Draft Genome Sequence of Zhihengliuella sp. Strain ISTPL4, a Psychrotolerant and Halotolerant Bacterium Isolated from Pangong Lake, India

Synergistic impact of Serendipita indica and Zhihengliuella sp. ISTPL4 on the mitigation of arsenic stress in rice

Arsenic (As) is a highly toxic metal that interferes with plant growth and disrupts various biochemical and molecular processes in plants. In this study, the harmful effects of As on rice were mitigated using combined inoculation of a root endophyte Serendipita indica and an actinobacterium Zhihengliuella sp. ISTPL4. A randomized experiment was conducted, in which rice plants were grown under controlled conditions and As-stressed conditions. The control and treatment groups consisted of untreated and non-stressed plants (C1), treated and non-stressed plants (C2), stressed and untreated plants (T1), and stressed and treated plants (T2). Various phenotypic characteristics such as shoot length (SL), root length (RL), shoot fresh weight (SFW), root fresh weight (RFW), shoot dry weight (SDW), and root dry weight (RDW) and biochemical parameters such as chlorophyll content, protein content, and antioxidant enzymatic activities were evaluated. The activity of various antioxidant enzymes was increased in T2 followed by T1 plants. Furthermore, high concentrations of phytohormones such as ethylene (ET), gibberellic acid (GA), and cytokinin (CK) were found at 4.11 μmol mg-1, 2.53 μmol mg-1, and 3.62 μmol mg-1 of FW of plant, respectively. The results of AAS indicated an increased As accumulation in roots of T2 plants (131.5 mg kg-1) than in roots of T1 plants (120 mg kg-1). It showed that there was an increased As accumulation and sequestration in roots of microbial-treated plants (T2) than in uninoculated plants (T1). Our data suggest that this microbial combination can be used to reduce the toxic effects of As in plants by increasing the activity of antioxidant enzymes such as SOD, CAT, PAL, PPO and POD. Furthermore, rice plants can withstand As stress owing to the active synthesis of phytohormones in the presence of microbial combinations.

Fungal-Bacterial Combinations in Plant Health under Stress: Physiological and Biochemical Characteristics of the Filamentous Fungus Serendipita indica and the Actinobacterium Zhihengliuella sp. ISTPL4 under In Vitro Arsenic Stress

Fungal-bacterial combinations have a significant role in increasing and improving plant health under various stress conditions. Metabolites secreted by fungi and bacteria play an important role in this process. Our study emphasizes the significance of secondary metabolites secreted by the fungus Serendipita indica alone and by an actinobacterium Zhihengliuella sp. ISTPL4 under normal growth conditions and arsenic (As) stress condition. Here, we evaluated the arsenic tolerance ability of S. indica alone and in combination with Z. sp. ISTPL4 under in vitro conditions. The growth of S. indica and Z. sp. ISTPL4 was measured in varying concentrations of arsenic and the effect of arsenic on spore size and morphology of S. indica was determined using confocal microscopy and scanning electron microscopy. The metabolomics study indicated that S. indica alone in normal growth conditions and under As stress released pentadecanoic acid, glycerol tricaprylate, L-proline and cyclo(L-prolyl-L-valine). Similarly, d-Ribose, 2-deoxy-bis(thioheptyl)-dithioacetal were secreted by a combination of S. indica and Z. sp. ISTPL4. Confocal studies revealed that spore size of S. indica decreased by 18% at 1.9 mM and by 15% when in combination with Z. sp. ISTPL4 at a 2.4 mM concentration of As. Arsenic above this concentration resulted in spore degeneration and hyphae fragmentation. Scanning electron microscopy (SEM) results indicated an increased spore size of S. indica in the presence of Z. sp. ISTPL4 (18 ± 0.75 µm) compared to S. indica alone (14 ± 0.24 µm) under normal growth conditions. Our study concluded that the suggested combination of microbial consortium can be used to increase sustainable agriculture by combating biotic as well as abiotic stress. This is because the metabolites released by the microbial combination display antifungal and antibacterial properties. The metabolites, besides evading stress, also confer other survival strategies. Therefore, the choice of consortia and combination partners is important and can help in developing strategies for coping with As stress.

