Analysis of copper tolerant rhizobacteria from the industrial belt of Gujarat, western India for plant growth promotion in metal polluted agriculture soils

Chronic industrial perturbation and seasonal change induces shift in the bacterial community from gammaproteobacteria to betaproteobacteria having catabolic potential for aromatic compounds at Amlakhadi canal

Escalating proportions of industrially contaminated sites are one of the major catastrophes faced at the present time due to the industrial revolution. The difficulties associated with culturing the microbes, has been circumvent by the direct use of metagenomic analysis of various complex niches. In this study, a metagenomic approach using next generation sequencing technologies was applied to exemplify the taxonomic abundance and metabolic potential of the microbial community residing in Amlakhadi canal, Ankleshwar at two different seasons. All the metagenomes revealed a predominance of Proteobacteria phylum. However, difference was observed within class level where Gammaproteobacteria was relatively high in polluted metagenome in Summer while in Monsoon the abundance shifted to Betaproteobacteria. Similarly, significant statistical differences were obtained while comparing the genera amongst contaminated sites where Serratia, Achromobacter, Stenotrophomonas and Pseudomonas were abundant in summer season and the dominance changed to Thiobacillus, Thauera, Acidovorax, Nitrosomonas, Sulfuricurvum, Novosphingobium, Hyphomonas and Geobacter in monsoon. Further upon functional characterization, the microbiomes revealed the diverse survival mechanisms, in response to the prevailing ecological conditions (such as degradation of aromatic compounds, heavy metal resistance, oxidative stress responses and multidrug resistance efflux pumps, etc.). The results have important implications in understanding and predicting the impacts of human-induced activities on microbial communities inhabiting natural niche and their responses in coping with the fluctuating pollution load.

Assessment of PGP traits of Bacillus cereus NDRMN001 and its influence on Cajanus cajan (L.) Millsp. phytoremediation potential on metal-polluted soil under controlled conditions

The current study looked at the plant growth-promoting (PGP) traits of the pre-isolated and metal-tolerant Bacillus cereus NDRMN001 as well as their stimulatory effect on the physiology, biomolecule content, and phytoremediation potential of Cajanus cajan (L.) Millsp. on metal-polluted soil. The bauxite mine, which is surrounded by farmland (1 km away), has been severely polluted by metals such as Cd (31.24 ± 1.68), Zn (769.57 ± 3.46), Pb (326.85 ± 3.43), Mn (2519.6 ± 5.71), and Cr (302.34 ± 1.62 mg kg^-1) that exceeded Indian standards. The metal-tolerant B. cereus NDRMN001 had excellent PGP activities such as synthesis of hydrogen cyanide (HCN), siderophore, indole acetic acid (IAA), N₂ fixation, and P solubilization. Furthermore, the optimal growth conditions (temperature of 30°C, pH 6.5, 6% glucose, 9% tryptophan, and 1.5% tricalcium phosphate) for effective synthesis and expression of PGP traits in B. cereus NDRMN001 were determined. Such metal-tolerant B. cereus NDRMN001 traits can significantly reduce metals in polluted soil, and their PGP traits significantly improve plant growth in polluted soil. Hence, this strain (B. cereus NDRMN001) significantly improved the growth and phytoremediation potential of C. cajan (L.) Millsp on metal-polluted soil without [study I: 2 kg of sieved and autoclaved metal-polluted soil seeded with bacterium-free C. cajan (L.) Millsp. seeds] and with [study II: 2 kg of sieved and autoclaved metal-polluted soil seeded with B. cereus NDRMN001-coated C. cajan (L.) Millsp. seeds] B. cereus NDRMN001 amalgamation. Fertile soil was used as control. The physiological parameters, biomolecule contents, and the phytoremediation (Cr: 7.74, Cd: 12.15, Zn: 16.72, Pb: 11.47, and Mn: 14.52 mg g^-1) potential of C. cajan (L.) Millsp. were significantly effective in study II due to the metal-solubilizing and PGP traits of B. cereus NDRMN001. These results conclude that the test bacteria B. cereus NDRMN001 considerably improved the phytoremediation competence of C. cajan (L.) Millsp. on metal-polluted soil in a greenhouse study.

