Enterobacter asburiae KE17 association regulates physiological changes and mitigates the toxic effects of heavy metals in soybean

Halotolerant Enterobacter asburiae A103 isolated from the halophyte Salix linearistipularis: Genomic analysis and growth-promoting effects on Medicago sativa under alkali stress

Soil salinization negatively affects plant growth and threatens food security. Halotolerant plant growth-promoting bacteria (PGPB) can alleviate salt stress in plants via diverse mechanisms. In the present study, we isolated salt-tolerant bacteria with phosphate-solubilizing abilities from the rhizosphere of Salix linearistipularis, a halophyte distributed in saline-alkali soils. Strain A103 showed high phosphate solubilization activity and was identified as Enterobacter asburiae based on genome analysis. In addition, it can produce indole-3-acetic acid (IAA), siderophores, and 1-aminocyclopropane-1-carboxylate (ACC) deaminase. Genome mining has also revealed the presence of several functional genes involved in the promotion of plant growth. Inoculation with A103 markedly improved alfalfa growth in the presence of 100 mM NaHCO3. Under alkali stress, the shoot and root dry weights after bacterial inoculation improved by 42.9 % and 21.9 %, respectively. Meanwhile, there was a 35.9-37.1 % increase in the shoot and root lengths after treatment with A103 compared to the NaHCO3-treated group. Soluble sugar content, peroxidase and catalase activities increased in A103-inoculated alfalfa under alkaline stress. A significant decrease in the malondialdehyde content was observed after treatment with strain A103. Metabolomic analysis indicated that strain A103 positively regulated alkali tolerance in alfalfa through the accumulation of metabolites, such as homocarnosine, panthenol, and sorbitol, which could reduce oxidative damage and act as osmolytes. These results suggest that halophytes are valuable resources for bioprospecting halotolerant beneficial bacteria and that the application of halotolerant growth-promoting bacteria is a natural and efficient strategy for developing sustainable agriculture.

Complete genome sequencing of Enterobacter ludwigii strain T977 revealed its great ability for starch degradation of Nicotiana tabacum L. Yunyan 97

Enterobacter ludwigii has been proven by numerous studies to be an effective plant growth promoter. Enterobacter ludwigii T977 was isolated from leaves of Nicotiana tabacum L. Yunyan 97 which showing high starch degrading ability. The optimal fermentation carbon source of strain T977 was starch, with optimal starch concentration as 2.5 g/L, and the most suitable fermentation nitrogen source for the strain T977 was ammonium acetate, with optimal concentration as 0.25 g/L. The spaying treatment of strain T977 could reduce the starch content of upper leaves from 3.77% to 1.43%, the total sugar and reducing sugar decreased slightly, the starch content of middle leaves decreased from 5.63% to 3.18%, the content of total sugar and reducing sugar increased in middle leaves, and the other chemical components were in the appropriate range. Here, we reported 4.77 MB whole genome of a starch-degrading E. ludwigii T977 that encodes 4501 proteins, 11 α-amylases in GH13 family were identified, and the amylase (GM000159) with signal peptide may play important role in degradation of starch in tobacco leaves. Our study may provide an effective microbiological mean for reducing starch content in tobacco leaves.

Gamma-aminobutyric acid interactions with phytohormones and its role in modulating abiotic and biotic stress in plants

Gamma-aminobutyric acid (GABA), a ubiquitous non-protein 4-carbon amino acid present in both prokaryotic and eukaryotic organisms. It is conventionally recognized as a neurotransmitter in mammals and plays a crucial role in plants. The context of this review centers on the impact of GABA in mitigating abiotic stresses induced by climate change, such as drought, salinity, heat, and heavy metal exposure. Beyond its neurotransmitter role, GABA emerges as a key player in diverse metabolic processes, safeguarding plants against multifaceted abiotic as well as biotic challenges. This comprehensive exploration delves into the GABA biosynthetic pathway, its transport mechanisms, and its intricate interplay with various abiotic stresses. The discussion extends to the nuanced relationship between GABA and phytohormones during abiotic stress acclimation, offering insights into the strategic development of mitigation strategies against these stresses. The delineation of GABA's crosstalk with phytohormones underscores its pivotal role in formulating crucial strategies for abiotic stress alleviation in plants.

