Isolation and characterization of endophytic bacterium LRE07 from cadmium hyperaccumulator Solanum nigrum L. and its potential for remediation

Halotolerant Endophytic Bacteria Priestia flexa 7BS3110 with Hg2+ Tolerance Isolated from Avicennia germinans in a Caribbean Mangrove from Colombia

The mangrove ecosystems of the Department of Atlántico (Colombian Caribbean) are seriously threatened by problems of hypersalinization and contamination, especially by heavy metals from the Magdalena River. The mangrove plants have developed various mechanisms to adapt to these stressful conditions, as well as the associated microbial populations that favor their growth. In the present work, the tolerance and detoxification capacity to heavy metals, especially to mercury, of a halotolerant endophytic bacterium isolated from the species Avicennia germinans located in the Balboa Swamp in the Department of Atlántico was characterized. Diverse microorganisms were isolated from superficially sterilized A. germinans leaves. Tolerance to NaCl was evaluated for each of the obtained isolates, and the most resistant was selected to assess its tolerance to Pb2+, Cu2+, Hg2+, Cr3+, Co2+, Ni2+, Zn2+, and Cd2+, many of which have been detected in high concentrations in the area of study. According to the ANI and AAI percentages, the most halotolerant strain was identified as Priestia flexa, named P. flexa 7BS3110, which was able to tolerate up to 12.5% (w/v) NaCl and presented a minimum inhibitory concentrations (MICs) of 0.25 mM for Hg, 10 mM for Pb, and 15 mM for Cr3+. The annotation of the P. flexa 7BS3110 genome revealed the presence of protein sequences associated with exopolysaccharide (EPS) production, thiol biosynthesis, specific proteins for chrome efflux, non-specific proteins for lead efflux, and processes associated with sulfur and iron homeostasis. Scanning electron microscopy (SEM) analysis showed morphological cellular changes and the transmission electron microscopy (TEM) showed an electrodense extracellular layer when exposed to 0.25 mM Hg2+. Due to the high tolerance of P. flexa 7BS3110 to Hg2+ and NaCl, its ability to grow when exposed to both stressors was tested, and it was able to thrive in the presence of 5% (w/v) NaCl and 0.25 mM of Hg2+. In addition, it was able to remove 98% of Hg2+ from the medium when exposed to a concentration of 14 mg/L of this metalloid. P. flexa 7BS3110 has the potential to bioremediate Hg2+ halophilic contaminated ecosystems.

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.

Trends in Harnessing Plant Endophytic Microbiome for Heavy Metal Mitigation in Plants: A Perspective

Plant microbiomes represent dynamic entities, influenced by the environmental stimuli and stresses in the surrounding conditions. Studies have suggested the benefits of commensal microbes in improving the overall fitness of plants, besides beneficial effects on plant adaptability and survival in challenging environmental conditions. The concept of 'Defense biome' has been proposed to include the plant-associated microbes that increase in response to plant stress and which need to be further explored for their role in plant fitness. Plant-associated endophytes are the emerging candidates, playing a pivotal role in plant growth, adaptability to challenging environmental conditions, and productivity, as well as showing tolerance to biotic and abiotic stresses. In this article, efforts have been made to discuss and understand the implications of stress-induced changes in plant endophytic microbiome, providing key insights into the effects of heavy metals on plant endophytic dynamics and how these beneficial microbes provide a prospective solution in the tolerance and mitigation of heavy metal in contaminated sites.

Adsorption capacity of Penicillium amphipolaria XK11 for cadmium and antimony

Heavy metal pollution is a global problem that affects both the environment and human health. Microorganisms play an important role in remediation. Most studies on the use of microorganisms for heavy metal remediation focus on single heavy metals. In this study, a strain of Penicillium amphipolaria, XK11 with high resistance to both antimony (Sb III) and cadmium (Cd II) was screened from the mineral slag. The strain also had a high phosphate solubilization capacity. The single-factor adsorption experiment results showed that the initial pH (pH₀), adsorption time (T), and initial solution concentration (C₀) all affected the adsorption of Sb and Cd by XK11. When the initial pH₀ (Cd = 6, Sb = 4) and adsorption time (T = 7 d) were constant, XK11 achieved the maximum removal rate of Cd (45.6%) and Sb (34.6%). These results confirm that XK11 has potential as a biomaterial or remediation of Sb and Cd pollution.

Sustainable Applications of Endophytic Bacteria and Their Physiological/Biochemical Roles on Medicinal and Herbal Plants: Review

Bacterial endophytes reside within the tissues of living plant species without causing any harm or disease to their hosts. These endophytes can be isolated, identified, characterized, and used as biofertilizers. Moreover, bacterial endophytes increase the plants' resistance against diseases, pests, and parasites, and are a promising source of pharmaceutically important bioactives. For instance, the production of antibiotics, auxins, biosurfactants, cytokinin's, ethylene, enzymes, gibberellins, nitric oxide organic acids, osmolytes, and siderophores is accredited to the existence of various bacterial strains. Thus, this manuscript intends to review the sustainable applications of endophytic bacteria to promote the growth, development, and chemical integrity of medicinal and herbal plants, as well as their role in plant physiology. The study of the importance of bacterial endophytes in the suppression of diseases in medicinal and herbal plants is crucial and a promising area of future investigation.