Variation in Peperomia pellucida growth and secondary metabolism after rhizobacteria inoculation

Peperomia pellucida L. Kunth is a herb well-known for its secondary metabolites (SM) with biological potential. In this study, the variations in the SM of P. pellucida during association with rhizobacteria were evaluated. Plants were inoculated with Enterobacter asburiae and Klebsiella variicola, which were identified by sequencing of the 16S rRNA gene. The data were evaluated at 7, 21, and 30-day post inoculation (dpi). Plant-bacteria symbiosis improved plant growth and weight. Total phenolic content and phenylalanine ammonia lyase enzyme activity had a significant increase mainly at 30 dpi. P. pellucida was mainly composed of phenylpropanoids (37.30-52.28%) and sesquiterpene hydrocarbons (39.28-49.42%). The phenylpropanoid derivative 2,4,5-trimethoxy-styrene (ArC2), the sesquiterpene hydrocarbon ishwarane, and the phenylpropanoid dillapiole were the major compounds. Principal component analysis (PCA) of the classes and compounds ≥ 2.0% indicated that plants colonized by E. asburiae had a reduction in the content of sesquiterpene hydrocarbons and an increase in phenylpropanoids and derivatives. Plants treated with this bacterium also had an increase in the content of 2,4,5-trimethoxystyrene at 30 dpi. Plants inoculated with K. variicola had significant increases only in the content of the classes monoterpene hydrocarbons and 'other compounds' (hydrocarbons, esters, ketones, etc.). These data suggest that the production of plant secondary metabolites can be modified depending on the type of rhizobacteria inoculated.

Mitigation of Copper Stress in Maize (Zea mays) and Sunflower (Helianthus annuus) Plants by Copper-resistant Pseudomonas Strains

Use of heavy metal (HM) resistant plant growth-promoting rhizobacteria (PGPR) is among the eco-friendly strategies to increase the resistance of crop plants against the HM stress. In this study, we investigated the effects of two copper (Cu)-resistant PGPR strains (Pseudomonas fluorescens P22 and Pseudomonas sp. Z6) on the growth and nutrition of maize (Zea mays) and sunflower (Helianthus annuus) plants grown in a Cu-contaminated soil under glasshouse conditions. Both PGPR strains significantly increased the plant vegetative parameters including shoot biomass, stem height and diameter, and chlorophyll (SPAD values) index in both crops. In both plants, the PGPR inoculations also significantly elevated the uptake of nutrients including potassium, phosphorus, calcium, magnesium (only by P. fluorescens P22), iron, zinc, manganese, and Cu. Magnitude of the nutritional effects varied between the PGPR strains, e.g., in sunflower, inoculation with P. fluorescens P22 and Pseudomonas sp. Z6 led to an increase in uptake of Zn by 42% and 114%, or Mn by 61% and 88%, respectively, in comparison with control plants. Improved performance of the inoculated plants can be attributed to the plant growth-promoting (e.g., production of auxin and siderophore, phosphate solubilization activities, etc.) and stress removal (e.g., production of ACC-deaminase to drop the ethylene level in stressed plants) properties of the PGPR strains, which were uncovered in our in vitro studies prior to the glasshouse experiment. Beside the plant growth-promoting traits of these PGPR strains, their high resistance to Cu toxicity seemed to be of particular importance for plant fitness improvement under Cu toxicity.

Effect of copper-resistant Stenotrophomonas maltophilia on maize (Zea mays) growth, physiological properties, and copper accumulation: potential for phytoremediation into biofortification

In this study, Cu-tolerant PGP bacteria were isolated from the contaminated soils of Tapi (Surat, Gujarat, India). From a set of 118 bacteria isolated from the contaminated soil, the isolate RBTS7 was found to be efficient in tolerating 0.3 g (w/v) Cu. The isolate was identified as Stenotrophomonas maltophilia, based on biochemical and 16S rRNA gene sequencing. Further, the isolate was also found to produce indole acetic acid (140 µg/ml) and siderophore, and solubilize potassium. Inoculation study was carried out in the presence and absence of Cu in the greenhouse. The results revealed that S. maltophilia enhanced plant growth and biomasses compared to control. In addition to plant growth attributes, the isolate also enhanced chlorophyll a and b (434.1 and 496.7%) contents and antioxidant properties such as proline (168.2%), total phenolic compounds (33.5%), and ascorbic acid oxidase (62.3%) compared to control with Cu and without Cu. Inoculation of S. maltophilia + Cu enhanced the uptake of Cu in maize root (77.4%) and stem (112.0%) compared to Cu-stressed control. The results clearly indicated the inoculation of S. maltophilia reduced the toxicity of Cu and in turn enhanced the plant growth and mobilization of Cu to the plant parts.

