Alleviation of heavy metals toxicity by the application of plant growth promoting rhizobacteria and effects on wheat grown in saline sodic field

Complete Genome Sequence of Pseudomonas psychrotolerans CS51, a Plant Growth-Promoting Bacterium, Under Heavy Metal Stress Conditions

In the current study, we aimed to elucidate the plant growth-promoting characteristics of Pseudomonas psychrotolerans CS51 under heavy metal stress conditions (Zn, Cu, and Cd) and determine the genetic makeup of the CS51 genome using the single-molecule real-time (SMRT) sequencing technology of Pacific Biosciences. The results revealed that inoculation with CS51 induced endogenous indole-3-acetic acid (IAA) and gibberellins (GAs), which significantly enhanced cucumber growth (root shoot length) and increased the heavy metal tolerance of cucumber plants. Moreover, genomic analysis revealed that the CS51 genome consisted of a circular chromosome of 5,364,174 base pairs with an average G+C content of 64.71%. There were around 4774 predicted protein-coding sequences (CDSs) in 4859 genes, 15 rRNA genes, and 67 tRNA genes. Around 3950 protein-coding genes with function prediction and 733 genes without function prediction were identified. Furthermore, functional analyses predicted that the CS51 genome could encode genes required for auxin biosynthesis, nitrate and nitrite ammonification, the phosphate-specific transport system, and the sulfate transport system, which are beneficial for plant growth promotion. The heavy metal resistance of CS51 was confirmed by the presence of genes responsible for cobalt-zinc-cadmium resistance, nickel transport, and copper homeostasis in the CS51 genome. The extrapolation of the curve showed that the core genome contained a minimum of 2122 genes (95% confidence interval = 2034.24 to 2080.215). Our findings indicated that the genome sequence of CS51 may be used as an eco-friendly bioresource to promote plant growth in heavy metal-contaminated areas.

Effects of EDTA and plant growth-promoting rhizobacteria on plant growth and heavy metal uptake of hyperaccumulator Sedum alfredii Hance

Phytoremediation is a cost-effective and environment-friendly strategy for decontaminating heavy-metal-contaminated soil. However, the practical use of phytoremediation is constrained by the low biomass of plants and low bioavailability of heavy metals in soil. A pot experiment was conducted to investigate the effects of the metal chelator ethylenediaminetetraacetic acid (EDTA) and EDTA in combination with plant growth-promoting rhizobacteria (Burkholderia sp. D54 or Burkholderia sp. D416) on the growth and metal uptake of the hyperaccumulator Sedum alfredii Hance. According to the results, EDTA application decreased shoot and root biomass by 50% and 43%, respectively. The soil respiration and Cd, Pb, Zn uptake were depressed, while the photosynthetic rate, glutathione and phytochelatin (PC) contents were increased by EDTA application. Interestingly, Burkholderia sp. D54 and Burkholderia sp. D416 inoculation significantly relieved the inhibitory effects of EDTA on plant growth and soil respiration. Compared with the control, EDTA + D416 treatment increased the Cd concentration in shoots and decreased the Pb concentration in shoots and roots, but did not change the Zn concentration in S. alfredii plants. Furthermore, EDTA, EDTA + D54 and EDTA + D416 application increased the cysteine and PC contents in S. alfredii (p < 0.05); among all tested PCs, the most abundant species was PC2, and compared with the control, the PC2 content was increased by 371.0%, 1158.6% and 815.6%, respectively. These results will provide some insights into the practical use of EDTA and PGPR in the phytoremediation of heavy-metal-contaminated soil by S. alfredii.

Effect of plant-growth-promoting rhizobacteria on phytoremediation efficiency of Scirpus triqueter in pyrene-Ni co-contaminated soils

The aim of this study was to investigate whether the plant-growth-promoting rhizobacteria (PGPR) could enhance phytoremediation efficiency of Scirpus triqueter (S.triqueter) in the pyrene-Ni co-contaminated soil. We also expected to reveal the possible mechanism for the affected phytoremediation efficiency induced by PGPR. We used three kinds of contaminated soils (Ni-contaminated soil, pyrene-contaminated soil and pyrene-Ni co-contaminated soil) to conduct this pot study. After harvest, plants growth indicators, polyphenol oxidase (PPO) activity and soil microbial community structure of each treatment were investigated to explain the different dissipation rates of pyrene and removal rates of Ni between treatments with and without PGPR. The results showed that PGPR-inoculated S. triqueter increased dissipation rates of pyrene and removal rates of Ni in all three contaminated soils, among which Ni removal rates in Ni single contaminated soil was elevated most significantly, from 0.895‰ to 8.8‰, increasing nearly 9 folds. However, Ni removal rate efficiency in co-contaminated soil was weakened because more toxic and complicated co-contaminated soil restrained plant growth and Ni absorption. We also observed that co-contamination harmed the soil microbial community more severely than that in single pyrene or Ni contaminated soil through phospholipid fatty acids analysis. Furthermore, dissipation rates of pyrene and removal rates of Ni were found positively correlated to the PPO activity and the abundance of branched and saturated fatty acids reflected by Pearson correlation analysis.