Heavy metal-resistant rhizobacteria fosters to alleviate the cadmium toxicity in Arabidopsis by upregulating the plant physiological responses

This study was designed to investigate the role of Morganella morganii strains in alleviating Cd stress in Arabidopsis seedlings under controlled conditions. Both M. morganii strains ABT3 (ON316873) and ABT9 (ON316874) strains isolated from salt-affected areas showed higher resistance against Cd and possess plant growth-promoting traits such as nitrogen fixation, indole-acetic acid production, ammonia production, phosphate solubilization, and, catalase, gelatinase and protease enzyme production. Plant inoculation assay showed that varying concentration of Cd (1.5 mM and 2.5 mM) significantly reduced Arabidopsis growth, quantum yield (56.70%-66.49%), and chlorophyll content (31.90%-42.70%). Cd toxicity also triggered different associations between lipid peroxidation (43.61%-69.77%) and enzymatic antioxidant mechanisms. However, when both strains were applied to the Arabidopsis seedlings, the shoot and root length and fresh and dry weights were improved in the control and Cd-stressed plants. Moreover, both strains enhanced the resistance against Cd stress by increasing antioxidant enzyme activities [catalase (19.47%-27.39%) and peroxidase (37.50%-48.07%)]that ultimately cause a substantial reduction in lipid peroxidation (27.71%-41.90%). Both strains particularly ABT3 also showed positive results in improving quantum yield (73.84%-98.64%) and chlorophyll content (41.13%-48.63%), thus increasing the growth of Arabidopsis seedlings. The study suggests that PGPR can protect plants from Cd toxicity, and Cd-tolerant rhizobacterial strains can remediate heavy metal polluted sites and improve plant growth.

Rhizobiome Transplantation: A Novel Strategy beyond Single-Strain/Consortium Inoculation for Crop Improvement

The growing human population has a greater demand for food; however, the care and preservation of nature as well as its resources must be considered when fulfilling this demand. An alternative employed in recent decades is the use and application of microbial inoculants, either individually or in consortium. The transplantation of rhizospheric microbiomes (rhizobiome) recently emerged as an additional proposal to protect crops from pathogens. In this review, rhizobiome transplantation was analyzed as an ecological alternative for increasing plant protection and crop production. The differences between single-strain/species inoculation and dual or consortium application were compared. Furthermore, the feasibility of the transplantation of other associated micro-communities, including phyllosphere and endosphere microbiomes, were evaluated. The current and future challenges surrounding rhizobiome transplantation were additionally discussed. In conclusion, rhizobiome transplantation emerges as an attractive alternative that goes beyond single/group inoculation of microbial agents; however, there is still a long way ahead before it can be applied in large-scale agriculture.

Recent progress on the microbial mitigation of heavy metal stress in soybean: overview and implications

Plants are adapted to defend themselves through programming, reprogramming, and stress tolerance against numerous environmental stresses, including heavy metal toxicity. Heavy metal stress is a kind of abiotic stress that continuously reduces various crops' productivity, including soybeans. Beneficial microbes play an essential role in improving plant productivity as well as mitigating abiotic stress. The simultaneous effect of abiotic stress from heavy metals on soybeans is rarely explored. Moreover, reducing metal contamination in soybean seeds through a sustainable approach is extremely needed. The present article describes the initiation of heavy metal tolerance mediated by plant inoculation with endophytes and plant growth-promoting rhizobacteria, the identification of plant transduction pathways via sensing annotation, and contemporary changes from molecular to genomics. The results suggest that the inoculation of beneficial microbes plays a significant role in rescuing soybeans under heavy metal stress. They create a dynamic, complex interaction with plants via a cascade called plant-microbial interaction. It enhances stress metal tolerance via the production of phytohormones, gene expression, and secondary metabolites. Overall, microbial inoculation is essential in mediating plant protection responses to heavy metal stress produced by a fluctuating climate.

The Effect of Cadmium Tolerant Plant Growth Promoting Rhizobacteria on Plant Growth Promotion and Phytoremediation: A Review

Cadmium (Cd) is a heavy metal of considerable toxicity with destructive impacts on plants, microbes and environments. Its toxicity is due to mishandling and manual hazards in plants and is primarily observed within the soil to cause decline of plants and microbial activity inside the rhizosphere. Cadmium accumulation in crops and the probability of Cd entering the food chain are grave for public health in the worldwide. Cadmium toxicity leads to depletion in seed germination, initial seedling growth, plant biomass, chlorosis, necrosis, hindrance of photosynthetic machinery and other physiological and biological activities in plants. Cadmium triggers the reactive oxygen species (ROS) that influences gene mutation and DNA damage that affects the cell cycle and cell division. Cd toxicity altered the levels of phenolic compounds, carbohydrates, glycine betaine, proline and organic acids in crops. Under stress conditions, the plant growth promoting rhizobacteria (PGPR) have various properties such as enzymatic activities, plant growth hormones production, phosphate solubilization, siderophores production and chelating agents that help the plants tolerate against Cd stress and also increase phenolic compound levels and osmolytes. Hence, this review highlights the crucial role of cadmium tolerant PGPR for crop production, declining metal phytoavailability and enhancing morphological and physiological boundaries of plants under stress conditions. It could be an environment friendly and cost effective technology under sustainable crop production.

