viz., Phosphate solubilization, Phytase production, Indole acetic acid (IAA) and Siderophore production. Quantitative study revealed isolate CDK25 to solubilize and produce maximum quantity of phosphate (281.59 μg/ml) and IAA (13.8 μg/ml) respectively. ZSB was applied in different treatments under pot culture assay, where T3 (seeds + CDK25) showed significant impact on plant growth parameters, besides showing maximum zinc content in fruit (0.25 mg/100 g). Hence, isolate CDK25 expresses highest potential throughout the experiments; as zinc solubilizer, PGP strain, and based on 16S rRNA gene sequencing identified as Bacillus megaterium. Therefore, meticulous use of this bacterium could aid in providing adequate amount of soluble zinc along with enhanced plants growth, nutrient uptake and yield in sustainable manner.

Endophyte: Understanding the Microbes and its Applications

The ability of endophytes to colonize every plant tissue has led to the opportunity of using the microorganism in a lot of biological applications. Endophytes are beneficial to their host cells as such its application is observed in every aspects of life. This study therefore endeavored to give an analysis of endophytes, what they were and what they had been used for till the present time. Sampling of several literature studies in endophytes was done in this study to enable a complete understanding of the mechanism of application of the actions of endophytes, so as to be able to do a thorough assessment of the current state in the knowledge of the microbes. From the complete analysis of the literature on the application and use of endophytes, in nutrient asquition and increase the stress tolerance in plants. This study provided a platform for further research gaps through the presentation of what endophytes were, what they had been used for till date, the mechanism of operation of the micro-organism and the type of interaction between them and their hosts. There are still ways to improve on the methods of application of endophytes as a type of biological organism. This will be done by adjusting to the current trends in biological studies using molecular mechanization, following an intensive further study on endophyte mechanisms.

In vivo removal of profenofos in agricultural soil and plant growth promoting activity on Vigna radiata by efficient bacterial formulation

This study evaluated the plant growth and profenofos (PF) removal efficiency of Acinetobacter sp.33F and Comamonas sp. 51 F bacteria as individual strains and in combination F1. Plant growth-promoting activities such as indole 3 acetic acid (IAA) production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, phosphate solubilization, ammonia production, and exopolysaccharide (EPS) production were observed in Acinetobacter sp. 33 F and Comamonas sp. 51 F. However, PGP properties observed were higher in Acinetobacter sp. 33 F as compared to the Comamonas sp. 51 F. In pot sand and pot soil studies, the physiological parameters such as sprout length, shoot length, root length, chlorophyll a, chlorophyll b, and carotenoids were higher for combination F1. PF degradation in pot sand and pot soil resulted in highest degradation by combination F1. In pot soil study, soil enzyme activities such as cellulase, dehydrogenase, urease, protease, and phosphate activities and root cross-section area, total stele area and xylem vessel area were recorded higher for the formulation F1. The study demonstrated that the together Acinetobacter sp. 33 F and Comamonas sp. 51 F as formulation has higher plant growth-promoting activities as compared to the individual bacteria.

Rhizosphere response to nickel in a facultative hyperaccumulator

This study faces the characterization of the culturable microbiota of the facultative Ni-hyperaccumulator Alyssoides utriculata to obtain a collection of bacterial and fungal strains for potential applications in Ni phytoextraction. Rhizosphere soil samples and adjacent bare soil associated with A. utriculata from serpentine and non-serpentine sites were collected together with plant roots and shoots. Rhizobacteria and fungi were isolated and characterized genotypically and phenotypically. Plants and soils were analyzed for total element concentration using Inductively Coupled Plasma Mass Spectrometry (ICP-MS). Serpentine and non-serpentine sites differ in terms of elements concentration in soil, plant roots and shoots. Ni and Co are significantly higher on serpentine site, while Ca is more abundant in non-serpentine site. Bacteria and fungi were significantly more abundant in rhizosphere than in bare soil and were dominated by genera Arthrobacter, Bacillus and Streptomyces, Penicillium and Mucor. The genus Pseudomonas was only found in rhizospheric serpentine soils (<2% of total serpentine isolates) and with Streptomyces sp. showed highest Ni-tolerance up to 15 mM. The same occurred for Trichoderma strain, belonging to the harzianum group (<2% of the total microfungal count) and Penicillium ochrochloron (<10% of the total microfungal count, tolerance up to Ni 20 mM). Among serpentine bacterial isolates, 8 strains belonging to 5 genera showed at least one PGPR activity (1-Aminocyclopropane-1-Carboxylic Acid (ACC) deaminase activity, production of indole-3-acetic acid (IAA), siderophores and phosphate solubilizing capacity), especially genera Pantoea, Pseudomonas and Streptomyces. Those microorganisms might thus be promising candidates for employment in bioaugmentation trials.

