Deciphering the Omics of Plant-Microbe Interaction: Perspectives and New Insights.

INTRODUCTION: Plants do not grow in isolation, rather they are hosts to a variety of microbes in their natural environments. While, few thrive in the plants for their own benefit, others may have a direct impact on plants in a symbiotic manner. Unraveling plant-microbe interactions is a critical component in recognizing the positive and negative impacts of microbes on plants. Also, by affecting the environment around plants, microbes may indirectly influence plants. The progress in sequencing technologies in the genomics era and several omics tools has accelerated in biological science. Studying the complex nature of plant-microbe interactions can offer several strategies to increase the productivity of plants in an environmentally friendly manner by providing better insights. This review brings forward the recent works performed in building omics strategies that decipher the interactions between plant-microbiome. At the same time, it further explores other associated mutually beneficial aspects of plant-microbe interactions such as plant growth promotion, nitrogen fixation, stress suppressions in crops and bioremediation; as well as provides better insights on metabolic interactions between microbes and plants through omics approaches. It also aims to explore advances in the study of Arabidopsis as an important avenue to serve as a baseline tool to create models that help in scrutinizing various factors that contribute to the elaborate relationship between plants and microbes. Causal relationships between plants and microbes can be established through systematic gnotobiotic experimental studies to test hypotheses on biologically derived interactions. CONCLUSION: This review will cover recent advances in the study of plant-microbe interactions keeping in view the advantages of these interactions in improving nutrient uptake and plant health.

Effect of endosulfan tolerant bacterial isolates (Delftia lacustris IITISM30 and Klebsiella aerogenes IITISM42) with Helianthus annuus on remediation of endosulfan from contaminated soil.

Endosulfan contaminated soil has become an important risk to the environment and human health worldwide. In the present study, endosulfan tolerant bacterial strain Delftia lacustris IITISM30 and Klebsiella aerogenes IITISM42 were isolated from pesticide stressed agricultural soil and tested for plant growth promoting activities. A pot experiment was performed using Helianthus annuus, grown in soil supplemented with endosulfan and inoculated with pure and consortium of bacterial strain IITISM30 and IITISM42. Inoculation increased plant biomass production and endosulfan degradation, maximum degradation (90% at 5 mg kg-1 of soil) was observed by inoculation with a consortium of bacterial strain IITISM30 and IITISM42. Moreover, there was significantly less endosulfan accumulation was observed in roots and shoots of bacterial inoculated plants as compared to uninoculated plants. Decrease in production of malonialdehyde (MDA) was noticed on inoculation of a bacterial strain. The study demonstrated that inoculation of a consortium of endosulfan tolerant plant growth promoting bacterial isolates could more effectively remediate endosulfan contaminated soils and decrease endosulfan residues in plants, than individual strains. Moreover, it revealed that combined use of H. annuus and endosulfan tolerant bacterial isolates IITISM30 and IITISM42 has great potential for remediating endosulfan contaminated soil.

Endosulfan Degradation by Selected Strains of Plant Growth Promoting Rhizobacteria.

Sixty endosulfan tolerant bacterial strains were isolated from pesticide stressed agricultural soils. Five most tolerant strains were tested for plant growth promoting (PGP) activities and endosulfan degradation under different optimizing conditions in broth and soil. The strains PRB101 and PRB77 were the most efficient in terms of endosulfan degradation and PGP activities and showed solubilization indexes of 3.3 and 3.1 mm, indole acetic acid production of 71 and 68 µg mL-1, siderophore zones of 13 mm each at the recommended dosage, respectively. Hydrogen cyanide and ammonia production remained unaffected in the presence of endosulfan. PRB101 and PRB77 strains were able to degrade 74% and 70% of endosulfan in broth and 67% and 63% in soil, respectively. Based on 16S rDNA analysis, the strains PRB101 and PRB77 exhibited 99% homology with Bacillus sp. KF984414 and Bacillus sp. LN849696, respectively.

Potential use of Solanum lycopersicum and plant growth promoting rhizobacterial (PGPR) strains for the phytoremediation of endosulfan stressed soil.