Effect of copper stress on Phaseolus coccineus in the presence of exogenous methyl jasmonate and/or Serratia plymuthica from the Spitsbergen soil

Copper stress in the presence of exogenous methyl jasmonate and Serratia plymuthica in a complete trifactorial design with copper (0, 50 µM), methyl jasmonate (0, 1, 10 µM) and Serratia plymuthica (without and with inoculation) was studied on the physiological parameters of Phaseolus coccineus. Copper application reduced biomass and allantoin content, but increased chlorophyll and carotenoids contents as well as catalase and peroxidases activities. Jasmonate did not modify biomass and organic acids levels under copper treatment, but additional inoculation elevated biomass and content of tartrate, malate and succinate. Jasmonate used alone or in combination with bacteria increased superoxide dismutase activity in copper application. With copper, allantoin content elevated at lower jasmonate concentration, but with additional inoculation - at higher jasmonate concentration. Under copper stress, inoculation resulted in higher accumulation of tartrate, malate and citrate contents in roots, which corresponded with lower allantoin concentration in roots. Combined with copper, inoculation reduced catalase and guaiacol peroxidase activities, whereas organic acids content was higher. Under metal stress, with bacteria, jasmonate reduced phenolics content, elevated superoxide dismutase and guaiacol peroxidase activities. The data indicate that jasmonate and S. plymuthica affected most physiological parameters of P. coccineus grown with copper and revealed some effect on biomass.

Alterations of endophytic microbial community function in Spartina alterniflora as a result of crude oil exposure

The 2010 Deepwater Horizon disaster remains one of the largest oil spills in history. This event caused significant damage to coastal ecosystems, the full extent of which has yet to be fully determined. Crude oil contains toxic heavy metals and substances such as polycyclic aromatic hydrocarbons that are detrimental to some microbial species and may be used as food and energy resources by others. As a result, oil spills have the potential to cause significant shifts in microbial communities. This study assessed the impact of oil contamination on the function of endophytic microbial communities associated with saltmarsh cordgrass (Spartina alterniflora). Soil samples were collected from two locations in coastal Louisiana, USA: one severely affected by the Deepwater Horizon oil spill and one relatively unaffected location. Spartina alterniflora seedlings were grown in both soil samples in greenhouses, and GeoChip 5.0 was used to evaluate the endophytic microbial metatranscriptome shifts in response to host plant oil exposure. Oil exposure was associated with significant shifts in microbial gene expression in functional categories related to carbon cycling, virulence, metal homeostasis, organic remediation, and phosphorus utilization. Notably, significant increases in expression were observed in genes related to metal detoxification with the exception of chromium, and both significant increases and decreases in expression were observed in functional gene subcategories related to hydrocarbon metabolism. These findings show that host oil exposure elicits multiple changes in gene expression from their endophytic microbial communities, producing effects that may potentially impact host plant fitness.

The endophytic bacterium Bacillus koreensis 181-22 promotes rice growth and alleviates cadmium stress under cadmium exposure

Recently, cadmium (Cd) contamination in paddy soils has become a highly concerning pollution problem. Endophytic microbes in rice not only affect the plant growth but also contribute to ion absorption by the roots. Therefore, they are a promising, ecologically sound means of reducing the Cd transport from soils to shoots and grains of the plant. In this study, a Cd-resistant endophytic bacterium, named 181-22, with high Cd absorption capacity (90.8%) was isolated from the roots of rice planting in heavily Cd-contaminated paddy soils and was identified as Bacillus koreensis CGMCC 19,468. The strain significantly increased fresh weight of roots and shoots (44.4% and 42.7%) and dry weight of roots and shoots (71.3% and 39.9%) and decreased Cd content in the rice roots (12.8%), shoots (34.3%), and grains (39.1%) under Cd stress compared to uninoculated plant by colonizing rice roots via seed inoculation. Moreover, colonization of 181-22 reprogrammed rice physiology to alleviate Cd stress by increasing pigment and total protein content, regulating Cd-induced oxidative stress enzymes such as superoxide dismutase and catalase and reducing malondialdehyde. Thus, B. koreensis 181-22 has the potential to protect rice against Cd stress and can be used as a biofertilizer to bioremediate paddy soils contaminated with Cd. KEY POINTS: • Bacillus koreensis 181-22 colonized the inside of rice roots at high numbers via seed inoculation. • B. koreensis 181-22 promoted rice growth and decreased Cd accumulation in grains. • B. koreensis 181-22 regulated the physiological response to alleviated Cd stress in rice.

Diversity of Endophytic Bacteria in Cardamine hupingshanensis and Potential of Culturable Selenium-Resistant Endophytes to Enhance Seed Germination Under Selenate Stress

The endophytic bacterial communities of Se hyperaccumulator Cardamine hupingshanensis collected from greenhouse and selenium mining area in Enshi City were investigated by Illumina sequencing technology. In addition, 14 culturable endophytic selenium-resistant strains were isolated and their selenium tolerance and plant growth promotion abilities were studied. The results showed that phylum Proteobacteria predominated in all the plants (> 70%) regardless of their habitats, with most of the OTUs related to Betaproteobacteria, Alphaproteobacteria, and Gammaproteobacteria. Roots harbored many more OTUs and showed higher alpha diversities than the leaves. Both growing environment and specific microflora selection of plants were found to have noticeable effects on endophytic bacterial community structure. The 14 culturable endophytes belonging to 11 bacterial genera were able to resist different levels of selenite and selenate, with their MIC ranges of 10-120 mM and 100-600 mM. Among them, Oceanobacillus and Terribacillus genera were firstly reported for the selenium-tolerant properties of their members. Inoculation experiment revealed that three endophytic strains (CHP07, CHP08, and CHP14) with excellent plant growth-promoting traits were beneficial for growth of Brassica chinensis seeds at germination stage under 0.19 mM selenate stress.