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

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

Heavy metal induced stress on wheat: phytotoxicity and microbiological management

Among many soil problems, heavy metal accumulation is one of the major agronomic challenges that has seriously threatened food safety. Due to these problems, soil biologists/agronomists in recent times have also raised concerns over heavy metal pollution, which indeed are unpleasantly affecting agro-ecosystems and crop production. The toxic heavy metals once deposited beyond certain permissible limits, obnoxiously affect the density, composition and physiological activities of microbiota, dynamics and fertility of soil leading eventually to reduction in wheat production and via food chain, human and animal health. Therefore, the metal induced phytotoxicity problems warrant urgent and immediate attention so that the physiological activities of microbes, nutrient pool of soils and concurrently the production of wheat are preserved and maintained in a constantly deteriorating environment. To mitigate the magnitude of metal induced changes, certain microorganisms have been identified, especially those belonging to the plant growth promoting rhizobacteria (PGPR) group endowed with the distinctive property of heavy metal tolerance and exhibiting unique plant growth promoting potentials. When applied, such metal-tolerant PGPR have shown variable positive impact on wheat production, even in soils contaminated with metals, by supplying macro and micro nutrients and secreting active biomolecules like EPS, melanins and metallothionein (MTs). Despite some reports here and there, the phytotoxicity of metals to wheat and how wheat production in metal-stressed soil can be enhanced is poorly explained. Thus, an attempt is made in this review to better understand the mechanistic basis of metal toxicity to wheat, and how such phytotoxicity can be mitigated by incorporating microbiological remediation strategies in wheat cultivation practices. The information provided here is likely to benefit wheat growers and consequently optimize wheat production inexpensively under stressed soils.

Among many soil problems, heavy metal accumulation is one of the major agronomic challenges that has seriously threatened food safety.

Bioaugmentation-assisted phytoremediation of lead and salinity co-contaminated soil by Suaeda salsa and Trichoderma asperellum

The combined application of plant Suaeda salsa and indigenous fungus Trichoderma asperellum on the treatment of a lead (Pb) and salinity (Na⁺ and Ca²⁺) co-contaminated soil was investigated by a flowerpot experiment. As demonstrated by plant growth and selected antioxidant parameters, S. salsa was able to tolerate and grow in the co-contaminated soil, especially bioaugmented with T. asperellum, which promoted plant growth (9-23% and 5-13% increases for plant height and fresh weight, respectively) and appeared to alleviate plant oxidative damage (7-85% and 7-49% decreases for plant malondialdehyde and peroxidase levels, respectively). The SDS-PAGE fingerprints indicated that the total protein contents of S. salsa were affected under Pb and salinity stresses. The interactions of Na⁺ and Ca²⁺ ions on the phytotoxicity of Pb remained hormesis phenomenon that low-dose alleviation and high-dose enhancement. The analysis of phytoextraction parameters and bioavailability demonstrated that Pb was mainly concentrated in plant roots and poorly translocated, indicating the phytostabilization served as a major repair pathway. On the contrary, the Na⁺ and Ca²⁺ ions were concentrated in plant by the following order: shoot > root. Moreover, bioaugmentation of planted soil with T. asperellum generally led to the 9-42%, 13-58%, and 19-30% decreases of plant Pb, Na⁺, and Ca²⁺ concentrations and translocations, respectively, as well as a 6-21% decrease of soil Pb bioavailability. This study provided a bioaugmentation-assisted phytoremediation technique to make up the deficiencies of the long-term remediation for heavy metals and salinity.

Genome sequencing and assessment of plant growth-promoting properties of a Serratia marcescens strain isolated from vermicompost

Background

Plant-bacteria associations have been extensively studied for their potential in increasing crop productivity in a sustainable manner. Serratia marcescens is a species of Enterobacteriaceae found in a wide range of environments, including soil.