This study aimed to assess the role of Solanum lycopersicum and plant growth promoting rhizobacterial (PGPR) strains to remove endosulfan present in the soil. S. lycopersicum was grown in endosulfan amended soil (5, 10, 25, and 50 mg kg-1) inoculated with PGPR strains for 40, 80, and 120 days. The influence of PGPR inoculation on endosulfan accumulation in plant tissues, endosulfan degradation in soil, and plant growth parameters were evaluated. The oxidative stress tolerance was assessed by determining the malondialdehyde formation in S. lycopersicum planted in endosulfan stressed soil inoculated with PGPR strains. The results showed that uptake of endosulfan followed root > shoot pathway in association with a reduction in endosulfan accumulation in inoculated plants as related to un-inoculated plants. Moreover, inoculation of PGPR strains showed a beneficial influence on the degradation of endosulfan, Bacillus sp. PRB101 showed maximum degradation (89% at 5 mg kg-1 of soil) of endosulfan at 120 days after sowing. Furthermore, the content of malondialdehyde was lower in inoculated plants as related to un-inoculated plants. Inoculation of PGPR strains efficiently enhanced plant biomass. The findings showed the effectiveness of PGPR strains to increase the decontamination of endosulfan stressed soil and decline endosulfan concentration in the plant tissues.

Circulating microRNAs as biomarkers of environmental exposure to polycyclic aromatic hydrocarbons: potential and prospects.

Exposure to polycyclic aromatic hydrocarbons (PAHs) produced from various pyrogenic and petrogenic sources in the environment has been linked to a variety of toxic effects in the human body. Genome-wide analyses have shown that microRNAs (miRNAs) can function as novel and minimally invasive biomarkers of environmental exposure to PAHs. The objective of this study is to explore miRNA signatures associated with early health effects in response to chronic environmental exposure to PAHs. We systematically searched Scopus and PubMed databases for studies related to exposure of PAHs with changes in miRNA expression patterns that represent early health effects in the exposed population. Based on previous studies, we included 15 cell-based and 9 each of animal model and human population-based studies for assessment. A total of 11 differentially expressed PAH-responsive miRNAs were observed each in two or more cell-based studies (miR-181a and miR-30c-1), animal model studies (miR-291a and miR-292), and human population-based studies (miR-126, miR-142-5p, miR-150-5p, miR-24-3p, miR-27a-3p, miR-28-5p, and miR-320b). In addition, miRNAs belonging to family miR-122, miR-199, miR-203, miR-21, miR-26, miR-29, and miR-92 were found to be PAH-responsive in both animal model and cell-based studies; let-7, miR-126, miR-146, miR-30, and miR-320 in both cell-based and human population-based studies; and miR-142, miR-150, and miR-27 were found differentially expressed in both animal model and human population-based studies. The only miRNA whose expression was found to be altered in all the three groups of studies is miR-34c. Association of environmental exposure to PAHs with altered expression of specific miRNAs indicates that selective miRNAs can be used as early warning biomarkers in PAH-exposed population.

Biosynthesis Pathways, Transport Mechanisms and Biotechnological Applications of Fungal Siderophores.

Iron (Fe) is the fourth most abundant element on earth and represents an essential nutrient for life. As a fundamental mineral element for cell growth and development, iron is available for uptake as ferric ions, which are usually oxidized into complex oxyhydroxide polymers, insoluble under aerobic conditions. In these conditions, the bioavailability of iron is dramatically reduced. As a result, microorganisms face problems of iron acquisition, especially under low concentrations of this element. However, some microbes have evolved mechanisms for obtaining ferric irons from the extracellular medium or environment by forming small molecules often regarded as siderophores. Siderophores are high affinity iron-binding molecules produced by a repertoire of proteins found in the cytoplasm of cyanobacteria, bacteria, fungi, and plants. Common groups of siderophores include hydroxamates, catecholates, carboxylates, and hydroximates. The hydroxamate siderophores are commonly synthesized by fungi. L-ornithine is a biosynthetic precursor of siderophores, which is synthesized from multimodular large enzyme complexes through non-ribosomal peptide synthetases (NRPSs), while siderophore-Fe chelators cell wall mannoproteins (FIT1, FIT2, and FIT3) help the retention of siderophores. S. cerevisiae, for example, can express these proteins in two genetically separate systems (reductive and nonreductive) in the plasma membrane. These proteins can convert Fe (III) into Fe (II) by a ferrous-specific metalloreductase enzyme complex and flavin reductases (FREs). However, regulation of the siderophore through Fur Box protein on the DNA promoter region and its activation or repression depend primarily on the Fe availability in the external medium. Siderophores are essential due to their wide range of applications in biotechnology, medicine, bioremediation of heavy metal polluted environments, biocontrol of plant pathogens, and plant growth enhancement.

