MALDI-TOF-MS and 16S rRNA characterization of lead tolerant metallophile bacteria isolated from saffron soils of Kashmir for their sequestration potential

Molecular and eco-physiological responses of soil-borne lead (Pb2+)-resistant bacteria for bioremediation and plant growth promotion under lead stress

Lead (Pb) is the 2nd known portentous hazardous substance after arsenic (As). Being highly noxious, widespread, non-biodegradable, prolonged environmental presence, and increasing accumulation, particularly in arable land, Pb pollution has become a serious global health concern requiring urgent remediation. Soil-borne, indigenous microbes from Pb-polluted sites have evolved diverse resistance strategies, involving biosorption, bioprecipitation, biomineralization, biotransformation, and efflux mechanisms, under continuous exposure to Pb in human-impacted surroundings. These strategies employ a wide range of functional bioligands to capture Pb and render it inaccessible for leaching. Recent breakthroughs in molecular technology and understanding of lead resistance mechanisms offer the potential for utilizing microbes as biological tools in environmental risk assessment. Leveraging the specific affinity and sensitivity of bacterial regulators to Pb2+ ions, numerous lead biosensors have been designed and deployed worldwide to monitor Pb bioavailability in contaminated sites, even at trace levels. Besides, the ongoing degradation of croplands due to Pb pollution poses a significant challenge to meet the escalating global food demands. The accumulation of Pb in plant tissues jeopardizes both food safety and security while severely impacting plant growth. Exploring Pb-resistant plant growth-promoting rhizobacteria (PGPR) presents a promising sustainable approach to agricultural practices. The active associations of PGPR with host plants have shown enhancements in plant biomass and stress alleviation under Pb influence. They thus serve a dual purpose for plants grown in Pb-contaminated areas. This review aims to offer a comprehensive understanding of the role played by Pb-resistant soil-borne indigenous bacteria in expediting bioremediation and improving the growth of Pb-challenged plants essential for potential field application, thus broadening prospects for future research and development.

Extremophiles and their expanding biotechnological applications

Microbial life is not restricted to any particular setting. Over the past several decades, it has been evident that microbial populations can exist in a wide range of environments, including those with extremes in temperature, pressure, salinity, and pH. Bacteria and Archaea are the two most reported types of microbes that can sustain in extreme environments, such as hot springs, ice caves, acid drainage, and salt marshes. Some can even grow in toxic waste, organic solvents, and heavy metals. These microbes are called extremophiles. There exist certain microorganisms that are found capable of thriving in two or more extreme physiological conditions simultaneously, and are regarded as polyextremophiles. Extremophiles possess several physiological and molecular adaptations including production of extremolytes, ice nucleating proteins, pigments, extremozymes and exopolysaccharides. These metabolites are used in many biotechnological industries for making biofuels, developing new medicines, food additives, cryoprotective agents etc. Further, the study of extremophiles holds great significance in astrobiology. The current review summarizes the diversity of microorganisms inhabiting challenging environments and the biotechnological and therapeutic applications of the active metabolites obtained as a response to stress conditions. Bioprospection of extremophiles provides a progressive direction with significant enhancement in economy. Moreover, the introduction to omics approach including whole genome sequencing, single cell genomics, proteomics, metagenomics etc., has made it possible to find many unique microbial communities that could be otherwise difficult to cultivate using traditional methods. These findings might be capable enough to state that discovery of extremophiles can bring evolution to biotechnology.

Evaluation of multi-heavy metal tolerance traits of soil-borne fungi for simultaneous removal of hazardous metals

The demand for environment-friendly cleanup techniques has arisen due to an increase in environmental pollutants. Fungi is the most prevalent and effective class of heavy metal-resistant microorganisms with the ability to leach metals. The objective of the present study was to isolate the fungi from the agricultural soil of Kashmir valley, investigate their multi-metal tolerance to heavy metals and evaluate the metal uptake capacities of the resistant fungi. The fungi were isolated and identified on the basis of morphological and molecular approach (ITS1 and ITS4). The tolerance limits of the isolated fungal strains to various doses of lead (Pb), cadmium (Cd), zinc (Zn), chromium (Cr), copper (Cu), nickel (Ni), and cobalt (Co) was evaluated. Five fungal strains, Aspergillus niger, Fusarium oxysporum, Fusarium verticillioides, Aspergillus fischeri, Epicoccum mackenziei were isolated from the soil samples. To the best of our knowledge, this is the first report on the study of metal resistance of Aspergillus fischeri and Epicoccum mackenziei. Among the identified fungal species, Aspergillus niger and Fusarium oxysporum were found to be most tolerant with a minimum inhibitory concentration (MIC) of 600 ppm against Cu and Cr respectively. Results indicated removal of considerable amount of heavy metals by some of the fungi. The highest metal uptake of 8.31 mg/g was found in Fusarium verticillioides for Zn. Surprisingly, these fungal strains demonstrated resistance to metal concentrations above the levels that are universally acceptable for polluted soils, and hence prove to be appealing contenders for use as bioremediation agents for cleaning up heavy metal-polluted environments.