Results

Here we describe the genome sequencing and assessment of plant growth-promoting abilities of S. marcescens UENF-22GI, a strain isolated from mature cattle manure vermicompost. In vitro, S. marcescens UENF-22GI is able to solubilize P and Zn, to produce indole compounds (likely IAA), to colonize hyphae and counter the growth of two phytopathogenic fungi. Inoculation of maize with this strain remarkably increased seedling growth and biomass under greenhouse conditions. The S. marcescens UENF-22GI genome has 5 Mb, assembled in 17 scaffolds comprising 4662 genes (4528 are protein-coding). No plasmids were identified. S. marcescens UENF-22GI is phylogenetically placed within a clade comprised almost exclusively of non-clinical strains. We identified genes and operons that are likely responsible for the interesting plant-growth promoting features that were experimentally described. The S. marcescens UENF-22GI genome harbors a horizontally-transferred genomic island involved in antibiotic production, antibiotic resistance, and anti-phage defense via a novel ADP-ribosyltransferase-like protein and possible modification of DNA by a deazapurine base, which likely contributes to its competitiveness against other bacteria.

Conclusions

Collectively, our results suggest that S. marcescens UENF-22GI is a strong candidate to be used in the enrichment of substrates for plant growth promotion or as part of bioinoculants for agriculture.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5130-y) contains supplementary material, which is available to authorized users.

Heavy metal induced oxidative damage and root morphology alterations of maize (Zea mays L.) plants and stress mitigation by metal tolerant nitrogen fixing Azotobacter chroococcum

Heavy metals are one of the major abiotic stresses that adversely affect the quantity and nutritive value of maize. Microbial management involving the use of plant growth promoting rhizobacteria (PGPR) is a promising inexpensive strategy for metal clean up from polluted soils. Considering these, metal tolerant plant growth promoting nitrogen fixing rhizobacterial strain CAZ3 identified by 16SrRNA gene sequence analysis as Azotobacter chroococcum was recovered from metal polluted chilli rhizosphere. When exposed to varying levels of metals, A. chroococcum survived up to 1400 and 2000 µg mL^-1 of Cu and Pb, respectively and expressed numerous plant growth promoting activities even under metal stress. Strain CAZ3 secreted 65.5 and 60.8 µg mL^-1 IAA at 400 µg mL^-1 each of Cu and Pb, respectively and produced siderophores, ammonia and ACC deaminase under metal pressure. The melanin extracted from A. chroococcum revealed metal chelating ability under EDX. Following application, strain CAZ3 enhanced growth and yield of maize grown both in the presence of Cu and Pb. The dry biomass of roots of inoculated plants grown with 2007 mg Cu kg^-1 and 585 mg Pb kg^-1 was increased by 28% and 20%, respectively. At 585 mg Pb kg^-1, the bioinoculant also increased the kernel attributes. At 2007 mg Cu kg^-1 strain CAZ3 enhanced the number, yield and protein of kernels by 10%, 45% and 6%, respectively. Interestingly, strain CAZ3 significantly reduced the levels of proline, malondialdehyde and antioxidant enzymes in foliage. The roots of inoculated plants accumulated greatest amounts of metals compared to other organs. In kernels, the concentration of Pb was more as compared to Cu. The metal concentrations in roots, shoots and kernels, however, declined following CAZ3 inoculation. Copper and lead had substantial distortive impact on root and leaf morphology while cell death were visible under CLSM and SEM. Conclusively, A. chroococcum CAZ3 could be a most suitable and promising option to increase maize production in metal polluted soils despite the soils being contaminated with heavy metals.

Leaching characteristic of toxic trace elements in soils amended by sewage sludge compost: A comparison of field and laboratory investigations

A 3-years field test and laboratory leaching test have been conducted to assess the environmental impact of land application of sewage sludge compost in conjunction with wheat and rice crops. Considering the complexity and variability of field conditions, we compared the result of laboratory test with the field test to understand the accuracy and uncertainty associated with using the laboratory test to evaluate the field scenario. The laboratory test with cycling of compost additions and water percolation was a high time-efficient and feasible method to simulate the annually repeated additions of compost in the field application scenario. The results of laboratory test were congruent to the 3-years field test regarding the leaching characteristics and geochemical speciation of toxic trace elements. Both the laboratory and the field test showed that repeated additions of compost to soils can increase leaching concentrations of toxic trace elements at neutral to alkaline pH. Increased toxic trace elements leaching was caused by the increase of organic matter from compost application and organic matter dissolution at alkaline pH. Uncertainties of the laboratory test mainly included the negligibility of crop growth and the strongly reducing condition formed with continuous percolation procedure.

