Bioremediation of toxic metals in mining site of Zamfara metropolis using resident bacteria (Pantoea agglomerans): A optimization approach

Pantoea trifolii sp. nov., a novel bacterium isolated from Trifolium rubens root nodules

A novel bacterium, designated strain MMK2T, was isolated from a surface-sterilised root nodule of a Trifolium rubens plant growing in south-eastern Poland. Cells were Gram negative, non-spore forming and rod shaped. The strain had the highest 16S rRNA gene sequence similarity with P. endophytica (99.4%), P. leporis (99.4%) P. rwandensis (98.8%) and P. rodasii (98.45%). Phylogenomic analysis clearly showed that strain MMK2T and an additional strain, MMK3, should reside in the genus Pantoea and that they were most closely related to P. endophytica and P. leporis. Genome comparisons showed that the novel strain shared 82.96-93.50% average nucleotide identity and 26.2-53. 2% digital DNA:DNA hybridization with closely related species. Both strains produced siderophores and were able to solubilise phosphates. The MMK2T strain was also able to produce indole-3-acetic acid. The tested strains differed in their antimicrobial activity, but both were able to inhibit the growth of Sclerotinia sclerotiorum 10Ss01. Based on the results of the phenotypic, phylogenomic, genomic and chemotaxonomic analyses, strains MMK2T and MMK3 belong to a novel species in the genus Pantoea for which the name Pantoea trifolii sp. nov. is proposed with the type strain MMK2T (= DSM 115063T = LMG 33049T).

Pan-metagenome reveals the abiotic stress resistome of cigar tobacco phyllosphere microbiome

The important role of microbial associations in mediating plant protection and responses to abiotic stresses has been widely recognized. However, there have been limited studies on the functional profile of the phyllosphere microbiota from tobacco (Nicotiana tabacum), hindering our understanding of the mechanisms underlying stress resilience in this representative and easy-to-cultivate model species from the solanaceous family. To address this knowledge gap, our study employed shotgun metagenomic sequencing for the first time to analyze the genetic catalog and identify putative plant growth promoting bacteria (PGPB) candidates that confer abiotic stress resilience throughout the growth period of cigar tobacco in the phyllosphere. We identified abundant genes from specific bacterial lineages, particularly Pseudomonas, within the cigar tobacco phyllospheric microbiome. These genes were found to confer resilience against a wide range of stressors, including osmotic and drought stress, heavy metal toxicity, temperature perturbation, organic pollutants, oxidative stress, and UV light damage. In addition, we conducted a virome mining analysis on the metagenome to explore the potential roles of viruses in driving microbial adaptation to environmental stresses. Our results identified a total of 3,320 scaffolds predicted to be viral from the cigar tobacco phyllosphere metagenome, with various phages infecting Pseudomonas, Burkholderia, Enterobacteria, Ralstonia, and related viruses. Within the virome, we also annotated genes associated with abiotic stress resilience, such as alkaline phosphatase D (phoD) for nutrient solubilization and glutamate-5-semialdehyde dehydrogenase (proA) for osmolyte synthesis. These findings shed light on the unexplored roles of viruses in facilitating and transferring abiotic stress resilience in the phyllospheric microbiome through beneficial interactions with their hosts. The findings from this study have important implications for agricultural practices, as they offer potential strategies for harnessing the capabilities of the phyllosphere microbiome to enhance stress tolerance in crop plants.

Roles and significance of chelating agents for potentially toxic elements (PTEs) phytoremediation in soil: A review

Phytoremediation is a biological remediation technique known for low-cost technology and environmentally friendly approach, which employs plants to extract, stabilise, and transform various compounds, such as potentially toxic elements (PTEs), in the soil or water. Recent developments in utilising chelating agents soil remediation have led to a renewed interest in chelate-induced phytoremediation. This review article summarises the roles of various chelating agents and the mechanisms of chelate-induced phytoremediation. This paper also discusses the recent findings on the impacts of chelating agents on PTEs uptake and plant growth and development in phytoremediation. It was found that the chelating agents have increased the rate of metal absorption and translocation up to 45% from roots to the aboveground plant parts during PTEs phytoremediation. Besides, it was also explored that the plants may experience some phytotoxicity after adding chelating agents to the soil. However, due to the leaching potential of synthetic chelating agents, the use of organic chelants have been explored to be used in PTEs phytoremediation. Finally, this paper also presents comprehensive insights on the significance of using chelating agents through SWOT analysis to discuss the advantages and limitations of chelate-induced phytoremediation.

Mirror proteorhodopsins

Proteorhodopsins (PRs), bacterial light-driven outward proton pumps comprise the first discovered and largest family of rhodopsins, they play a significant role in life on the Earth. A big remaining mystery was that up-to-date there was no described bacterial rhodopsins pumping protons at acidic pH despite the fact that bacteria live in different pH environment. Here we describe conceptually new bacterial rhodopsins which are operating as outward proton pumps at acidic pH. A comprehensive function-structure study of a representative of a new clade of proton pumping rhodopsins which we name "mirror proteorhodopsins", from Sphingomonas paucimobilis (SpaR) shows cavity/gate architecture of the proton translocation pathway rather resembling channelrhodopsins than the known rhodopsin proton pumps. Another unique property of mirror proteorhodopsins is that proton pumping is inhibited by a millimolar concentration of zinc. We also show that mirror proteorhodopsins are extensively represented in opportunistic multidrug resistant human pathogens, plant growth-promoting and zinc solubilizing bacteria. They may be of optogenetic interest.

Bioremediation of hazardous pollutants from agricultural soils: A sustainable approach for waste management towards urban sustainability

Soil contamination is perhaps the most hazardous issue all over the world; these emerging pollutants ought to be treated to confirm the safety of our living environment. Fast industrialization and anthropogenic exercises have resulted in different ecological contamination and caused serious dangerous health effects to humans and animals. Agro wastes are exceptionally directed because of their high biodegradability. Effluents from the agro-industry are a possibly high environmental risk that requires suitable, low-cost, and extensive treatment. Soil treatment using a bioremediation method is considered an eco-accommodating and reasonable strategy for removing toxic pollutants from agricultural fields. The present review was led to survey bioremediation treatability of agro soil by microbes, decide functional consequences for microbial performance and assess potential systems to diminish over potentials. The presence of hazardous pollutants in agricultural soil and sources, and toxic health effects on humans has been addressed in this review. The present review emphasizes an outline of bioremediation for the effective removal of toxic contaminants in the agro field. In addition, factors influencing recent advancements in the bioremediation process have been discussed. The review further highlights the roles and mechanisms of micro-organisms in the bioremediation of agricultural fields.