Valorisation of hydrothermal liquefaction wastewater in agriculture: effects on tobacco plants and rhizosphere microbiota

Industrial wastewater obtained from hydrothermal liquefaction (HTL-WW) of food wastes for biofuels production could represent a source of crop nutrients since it is characterized by a high amount of organic and inorganic compounds. In the present work, the potential use of HTL-WW as irrigation water for industrial crops was investigated. The composition of the HTL-WW was rich in nitrogen, phosphorus, and potassium with high level of organic carbon. A pot experiment with Nicotiana tabacum L. plants was conducted using diluted wastewater to reduce the concentration of some chemical elements below the official accepted threshold values. Plants were grown in the greenhouse under controlled conditions for 21 days and irrigated with diluted HTL-WW every 24 hours. Soils and plants were sampled every seven days to evaluate, over time, the effect of wastewater irrigation both on soil microbial populations, through high-throughput sequencing, and plant growth parameters, through the measurement of different biometric indices. Metagenomic results highlighted that, in the HTL-WW treated rhizosphere, the microbial populations shifted via their mechanisms of adaptation to the new environmental conditions, establishing a new balance among bacterial and fungal communities. Identification of microbial taxa occurring in the rhizosphere of tobacco plants during the experiment highlighted that the HTL-WW application improved the growth of Micrococcaceae, Nocardiaceae and Nectriaceae, which included key species for denitrification, organic compounds degradation and plant growth promotion. As a result, irrigation with HTL-WW improved the overall performance of tobacco plants which showed higher leaf greenness and increased number of flowers compared to irrigated control plants. Overall, these results demonstrate the potential feasibility of using of HTL-WW in irrigated agriculture.

Novel Cesium Resistance Mechanism of Alkaliphilic Bacterium Isolated From Jumping Spider Ground Extract

The radionuclide isotopes (¹³⁴Cs and ¹³⁷Cs) of Cesium (Cs), an alkali metal, are attracting attention as major causes of radioactive contamination. Although Cs⁺ is harmful to the growth of plants and bacteria, alkaliphilic bacterium Microbacterium sp. TS-1, isolated from a jumping spider, showed growth even in the presence of 1.2 M CsCl. The maximum concentration of Cs⁺ that microorganisms can withstand has been reported to be 700 mM till date, suggesting that the strain TS-1 is resistant to a high concentration of Cs ions. Multiple reports of cesium ion-resistant bacteria have been reported, but the detailed mechanism has not yet been elucidated. We obtained Cs ion-sensitive mutants and their revertant mutants from strain TS-1 and identified a Cs ion resistance-related gene, MTS1_00475, by performing SNP analysis of the whole-genome sequence data. When exposed to more than 200 mM Cs⁺ concentration, the intracellular Cs⁺ concentration was constantly lowered by MTS1_00475, which encodes the novel low-affinity Cs⁺/H⁺ antiporter. This study is the first to clarify the mechanism of cesium resistance in unexplained cesium-resistant microorganisms. By clarifying the new cesium resistance mechanism, it can be expected to be used as a bioremediation tool for treating radioactive Cs⁺ contaminated water.

A comparative metagenomic study reveals microbial diversity and their role in the biogeochemical cycling of Pangong lake