Current Trends and Potential Applications of Microbial Interactions for Human Welfare

For a long time, it was considered that interactions between microbes are only inhibitory in nature. However, latest developments in research have demonstrated that within our environment, several classes of microbes exist which produce different products upon interaction and thus embrace a wider scope of useful and potentially valuable aspects beyond simple antibiosis. Therefore, the current review explores different types of microbial interactions and describes the role of various physical, chemical, biological, and genetic factors regulating such interactions. It further explains the mechanism of action of biofilm formation and role of secondary metabolites regulating bacteria-fungi interaction. Special emphasis and focus is placed on microbial interactions which are important in medicine, food industry, agriculture, and environment. In short, this review reveals the recent contributions of microbial interaction for the benefit of mankind.

Role of Burkholderia cepacia CS8 in Cd-stress alleviation and phytoremediation by Catharanthus roseus

The current study was performed to assess the effect of Burkholderia cepacia CS8 on the phytoremediation of cadmium (Cd) by Catharanthus roseus grown in Cd-contaminated soil. The plants cultivated in Cd amended soil showed reduced growth, dry mass, gas-exchange capacity, and chlorophyll contents. Furthermore, the plants exhibited elevated levels of malondialdehyde (MDA) and hydrogen peroxide (H₂O₂) under Cd stress. The bacterized plants showed higher shoot length, root length; fresh and dry weight. The improved stress tolerance in inoculated plants was attributed to the reduced quantity of MDA and H₂O₂, enhanced synthesis of protein, proline, phenols, flavonoids, and improved activity of antioxidant enzymes including peroxidase, superoxide dismutase, ascorbate peroxidase, and catalase. Similarly, the 1-aminocyclopropane-1-carboxylate deaminase activity, phosphate solubilization, auxin, and siderophore production capability of B. cepacia CS8 improved growth and stress alleviation in treated plants. The bacterial inoculation enhanced the amount of water extractable Cd from soil. Furthermore, the inoculated plants showed higher bioconcentration factor and translocation factor. The current study exhibits that B. cepacia CS8 improves stress alleviation and phytoextraction potential of C. roseus plants growing under Cd stress.

Heavy Metal Stress, Signaling, and Tolerance Due to Plant-Associated Microbes: An Overview

Several anthropogenic activities including mining, modern agricultural practices, and industrialization have long-term detrimental effect on our environment. All these factors lead to increase in heavy metal concentration in soil, water, and air. Soil contamination with heavy metals cause several environmental problems and imparts toxic effect on plant as well as animals. In response to these adverse conditions, plants evolve complex molecular and physiological mechanisms for better adaptability, tolerance, and survival. Nowadays conventional breeding and transgenic technology are being used for development of metal stress resistant varieties which, however, are time consuming and labor intensive. Interestingly the use of microbes as an alternate technology for improving metal tolerance of plants is gaining momentum recently. The use of these beneficial microorganisms is considered as one of the most promising methods for safe crop-management practices. Interaction of plants with soil microorganisms can play a vital role in acclimatizing plants to metalliferous environments, and can thus be explored to improve microbe-assisted metal tolerance. Plant-associated microbes decrease metal accumulation in plant tissues and also help to reduce metal bioavailability in soil through various mechanisms. Nowadays, a novel phytobacterial strategy, i.e., genetically transformed bacteria has been used to increase remediation of heavy metals and stress tolerance in plants. This review takes into account our current state of knowledge of the harmful effects of heavy metal stress, the signaling responses to metal stress, and the role of plant-associated microbes in metal stress tolerance. The review also highlights the challenges and opportunities in this continued area of research on plant-microbe-metal interaction.

Diversity of the Bacterial Microbiome in the Roots of Four Saccharum Species: S. spontaneum, S. robustum, S. barberi, and S. officinarum

Endophytic bacteria are nearly ubiquitously present in the internal tissues of plants, and some endophytes can promote plant growth. In this study, we sampled the roots of four ancestral species of sugarcane (two genotypes per species) and two sugarcane cultivars, and used 16S rRNA and nifH gene sequencing to characterize the root endophytic bacterial communities and diazotroph diversity. A total of 7,198 operational taxonomic units (OTUs) were detected for the endophytic bacteria community. The endophytic bacterial communities exhibited significantly different α- and β-diversities. From the 202 detected families in the sugarcane roots, a core microbiome containing 13 families was identified. The nifH gene was successfully detected in 9 of 30 samples from the four sugarcane species assayed, and 1,734 OTUs were merged for endophytic diazotrophs. In the tested samples, 43 families of endophytic diazotrophs were detected, and six families showed differences across samples. Among the 20 most abundant detected genera, 10 have been reported to be involved in nitrogen fixation in sugarcane. These findings demonstrate the diversity of the microbial communities in different sugarcane germplasms and shed light on the mechanism of biological nitrogen fixation in sugarcane.