Marine Bacteria and Omic Approaches: A Novel and Potential Repository for Bioremediation Assessment

Microbial valorization of kraft black liquor for production of platform chemicals, biofuels, and value-added products: A critical review

The proper treatment and utilization of kraft black liquor, generated from the pulp and paper industry through the kraft pulping method, is required to reduce environmental impacts prior to the final disposal. It also improves the economic performance through the utilization of waste. Microbial valorization appears to demonstrates the dual benefits of waste management and resource recovery by providing an innovative solution to convert kraft black liquor into resource for reuse. A comprehensive review on the microbial valorization of kraft black liquor, describing the role in valorization and management, is still lacking in the literature, forming the rationale of this article. Thus, the present study reviews and systematically discusses the potential of utilizing microorganisms to valorize kraft black liquor as a sustainable feedstock to develop a numerous portfolio of platform chemicals, bioenergy, and other value-added products. This work contributes to sustainability and resource efficiency within the pulp and paper industry. The recent developments in utilization of synthetic biology tools and molecular techniques, including omics approaches for engineering novel microbial strains, for enhancing kraft black liquor valorization has been presented. This review explores how the better utilization of kraft black liquor in the pulp and paper industry contributes to achieving UN Sustainable Development Goals (SDGs), particularly clean water and sanitation (SDG 6) as well as the affordable and clean energy goal (SDG 7). The current review also addresses challenges related to toxicity, impurities, low productivity, and downstream processing that serve as obstacles to the progress of developing highly efficient bioproducts. The new directions for future research efforts to fill the critical knowledge gaps are proposed. This study concludes that by implementing microbial valorization techniques, the pulp and paper industry can transition from a linear to a circular bioeconomy and eco-friendly manage the kraft black liuor. This approach showed to be effective towards resource recovery, while simultaneously minimizing the environmental burden.

Microbial oases in the ice: A state-of-the-art review on cryoconite holes as diversity hotspots and their scientific connotations

Cryoconite holes, small meltwater pools on the surface of glaciers and ice sheets, represent extremely cold ecosystems teeming with diverse microbial life. Cryoconite holes exhibit greater susceptibility to the impacts of climate change, underlining the imperative nature of investigating microbial communities as an essential module of polar and alpine ecosystem monitoring efforts. Microbes in cryoconite holes play a critical role in nutrient cycling and can produce bioactive compounds, holding promise for industrial and pharmaceutical innovation. Understanding microbial diversity in these delicate ecosystems is essential for effective conservation strategies. Therefore, this review discusses the microbial diversity in these extreme environments, aiming to unveil the complexity of their microbial communities. The current study envisages that cryoconite holes as distinctive ecosystems encompass a multitude of taxonomically diverse and functionally adaptable microorganisms that exhibit a rich microbial diversity and possess intricate ecological functions. By investigating microbial diversity and ecological functions of cryoconite holes, this study aims to contribute valuable insights into the broader field of environmental microbiology and enhance further understanding of these ecosystems. This review seeks to provide a holistic overview regarding the formation, evolution, characterization, and molecular adaptations of cryoconite holes. Furthermore, future research directions and challenges underlining the need for long-term monitoring, and ethical considerations in preserving these pristine environments are also provided. Addressing these challenges and resolutely pursuing future research directions promises to enrich our comprehension of microbial diversity within cryoconite holes, revealing the broader ecological and biogeochemical implications. The inferences derived from the present study will provide researchers, ecologists, and policymakers with a profound understanding of the significance and utility of cryoconite holes in unveiling the microbial diversity and its potential applications.

Revitalizing contaminated lands: A state-of-the-art review on the remediation of mine-tailings using phytoremediation and genomic approaches