Gene sdaB Is Involved in the Nematocidal Activity of Enterobacter ludwigii AA4 Against the Pine Wood Nematode Bursaphelenchus xylophilus

Bursaphelenchus xylophilus, a plant parasitic nematode, is the causal agent of pine wilt, a devastating forest tree disease. Essentially, no efficient methods for controlling B. xylophilus and pine wilt disease have yet been developed. Enterobacter ludwigii AA4, isolated from the root of maize, has powerful nematocidal activity against B. xylophilus in a new in vitro dye exclusion test. The corrected mortality of the B. xylophilus treated by E. ludwigii AA4 or its cell extract reached 98.3 and 98.6%, respectively. Morphological changes in B. xylophilus treated with a cell extract from strain AA4 suggested that the death of B. xylophilus might be caused by an increased number of vacuoles in non-apoptotic cell death and the damage to tissues of the nematodes. In a greenhouse test, the disease index of the seedlings of Scots pine (Pinus sylvestris) treated with the cells of strain AA4 plus B. xylophilus or those treated by AA4 cell extract plus B. xylophilus was 38.2 and 30.3, respectively, was significantly lower than 92.5 in the control plants treated with distilled water and B. xylophilus. We created a sdaB gene knockout in strain AA4 by deleting the gene that was putatively encoding the beta-subunit of L-serine dehydratase through Red homologous recombination. The nematocidal and disease-suppressing activities of the knockout strain were remarkably impaired. Finally, we revealed a robust colonization of P. sylvestris seedling needles by E. ludwigii AA4, which is supposed to contribute to the disease-controlling efficacy of strain AA4. Therefore, E. ludwigii AA4 has significant potential to serve as an agent for the biological control of pine wilt disease caused by B. xylophilus.

Influence of Endophytic Bacterium, Cellulosimicrobium sp. FRR2 on Plant Growth of Amaranthus campestris L. and Bacterial Survival at Adverse Environmental Conditions

The endophytic microorganisms are believed to be an important bio-resource for modern agriculture because of their beneficial effects on plant growth promotion, biocontrol, stress tolerance, and diseases resistance. This study was focused to know the beneficial effect of endophytic bacterium (FRR2) isolated from the roots of Ficus religiosa L. on Amaranthus campestris L. and their tolerance ability against salinity and heavy metals. The strain FRR2 was recognized as Cellulosimicrobium sp. by 16s rRNA sequencing and phylogenetic study. The bacterial isolate FRR2 showed salt (at 150 mM NaCl) and metal (at 150 µM CuSO4 and 100 µM ZnSO4) tolerance ability and significantly higher growth rate of Amaranthus campestris in a green leafy vegetable might be due to the nitrogen fixation, indole acetic acid production, amylase and protease activities. In addition, the endophyte FRR2 application slightly increased the antioxidants activity than their controls. The results of this study revealed that Cellulosimicrobium sp. strain FRR2 would be an effective endophyte to increase the growth of green leafy vegetables.

Biofilm Formation, Production of Matrix Compounds and Biosorption of Copper, Nickel and Lead by Different Bacterial Strains

Bacterial biofilms play a key role in metal biosorption from wastewater. Recently, Enterobacter asburiae ENSD102, Enterobacter ludwigii ENSH201, Vitreoscilla sp. ENSG301, Acinetobacter lwoffii ENSG302, and Bacillus thuringiensis ENSW401 were shown to form air–liquid (AL) and solid–air–liquid (SAL) biofilms in a static condition at 28 and 37°C, respectively. However, how environmental and nutritional conditions affect biofilm formation; production of curli and cellulose; and biosorption of copper (Cu), nickel (Ni), and lead (Pb) by these bacteria have not been studied yet. In this study, E. asburiae ENSD102, E. ludwigii ENSH201, and B. thuringiensis ENSW401 developed the SAL biofilms at pH 8, while E. asburiae ENSD102 and Vitreoscilla sp. ENSG301 constructed the SAL biofilms at pH 4. However, all these strains produced AL biofilms at pH 7. In high osmolarity and ½-strength media, all these bacteria built fragile AL biofilms, while none of these strains generated the biofilms in anaerobic conditions. Congo red binding results showed that both environmental cues and bacterial strains played a vital role in curli and cellulose production. Calcofluor binding and spectrophotometric results revealed that all these bacterial strains produced significantly lesser amounts of cellulose at 37°C, pH 8, and in high osmotic conditions as compared to the regular media, at 28°C, and pH 7. Metal biosorption was drastically reduced in these bacteria at 37°C than at 28°C. Only Vitreoscilla sp. ENSG301 and B. thuringiensis ENSW401 completely removed (100%) Cu and Ni at an initial concentration of 12.5 mg l^–1, while all these bacteria totally removed (100%) Pb at concentrations of 12.5 and 25 mg l^–1 at pH 7 and 28°C. At an initial concentration of 100 mg l^–1, the removal of Cu (92.5 to 97.8%) and Pb (89.3 to 98.3%) was the highest at pH 6, while it was higher (84.7 to 93.9%) for Ni at pH 7. Fourier transform infrared spectroscopy results showed metal-unloaded biomass biofilms contained amino, hydroxyl, carboxyl, carbonyl, and phosphate groups. The peak positions of these groups were shifted responding to Cu, Ni, and Pb, suggesting biosorption of metals. Thus, these bacterial strains could be utilized to remove Cu, Ni, and Pb from aquatic environment.