Implications of plant growth promoting Klebsiella sp. CPSB4 and Enterobacter sp. CPSB49 in luxuriant growth of tomato plants under chromium stress.

The present study explores the potential of two chromium tolerant and plant growth promoting bacterial strains, Klebsiella sp. and Enterobacter sp. in luxuriant growth of tomato plants under chromium stress conditions. For the assessment of potentiality of the two selected strains, a pot scale experiment was setup with tomato plant under different levels of chromium contamination. In pot experiment, different plant growth parameters, oxidative stress tolerance and chromium bioremediation potential were studied upon inoculation of the selected bacterial strains. The results of pot experiment showed that both the strains were effective in promotion of plant growth and enhanced the plant biomass but Enterobacter sp. was more prominent in enhancement of root length, shoot length, fresh and dry weight, and nutrient uptake in tomato plant. The enhancement of enzymes to combat oxidative stress in tomato plant under chromium stress was also observed for both the strains. Both strains enhanced the levels of superoxide dismutase, catalase, peroxidase, total phenolic, and ascorbic acid in tomato plant under different levels of chromium stress conditions. The chromium phytoremediation potential of tomato plant upon inoculation of both the strains was also studied. The results of phytoremediation showed greater chromium accumulation in roots with poor translocation in shoot upon inoculation of Klebsiella sp. while no significant enhancement in chromium uptake by tomato plant was observed on inoculation of Enterobacter sp. compared to control. Thus, these two strains can effectively be used in luxuriant growth of tomato plant under metal stress conditions.

Influence of plant growth promoting rhizobacterial strains Paenibacillus sp. IITISM08, Bacillus sp. PRB77 and Bacillus sp. PRB101 using Helianthus annuus on degradation of endosulfan from contaminated soil.

Endosulfan is a broad spectrum insecticide used in agriculture for protection of various food and non-food crops. It is persistent in nature and hence found in soil, air and water. The potential use of plants and microorganisms for the removal of endosulfan from soil was studied. Helianthus annuus plant was grown in soil spiked with 5, 10, 25 and 50 mg kg-1 concentrations of endosulfan and inoculated with plant growth promoting rhizobacterial strains Paenibacillus sp. IITISM08, Bacillus sp. PRB77 and Bacillus sp. PRB101 for 40, 80 and 120 days. Potential of plant for endosulfan uptake was evaluated by investigating the endosulfan levels in plant tissues (root and shoot). The results indicated that endosulfan accumulation followed the pattern of root > shoot as well as decrease in uptake of endosulfan in root and shoot of a plant grown in bacterial inoculated soil as compared to un-inoculated soil. Bacterial inoculation had a positive effect on endosulfan degradation. Maximum degradation of 92% at 5 mg kg-1 of endosulfan in soil was observed on inoculation with PRB101 after 120 days of inoculation. The results showed that plant growth promoting bacteria enhances plant biomass production. Lipid peroxidation was also estimated by determining the malondialdehyde (MDA) production, which is a biomarker of oxidative damage. Decrease in MDA formation by root and leaves of plants grown in the bacteria inoculated plant was also observed. The results suggested the effectiveness of plant growth promoting rhizobacteria to boost accumulation potential, biomass production and enhance remediation of endosulfan contaminated soil.

A comparative evaluation towards the potential of Klebsiella sp. and Enterobacter sp. in plant growth promotion, oxidative stress tolerance and chromium uptake in Helianthus annuus (L.).

Prevalence of metal pollutants exerts negative effects on human health and environment, thus propounding an urgent need for a safer substitute. This study was conducted to compare the chromium bioremediation and plant growth promotion ability of two bacterial strains, Klebsiella sp. strain CPSB4 (MH266218) and Enterobacter sp. strain CPSB49 (MH532567), isolated from the rhizospheric soils. A pot scale experiment was setup with Helianthus annuus (L.) as a test plant to compare the efficiency of both isolates in enhancement of plant growth, nutrients uptake, anti-oxidative enzymes production, lipid peroxidation, and chromium bioremediation. Inoculation of strains, CPSB4 and CPSB49 enhanced plant biomass, plant growth, nutrient uptake, anti-oxidative enzymes, and chromium bioremediation, while reduction in lipid peroxidation was observed compared to uninoculated control under chromium stress. The maximum increase in plant growth and nutrient uptake was found in treatments inoculated with CPSB49, while maximum chromium uptake by sunflower was observed in treatments inoculated with CPSB4. Moreover, an increase in anti-oxidative enzyme production and decrease in lipid peroxidation was observed on inoculation of the selected strains. Thus, the strains Klebsiella sp. and Enterobacter sp. can be effectively used in chromium bioremediation and plant growth promotion under chromium stress conditions.