The mining industry has historically served as a critical reservoir of essential raw materials driving global economic progress. Nevertheless, the consequential by-product known as mine tailings has consistently produced a substantial footprint of environmental contamination. With annual discharges of mine tailings surpassing 10 billion tons globally, the need for effective remediation strategies is more pressing than ever as traditional physical and chemical remediation techniques are hindered by their high costs and limited efficacy. Phytoremediation utilizing plants for remediation of polluted soil has developed as a promising and eco-friendly approach to addressing mine tailings contamination. Furthermore, sequencing of genomic DNA and transcribed RNA extracted from mine tailings presents a pivotal opportunity to provide critical supporting insights for activities directed towards the reconstruction of ecosystem functions on contaminated lands. This review explores the growing prominence of phytoremediation and metagenomics as an ecologically sustainable techniques for rehabilitating mine-tailings. The present study envisages that plant species such as Solidago chilensis, Festuca arundinacea, Lolium perenne, Polygonum capitatum, Pennisetum purpureum, Maireana brevifolia, Prosopis tamarugo etc. could be utilized for the remediation of mine-tailings. Furthermore, a critical evaluation of the organic and inorganic ammendments that optimize conditions for the remediation of mine tailings is also provided. The focus of this review extends to the exploration of environmental genomics to characterize microbial communities in mining sites. By delving into the multifaceted dimensions of phytoremediation and genomics for mine tailings, this study contributes to the ongoing efforts to revitalize contaminated lands for a sustainable and environmentally friendly future.

Strategies for mitigation of pesticides from the environment through alternative approaches: A review of recent developments and future prospects

Chemical-based peticides are having negative impacts on both the healths of human beings and plants as well. The World Health Organisation (WHO), reported that each year, >25 million individuals in poor nations are having acute pesticide poisoning cases along with 20,000 fatal injuries at global level. Normally, only ∼0.1% of the pesticide reaches to the intended targets, and rest amount is expected to come into the food chain/environment for a longer period of time. Therefore, it is crucial to reduce the amounts of pesticides present in the soil. Physical or chemical treatments are either expensive or incapable to do so. Hence, pesticide detoxification can be achieved through bioremediation/biotechnologies, including nano-based methodologies, integrated approaches etc. These are relatively affordable, efficient and environmentally sound methods. Therefore, alternate strategies like as advanced biotechnological tools like as CRISPR Cas system, RNAi and genetic engineering for development of insects and pest resistant plants which are directly involved in the development of disease- and pest-resistant plants and indirectly reduce the use of pesticides. Omics tools and multi omics approaches like metagenomics, genomics, transcriptomics, proteomics, and metabolomics for the efficient functional gene mining and their validation for bioremediation of pesticides also discussed from the literatures. Overall, the review focuses on the most recent advancements in bioremediation methods to lessen the effects of pesticides along with the role of microorganisms in pesticides elimination. Further, pesticide detection is also a big challenge which can be done by using HPLC, GC, SERS, and LSPR ELISA etc. which have also been described in this review.

Exploring the bioremediation capability of petroleum-contaminated soils for enhanced environmental sustainability and minimization of ecotoxicological concerns

The bioremediation of soils contaminated with petroleum hydrocarbons (PHCs) has emerged as a promising approach, with its effectiveness contingent upon various types of PHCs, i.e., crude oil, diesel, gasoline, and other petroleum products. Strategies like genetically modified microorganisms, nanotechnology, and bioaugmentation hold potential for enhancing remediation of polycyclic aromatic hydrocarbon (PAH) contamination. The effectiveness of bioremediation relies on factors such as metabolite toxicity, microbial competition, and environmental conditions. Aerobic degradation involves enzymatic oxidative reactions, while bacterial anaerobic degradation employs reductive reactions with alternative electron acceptors. Algae employ monooxygenase and dioxygenase enzymes, breaking down PAHs through biodegradation and bioaccumulation, yielding hydroxylated and dihydroxylated intermediates. Fungi contribute via mycoremediation, using co-metabolism and monooxygenase enzymes to produce CO2 and oxidized products. Ligninolytic fungi transform PAHs into water-soluble compounds, while non-ligninolytic fungi oxidize PAHs into arene oxides and phenols. Certain fungi produce biosurfactants enhancing degradation of less soluble, high molecular-weight PAHs. Successful bioremediation offers sustainable solutions to mitigate petroleum spills and environmental impacts. Monitoring and assessing strategy effectiveness are vital for optimizing biodegradation in petroleum-contaminated soils. This review presents insights and challenges in bioremediation, focusing on arable land safety and ecotoxicological concerns.