Advances in microbial remediation for heavy metal treatment: a mini review

Abstract

In recent years, microbiological treatment to remediate contamination by heavy metals has aroused public attention as such pollution has seriously threatens ecosystems and human health and impedes sustainable development. However, the aspect of actual industrial wastewater and solid waste remediation by microorganisms is not explored sufficiently. And what we focus on is technical field of microbial remediation. Therefore, in this review, we discuss and summarize heavy metal treatment via microbiological approaches in different media, including wastewater, solid waste from industrial factories and polluted sites. We also clarify the technical applicability from the perspective of biosorption, bioleaching, biominerization, etc. In particular, the exploration of the combination of microbiological approaches with chemical methods or phytoextraction are scrutinized in this review relative to real waste heavy metal remediation. Furthermore, we highlight the importance of hyperaccumulator endophytes.

Graphical abstract

Co-culturing microalgae with endophytic bacteria increases nutrient removal efficiency for biogas purification

Endophytic bacteria were isolated from Chlorella vulgaris and co-cultured with its host microalgae to determine whether this symbiotic system is suitable for purifying biogas and biogas slurry. Results showed that endophytic bacteria S395-1 and S395-2 belonged to different genera. Both strains promoted microalgae growth while improving photosynthetic performance, carbonic anhydrase activity, nutrient removal efficiency, and CO₂ fixation. The optimal bacteria (S395-2)-to-microalgae ratio and co-culture duration were 10:1 and 7 days. Under this condition, the growth rate and carbonic anhydrase activity were 0.196 ± 0.06 d^-1 and 31.24 ± 0.28 EU/cell, respectively. The symbiotic system had removal efficiencies of 88.29 ± 5.03%, 88.31 ± 4.29%, 88.21 ± 4.51%, and 68.13 ± 1.69% for chemical oxygen demand, nitrogen, phosphorus, and CO₂, respectively. These results will provide a framework for constructing a microalgal-bacterial consortium that can improve wastewater treatment and enhance biogas quality.

Aqueous extracts from the selected hyperaccumulators used as soil additives significantly improve accumulation capacity of Solanum nigrum L. for Cd and Pb

The effects of soil treatment with aqueous extracts from three hyperaccumulators on Cd and Pb accumulation by Solanum nigrum L. were determined. The stem (S-RG) and leaf extracts (L-RG) of Rorippaglobosa (Turcz.) Thell., and stem extract (S-BP) of Bidens pilosa L. significantly enhanced Cd and Pb total accumulation capacity of S. nigrum compared to control (by 44 %, 47 %, and 29 % for Cd and by 28 %, 28 % and 21 % for Pb, respectively), while EDTA caused its 9 % and 15 % decrease due to the plant biomass reduction (by 33 %). The leaching experiments reflected affinity of additives to metal mobilization in soils. The concentrations of total organic acid in S-RG, L-RG and S-BP were the highest among studied extracts, which besides the beneficial effect on the soil environment (microbe number and enzyme activities), may be partial reasons of strong promotion of S. nigrum accumulation capacity for Cd and Pb. It was shown that hyperaccumulation properties of a plant are not a prerequisite of enhancing effect of the plant-based soil additive on the metal accumulation capacity of the target living hyperaccumultor. The plant-based chelators were found to be promising candidates for EDTA and other chemicals replacement in promoting efficient and environmentally safe phytoremediation.

Physiological, biochemical and proteomic insight into integrated strategies of an endophytic bacterium Burkholderia cenocepacia strain YG-3 response to cadmium stress

An endophytic bacterium YG-3 with high cadmium (Cd) resistance was isolated from poplar grown in a composite mine tailing. It was identified as Burkholderia cenocepacia based on genomic, physiological and biochemical analyses. The Cd removal rate by YG-3 could reach about 60.0% in Cd aqueous solution with high concentrations of both 100 and 500 mg L-1. Meanwhile, various absorption and adsorption strategies were found in the two different Cd concentrations. The global resistance mechanisms of YG-3 were investigated in several levels, i.e., physiological observation, such as scanning electron microscopy and transmission electron microscopy; biochemical detection for active compound production and infrared spectroscopy; label-free quantitative proteomic profile analysis. The results indicated that YG-3 possesses a complex mechanism to adapt to Cd stress: (1) binding of Cd to prevent it from entering the cell by the cell wall components, as well as secreted siderophores and exopolysaccharides; (2) intracellular sequestration of Cd by metalloproteins; (3) excretion of Cd from the cell by efflux pumps; (4) alleviation of Cd toxicity by antioxidants. Our results demonstrate that endophyte YG-3 is well adjusted to largely remove Cd and has potential to cooperate with its host to improve phytoremediation efficiency in heavy metal-contaminated sites.

Isolation, characterization and inoculation of Cd tolerant rice endophytes and their impacts on rice under Cd contaminated environment

Cadmium (Cd) contamination in paddy soil becomes increasingly prominent in recent years, which endangers the safe production of food crops. Cd-tolerant endophytes are ideal mediators for decreasing Cd content in rice plants, but their effects on the rice endophytic microbial community and gene expression profile have not yet been well elucidated. In this study, 58 endophytic bacteria from rice seeds were isolated and characterized. Five strains of them were selected based on their potential growth-promoting traits and strong Cd tolerance that could grow well under 4 mM Cd²⁺. By 16S ribosomal RNA (rRNA) identification, these five strains were designated as Enterobacter tabaci R2-7, Pantoea agglomerans R3-3, Stenotrophomonas maltophilia R5-5, Sphingomonas sanguinis R7-3 and Enterobacter tabaci R3-2. Pot experiments in relieving Cd stress in rice plants showed that the S. maltophilia R5-5 performed the strongest potential for reducing the Cd content in root and blade by 81.33% and 77.78%, respectively. The endophytic microbial community diversity, richness and composition were significantly altered in S. maltophilia R5-5 inoculated rice plants. Reverse-transcription qPCR (RT-qPCR) showed that the expression of Cd transporters, OsNramp5 and OsHMA2, were down-regulated in S. maltophilia R5-5-innoculated rice roots. The results indicate that the inoculation of endophytic bacteria S. maltophilia R5-5 provides a reference for alleviating the heavy metal contamination in paddy fields and can be a better alternative for guaranteeing the safe production of crops. Changes in the relative abundance of Cd-resistant microorganisms and the expression of Cd transporters might be the intrinsic factors affecting cadmium content in rice.