Arbuscular mycorrhizal fungi effect growth and photosynthesis of Phragmites australis (Cav.) Trin ex. Steudel under copper stress

Arbuscular mycorrhizal fungi (AMF) is an effective way to remove heavy metals' inhibition on plants, however, few relevant research attempts have been made to determine the contribution of AMF to the physiological and biochemical changes related to the enhanced copper tolerance of Phragmites australis under metal-stressed conditions. In this study, the effects of AMF inoculation on P. australis under different concentrations of copper stress were investigated according to the changes in the parameters related to growth and development, and photosynthetic charateristics. Then, differentially expressed proteins (DEPs) were evaluated by the Isobaric Tag for Relative and Absolute Quantification (iTRAQ) system, which could accurately quantify the DEPs by measuring peak intensities of reporter ions in tandem mass spectrometry (MS/MS) spectra. It was found that AMF inoculation may relieve the photosynthesis inhibition caused by copper stress on P. australis and thus promote growth. Proteomic analysis results showed that under copper stress, the inoculation of R. irregularis resulted in a total of 459 differently-expressed proteins (200 up-regulated and 259 down-regulated) in root buds. In addition, the photosynthetic changes caused by AMF inoculation mainly involve the up-regulated expression of transmembrane protein-pigment complexes CP43 (photosystem II) and FNR (ferredoxin-NADP+ oxidoreductase related to photosynthetic electron transport). These results indicate that AMF could effectively improve the growth and physiological activity of P. australis under copper stress, and thus provides a new direction and instructive evidence for determining the mechanisms by which AMF inoculation enhances the copper tolerance of plants.

The speciation and distribution characteristics of Cu in Phragmites australis (Cav.) Trin ex. Steudel

Heavy metal allocation and the mechanism(s) of metal sequestration in different clonal organs, micro-domains and subcellular structures has not been systematically studied for rhizomatous perennial plants. It is thus pertinent to investigate knowledge of the speciation and distribution characteristics of Cu in Phragmites australis to elucidating the mobility of metals in wetland plants after their uptake via root systems so as to facilitate development of strategies to enhance Cu tolerance. This study investigated the distributions of Cu in P. australis root, stem and leaf using ICP-MS, synchrotron-based X-ray micro-fluorescence and X-ray absorption spectroscopy, then evaluated the effects of Cu on cellular structure and ultrastructure via transmission electron microscopy. The results indicate a clear preferential localisation of Cu in the roots as compared with the shoots (stems and leaves). The intensity of Cu in the vascular bundles was higher than that in the surrounding epidermis and the endodermis and parenchyma outside the medullary cavity. The dominant chemical form of Cu in P. australis was similar to Cu citrate. The results suggest that although Cu can be easily transported into the vascular tissues in roots and stems via Cu citrate, most of the metal absorbed by plants is retained in the roots because if its high binding to the cell wall, thus preventing metal translocation to aerial parts of the plants. Therefore, P. australis showed a high capacity to accumulate Cu in roots, being therefore a suitable species for phytostabilisation interventions.

Bacterial Isolate Inhabiting Spitsbergen Soil Modifies the Physiological Response of Phaseolus coccineus in Control Conditions and under Exogenous Application of Methyl Jasmonate and Copper Excess

