Immobilized cells of a novel bacterium increased the degradation of N-methylated carbamates under low temperature conditions

Enhanced remediation of co-contaminated agricultural soils under cold stress by immobilized bacterial agents: A perspective based on abundance differences

This study explored the enhanced remediation effects and microbial mechanisms of the immobilized microbial agent B&Ma19, compared to the microbial agent Ma19, in cold-region farmland co-contaminated with antibiotics and heavy metals during winter. B&Ma19 achieved superior fluoroquinolone degradation and significantly reduced the bioavailability of copper and zinc, while Ma19 treatment only reduced the content of available zinc. Microbial community analysis revealed that B&Ma19 promoted the proliferation of Firmicutes and increased the relative abundance of rare taxa during the freeze-thaw and freezing phases. Functional predictions indicated that B&Ma19 enhanced the expression of proteins in the winter microbial community involved in resistance to antibiotics, metabolic activity, and nutrient acquisition capacity. A random forest model identified Sporosarcina as a potential key genus for co-contamination remediation. Moreover, increased in overall community dispersal limitation and reduced drift-driven succession were observed. The co-occurrence network became more stable, characterized by a higher proportion of moderately abundant keystone taxa. Mantel tests showed that B&Ma19 weakened the correlation between antibiotic resistance genes (ARGs) and mobile genetic elements, and reduced the impact of temperature fluctuations on contaminant concentrations. In contrast, Ma19 strengthened ARG-antibiotic associations. These findings provide a theoretical basis for bioremediation of co-contaminated farmland in cold regions.

An Overview of Microorganisms Immobilized in a Gel Structure for the Production of Precursors, Antibiotics, and Valuable Products

Using free microorganisms for industrial processes has some limitations, such as the extensive consumption of substrates for growth, significant sensitivity to the microenvironment, and the necessity of separation from the product and, therefore, the cyclic process. It is widely acknowledged that confining or immobilizing cells in a matrix or support structure enhances enzyme stability, facilitates recycling, enhances rheological resilience, lowers bioprocess costs, and serves as a fundamental prerequisite for large-scale applications. This report summarizes the various cell immobilization methods, including several synthetic (polyvinylalcohol, polyethylenimine, polyacrylates, and Eudragit) and natural (gelatin, chitosan, alginate, cellulose, agar-agar, carboxymethylcellulose, and other polysaccharides) polymeric materials in the form of thin films, hydrogels, and cryogels. Advancements in the production of well-known antibiotics like penicillin and cephalosporin by various strains were discussed. Additionally, we highlighted cutting-edge research related to strain producers of peptide-based antibiotics (polymyxin B, Subtilin, Tyrothricin, varigomycin, gramicidin S, friulimicin, and bacteriocin), glusoseamines, and polyene derivatives. Crosslinking agents, especially covalent linkers, significantly affect the activity and stability of biocatalysts (penicillin G acylase, penicillinase, deacetoxycephalosporinase, L-asparaginase, β-glucosidase, Xylanase, and urease). The molecular weight of polymers is an important parameter influencing oxygen and nutrient diffusion, the kinetics of hydrogel formation, rigidity, rheology, elastic moduli, and other mechanical properties crucial for long-term utilization. A comparison of stability and enzymatic activity between immobilized enzymes and their free native counterparts was explored. The discussion was not limited to recent advancements in the biopharmaceutical field, such as microorganism or enzyme immobilization, but also extended to methods used in sensor and biosensor applications. In this study, we present data on the advantages of cell and enzyme immobilization over microorganism (bacteria and fungi) suspension states to produce various bioproducts and metabolites-such as antibiotics, enzymes, and precursors-and determine the efficiency of immobilization processes and the optimal conditions and process parameters to maximize the yield of the target products.

Application of cold-adapted microbial agents in soil contaminate remediation: biodegradation mechanisms, case studies, and safety assessments

The microbial agent technology has made significant progress in remediating nitro-aromatic compounds (NACs), such as p-nitrophenol, 2,4-dinitrophenol, and 2,4,6-Trinitrotoluene, in farmland soil over the past decade. However, there are still gaps in our understanding of the bioavailability and degradation mechanisms of these compounds in low-temperature environments. In this review, we provide a comprehensive summary of the strategies employed by cold-adapted microorganisms and elucidate the degradation pathways of NACs pollutants. To further analyze their metabolic mechanisms, we propose using mass balance to improve our understanding of biochemical processes and refine the degradation pathways through stoichiometry analysis. Additionally, we suggest employing 13C-metabolic flux analysis to track enzyme activity and intermediate products during bio-degradation processes with the aim of accelerating the remediation of nitro-aromatic compounds, particularly in cold regions. Through a comprehensive analysis of pollutant metabolic activities and a commitment to the 'One Health' approach, with an emphasis on selecting non-pathogenic strains, the environmental management strategies for soil remediation could be positioned to develop and implement safe and effective measure.

Rapid Degradation of Hazardous Amides by Immobilized Engineered Pseudomonas putida KT2440 Based on a Novel Gene Expression Vector

The amides 4-trifluoromethylnicotinamide, acrylamide, and benzamide are widely used in agriculture and industry, posing hazards to the environment and animals. Immobilized bacteria are preferred in wastewater treatment, but degradation of these amides by immobilized engineered bacteria has not been explored. Here, engineered Pseudomonas putida KT2440 pLSJ15-amiA was constructed by introducing a new amidase gene expression vector into environmentally safe P. putida KT2440. P. putida KT2440 pLSJ15-amiA had high amidase activity, even at 80 °C. P. putida KT2440 pLSJ15-amiA immobilized with calcium alginate exhibited a greater environmental tolerance than free cells. The amides were rapidly degraded by the immobilized cells, but the activity was inhibited by high concentrations of substrates. The substrate inhibition model revealed that the optimum initial concentrations of 4-trifluoromethylnicotinamide, acrylamide, and benzamide for degradation by immobilized cells were 197.65, 350.76, and 249.40 μmol/L, respectively. This study develops a novel and excellent immobilized biocatalyst for remediation of wastewater containing hazardous amides.