Rhizosphere assisted biodegradation of benzo(a)pyrene by cadmium resistant plant-probiotic Serratia marcescens S2I7, and its genomic traits

Melia azedarach-rhizosphere mediated degradation of benzo(a)pyrene (BaP), in the presence of cadmium (Cd) was studied, using efficient rhizobacterial isolate. Serratia marcescens S2I7, isolated from the petroleum-contaminated site, was able to tolerate up to 3.25 mM Cd. In the presence of Cd, the isolate S2I7 exhibited an increase in the activity of stress-responsive enzyme, glutathione-S-transferase. Gas Chromatography-Mass spectroscopy analysis revealed up to 59% in -vitro degradation of BaP after 21 days, while in the presence of Cd, the degradation was decreased by 14%. The bacterial isolate showed excellent plant growth-promoting attributes and could enhance the growth of host plant in Cd contaminated soil. The 52,41,555 bp genome of isolate S. marcescens S2I7 was sequenced, assembled and annotated into 4694 genes. Among these, 89 genes were identified for the metabolism of aromatic compounds and 172 genes for metal resistance, including the efflux pump system. A 2 MB segment of the genome was identified to contain operons for protocatechuate degradation, catechol degradation, benzoate degradation, and an IclR type regulatory protein pcaR, reported to be involved in the regulation of protocatechuate degradation. A pot trial was performed to validate the ability of S2I7 for rhizodegradation of BaP when applied through Melia azedarach rhizosphere. The rhizodegradation of BaP was significantly higher when augmented with S2I7 (85%) than degradation in bulk soil (68%), but decreased in the presence of Cd (71%).

Bacillus Cereus Enhanced Phytoremediation Ability of Rice Seedlings under Cadmium Toxicity

Cadmium (Cd+2) is a highly toxic metal, which significantly alters different biochemical and metabolic processes in plants. Massive amounts of Cd+2 is being released into the environment by different anthropogenic activities. In the present study, plant growth promoting activities of bacterial strain Bacillus cereus was evaluated under Cd+2 stress in two rice cultivars Basmati-385 and Shaheen Basmati. Cd+2 stress significantly decreased plant growth and biomass production in both cultivars. However, with the inoculation of B. cereus under Cd+2 treatments, reduced Cd+2 uptake and increased antioxidant enzymes activities in rice cultivars lead to enhanced plant growth, biomass production, photosynthetic pigments, micronutrients, and lowered electrolytes leakage. This study suggests that B. cereus has the ability to alleviating Cd toxicity and increased phytoremediation efficiency of rice seedling under Cd stress.

Combined use of Enterobacter sp. MN17 and zeolite reverts the adverse effects of cadmium on growth, physiology and antioxidant activity of Brassica napus

The objective of the study was to evaluate role of zeolite and Enterobacter sp. MN17 on Cd uptake, growth, physiological and biochemical responses of Brassica napus on Cd-contaminated soil. A sandy clay loam soil in plastic pots was spiked with Cd (0 and 80 mg kg-1) and amended with zeolite (0 and 10 g kg-1). Seeds of B. napus were inoculated with Enterobacter sp. MN17. Both inoculated and non-inoculated seeds of B. napus were sown and plants were harvested after 60 days of growth and data were collected. Although sole application of zeolite and seed inoculation reverted adverse effects of Cd in B. napus plants, the combined use resulted in even higher growth and physiological responses compared to control plants. The combined use under Cd stress increased plant height, root length, dry biomass of shoot and root up to 32%, 57%, 42% and 64%, respectively compared to control. The different physiological attributes (photosynthetic rate, chlorophyll content, transpiration rate, stomatal conductance) of B. napus were improved from 6% to 137%. Moreover, combined use of zeolite and seed inoculation on Cd-contaminated soil reduced the stress to plants as antioxidant activities decreased up to 25-64%, however enzyme activities were still higher than plants grown on normal soil. Root and shoot analysis of B. napus for Cd content depicted that zeolite and bacterium decreased Cd uptake from soil. It is concluded that combined use of zeolite and strain MN17 reduces Cd uptake from soil and improves physiological and biochemical responses of B. napus which is helpful to alleviate Cd toxicity to plants.

Optimization of Direct Blue-14 dye degradation by Bacillus fermus (Kx898362) an alkaliphilic plant endophyte and assessment of degraded metabolite toxicity

Alkaliphilic bacteria possesses the ability to survive in the extreme conditions with high salt concentrations. The adaptability of alkaliphilic bacteria to extreme conditions has made them predominant degrader in the field of biodegradation. A moderately alkaliphilic endophyte was isolated from Centella asiatica with a potential to degrade a di-azo dye Direct Blue-14(DB-14). The isolate was identified as Bacillus fermus with 97% similarity strain Xmb064. On optimization, maximum of 92.76% biodegradation was attained with dye concentration at 68.78 ppm supplemented with 1 g of sucrose and 2.5% (v/v) of inoculum for 72 h incubation. Characterization of the biodegraded product carried out using UV-vis spectrophotometry, FT-IR and LC-MS confirmed the destabilization of di-azo bond followed with the degradation of DB-14. Cytogenotoxicity studies revealed the biodegraded products to be less toxic. The current study is the first report on the optimization, biotransformation and cytogenotoxicity of DB-14 by B. fermus strain Centella.