New roles for Bacillus thuringiensis in the removal of environmental pollutants

For a long time, the well-known Gram-positive bacterium Bacillus thuringiensis (Bt) has been extensively studied and developed as a biological insecticide for Lepidoptera and Coleoptera pests due to its ability to secrete a large number of specific insecticidal proteins. In recent years, studies have found that Bt strains can also potentially biodegrade residual pollutants in the environment. Many researchers have isolated Bt strains from multiple sites polluted by exogenous compounds and characterized and identified their xenobiotic-degrading potential. Furthermore, its pathway for degradation was also investigated at molecular level, and a number of major genes/enzymes responsible for degradation have been explored. At present, a variety of xenobiotics involved in degradation in Bt have been reported, including inorganic pollutants (used in the field of heavy metal biosorption and recovery and precious metal recovery and regeneration), pesticides (chlorpyrifos, cypermethrin, 2,2-dichloropropionic acid, etc.), organic tin, petroleum and polycyclic aromatic hydrocarbons, reactive dyes (congo red, methyl orange, methyl blue, etc.), and ibuprofen, among others. In this paper, the biodegrading ability of Bt is reviewed according to the categories of related pollutants, so as to emphasize that Bt is a powerful agent for removing environmental pollutants.

Integrated genomics and transcriptomics reveal the extreme heavy metal tolerance and adsorption potentiality of Staphylococcus equorum

In this study, we successfully isolated 11 species of cadmium-tolerant bacterium from Pu-erh rhizosphere soil, of which Staphylococcus equorum PU1 showed the highest cadmium tolerance, with a minimum inhibitory concentration (MIC) value of 500 mg/L. The cadmium removal efficiency of PU1 in 400 mg/L cadmium medium reached 58.7 %. Based on the Nanopore PromethION and Illumina NovaSeq platforms, we successfully obtained the complete PU1 genome with a size of 2,705,540 bp, which encoded 2729 genes. We further detected 82 and 44 indel mutations in the PU1 genome compared with the KS1039 and KM1031 genomes from the database. Transcriptional analysis showed that the expression of 11 genes in PU1 increased with increasing cadmium concentrations (from 0 to 200, then to 400 mg/L), which encoded cadmium resistance, cadmium transport, and mercury resistance genes. In addition, some genes showed differential expression patterns with changes in cadmium concentration, including quinone oxidoreductase-like protein, ferrous iron transport protein, and flavohemoprotein. Gene Ontology (GO) functions, including oxidation reduction process and oxidoreductase activity functions, and KEGG pathways, including glycolysis/gluconeogenesis and biosynthesis of secondary metals, were also considered closely related to the extreme cadmium tolerance of PU1. This study provides novel insight into the cadmium tolerance mechanism of bacteria.

MALDI-TOF MS: application in diagnosis, dereplication, biomolecule profiling and microbial ecology

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has revolutionized scientific research over the past few decades and has provided a unique platform in ongoing technological developments. Undoubtedly, there has been a bloom chiefly in the field of biological sciences with this emerging technology, and has enabled researchers to generate critical data in the field of disease diagnoses, drug development, dereplication. It has received well acceptance in the field of microbial identification even at strain level, as well as diversified field like biomolecule profiling (proteomics and lipidomics) has evolved tremendously. Additionally, this approach has received a lot more attention over conventional technologies due to its high throughput, speed, and cost effectiveness. This review aims to provide a detailed insight regarding the application of MALDI-TOF MS in the context of medicine, biomolecule profiling, dereplication, and microbial ecology. In general, the expansion in the application of this technology and new advancements it has made in the field of science and technology has been highlighted.

In vitro Sequestration of Molecular and Mass Spectra Characterized Metallophilic Cadmium Tolerant Bacteria for Sustainable Agriculture

Due to industrialization, the contamination of toxic metals in soils is currently one of the major concerns to scientists worldwide. The presence of high concentrations of heavy metals including cadmium in the environment is mainly attributed to human activities. Being a highly toxic metal, cadmium can enter plant cell transporters usually used for the uptake of essential cations, such as iron, calcium, and zinc. This study deals with the appraisement of response and tolerance shown by various bacteria in varied cadmium concentrations (100-1,000 ppm). The optical density (OD) of the isolates was measured to determine the minimum inhibitory concentration (MIC) of cadmium. Isolated bacteria have been identified using 16S rRNA gene sequence and Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Among the 72 isolates, 07 (Bacillus pumilus, Enterobacter kobei, Klebsiella pneumonia, Pseudomonas mandelii, Pseudomonas putida, Pseudomonas avellanae, and Staphylococcus equorum), isolates had efficacy for cadmium tolerance and showed sequestration potential at varying MIC. Furthermore, K. pneumonia was observed to have the highest (900 ppm) tolerance for cadmium and the lowest (600 ppm) was shown by E. kobei. Besides, K. pneumonia showed the highest (75.2%) sequestration potential while the least (52.4%) potential was observed for P. putida. These cadmium tolerant species can be implemented in contaminated environments for detoxification and elimination of cadmium from these agricultural fields. Graphical Abstract.