Seed Priming Modulates Physiological and Agronomic Attributes of Maize (Zea mays L.) under Induced Polyethylene Glycol Osmotic Stress

Drought and osmotic stresses are major threats to agricultural crops as they affect plants during their life cycle. The seeds are more susceptible to these stresses during germination and establishment of seedlings. To cope with these abiotic stresses, various seed priming techniques have broadly been used. The present study aimed to assess seed priming techniques under osmotic stress. Osmo-priming with chitosan (1 and 2%), hydro-priming with distilled water, and thermo-priming at 4 °C were used on the physiology and agronomy of Zea mays L. under polyethylene glycol (PEG-4000)-induced osmotic stress (-0.2 and -0.4 MPa). The vegetative response, osmolyte content, and antioxidant enzymes of two varieties (Pearl and Sargodha 2002 White) were studied under induced osmotic stress. The results showed that seed germination and seedling growth were inhibited under osmotic stress and germination percentage, and the seed vigor index was enhanced in both varieties of Z. mays L. with chitosan osmo-priming. Osmo-priming with chitosan and hydro-priming with distilled water modulated the level of photosynthetic pigments and proline, which were reduced under induced osmotic stress; moreover, the activities of antioxidant enzymes were improved significantly. In conclusion, osmotic stress adversely affects the growth and physiological attributes; on the contrary, seed priming ameliorated the stress tolerance resistance of Z. mays L. cultivars to PEG-induced osmotic stress by activating the natural antioxidation enzymatic system and accumulating osmolytes.

Deciphering the recent trends in pesticide bioremediation using genome editing and multi-omics approaches: a review

Pesticide pollution in recent times has emerged as a grave environmental problem contaminating both aquatic and terrestrial ecosystems owing to their widespread use. Bioremediation using gene editing and system biology could be developed as an eco-friendly and proficient tool to remediate pesticide-contaminated sites due to its advantages and greater public acceptance over the physical and chemical methods. However, it is indispensable to understand the different aspects associated with microbial metabolism and their physiology for efficient pesticide remediation. Therefore, this review paper analyses the different gene editing tools and multi-omics methods in microbes to produce relevant evidence regarding genes, proteins and metabolites associated with pesticide remediation and the approaches to contend against pesticide-induced stress. We systematically discussed and analyzed the recent reports (2015-2022) on multi-omics methods for pesticide degradation to elucidate the mechanisms and the recent advances associated with the behaviour of microbes under diverse environmental conditions. This study envisages that CRISPR-Cas, ZFN and TALEN as gene editing tools utilizing Pseudomonas, Escherichia coli and Achromobacter sp. can be employed for remediation of chlorpyrifos, parathion-methyl, carbaryl, triphenyltin and triazophos by creating gRNA for expressing specific genes for the bioremediation. Similarly, systems biology accompanying multi-omics tactics revealed that microbial strains from Paenibacillus, Pseudomonas putida, Burkholderia cenocepacia, Rhodococcus sp. and Pencillium oxalicum are capable of degrading deltamethrin, p-nitrophenol, chlorimuron-ethyl and nicosulfuron. This review lends notable insights into the research gaps and provides potential solutions for pesticide remediation by using different microbe-assisted technologies. The inferences drawn from the current study will help researchers, ecologists, and decision-makers gain comprehensive knowledge of value and application of systems biology and gene editing in bioremediation assessments.

Apoptotic, cytotoxic, antioxidant, and antibacterial activities of biosynthesized silver nanoparticles from nettle leaf

Here, we reported the biosynthesis of silver nanoparticles (AgNPs) using Urtica dioica (nettle) leaf extract as green reducing and capping agents and investigate their anticancer and antibacterial, activity. The Nettle-mediated biosynthesized AgNPs was characterized by UV-Vis a spectrophotometer. Their size, shape and elemental analysis were determined with the using of SEM and TEM. The crystal structure was determined by XRD and the biomolecules responsible for the reduction of Ag⁺ were determined using FTIR analysis. Nettle-mediated biosynthesis AgNPs indicated strong antibacterial activity against pathogenic microorganisms. Again, the antioxidant activity of AgNPs is quite high when compared to ascorbic acid. Anticancer effect of AgNPs, IC₅₀ dose was determined by XTT analysis using MCF-7 cell line and the IC₅₀ value was found to be 0.243 ± 0.014 μg/mL (% w/v).