Streptomyces Dominate the Soil Under Betula Trees That Have Naturally Colonized a Red Gypsum Landfill

The successful restoration of well-engineered tailings storage facilities is needed to avoid mine tailings problems. This study characterized the bacterial communities from vegetated and non-vegetated soils from a red gypsum landfill resulting from the industrial extraction of titanium. A set of 275 bacteria was isolated from vegetated soil and non-vegetated soil areas and taxonomically characterized using BOX-PCR. The study also evaluated the ability of a subset of 88 isolated bacteria on their ability to produce plant growth promoting (PGP) traits [indoleacetic acid (IAA) production, phosphate solubilization, and siderophore production] and their tolerance to potentially toxic elements (PTEs). Twenty strains were chosen for further analysis to produce inoculum for birch-challenging experiments. Principal component analysis (PCA) showed that the set of pedological parameters (pH, granulometry, carbon, organic matter, and Mg content) alone explained approximately 40% of the differences between the two soils. The highest density of total culturable bacteria was found in the vegetated soil, and it was much higher than that in the non-vegetated soil. The Actinobacteria phyla dominated the culturable soil community (70% in vegetated soil and 95% in non-vegetated soil), while the phyla Firmicutes (including the genus Bacillus) and Bacteroides (including the genera Pedobacter and Olivibacter) were found only in the vegetated soil fraction. Additional genera (Rhizobium, Variovorax, and Ensifer) were found solely in the vegetated soil. The vegetated soil bacteria harbored the most beneficial PGP bacteria with 12% of the isolates showing three or more PGP traits. The strains with higher metal tolerances in our study were Phyllobacterium sp. WR140 (RO1.15), Phyllobacterium sp. WR140 (R01.34), and Streptomyces sp. (R04.15), all isolated from the vegetated soil. Among the isolates tested in challenging experiments, Phyllobacterium (R01.34) and Streptomyces sp. (R05.33) have the greatest potential to act as PGP rhizobacteria and therefore to be used in the biological restoration of tailings dumps.

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.

Mechanism of arsenic resistance in endophytic bacteria isolated from endemic plant of mine tailings and their arsenophore production

Arsenic contamination is an important environmental problem around the world since its high toxicity, and bacteria resist to this element serve as valuable resource for its bioremediation. Aiming at searching the arsenic-resistant bacteria and determining their resistant mechanism, a total of 27 strains isolated from roots of Prosopis laevigata and Spharealcea angustifolia grown in a heavy metal-contaminated region in Mexico were investigated. The minimum inhibitory concentration (MIC) and transformation abilities of arsenate (As⁵⁺) and arsenite (As³⁺), arsenophore synthesis, arsenate uptake, and cytoplasmatic arsenate reductase (arsC), and arsenite transporter (arsB) genes were studied for these strains. Based on these results and the 16S rDNA sequence analysis, these isolates were identified as arsenic-resistant endophytic bacteria (AREB) belonging to the genera Arthrobacter, Bacillus, Brevibacterium, Kocuria, Microbacterium, Micrococcus, Pseudomonas, and Staphylococcus. They could tolerate high concentrations of arsenic with MIC from 20 to > 100 mM for As⁵⁺ and 10-20 mM for As³⁺. Eleven isolates presented dual abilities of As⁵⁺ reduction and As³⁺ oxidation. As the most effective strains, Micrococcus luteus NE2E1 reduced 94% of the As⁵⁺ and Pseudomonas zhaodongensis NM2E7 oxidized 46% of As³⁺ under aerobic condition. About 70 and 44% of the test strains produced arsenophores to chelate As⁵⁺ and As³⁺, respectively. The AREB may absorb arsenate via the same receptor of phosphate uptake or via other way in some case. The cytoplasmic arsenate reductase and alternative arsenate reduction pathways exist in these AREB. Therefore, these AREB could be candidates for the bioremediation process.

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.

Complete genome analysis of Serratia marcescens RSC-14: A plant growth-promoting bacterium that alleviates cadmium stress in host plants

Serratia marcescens RSC-14 is a Gram-negative bacterium that was previously isolated from the surface-sterilized roots of the Cd-hyperaccumulator Solanum nigrum. The strain stimulates plant growth and alleviates Cd stress in host plants. To investigate the genetic basis for these traits, the complete genome of RSC-14 was obtained by single-molecule real-time sequencing. The genome of S. marcescens RSC-14 comprised a 5.12-Mbp-long circular chromosome containing 4,593 predicted protein-coding genes, 22 rRNA genes, 88 tRNA genes, and 41 pseudogenes. It contained genes with potential functions in plant growth promotion, including genes involved in indole-3-acetic acid (IAA) biosynthesis, acetoin synthesis, and phosphate solubilization. Moreover, annotation using NCBI and Rapid Annotation using Subsystem Technology identified several genes that encode antioxidant enzymes as well as genes involved in antioxidant production, supporting the observed resistance towards heavy metals, such as Cd. The presence of IAA pathway-related genes and oxidative stress-responsive enzyme genes may explain the plant growth-promoting potential and Cd tolerance, respectively. This is the first report of a complete genome sequence of Cd-tolerant S. marcescens and its plant growth promotion pathway. The whole-genome analysis of this strain clarified the genetic basis underlying its phenotypic and biochemical characteristics, underpinning the beneficial interactions between RSC-14 and plants.