Bioaugmented Phytoremediation of Metal-Contaminated Soils and Sediments by Hemp and Giant Reed

We assessed the effects of EDTA and selected plant growth-promoting rhizobacteria (PGPR) on the phytoremediation of soils and sediments historically contaminated by Cr, Ni, and Cu. A total of 42 bacterial strains resistant to these heavy metals (HMs) were isolated and screened for PGP traits and metal bioaccumulation, and two Enterobacter spp. strains were finally selected. Phytoremediation pot experiments of 2 months duration were carried out with hemp (Cannabis sativa L.) and giant reed (Arundo donax L.) grown on soils and sediments respectively, comparing in both cases the effects of bioaugmentation with a single PGPR and EDTA addition on plant and root growth, plant HM uptake, HM leaching, as well as the changes that occurred in soil microbial communities (structure, biomass, and activity). Good removal percentages on a dry mass basis of Cr (0.4%), Ni (0.6%), and Cu (0.9%) were observed in giant reed while negligible values (<100‰) in hemp. In giant reed, HMs accumulated differentially in plant (rhizomes > > roots > leaves > stems) with largest quantities in rhizomes (Cr 0.6, Ni 3.7, and Cu 2.2 g plant^–1). EDTA increased Ni and Cu translocation to aerial parts in both crops, despite that in sediments high HM concentrations in leachates were measured. PGPR did not impact fine root diameter distribution of both crops compared with control while EDTA negatively affected root diameter class length (DCL) distribution. Under HM contamination, giant reed roots become shorter (from 5.2 to 2.3 mm cm^–3) while hemp roots become shorter and thickened from 0.13 to 0.26 mm. A consistent indirect effect of HM levels on the soil microbiome (diversity and activity) mediated by plant response (root DCL distribution) was observed. Multivariate analysis of bacterial diversity and activity revealed not only significant effects of plant and soil type (rhizosphere vs. bulk) but also a clear and similar differentiation of communities between control, EDTA, and PGPR treatments. We propose root DCL distribution as a key plant trait to understand detrimental effect of HMs on microbial communities. Positive evidence of the soil-microbe-plant interactions occurring when bioaugmentation with PGPR is associated with deep-rooting perennial crops makes this combination preferable over the one with chelating agents. Such knowledge might help to yield better bioaugmented bioremediation results in contaminated sites.

Rhizospheric Phosphate Solubilizing Bacillus atrophaeus GQJK17 S8 Increases Quinoa Seedling, Withstands Heavy Metals, and Mitigates Salt Stress

Introduction of quinoa (Chenopodium quinoa willd.), a gluten-free nutritious pseudo-cereal, outside its traditional growing areas exposed it to seedling damping-off. Here, we isolated eleven phosphate-solubilizing bacteria from the quinoa rhizosphere and assessed their effect on germination and seedlings growth. All isolates solubilized phosphate, produced indole3-acetic acid, hydrocyanic acid, siderophores, and ammonia. Genotypic analysis revealed that our strains are related to the genus of Bacillus, Pseudomonas, and Enterobacter. Strains Enterobacter asburiae (QD14, QE4, QE6, and QE16), Enterobacter sp. QE3, and Enterobacter hormaechei QE7 withstood 1.5 mg·L−1 of cadmium sulfate, 0.5 mg·mL−1 of nickel nitrate, and 1 mg·mL−1 of copper sulfate. Moreover, all strains solubilized zinc from ZnO; P. Stutzeri QD1 and E. asburiae QD14 did not solubilize Zn3(PO4)2 and CO3Zn, whereas CO3Zn was not solubilized by E. asburiae QE16. Bacillus atrophaeus S8 tolerated 11% NaCl. P. frederiksbergensis S6 and Pseudomonas sp. S7 induced biofilm formation. Anti-fusarium activity was demonstrated for E.asburiae QE16, P. stutzeri QD1, P. frederiksbergensis S6, Pseudomonas sp. S7, and B. atrophaeus S8. Lastly, inoculation of quinoa seeds with B. atrophaeus S8 and E. asburiae QB1 induced the best germination rate and seedling growth, suggesting their potential use as inoculants for salty and heavy metal or zinc contaminated soils.