Enhanced soil fertility, plant growth promotion and microbial enzymatic activities of vermicomposted fly ash.

It is reported that coal consumption in the Asia-Pacific region is going to increase to about 87.2 percent by 2035. Management of coal combustion residues (CCRs) generated by industries is a major bottleneck towards handling the repercussions of coal usage. The present study investigates a management technique for these potentially hazardous wastes by means of vermicomposting. In the present investigation, studies were made on the effects of various concentrations of vermicomposted fly ash (VCF) added to agricultural soil, on the growth and yield of tomato (Lycopersicon esculentum Mill.) and brinjal (Solanum melongena L.) plants. The toxicity of trace elements in VCF were estimated using coefficient of pollution and potential ecological risk index, which revealed no apparent risks to the environment. A gradual increase in VCF concentrations in the agricultural soil improved the physico-chemical properties, enzymatic activities, microbial biomass, carbon and microbial population upto 90 days after sowing of seeds. The VCF amendments significantly (p < 0.05) improved the soil quality (2.86% nitrogen and 1.05% Phosphorous) and germination percentage (82.22%) of seeds in L. esculentum and also in S. melongena. The results of this study reveal that, CCRs can be effectively managed in agriculture specially in developing economies.

Potential applications of Pseudomonas sp. (strain CPSB21) to ameliorate Cr6+ stress and phytoremediation of tannery effluent contaminated agricultural soils.

Contamination of agricultural soil with heavy metals has become a serious concern worldwide. In the present study, Cr6+ resistant plant growth promoting Pseudomonas sp. (strain CPSB21) was isolated from the tannery effluent contaminated agricultural soils and evaluated for the plant growth promoting activities, oxidative stress tolerance, and Cr6+ bioremediation. Assessment of different plant growth promotion traits, such as phosphate solubilization, indole-3-acetic acid production, siderophores, ammonia and hydrogen cyanide production, revealed that the strain CPSB21 served as an efficient plant growth promoter under laboratory conditions. A pot experiment was performed using sunflower (Helianthus annuus L.) and tomato (Solanum lycopersicum L.) as a test crop. Cr6+ toxicity reduced plant growth, pigment content, N and P uptake, and Fe accumulation. However, inoculation of strain CPSB21 alleviated the Cr6+ toxicity and enhanced the plant growth parameters and nutrient uptake. Moreover, Cr toxicity had varied response on oxidative stress tolerance at graded Cr6+ concentration on both plants. An increase in superoxide dismutase (SOD) and catalase (CAT) activity and reduction in malonialdehyde (MDA) was observed on inoculation of strain CPSB21. Additionally, inoculation of CPSB21 enhanced the uptake of Cr6+ in sunflower plant, while no substantial enhancement was observed on inoculation in tomato plant.

Phosphate solubilization and chromium (VI) remediation potential of Klebsiella sp. strain CPSB4 isolated from the chromium contaminated agricultural soil.

In this study, an effort was made to identify an efficient phosphate solubilizing bacterial strain from chromium contaminated agricultural soils. Based on the formation of a solubilized halo around the colonies on Pikovskaya's agar amended with chromium (VI), 10 strains were initially screened out. Out of 10, strain CPSB4, which showed significantly high solubilization zone at different chromium concentrations, was selected for further study. The strain CPSB4 showed significant plant growth promotion traits with chromium (VI) stress under in-vitro conditions in broth. The plant growth promotion activities of the strain decreased regularly, but were not completely lost with the increase in concentration of chromium up to 200 mg L-1. On subjected to FT-IR analysis, the presence of the functional group, indicating the organic acid aiding in phosphate solubilization was identified. At an optimal temperature of 30 °C and pH 7.0, the strain showed around 93% chromium (VI) reduction under in-vitro conditions in broth study. In soil condition, the maximum chromium (VI) reduction obtained was 95% under in-vitro conditions. The strain CPSB4 was identified as Klebsiella sp. on the basis of morphological, biochemical and 16S rRNA gene sequencing. This study shows that the diverse role of the bacterial strain CPSB4 would be useful in the chromium contaminated soil as a good bioremediation and plant growth promoting agent as well.