Cultivable endophytic bacteria from heavy metal(loid)-tolerant plants

To evaluate the interactions among endophytes, plants and heavy metal/arsenic contamination, root endophytic bacteria of Prosopis laevigata (Humb and Bonpl. ex Willd) and Sphaeralcea angustifolia grown in a heavy metal(loid)-contaminated zone in San Luis Potosi, Mexico, were isolated and characterized. Greater abundance and species richness were found in Prosopis than in Sphaeralcea and in the nutrient Pb-Zn-rich hill than in the poor nutrient and As-Cu-rich mine tailing. The 25 species identified among the 60 isolates formed three groups in the correspondence analysis, relating to Prosopis/hill (11 species), Prosopis/mine tailing (4 species) and Sphaeralcea/hill (4 species), with six species ungrouped. Most of the isolates showed high or extremely high resistance to arsenic, such as ≥100 mM for As(V) and ≥20 mM for As(III), in mineral medium. These results demonstrated that the abundance and community composition of root endophytic bacteria were strongly affected by the concentration and type of the heavy metals and metalloids (arsenic), as well as the plant species.

Beneficial role of bacterial endophytes in heavy metal phytoremediation

Phytoremediation is an emerging technology that uses plants and their associated microbes to clean up pollutants from the soil, water and air. In recent years, phytoremediation assisted by bacterial endophytes has been highly recommended for cleaning up of metal polluted soils since endophytic bacteria can alleviate metal toxicity in plant through their own metal resistance system and facilitate plant growth under metal stress. Endophytic bacteria improve plant growth in metal polluted soils in two different ways: 1) directly by producing plant growth beneficial substances including solubilization/transformation of mineral nutrients (phosphate, nitrogen and potassium), production of phytohormones, siderophores and specific enzymes; and 2) indirectly through controlling plant pathogens or by inducing a systemic resistance of plants against pathogens. Besides, they also alter metal accumulation capacity in plants by excreting metal immobilizing extracellular polymeric substances, as well as metal mobilizing organic acids and biosurfactants. The present work aims to review the progress of recent research on the isolation, identification and diversity of metal resistant endophytic bacteria and illustrate various mechanisms responsible for plant growth promotion and heavy metal detoxification/phytoaccumulation/translocation in plants.

Improvement in phytoremediation potential of Solanum nigrum under cadmium contamination through endophytic-assisted Serratia sp. RSC-14 inoculation

The growth of hyperaccumulator plants is often compromised by increased toxicity of metals like cadmium (Cd). However, extraction of such metals from the soil can be enhanced by endophytic microbial association. Present study was aimed to elucidate the potential of microbe-assisted Cd phytoextraction in hyperaccumulator Solanum nigrum plants and their interactions under varied Cd concentrations. An endophytic bacteria Serratia sp. RSC-14 was isolated from the roots of S. nigrum. In addition to Cd tolerance up to 4 mM, the RSC-14 exhibited phosphate solubilization and secreted plant growth-promoting phytohormones such as indole-3-acetic acid (54 μg/mL). S. nigrum plants were inoculated with RSC-14 and were grown in different concentrations of Cd (0, 10, and 30 mg Cd kg(-1) sand). Results revealed that Cd treatment caused significant cessation in plant growth, biomass, and chlorophyll content, whereas significantly higher malondialdehyde (MDA) and electrolyte production in leaves were observed in a dose-dependent manner. Conversely, RSC-14 inoculation relived the toxic effects of Cd-induced stress by significantly increasing root/shoot growth, biomass production, and chlorophyll content and decreasing MDA and electrolytes contents. Ameliorative effects on host growth were also observed by the regulation of metal-induced oxidative stress enzymes such as catalase, peroxidase, and polyphenol peroxidase. Activities of these enzymes were significantly reduced in RSC-14 inoculated plants as compared to control plants under Cd treatments. The lower activities of stress responsive enzymes suggest modulation of Cd stress by RSC-14. The current findings support the beneficial uses of Serratia sp. RSC-14 in improving the phytoextraction abilities of S. nigrum plants in Cd contamination.

Characterization of arsenic-resistant endophytic bacteria from hyperaccumulators Pteris vittata and Pteris multifida

We isolated and characterized As-resistant endophytic bacteria (AEB) from two arsenic hyperaccumulators. Their plant growth promoting traits and the relation between As tolerance and transformation were evaluated. A total of 41 and 33 AEB were isolated from Pteris vittata (PV) and Pteris multifida (PM) respectively. PV AEB represented 2genera while PM AEB comprised of 12 genera, with Bacillus sp. being the most dominant bacteria from both plants. All AEB had limited ability in solubilizing P and producing indole acetic acid (IAA) and siderophore. All isolates tolerated 10mM arsenate (As(V)), with PV isolates being more tolerant to As(V) and PM more tolerant to arsenite (As(III)). Bacterial arsenic tolerance was related to their ability in As(III) oxidation and As(V) reduction as well as their ability to retain As in the biomass to a varying extent. Though AEB showed limited plant growth promoting traits, they were important in arsenic tolerance and speciation in plants.

Regeneration of Solanum nigrum by somatic embryogenesis, involving frog egg-like body, a novel structure

A new protocol was established for the regeneration of Solanum nigrum by frog egg-like bodies (FELBs), which are novel somatic embryogenesis (SE) structures induced from the root, stem, and leaf explants. The root, stem, and leaf explants (93.33%, 85.10%, and 100.00%, respectively) were induced to form special embryonic calli on Murashige and Skoog (MS) medium containing 1.0 mg/L 2,4-dichlorophenoxyacetic acid, under dark condition. Further, special embryonic calli from the root, stem, and leaf explants (86.97%, 83.30%, and 99.47%, respectively) were developed into FELBs. Plantlets of FELBs from the three explants were induced in vitro on MS medium supplemented with 5.0 mg/L 6-benzylaminopurine and 0.1 mg/L gibberellic acid, and 100.00% plantlet induction rates were noted. However, plantlet induction in vivo on MS medium supplemented with 20 mg/L thidiazuron showed rates of 38.63%, 15.63%, and 61.30% for the root, stem, and leaf explants, respectively, which were lower than those of the in vitro culture. Morphological and histological analyses of FELBs at different development stages revealed that they are a novel type of SE structure that developed from the mesophyll (leaf) or cortex (stem and root) cells of S. nigrum.