The versatile GABA in plants

Gamma-aminobutyric acid (GABA) is a ubiquitous four-carbon, non-protein amino acid. GABA has been widely studied in animal central nervous systems, where it acts as an inhibitory neurotransmitter. In plants, it is metabolized through the GABA shunt pathway, a bypass of the tricarboxylic acid (TCA) cycle. Additionally, it can be synthesized through the polyamine metabolic pathway. GABA acts as a signal in Agrobacterium tumefaciens-mediated plant gene transformation and in plant development, especially in pollen tube elongation (to enter the ovule), root growth, fruit ripening, and seed germination. It is accumulated during plant responses to environmental stresses and pathogen and insect attacks. A high concentration of GABA elevates plant stress tolerance by improving photosynthesis, inhibiting reactive oxygen species (ROS) generation, activating antioxidant enzymes, and regulating stomatal opening in drought stress. The transporters of GABA in plants are reviewed in this work. We summarize the recent research on GABA function and transporters with the goal of providing a review of GABA in plants.

Double infection of Wolbachia and Spiroplasma alters induced plant defense and spider mite fecundity

BACKGROUND

Herbivore-associated bacterial symbionts can change plant physiology and influence herbivore fitness. The spider mite Tetranychus truncatus is a notorious pest harboring various bacterial symbionts; however, the effect of bacterial symbionts on host plant physiology remains unclear. Here, we investigated whether infection with the endosymbionts Wolbachia and Spiroplasma altered spider mite performance on tomato plants and affected plant-induced defenses.

RESULTS

Wolbachia and Spiroplasma were mainly located in the gnathosoma and ovaries of their spider mite hosts. Wolbachia and Spiroplasma significantly improved spider mite reproductive performance in cultivated and wild-type tomato. However, in plants deficient in jasmonic acid (JA) and salicylic acid (SA), there were no significant differences in reproduction between spider mites infected with Wolbachia and Spiroplasma and uninfected mites. The results indicated that the reproduction benefits conferred by endosymbionts may relate to plant defenses. Both spider mites infected with Wolbachia and Spiroplasma and uninfected mites induced similar levels of JA and SA accumulation in tomato, whereas tomato plants damaged by spider mites infected with both Wolbachia and Spiroplasma showed lower expression levels of JA- and SA-responsive genes than those damaged by uninfected spider mites. In addition, mites infected with Wolbachia and Spiroplasma mites consumed more tomato amino acids compared to uninfected spider mites, which may have contributed to host fecundity.

CONCLUSIONS

Our results suggest that the reproduction benefits conferred by endosymbionts may be associated with changes in plant defense parameters and the concentrations of plant amino acids. The results highlight the importance of endosymbionts in interactions between spider mites and their host plants. © 2020 Society of Chemical Industry.

Genome-wide association study (GWAS) reveals genetic loci of lead (Pb) tolerance during seedling establishment in rapeseed (Brassica napus L.)

BACKGROUND

Lead (Pb) pollution in soil has become one of the major environmental threats to plant growth and human health. Safe utilization of Pb contaminated soil by phytoremediation require Pb-tolerant rapeseed (Brassica napus L.) accessions. However, breeding of new B. napus cultivars tolerance to Pb stress has been restricted by limited knowledge on molecular mechanisms involved in Pb tolerance. This work was carried out to identify genetic loci related to Pb tolerance during seedling establishment in rapeseed.

RESULTS

Pb tolerance, which was assessed by quantifying radicle length (RL) under 0 or 100 mg/L Pb stress condition, shown an extensive variation in 472 worldwide-collected rapeseed accessions. Based on the criterion of relative RL > 80%, six Pb-tolerant genotypes were selected. Four quantitative trait loci (QTLs) associated with Pb tolerance were identified by Genome-wide association study. The expression level of nine promising candidate genes, including GSTUs, BCATs, UBP13, TBR and HIPP01, located in these four QTL regions, were significantly higher or induced by Pb in Pb-tolerant accessions in comparison to Pb-sensitive accessions.

CONCLUSION

To our knowledge, this is the first study on Pb-tolerant germplasms and genomic loci in B. napus. The findings can provide valuable genetic resources for the breeding of Pb-tolerant B. napus cultivars and understanding of Pb tolerance mechanism in Brassica species.

Supplementation with plant growth promoting rhizobacteria (PGPR) alleviates cadmium toxicity in Solanum lycopersicum by modulating the expression of secondary metabolites