New Caledonian ultramafic conditions structure the features of Curtobacterium citreum strains that play a role in plant adaptation

The present study focused on the characterization of 10 Curtobacterium citreum strains isolated from the rhizosphere of pioneer plants growing on ultramafic soils from New Caledonia. Taxonomic status was investigated using a polyphasic approach. Three strains (BE, BB, and AM) were selected in terms of multiple-metal resistance and plant-growth-promoting traits. They were tested on sorghum growing on ultramafic soil and compared with the reference strain C. citreum DSM20528^T. To better understand the bacterial mechanisms involved, biosorption, bioaccumulation, and biofilm formation were investigated for the representative strain of the ultramafic cluster (strain BE) versus C. citreum DSM20528^T. The polyphasic approach confirmed that all native isolates belong to the same cluster and are C. citreum. The inoculation of sorghum with strains BE and BB significantly reduced Ni content in shoots compared with inoculation with C. citreum DSM20528^T and control values. This result was related to the higher Ni tolerance of the ultramafic strains compared with C. citreum DSM20528^T. Ni biosorption and bioaccumulation showed that BE exhibited a lower Ni content, which is explained by the ability of this strain to produce exopolysaccharides involved in Ni chelation. We suggested that ultramafic C. citreum strains are more adapted to this substrate than is C. citreum DSM20528^T, and their features allow them to enhance plant metal tolerance.

Assessing nickel tolerance of bacteria isolated from serpentine soils

Serpentine soils present unique characteristics such as a low Ca/Mg ratio, low concentration of nutrients, and a high concentration of heavy metals, especially nickel. Soil bacterial isolates from an ultramafic complex located in the tropical savanna known as the Brazilian Cerrado were studied. Nickel-tolerant bacteria were obtained, and their ability to remove nickel from a culture medium was assessed. Bacterial isolates presented higher tolerance to nickel salts than previously reported for bacteria obtained from serpentine environments in other regions of the world. In addition, the quantification of nickel in cell pellets indicated that at least four isolates may adsorb soluble forms of nickel. It is expected that information gathered in this study will support future efforts to exploit serpentine soil bacteria for biotechnological processes involving nickel decontamination from environmental samples.

Phylogenetic analyses and characteristics of the microbiomes from five mealybugs (Hemiptera: Pseudococcidae)

Associations between Sternorrhyncha insects and intracellular bacteria are common in nature. Mealybugs are destructive pests that seriously threaten the production of agriculture and forestry. Mealybugs have evolved intimate endosymbiotic relationships with bacteria, which provide them with essential amino acids, vitamins, and other nutrients. In this study, the divergence of five mealybugs was analyzed based up the sequences of the mitochondrial cytochrome oxidase I (mtCOI). Meanwhile, the distinct regions of the 16S rRNA gene of primary symbionts in the mealybugs were sequenced. Finally, high-throughput sequencing (HTS) techniques were used to study the microbial abundance and diversity in mealybugs. Molecular phylogenetic analyses revealed that these five mealybugs were subdivided into two different clusters. One cluster of mealybugs (Dysmicoccus neobrevipes, Pseudococcus comstocki, and Planococcus minor) harbored the primary endosymbiont "Candidatus Tremblaya princeps," and another cluster (Phenacoccus solenopsis and Phenacoccus solani) harbored "Ca. Tremblaya phenacola." The mtCOI sequence divergence between the two clusters was similar to the 16S rRNA sequence divergence between T. princeps and T. phenacola. Thus, we concluded that the symbiont phylogeny was largely concordant with the host phylogeny. The HTS showed that the microbial abundance and diversity within P. solani and P. solenopsis were highly similar, and there was lower overall species richness compared to the other mealybugs. Among the five mealybugs, we also found significant differences in Shannon diversity and observed species. These results provide a theoretical basis for further research on the coevolution of mealybugs and their symbiotic microorganisms. These findings are also useful for research on the effect of symbiont diversity on the pest status of mealybugs in agricultural systems.