LEAFY COTYLEDON2 (LEC2) promotes embryogenic induction in somatic tissues of Arabidopsis, via YUCCA-mediated auxin biosynthesis

The LEAFY COTYLEDON2 (LEC2) transcription factor with a plant-specific B3 domain plays a central role in zygotic and somatic embryogenesis (SE). LEC2 overexpression induced in planta leads to spontaneous somatic embryo formation, but impairs the embryogenic response of explants cultured in vitro under auxin treatment. The auxin-related functions of LEC2 appear during SE induction, and the aim of the present study was to gain further insights into this phenomenon. To this end, the effect of LEC2 overexpression on the morphogenic responses of Arabidopsis explants cultured in vitro under different auxin treatments was evaluated. The expression profiles of the auxin biosynthesis genes were analysed in embryogenic cultures with respect to LEC2 activity. The results showed that LEC2 overexpression severely modifies the requirement of cultured explants for an exogenous auxin concentration at a level that is effective in SE induction and suggested an increase in the auxin content in 35S::LEC2-GR transgenic explants. The assumption of an LEC2 promoted increase in endogenous auxin in cultured explants was further supported by the expression profiling of the genes involved in auxin biosynthesis. The analysis indicated that YUCCAs and TAA1, working in the IPA-YUC auxin biosynthesis pathway, are associated with SE induction, and that the expression of three YUCCA genes (YUC1, YUC4 and YUC10) is associated with LEC2 activity. The results also suggest that the IAOx-mediated auxin biosynthesis pathway involving ATR1/MYB34 and CYP79B2 does not seem to be involved in SE induction. We conclude that de novo auxin production via the tryptophan-dependent IPA-YUC auxin biosynthesis pathway is implicated in SE induction, and that LEC2 plays a key role in this mechanism.

LEAFY COTYLEDON2 (LEC2) promotes embryogenic induction in somatic tissues of Arabidopsis, via YUCCA-mediated auxin biosynthesis

The LEAFY COTYLEDON2 (LEC2) transcription factor with a plant-specific B3 domain plays a central role in zygotic and somatic embryogenesis (SE). LEC2 overexpression induced in planta leads to spontaneous somatic embryo formation, but impairs the embryogenic response of explants cultured in vitro under auxin treatment. The auxin-related functions of LEC2 appear during SE induction, and the aim of the present study was to gain further insights into this phenomenon. To this end, the effect of LEC2 overexpression on the morphogenic responses of Arabidopsis explants cultured in vitro under different auxin treatments was evaluated. The expression profiles of the auxin biosynthesis genes were analysed in embryogenic cultures with respect to LEC2 activity. The results showed that LEC2 overexpression severely modifies the requirement of cultured explants for an exogenous auxin concentration at a level that is effective in SE induction and suggested an increase in the auxin content in 35S::LEC2-GR transgenic explants. The assumption of an LEC2 promoted increase in endogenous auxin in cultured explants was further supported by the expression profiling of the genes involved in auxin biosynthesis. The analysis indicated that YUCCAs and TAA1, working in the IPA-YUC auxin biosynthesis pathway, are associated with SE induction, and that the expression of three YUCCA genes (YUC1, YUC4 and YUC10) is associated with LEC2 activity. The results also suggest that the IAOx-mediated auxin biosynthesis pathway involving ATR1/MYB34 and CYP79B2 does not seem to be involved in SE induction. We conclude that de novo auxin production via the tryptophan-dependent IPA-YUC auxin biosynthesis pathway is implicated in SE induction, and that LEC2 plays a key role in this mechanism.

Effect of endophyte-infection on growth parameters and Cd-induced phytotoxicity of Cd-hyperaccumulator Solanum nigrum L

The aim of this work was to evaluate effects of endophytic bacterium inoculation on plant growth and assess the possible mechanism of endophyte in heavy metal phytoremediation. Seeds of Solanum nigrum L. were inoculated with endophyte Serratia nematodiphila LRE07 and were subjected to Cd in the growing medium. Cd produced a significant inhibition on plant growth and a reduction in the content of photosynthetic pigments. The inoculation of endophytic bacterium alleviated the Cd-induced changes, resulting in more biomass production and higher photosynthetic pigments content of leaves compared with non-symbiotic ones. The beneficial effect was more obvious at relatively low Cd concentration (10 μM). Based on the alteration of nutrient uptake and activated oxygen metabolism in infected plants, the possible mechanisms of endophytic bacterium in Cd phytotoxicity reduction can be concluded as uptake enhancement of essential mineral nutrition and improvement in the antioxidative enzymes activities in infected plant.

Approaches for enhanced phytoextraction of heavy metals

The contamination of the environment with toxic metals has become a worldwide problem. Metal toxicity affects crop yields, soil biomass and fertility. Soils polluted with heavy metals pose a serious health hazard to humans as well as plants and animals, and often requires soil remediation practices. Phytoextraction refers to the uptake of contaminants from soil or water by plant roots and their translocation to any harvestable plant part. Phytoextraction has the potential to remove contaminants and promote long-term cleanup of soil or wastewater. The success of phytoextraction as a potential environmental cleanup technology depends on factors like metal availability for uptake, as well as plants ability to absorb and accumulate metals in aerial parts. Efforts are ongoing to understand the genetics and biochemistry of metal uptake, transport and storage in hyperaccumulator plants so as to be able to develop transgenic plants with improved phytoremediation capability. Many plant species are being investigated to determine their usefulness for phytoextraction, especially high biomass crops. The present review aims to give an updated version of information available with respect to metal tolerance and accumulation mechanisms in plants, as well as on the environmental and genetic factors affecting heavy metal uptake. The genetic tools of classical breeding and genetic engineering have opened the door to creation of 'remediation' cultivars. An overview is presented on the possible strategies for developing novel genotypes with increased metal accumulation and tolerance to toxicity.