The current study evaluated the synergistic role of Plant growth promoting rhizobacteria (PGPR), Pseudomonas aeruginosa and Burkholderia gladioli on different physiological, biochemical and molecular activities of 10-days old Solanum lycopersicum seedlings under Cd stress. Cd toxicity altered the levels of phenolic compounds (total phenols (30.2%), flavonoids (92.7%), anthocyanin (59.5%), polyphenols (368.7%)), osmolytes (total osmolytes (10.3%), total carbohydrates (94%), reducing sugars (64.5%), trehalose (112.5%), glycine betaine (59%), proline (54.8%), and free amino acids (63%)), and organic acids in S. lycopersicum seedlings. Inoculation of P. aeruginosa and B. gladioli alleviated Cd-induced toxicity, which was manifested through enhanced phenolic compound levels and osmolytes. Additionally, the levels of low molecular weight organic acids (fumaric acid, malic acid, succinic acid, and citric acid) were also elevated. The expression of genes encoding enzymes for phenols and organic acid metabolism were also studied to be modulated that included CHS (chalcone synthase; 138.4%), PAL (phenylalanine ammonia lyase; 206.7%), CS (citrate synthase; 61.3%), SUCLG1 (succinyl Co-A ligase; 33.6%), SDH (succinate dehydrogenase; 23.2%), FH (fumarate hydratase; 12.4%), and MS (malate synthase; 41.2%) and found to be upregulated in seedlings inoculated independently with P. aeruginosa and B. gladioli. The results provide insights into the role of micro-organisms in alleviating Cd-induced physiological damage by altering levels of different metabolites.

Metal resistant PGPR lowered Cd uptake and expression of metal transporter genes with improved growth and photosynthetic pigments in Lycopersicon esculentum under metal toxicity

Plant growth promoting rhizobacteria (PGPRs) are very effective in immobilization of heavy metals and reducing their translocation in plants via precipitation, complex formation and adsorption. The present study was therefore designed to understand the role of Pseudomonas aeruginosa and Burkholderia gladioli in mitigation of Cd stress (0.4 mM) in 10-days old L. esculentum seedlings. The present work investigated growth characteristics, photosynthetic pigments, metal tolerance index, metal uptake and the contents of metal chelating compounds (protein bound and non-protein bound thiols, total thiols) in microbes inoculated Cd treated L. esculentum seedlings. The gene expression profiling of different metal transporters was conducted in order to investigate the quantitative analysis. Our results revealed Cd generated toxicity in seedlings in terms of reduced growth (root length, shoot length and fresh weight) and photosynthetic pigments (chlorophyll, carotenoid and xanthophyll) which enhanced upon inoculations of P. aeruginosa and B. gladioli. Further, the metal uptake along with levels of protein and non-protein bound thiols was also enhanced in Cd-treated seedlings. Gene expression studies suggested enhanced expression in the metal transporter genes which were further declined in the microbe supplemented seedlings. Therefore, micro-organisms possess growth promoting traits that enable them to reduce metal toxicity in plants.

Metal resistant PGPR lowered Cd uptake and expression of metal transporter genes with improved growth and photosynthetic pigments in Lycopersicon esculentum under metal toxicity

Plant growth promoting rhizobacteria (PGPRs) are very effective in immobilization of heavy metals and reducing their translocation in plants via precipitation, complex formation and adsorption. The present study was therefore designed to understand the role of Pseudomonas aeruginosa and Burkholderia gladioli in mitigation of Cd stress (0.4 mM) in 10-days old L. esculentum seedlings. The present work investigated growth characteristics, photosynthetic pigments, metal tolerance index, metal uptake and the contents of metal chelating compounds (protein bound and non-protein bound thiols, total thiols) in microbes inoculated Cd treated L. esculentum seedlings. The gene expression profiling of different metal transporters was conducted in order to investigate the quantitative analysis. Our results revealed Cd generated toxicity in seedlings in terms of reduced growth (root length, shoot length and fresh weight) and photosynthetic pigments (chlorophyll, carotenoid and xanthophyll) which enhanced upon inoculations of P. aeruginosa and B. gladioli. Further, the metal uptake along with levels of protein and non-protein bound thiols was also enhanced in Cd-treated seedlings. Gene expression studies suggested enhanced expression in the metal transporter genes which were further declined in the microbe supplemented seedlings. Therefore, micro-organisms possess growth promoting traits that enable them to reduce metal toxicity in plants.

Structural development and assembly patterns of the root-associated microbiomes during phytoremediation

Successful in situ phytoremediation depends on beneficial interactions between roots and microbes. However, the assembly strategies of root-associated microbiome during phytoremediation are not well known. Here we investigated the assembly patterns of root-associated microbiomes during phytoremediation as well as its regulation by both plants and heavy metals. Plant cultivation and soil amendment increased microbial diversity and restructured microbial communities. Rhizo-compartmentalization was the largest source of variation in root-associated microbiomes, with endosphere being the most independent and exclusive compartment. Soil type explained a larger amount of microbiomes variation in bulk soil and rhizosphere than that in endosphere. A specific core root microbiome was likely to be selected by the metal-tolerant plant H. cannabinus, with Enterobacteriaceae, Pseudomonadaceae and Comamonadaceae which contain a large number of metal-tolerant and plant growth-promoting bacteria (PGPB) being the most abundant families. The root-associated microbial community tended to proceed a niche-assembled patterns and formed a smaller bacterial pool dominant by Proteobacteria, Actinobacteria and Chloroflexi under metal-contaminated conditions. Among these genera, potential metal-tolerant PGPB species have taken up the keystone positions in the microbial co-occurrence networks, revealing their key roles in metal-contaminated environment due to niche selection. We also detected a keystone functional group reducing metal bioavailability which might work as vanguards and devote to maintaining the structure and function of the whole microbial community. In conclusion, this study suggested a specific assembly pattern of root-associated microbiomes of the metal-tolerant plant H. cannabinus during phytoremediation, showing the directional selections of the associated microbiomes by both the plant and metal-contaminated conditions in such a system.