Integrated phytobial heavy metal remediation strategies for a sustainable clean environment - A review

Heavy metal contamination in the environment is a global threat which accelerated after the industrial revolution. Remediation of these noxious elements has been widely investigated and multifarious technologies have been practiced for many decades. Phytoremediation has attracted much attention from researchers. Under this technology, heavy metal hyperaccumulator plants have been extensively employed to extract extraordinary concentrations of heavy metals but slow growth, limited biomass and stresses caused by heavy metals imperil the efficiency of hyperaccumulators. Plant growth promoting rhizobacteria (PGPR) can help overcome/lessen heavy metal-induced adversities. PGPR produce several metabolites, including growth hormones, siderophores and organic acids, which aid in solubilization and provision of essential nutrients (e.g. Fe and Mg) to the plant. Hyperaccumulator plants may be employed to remediate metal contaminated sites. Use of PGPR to enhance growth of hyperaccumulator plant species may enhance their metal accumulating capacity by increasing metal availability and also by alleviating plant stress induced by the heavy metals. Combined use of hyperaccumulator plants and PGPR may prove to be a cost effective and environmentally friendly technology to clean heavy metal contaminated sites on a sustainable basis. This review discusses the current status of PGPR in improving the growth and development of hyperaccumulator plants growing in metal contaminated environments. The mechanisms used by these rhizosphere bacteria in increasing the availability of heavy metals to plants and coping with heavy metal stresses are also described.

Use of plant growth promoting rhizobacteria (PGPRs) with multiple plant growth promoting traits in stress agriculture: Action mechanisms and future prospects

Increased incidence of abiotic stresses impacting adversely plant growth and productivity in major crops is being witnessed all over the world. Therefore, as a result of such stress factors, plant growth under the stress conditions will be less than the non-stress conditions. Growing concerns and global demand for correct, environmentally-friendly techniques exist to reduce the adverse effects of plant stress. Under such stressful conditions, the role of interactions of plant and beneficial microorganisms is of great significance. Application of plant growth promoting rhizobacteria (PGPRs) is a useful option to decrease these stresses and is now widely in practice. Plants inoculated with PGPRs induce morphological and biochemical modifications resulting in increased tolerance to abiotic stresses defined as IST (induced systemic tolerance). PGPRs increase plant growth and resistance to abiotic stresses through various mechanisms (more than one mechanism of action) such as production of ACC (1-aminocyclopropane-1-carboxylate) deaminase, reducing production of stress ethylene, modifications in phytohormonal content, induction of synthezing plant antioxidative enzymes, improvement in the uptake of essential mineral elements, extracellular polymeric substance (EPS) production, decrease in the absorbtion of excess nutrients/heavy metals, and induction of abiotic stress resistance genes. Experimental evidence also suggests that stimulated plant growth by these bacteria is the net result of various mechanisms of action that are activated simultaneously. In this review paper, we reviewed the action mechanisms through which PGPRs could alleviate abiotic stresses (salinity, drought, heavy metal toxicity, and nutritional imbalance) in plants. Use of PGPRs is predicted to become a suitable strategy and an emerging trend in sustainable enhancement of plant growth. Generally, ACC deaminase and IAA-producing bacteria can be a good option for optimal crop production and production of bio-fertilizers in the future due to having multiple potentials in alleviating stresses of salinity, drought, nutrient imbalance, and heavy metals toxicity in plants. This review paper also emphasizes future research needs about the combined utilization of stress tolerant-PGPRs with multiple plant growth promoting (PGP) characteristics under environmental stresses.

Genetic diversity and characterization of arsenic-resistant endophytic bacteria isolated from Pteris vittata, an arsenic hyperaccumulator

Background

Alleviating arsenic (As) contamination is a high-priority environmental issue. Hyperaccumulator plants may harbor endophytic bacteria able to detoxify As. Therefore, we investigated the distribution, diversity, As (III) resistance levels, and resistance-related functional genes of arsenite-resistant bacterial endophytes in Pteris vittata L. growing in a lead-zinc mining area with different As contamination levels.

Results

A total of 116 arsenite-resistant bacteria were isolated from roots of P. vittata with different As concentrations. Based on the 16S rRNA gene sequence analysis of representative isolates, the isolates belonged to Proteobacteria, Actinobacteria, and Firmicutes. Major genera found were Agrobacterium, Stenotrophomonas, Pseudomonas, Rhodococcus, and Bacillus. The most highly arsenite-resistant bacteria (minimum inhibitory concentration > 45 mM) were isolated from P. vittata with high As concentrations and belonged to the genera Agrobacterium and Bacillus. The strains with high As tolerance also showed high levels of indole-3-acetic acid (IAA) production and carried arsB/ACR3(2) genes. The arsB and ACR3(2) were most likely horizontally transferred among the strains.