A Review Unveiling Various Machine Learning Algorithms Adopted for Biohydrogen Productions from Microalgae

Biohydrogen production from microalgae is a potential alternative energy source that is now intensively being researched. The complex natures of the biological processes involved have afflicted the accuracy of traditional modelling and optimization, besides being costly. Accordingly, machine learning algorithms have been employed to overcome setbacks, as these approaches have the capability to predict nonlinear interactions and handle multivariate data from microalgal biohydrogen studies. Thus, the review focuses on revealing the recent applications of machine learning techniques in microalgal biohydrogen production. The working principles of random forests, artificial neural networks, support vector machines, and regression algorithms are covered. The applications of these techniques are analyzed and compared for their effectiveness, advantages and disadvantages in the relationship studies, classification of results, and prediction of microalgal hydrogen production. These techniques have shown great performance despite limited data sets that are complex and nonlinear. However, the current techniques are still susceptible to overfitting, which could potentially reduce prediction performance. These could be potentially resolved or mitigated by comparing the methods, should the input data be limited.

Microbiome enrichment from contaminated marine sediments unveils novel bacterial strains for petroleum hydrocarbon and heavy metal bioremediation

Petroleum hydrocarbons and heavy metals are some of the most widespread contaminants affecting marine ecosystems, urgently needing effective and sustainable remediation solutions. Microbial-based bioremediation is gaining increasing interest as an effective, economically and environmentally sustainable strategy. Here, we hypothesized that the heavily polluted coastal area facing the Sarno River mouth, which discharges >3 tons of polycyclic aromatic hydrocarbons (PAHs) and ∼15 tons of heavy metals (HMs) into the sea annually, hosts unique microbiomes including marine bacteria useful for PAHs and HMs bioremediation. We thus enriched the microbiome of marine sediments, contextually selecting for HM-resistant bacteria. The enriched mixed bacterial culture was subjected to whole-DNA sequencing, metagenome-assembled-genomes (MAGs) annotation, and further sub-culturing to obtain the major bacterial species as pure strains. We obtained two novel isolates corresponding to the two most abundant MAGs (Alcanivorax xenomutans strain-SRM1 and Halomonas alkaliantarctica strain-SRM2), and tested their ability to degrade PAHs and remove HMs. Both strains exhibited high PAHs degradation (60-100%) and HMs removal (21-100%) yield, and we described in detail >60 genes in their MAGs to unveil the possible genetic basis for such abilities. Most promising yields (∼100%) were obtained towards naphthalene, pyrene and lead. We propose these novel bacterial strains and related genetic repertoire to be further exploited for effective bioremediation of marine environments contaminated with both PAHs and HMs.

A comparative study on biopharmaceutical function of curcumin and miR-34a by multistimuli-responsive nanoniosome carrier: In-vitro and in-vivo

This research conducted a comparative study on nanoscaled niosomal structures consisting of Tween-80, Tween-60, cholesterol, and dioleoyl-3-trimethylammonium propane (DOTAP). Thin-film hydration technique was used for the preparation and entrapment of curcumin and miRNA in niosomal formulations for enhancing the stability and delivery rate of the agents. Herein, the influence of Tween-80, Tween-60, cholesterol, and DOTAP on the entrapment efficiency (EE%) of curcumin and the physicochemical properties of the carrier are fully discussed. The optimum engineered formulation resulted in a positive charge of +11.23 mV, high EE (100%), smooth surface, spherical shape, small diameter (90 nm), and good stability in physiological buffers. Also, an accelerated cellular uptake, as well as drug release in PBS (pH 7.4, 37°C) after 72 h, were observed. The cytotoxic activity of curcumin (Cur)/miR-34a-loaded nanoparticles was determined by the MTT assay. The results displayed an improved cytotoxic activity of Cur-niosome towards cancer cells compared to free-dispersed Cur. The uptake of Cur-loaded niosome by A280s and A280cp-1 cancer cell lines faced 2.5 folds drop in the concentration compared to its free form. Generally, Cur-niosome exhibits a significant accumulation of superior anti-cancer properties. Likewise, the cytotoxicity of miR-34a-niosome against tumor cells was higher in comparison with its free form. The anti-cancer effects of the gene/drug delivery were investigated in the 4T1 xenografted Balb/C mouse tumor model. According to the in vitro and in vivo results, gene delivery from the modified niosome nanoparticles was distinctly greater than Cur delivery. Therefore, it was concluded that encapsulation of genes in the nano-niosomal delivery system is a promising procedure for the treatment of cancer cells.