Effects of organochlorine pesticides on plant growth-promoting traits of phosphate-solubilizing rhizobacterium, Paenibacillus sp. IITISM08.

The study aimed to identify an effective phosphate-solubilizing and organochlorine pesticide-tolerant bacterial strain(s). A total of 50 phosphate-solubilizing bacterial (PSB) strains were isolated from pesticide-stressed soil. Ten isolates showing higher solubilization were selected for organochlorine pesticides (endosulfan, aldrin, and lindane) tolerance. The strain IITISM08 showed the maximum potential of phosphorous solubilization in Pikovaskya agar medium (solubilization index = 3.2) and in broth medium (348 ± 2 µg mL-1) and tolerated up to 250 µg mL-1 of organochlorine pesticides. During phosphorous solubilization, the presence of functional group and organic acid production were also observed using FT-IR and HPLC. The plant growth-promoting (PGP) traits of the strain IITISM08 was highly inhibited in presence of endosulfan among the three organochlroine pesticides. The strain IITISM08 degraded aldrin (79%), lindane (68%), and endosulfan (51%) at a concentration of 50 µg mL-1. The strain IITISM08 was identified using 16S rDNA gene sequencing as Paenibacillus sp. (IITISM08). The study revealed that the strain IITISM08 can be used as PGP candidate even under organochlorine pesticide-stressed condition.

Spatial characterization and prioritization of heavy metal contaminated soil-water resources in peri-urban areas of National Capital Territory (NCT), Delhi.

Due to rapid industrialization and urbanization during last two decades, contamination of soils by heavy metals is on an increase globally. Lands under peri-urban agriculture are the worst affected. In NCT, Delhi about 14.4% of land area is chemically degraded. In order to take care of this problem, recently the Supreme Court of India ordered to shift various non-confirming (about 39,000 units) industries to regions outside NCT, Delhi. However in spite of this, there have been several reports and parliamentary debates on the phyto-toxicity and extensive accumulation of heavy metals in the region. Literature review revealed that the basis of these debates is a few studies on some point locations in/around Delhi. It was further observed that information on the distribution and extent of heavy metal pollution problem in the region was completely missing. The present study was thus basically aimed at assessing the spatial distribution/extent and type of heavy metal pollution in the study area, for enabling future designing of appropriate site-specific management measures by the decision makers. For this, detailed spatial information on bio-available heavy metal concentrations in the soils and surface/sub-surface waters of NCT (Delhi) was generated through actual soil/water surveys, standard laboratory methods and GIS techniques. The study showed that concentration of all micronutrients (viz. Zn: 0.05-0.18 ppm; Cu: in traces; Fe: 0-0.5 ppm; and Mn: 0-1.2 ppm) and most heavy metals (viz. Ni: 0-0.7 ppm; Pb: 0-0.15 ppm and Cd: in traces) in the surface/sub-surface irrigation waters were well within permissible limits. However Cr concentrations in irrigation waters of Alipur and Shahdara blocks were far above their maximum permissible limit of 1 ppm. It was further observed that Ni and Cr concentrations in the drinking waters of almost entire test area were far above maximum permissible levels of 0.02 and 0.01 ppm, respectively. Bio-available concentrations of several heavy metals (viz. Pb: 0.1-2 ppm; Cd: traces; Ni: 0.05-2 ppm and Cr: 0-0.4 ppm) in the study area soils were also observed to be well within the maximum permissible limits. However there were point Cu contaminations (5-10 ppm) in the sewage-sludge amended soils of vegetable growing areas near south Shahdara block. This was attributed to increased Cu availability due to oxidized acidic conditions generated by over-irrigation of agricultural lands. Available Mn concentrations in Kanjhawala, western Najafgarh and Alipur soils were also observed to be above maximum permissible limit of 10 ppm. This was observed to be mainly due to the geology (i.e. presence of Mn rich sedimentary rocks) and prevalence of reduced acidic conditions, due to paddy cultivation, in these areas. It was further observed that there is acute zinc (Zn) deficiency (< 0.6 ppm) in paddy growing soils of north Kanjhawala, Alipur and some parts of Najafgarh and Shahdara blocks due to extensive leaching of available Zn fractions to lower soil horizons. Similar available Zn deficiencies in high pH (8.5) soils of areas around Bamnoli village in E-Najafgarh block were also observed.