Conclusion

The results of this study suggest that P. vittata plants with high As concentrations may select diverse arsenite-resistant bacteria; this diversity might, at least partly, be a result of horizontal gene transfer. These diverse endophytic bacteria are potential candidates to enhance phytoremediation techniques.

The Role of Strigolactone in the Cross-Talk Between Arabidopsis thaliana and the Endophytic Fungus Mucor sp

Over the last years the role of fungal endophytes in plant biology has been extensively studied. A number of species were shown to positively affect plant growth and fitness, thus attempts have been made to utilize these microorganisms in agriculture and phytoremediation. Plant-fungi symbiosis requires multiple metabolic adjustments of both of the interacting organisms. The mechanisms of these adaptations are mostly unknown, however, plant hormones seem to play a central role in this process. The plant hormone strigolactone (SL) was previously shown to activate hyphae branching of mycorrhizal fungi and to negatively affect pathogenic fungi growth. Its role in the plant-endophytic fungi interaction is unknown. The effect of the synthetic SL analog GR24 on the endophytic fungi Mucor sp. growth, respiration, H2O2 production and the activity of antioxidant enzymes was evaluated. We found fungi colony growth rate was decreased in a GR24 concentration dependent manner. Additionally, the fungi accumulated more H2O2 what was accompanied by an altered activity of antioxidant enzymes. Symbiosis with Mucor sp. positively affected Arabidopsis thaliana growth, but SL was necessary for the establishment of the beneficial interaction. A. thaliana biosynthesis mutants max1 and max4, but not the SL signaling mutant max2 did not develop the beneficial phenotype. The negative growth response was correlated with alterations in SA homeostasis and a significant upregulation of genes encoding selected plant defensins. The fungi were also shown to be able to decompose SL in planta and to downregulate the expression of SL biosynthesis genes. Additionally, we have shown that GR24 treatment with a dose of 1 μM activates the production of SA in A. thaliana. The results presented here provide evidence for a role of SL in the plant-endophyte cross-talk during the mutualistic interaction between Arabidopsis thaliana and Mucor sp.

Isolation of vanadium-resistance endophytic bacterium PRE01 from Pteris vittata in stone coal smelting district and characterization for potential use in phytoremediation

This study investigates the V-resistant endophytic bacteria isolated from V-accumulator Pteris vittata grown on stone coal smelting district. Among all the ten isolates, the strain PRE01 identified as Serratia marcescens ss marcescens by Biolog GEN III MicroPlate™ was screened out by ranking first in terms of heavy metal resistance and plant growth promoting traits. The S. marcescens PRE01 had strong V, Cr and Cd resistance especially for V up to 1500mg/L. In addition, it exhibited ACC deaminase activity, siderophore production and high indoleacetic acid production (60.14mg/L) and solubilizing P potential (336.41mg/L). For heavy metal detoxification tests, PRE01 could specifically assimilate 97.6%, 21.7% and 6.6% of Cd(II), Cr(VI) and V(V) within 72h incubation. Despite the poor absorption of the two anions, most V(V) and Cr(VI) were detoxified and reduced to lower valence states by the strain. Furthermore, the isolate had the potential to facilitate the metals uptake of their hosts by changing heavy metal speciation. Our research may open up further scope of utilizing the endophyte for enhancing phytoextraction of vanadium industry contaminated soils.

Bisphenol-A removal by the halophyte Juncus acutus in a phytoremediation pilot: Characterization and potential role of the endophytic community

A phytoremediation pilot emulating a shallow aquifer planted with Juncus acutus showed to be effective for remediating Bisphenol-A (BPA) contaminated groundwater. Biostimulation with root exudates, low molecular weight organic acids, of J. acutus did not improve BPA-degradation rates. Furthermore, the endophytic bacterial community of J. acutus was isolated and characterized. Many strains were found to possess increased tolerance to metals such as Zn, Ni, Pb and Cd. Moreover, several endophytic bacterial strains tolerated and even used BPA and/or two antibiotics (ciprofloxacin and sulfamethoxazole) as a sole carbon source. Our results demonstrate that the cultivable bacterial endophytic community of J. acutus is able to use organic contaminants as carbon sources, tolerates metals and is equipped with plant-growth promoting traits. Therefore, J. acutus has potential to be exploited in constructed wetlands when co-contamination is one of the restricting factors.