Mechanisms of Cr(VI) resistance by endophytic Sphingomonas sp. LK11 and its Cr(VI) phytotoxic mitigating effects in soybean (Glycine max L.)

Chromium Cr(VI) is highly toxic and leads to impaired phenotypic plasticity of economically important crops. The current study assessed an endophytic-bacteria assisted metal bio-remediation strategy to understand stress-alleviating mechanisms in Glycine max L (soybean) plants inoculated with Sphingomonas sp. LK11 under severe Cr(VI) toxicity. The screening analysis showed that high Cr concentrations (5.0 mM) slightly suppressed LK11 growth and metal uptake by LK11 cells, while significantly enhancing indole-3-acetic acid (IAA) production. Endophytic LK11 significantly upregulated its antioxidant system compared to control by enhancing reduced glutathione (GSH), catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD) activities to counteract Cr-induced oxidative stress. Cr toxicity induced cell morphological alteration, as shown by SEM-EDX analysis and triggered significant lipid peroxidation. The interaction between LK11 and soybean in Cr-contaminated soil significantly increased plant growth attributes and down-regulated the synthesis of endogenous defense-related phytohormones, salicylic acid and abscisic acid, by 20% and 37%, respectively, and reduced Cr translocation to the roots, shoot, and leaves. Additionally, Cr-induced oxidative stress was significantly reduced in LK11-inoculated soybean, regulating metal responsive reduced GSH and enzymatic antioxidant CAT. Current findings indicate that LK11 may be a suitable candidate for the bioremediation of Cr-contaminated soil and stimulation of host physiological homeostasis.

Comparative analysis of Cd-responsive maize and rice transcriptomes highlights Cd co-modulated orthologs

Background

Metal tolerance is often an integrative result of metal uptake and distribution, which are fine-tuned by a network of signaling cascades and metal transporters. Thus, with the goal of advancing the molecular understanding of such metal homeostatic mechanisms, comparative RNAseq-based transcriptome analysis was conducted to dissect differentially expressed genes (DEGs) in maize roots exposed to cadmium (Cd) stress.

Results

To unveil conserved Cd-responsive genes in cereal plants, the obtained 5166 maize DEGs were compared with 2567 Cd-regulated orthologs in rice roots, and this comparison generated 880 universal Cd-responsive orthologs groups composed of 1074 maize DEGs and 981 rice counterparts. More importantly, most of the orthologous DEGs showed coordinated expression pattern between Cd-treated maize and rice, and these include one large orthologs group of pleiotropic drug resistance (PDR)-type ABC transporters, two clusters of amino acid transporters, and 3 blocks of multidrug and toxic compound extrusion (MATE) efflux family transporters, and 3 clusters of heavy metal-associated domain (HMAD) isoprenylated plant proteins (HIPPs), as well as all 4 groups of zinc/iron regulated transporter protein (ZIPs). Additionally, several blocks of tandem maize paralogs, such as germin-like proteins (GLPs), phenylalanine ammonia-lyases (PALs) and several enzymes involved in JA biosynthesis, displayed consistent co-expression pattern under Cd stress.

Out of the 1074 maize DEGs, approximately 30 maize Cd-responsive genes such as ZmHIPP27, stress-responsive NAC transcription factor (ZmSNAC1) and 9-cis-epoxycarotenoid dioxygenase (NCED, vp14) were also common stress-responsive genes reported to be uniformly regulated by multiple abiotic stresses. Moreover, the aforementioned three promising Cd-upregulated genes with rice counterparts were identified to be novel Cd-responsive genes in maize.

Meanwhile, one maize glutamate decarboxylase (ZmGAD1) with Cd co-modulated rice ortholog was selected for further analysis of Cd tolerance via heterologous expression, and the results suggest that ZmGAD1 can confer Cd tolerance in yeast and tobacco leaves.

Conclusions

These novel findings revealed the conserved function of Cd-responsive orthologs and paralogs, which would be valuable for elucidating the genetic basis of the plant response to Cd stress and unraveling Cd tolerance genes.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5109-8) contains supplementary material, which is available to authorized users.