Application of phosphate-solubilizing bacteria for enhancing bioavailability and phytoextraction of cadmium (Cd) from polluted soil

In this study, phosphate-solubilizing bacteria (PSB), Bacillus megaterium, were used to enhance Cd bioavailability and phytoextractability of Cd from contaminated soils. This strain showed a potential for directly solubilizing phosphorous from soils more than 10 folds greater than the control without inoculation. The results of pot experiments revealed that inoculation with B. megaterium significantly increased the extent of Cd accumulation in Brassica juncea and Abutilon theophrasti by two folds relative to the uninoculated control. The maximum Cd concentrations due to inoculation were 1.6 and 1.8 mg Cd g(-1) plant for B. juncea and A. theophrasti after 10 wk, respectively. The total biomass of A. theophrasti was not significantly promoted by the inoculation treatment, yet the total biomass of B. juncea increased from 0.087 to 0.448 g. It is also worth to mention that B. juncea predominantly accumulates Cd in its stems (39%) whereas A. theophrasti accumulates it in its leaves (68%) after 10 wk. The change of the Cd speciation indicated that inoculation of B. megaterium as PSB increased the bioavailabilty of Cd and consequently enhanced its uptake by plants. The present study may provide a new insight for improving phytoremediation using PSB in the Cd-contaminated soils.

Combined remediation of DDT congeners and cadmium in soil by Sphingobacterium sp. D-6 and Sedum alfredii Hance

Combined pollution of 1,1,1-trichloro-2,2-bis (4-chlorophenyl) ethane (DDT) and cadmium (Cd) in agricultural soils is of great concern because they present serious risk to food security and human health. In order to develop a cost-effective and safe method for the removal of DDTs and Cd in soil, combined remediation of DDTs and Cd in soil by Sphingobacterium sp. D-6 and the hyperaccumulator, Sedum alfredii Hance was investigated. After treatment for 210 days, the degradation half-lives of DDTs in soils treated by strain D-6 decreased by 8.1% to 68.0% compared with those in the controls. The inoculation of strain D-6 into soil decreased the uptake of DDTs by pak choi and S. alfredii. The shoots/roots ratios of S. alfredii for the Cd accumulation ranged from 12.32 to 21.75. The Cd concentration in soil decreased to 65.8%-71.8% for S. alfredii treatment and 14.1%-58.2% for S. alfredii and strain D-6 combined treatment, respectively, compared with that in the control. The population size of the DDTs-degrading strain, Simpson index (1/D) and soil respiratory rate decreased in the early stage of treatment and then gradually increased, ultimately recovering to or exceeding the initial level. The results indicated that synchronous incorporation of strain D-6 and S. alfredii into soil was found to significantly (p < or = 0.05) enhance the degradation of DDTs in soil and the hyperaccumulation of Cd in S. alfredii. It was concluded that strain D-6 and S. alfredii could be used successfully to control DDTs and Cd in contaminated soil.

Analysis and characterization of cultivable heavy metal-resistant bacterial endophytes isolated from Cd-hyperaccumulator Solanum nigrum L. and their potential use for phytoremediation

This study investigates the heavy metal-resistant bacterial endophytes of Cd-hyperaccumulator Solanum nigrum L. grown on a mine tailing by using cultivation-dependent technique. Thirty Cd-tolerant bacterial endophytes were isolated from roots, stems, and leaves of S. nigrum L. and classified by amplified ribosomal DNA-restriction analysis into 18 different types. Phylogenetic analysis based on 16S rDNA sequences showed that these isolates belonged to four groups: Actinobacteria (43%), Proteobacteria (23%), Bacteroidetes (27%) and Firmicutes (7%). All the isolates were then characterized for their plant growth promoting traits as well as their resistances to different heavy metals; and the actual plant growth promotion and colonization ability were also assessed. Four isolates were re-introduced into S. nigrum L. under Cd stress and resulted in Cd phytotoxicity decrease, as dry weights of roots increased from 55% to 143% and dry weights of above-ground from 64% to 100% compared to the uninoculated ones. The total Cd accumulation of inoculated plants increased from 66% to 135% (roots) and from 22% to 64% (above-ground) compared to the uninoculated ones. Our research suggests that bacterial endophytes are a most promising resource and may be the excellent candidates of bio-inoculants for enhancing the phytoremediation efficiency.

Soil microbes and plant fertilization

With respect to the adverse effects of chemical fertilization on the environment and their related expenses, especially when overused, alternative methods of fertilization have been suggested and tested. For example, the combined use of chemical fertilization with organic fertilization and/or biological fertilization is among such methods. It has been indicated that the use of organic fertilization with chemical fertilization is a suitable method of providing crop plants with adequate amount of nutrients, while environmentally and economically appropriate. In this article, the importance of soil microbes to the ecosystem is reviewed, with particular emphasis on the role of plant growth-promoting rhizobacteria, arbuscular mycorrhizal fungi, and endophytic bacteria in providing necessary nutrients for plant growth and yield production. Such microbes are beneficial to plant growth through colonizing plant roots and inducing mechanisms by which plant growth increases. Although there has been extensive research work regarding the use of microbes as a method of fertilizing plants, it is yet a question how the efficiency of such microbial fertilization to the plant can be determined and increased. In other words, how the right combination of chemical and biological fertilization can be determined. In this article, the most recent advances regarding the effects of microbial fertilization on plant growth and yield production in their combined use with chemical fertilization are reviewed. There are also some details related to the molecular mechanisms affecting the microbial performance and how the use of biological techniques may affect the efficiency of biological fertilization.