The aim of the study was to demonstrate the potential of the promotion and regulation of plant physiology and growth under control and copper stress conditions, and the impact of the exogenous application of methyl jasmonate on this potential. Runner bean plants were treated with methyl jasmonate (1 or 10 µM) (J; J1 or J10) and Cu (50 µM), and inoculated with a bacterial isolate (S17) originating from Spitsbergen soil, and identified as Pseudomonas luteola using the analytical profile index (API) test. Above- and under-ground plant parts were analyzed. The growth parameters; the concentration of the photosynthetic pigments, elements, flavonoids (FLAVO), phenolics (TPC), allantoin (ALLA), and low molecular weight organic acids (LMWOAs); the activity of antioxidant enzymes and enzymes of resistance induction pathways (e.g., superoxide dismutase (SOD), catalase (CAT), ascorbate (APX) and guaiacol (GPX) peroxidase, glucanase (GLU), and phenylalanine (PAL) and tyrosine ammonia-lyase (TAL)), and the antioxidant capacity (AC) were studied. The leaves exhibited substantially higher ALLA and LMWOA concentrations as well as PAL and TAL activities, whereas the roots mostly had higher activities for a majority of the enzymes tested (i.e., SOD, CAT, APX, GPX, and GLU). The inoculation with S17 mitigated the effect of the Cu stress. Under the Cu stress and in the presence of J10, isolate S17 caused an elevation of the shoot fresh weight, K concentration, and TAL activity in the leaves, and APX and GPX (also at J1) activities in the roots. In the absence of Cu, isolate S17 increased the root length and the shoot-to-root ratio, but without statistical significance. In these conditions, S17 contributed to a 236% and 34% enhancement of P and Mn, respectively, in the roots, and a 19% rise of N in the leaves. Under the Cu stress, S17 caused a significant increase in FLAVO and TPC in the leaves. Similarly, the levels of FLAVO, TPC, and AC were enhanced after inoculation with Cu and J1. Regardless of the presence of J, inoculation at Cu excess caused a reduction of SOD and CAT activities, and an elevation of GPX. The effects of inoculation were associated with the application of Cu and J, which modified plant response mainly in a concentration-dependent manner (e.g., PAL, TAL, and LMWOA levels). The conducted studies demonstrated the potential for isolate S17 in the promotion of plant growth.

The bacterial community structure and functional profile in the heavy metal contaminated paddy soils, surrounding a nonferrous smelter in South Korea

The pollution of agricultural soils by the heavy metals affects the productivity of the land and has an impact on the quality of the surrounding ecosystems. This study investigated the bacterial community structure in the heavy metal contaminated sites along a smelter and a distantly located paddy field to elucidate the factors that are related to the alterations of the bacterial communities under the conditions of heavy metal pollution. Among the study sites, the bacterial communities in the soil did not show any significant differences in their richness and diversity. The soil bacterial communities at the three study sites were distinct from one another at each site, possessing a distinct set of bacterial phylotypes. Among the study sites, significant changes were observed in the abundances of the bacterial phyla and genera. The variations in the bacterial community structure were mostly related to the general soil properties at the phylum level, while at the finer taxonomic levels, the concentrations of arsenic (As) and lead (Pb) were the significant factors, affecting the community structure. The relative abundances of the genera Desulfatibacillum and Desulfovirga were negatively correlated to the concentrations of As, Pb, and cadmium (Cd) in the soil, while the genus Bacillus was positively correlated to the concentrations of As and Cd. According to the results of the prediction of bacterial community functions, the soil bacterial communities of the heavy metal polluted sites were characterized by the more abundant enzymes involved in DNA replication and repair, translation, transcription, and the nucleotide metabolism pathways, while the amino acid and lipid metabolism, as well as the biodegradation potential of xenobiotics, were reduced. Our results showed that the adaptation of the bacterial communities to the heavy metal contamination was predominantly attributed to the replacement process, while the changes in community richness were linked to the variations in the soil pH values.

Phytostabilization-Management Strategy for Stabilizing Trace Elements in Contaminated Soils

Contamination of soil by copper (Cu) has become a serious problem throughout the world, causing the reduction of agricultural yield and harmful effects on human health by entering the food chain. A glasshouse pot experiment was designed to evaluate the potential use of halloysite as an immobilizing agent in the aided phytostabilization of Cu-contaminated soil, using Festuca rubra L. The content of Cu in plants, i.e., total and extracted by 0.01 M CaCl₂, was determined using the method of spectrophotometry. Cu content in the tested parts of F. rubra differed significantly when halloysite was applied to the soil, as well as with increasing concentrations of Cu. The addition of halloysite significantly increased plant biomass. Cu accumulated in the roots, thereby reducing its toxicity to the aerial parts of the plant. The obtained values of bioconcentration and translocation factors observed for halloysite treatment indicate the effectiveness of using F. rubra in phytostabilization techniques.