Metabolism-mediated induction of zinc tolerance in Brassica rapa by Burkholderia cepacia CS2-1

Brassica rapa (Chinese cabbage) is an essential component of traditional Korean food. However, the crop is often subject to zinc (Zn⁺) toxicity from contaminated irrigation water, which, as a result, compromises plant growth and production, as well as the health of human consumers. The present study investigated the bioaccumulation of Zn⁺ by Burkholderia cepacia CS2-1 and its effect on the heavy metal tolerance of Chinese cabbage. Strain CS2-1 was identified and characterized on the basis of 16S rRNA sequences and phylogenetic analysis. The strain actively produced indole-3-acetic acid (3.08 ± 0.21 μg/ml) and was also able to produce siderophore, solubilize minerals, and tolerate various concentrations of Zn⁺. The heavy metal tolerance of B. rapa plants was enhanced by CS2-1 inoculation, as indicated by growth attributes, Zn⁺ uptake, amino acid synthesis, antioxidant levels, and endogenous hormone (ABA and SA) synthesis. Without inoculation, the application of Zn⁺ negatively affected the growth and physiology of B. rapa plants. However, CS2-1 inoculation improved plant growth, lowered Zn⁺ uptake, altered both amino acid regulation and levels of flavonoids and phenolics, and significantly decreased levels of superoxide dismutase, endogenous abscisic acid, and salicylic acid. These findings indicate that B. cepacia CS2-1 is suitable for bioremediation against Zn⁺-induced oxidative stress.

Diversity of microbiota found in coffee processing wastewater treatment plant

Cultivable microbiota presents in a coffee semi-dry processing wastewater treatment plant (WTP) was identified. Thirty-two operational taxonomic units (OTUs) were detected, these being 16 bacteria, 11 yeasts and 4 filamentous fungi. Bacteria dominated the microbial population (11.61 log CFU mL^- 1), and presented the highest total diversity index when observed in the WTP aerobic stage (Shannon = 1.94 and Simpson = 0.81). The most frequent bacterial species were Enterobacter asburiae, Sphingobacterium griseoflavum, Chryseobacterium bovis, Serratia marcescens, Corynebacterium flavescens, Acetobacter orientalis and Acetobacter indonesiensis; these showed the largest total bacteria populations in the WTP, with approximately 10 log CFU mL^- 1. Yeasts were present at 7 log CFU mL^- 1 of viable cells, with Hanseniaspora uvarum, Wickerhamomyces anomalus, Torulaspora delbrueckii, Saturnispora gosingensis, and Kazachstania gamospora being the prevalent species. Filamentous fungi were found at 6 log CFU mL^- 1, with Fusarium oxysporum the most populous species. The identified species have the potential to act as a biological treatment in the WTP, and the application of them for this purpose must be better studied.

Bacillus: A Biological Tool for Crop Improvement through Bio-Molecular Changes in Adverse Environments

Crop productivity is affected by environmental and genetic factors. Microbes that are beneficial to plants are used to enhance the crop yield and are alternatives to chemical fertilizers and pesticides. Pseudomonas and Bacillus species are the predominant plant growth-promoting bacteria. The spore-forming ability of Bacillus is distinguished from that of Pseudomonas. Members of this genus also survive for a long time under unfavorable environmental conditions. Bacillus spp. secrete several metabolites that trigger plant growth and prevent pathogen infection. Limited studies have been conducted to understand the physiological changes that occur in crops in response to Bacillus spp. to provide protection against adverse environmental conditions. This review describes the current understanding of Bacillus-induced physiological changes in plants as an adaptation to abiotic and biotic stresses. During water scarcity, salinity and heavy metal accumulate in soil, Bacillus spp. produce exopolysaccharides and siderophores, which prevent the movement of toxic ions and adjust the ionic balance and water transport in plant tissues while controlling the pathogenic microbial population. In addition, the synthesis of indole-3-acetic acid, gibberellic acid and1-aminocyclopropane-1-carboxylate (ACC) deaminase by Bacillus regulates the intracellular phytohormone metabolism and increases plant stress tolerance. Cell-wall-degrading substances, such as chitosanase, protease, cellulase, glucanase, lipopeptides and hydrogen cyanide from Bacillus spp. damage the pathogenic bacteria, fungi, nematodes, viruses and pests to control their populations in plants and agricultural lands. The normal plant metabolism is affected by unfavorable environmental stimuli, which suppress crop growth and yield. Abiotic and biotic stress factors that have detrimental effects on crops are mitigated by Bacillus-induced physiological changes, including the regulation of water transport, nutrient up-take and the activation of the antioxidant and defense systems. Bacillus association stimulates plant immunity against stresses by altering stress-responsive genes, proteins, phytohormones and related metabolites. This review describes the beneficial effect of Bacillus spp. on crop plants, which improves plant productivity under unfavorable climatic conditions, and the current understanding of the mitigation mechanism of Bacillus spp. in stress-tolerant and/or stress-resistant plants.