The environment of a high altitude brackish water lake presents an unprecedented reservoir for the microbial community with adaptability towards surviving stressful conditions. Pangong lake is a high altitude brackish water lake of the Himalayas situated in the eastern part of Ladakh (Indian Tibet), at the height of 4250 m above the sea level. Shotgun metagenomics sequencing of Pangong Lake sediments was performed to examine the taxonomic diversity and functional adaptations of the resident psychrophilic and psychrotolerant microbial communities of the lake (September; a temperature of ±10 °C). Proteobacteria was the most prominent phylum, and Methylophaga, Halomonas, and Marinobacter were mainly abundant at the genus level. Enzyme pathways responsible for methane metabolism, nitrogen metabolism, sulfur reduction, benzoate, and xylene degradation appeared to be complete in the metagenomic dataset. Stress response genes responsible for adaption to pH, cold, salt tolerance, osmotic stress, and oxidative stress were also found in abundance in the metagenome. We compared the Pangong lake metagenome sample to sediments and water samples from three different aquatic habitats, namely saline lake, freshwater lakes and marine ecosystem using MG-RAST server against RefSeq and Subsystem databases. The Pangong lake microbial community contains six unique genera. Regression analysis using metagenome samples suggested that Pangong lake was most closely related to the Trophic South Pacific Ocean (R² = 0.971) and Socompa lake ecosystem (R² = 0.991) at phylum and functional level II, respectively. Our study signifies that the functional metabolic potentiality of Pangong lake is strongly influenced by the taxonomic structure and environmental conditions. We are reporting the metagenome of the sediment sample of the Pangong lake, which unveils the microbial diversity and their functional potential.

Environmental DNA and RNA as Records of Human Exposome, Including Biotic/Abiotic Exposures and Its Implications in the Assessment of the Role of Environment in Chronic Diseases

Most of environment-related diseases often result from multiple exposures of abiotic and/or biotic stressors across various life stages. The application of environmental DNA/RNA (eDNA/eRNA) to advance ecological understanding has been very successfully used. However, the eminent extension of eDNA/eRNA-based approaches to estimate human exposure to biotic and/or abiotic environmental stressors to understand the environmental causes of chronic diseases has yet to start. Here, we introduce the potential of eDNA/eRNA for bio-monitoring of human exposome and health effects in the real environmental or occupational settings. This review is the first of its kind to discuss how eDNA/eRNA-based approaches can be applied for assessing the human exposome. eDNA-based exposome assessment is expected to rely on our ability to capture the genome- and epigenome-wide signatures left behind by individuals in the indoor and outdoor physical spaces through shedding, excreting, etc. Records of eDNA/eRNA exposome may reflect the early appearance, persistence, and presence of biotic and/or abiotic-exposure-mediated modifications in these nucleic acid molecules. Functional genome- and epigenome-wide mapping of eDNA offer great promise to help elucidate the human exposome. Assessment of longitudinal exposure to physical, biological, and chemical agents present in the environment through eDNA/eRNA may enable the building of an integrative causal dynamic stochastic model to estimate environmental causes of human health deficits. This model is expected to incorporate key biological pathways and gene networks linking individuals, their geographic locations, and random multi-hits of environmental factors. Development and validation of monitoring of eDNA/eRNA exposome should seriously be considered to introduce into safety and risk assessment and as surrogates of chronic exposure to environmental stressors. Here we highlight that eDNA/eRNA reflecting longitudinal exposure of both biotic and abiotic environmental stressors may serve as records of human exposome and discuss its application as molecular tools for understanding the toxicogenomics basis of environment-related health deficits.

Synthesis of calcite-based bio-composite biochar for enhanced biosorption and detoxification of chromium Cr (VI) by Zhihengliuella sp. ISTPL4

The current study presents a comprehensive analysis of the potential of actinobacterium Zhihengliuella sp. ISTPL4 and different composite materials for the removal of hexavalent chromium [Cr (VI)]. Genome analysis of strain indicated the presence of several oxidoreductases which includes chromate reductase, nitrate reductase, thioredoxin, superoxide dismutase and hydrogenase are other major candidate genes. Catalytic calcite-based bio-composite material was absorbed on biochar had highest Cr removal efficiency. The main mechanism involved in Cr biosorption by this strain was explained by the Langmuir isotherm model; under equilibrium conditions the maximum adsorption was observed 49 ± 0.3 mgg^-1. Kinetic studies showed that biosorption of Cr (VI) by this strain was a rate-limiting step and followed a pseudo-second-order kinetics (R2 = 0.99). SEM analysis is in line with EDX result indicating highest Cr removal by calcined biochar. MTT assay shown that the bacteria successfully convert toxic Cr (VI) to comparatively less toxic form such as Cr (III).