Elucidated potential of immobilized Janibacter sp. for saline wastewater phenol removal

Phenolic compounds are commonly found in industrial effluents and can be hazardous to organisms even at low concentrations. Over the years, researchers have demonstrated that bioremediation is a cost-effective and environmentally friendly alternative to physicochemical approaches used to remove phenol. The aim of this study was to investigate the removal of phenol from saline wastewaters by a halotolerant strain of the genus Janibacter. For this purpose, bacterial cells were immobilized on different supports, from which mica and zeolite were ultimately chosen due to their higher removal efficiency. The wet weight of immobilized cells per 1 g of mica and zeolite was 0.51 and 0.48 g, respectively. Free cells consumed 100 mg/L of phenol in 88 h, while immobilized cells used it in 40 h. Immobilized cells revealed a higher thermostability and could operate over a wider pH range and salinity. Unlike free cells, immobilized cells could remove 700 mg/L of phenol and could be reused for at least nine cycles. Interestingly the phenol removal efficiency of zeolite-immobilized cells remained unchanged after 4 months of storage at 4 and - 20 °C, which could be of great advantage for industrial applications. Complete destruction of phenol was observed through the meta pathway comprising phenol hydroxylase and catechol 2,3-dioxygenase enzymes. KEY POINTS: • Mica- and zeolite-immobilized cells were able to consume high concentrations of phenol. • Cells immobilized on mica and zeolite had considerable operational and storage stability. • Immobilized cells could be a good candidate for phenol removal in saline environments.

Microbial elimination of carbamate pesticides: specific strains and promising enzymes

Carbamate pesticides are widely used in the environment, and compared with other pesticides in nature, they are easier to decompose and have less durability. However, due to the improper use of carbamate pesticides, some nontarget organisms still may be harmed. To this end, it is necessary to investigate effective removal or elimination methods for carbamate pesticides. Current effective elimination methods could be divided into four categories: physical removal, chemical reaction, biological degradation, and enzymatic degradation. Physical removal primarily includes elution, adsorption, and supercritical fluid extraction. The chemical reaction includes Fenton oxidation, photo-radiation, and net electron reduction. Biological degradation is an environmental-friendly manner, which achieves degradation by the metabolism of microorganisms. Enzymatic degradation is more promising due to its high substrate specificity and catalytic efficacy. All in all, this review primarily summarizes the property of carbamate pesticides and the traditional degradation methods as well as the promising biological elimination. KEY POINTS: • The occurrence and toxicity of carbamate pesticides were shown. • Biological degradation strains against carbamate pesticides were presented. • Promising enzymes responsible for the degradation of carbamates were discussed.

Microbial adaptation and impact into the pesticide's degradation

The imprudent use of agrochemicals to control agriculture and household pests is unsafe for the environment. Hence, to protect the environment and diversity of living organisms, the degradation of pesticides has received widespread attention. There are different physical, chemical, and biological methods used to remediate pesticides in contaminated sites. Compared to other methods, biological approaches and their associated techniques are more effective, less expensive and eco-friendly. Microbes secrete several enzymes that can attach pesticides, break down organic compounds, and then convert toxic substances into carbon and water. Thus, there is a lack of knowledge regarding the functional genes and genomic potential of microbial species for the removal of emerging pollutants. Here we address the knowledge gaps by highlighting systematic biology and their role in adaptation of microbial species from agricultural soils with a history of pesticide usage and profiling shifts in functional genes and microbial taxa abundance. Moreover, by co-metabolism, the microbial species fulfill their nutritional requirements and perform more efficiently than single microbial-free cells. But in an open environment, free cells of microbes are not much prominent in the degradation process due to environmental conditions, incompatibilities with mechanical equipment and difficulties associated with evenly distributing inoculum through the agroecosystem. This review highlights emerging techniques involving the removal of pesticides in a field-scale environment like immobilization, biobed, biocomposites, biochar, biofilms, and bioreactors. In these techniques, different microbial cells, enzymes, natural fibers, and strains are used for the effective biodegradation of xenobiotic pesticides.

Insights into the microbial degradation and biochemical mechanisms of carbamates

Carbamate compounds are commonly applied in agricultural sectors as alternative options to the recalcitrant organochlorine pesticides due to their easier breakdown and less persistent nature. However, the large-scale use of carbamates also leads to toxic environmental residues, causing severe toxicity in various living systems. The toxic effects of carbamates are due to their inhibitor activity against the acetylchlolinesterase enzyme. This enzyme is crucial for neurotransmission signaling in living beings. Hence, from the environmental point of view, the elimination of carbamates is a worldwide concern and priority. Microbial technology can be deliberated as a potential tool that can work efficiently and as an ecofriendly option for the dissipation of carbamate insecticides from contaminated environments by improving biodegradation processes via metabolic activities of microorganisms. A variety of bacterial and fungal species have been isolated and characterized and are capable of degrading a broad range of carbamates in soil and water environments. In addition, microbial carbamate hydrolase genes (mcd, cehA, cahA, cfdJ, and mcbA) were strongly implicated in the evolution of new metabolic functions and carbamate hydrolase enzymes. However, the accurate localization and appropriate functions of carbamate hydrolase enzymes/genes are very limited. To explore the information on the degradation routes of carbamates and promote the application of biodegradation, a study of molecular techniques is required to unlock insights regarding the degradation specific genes and enzymes. Hence, this review discusses the deep understanding of carbamate degradation mechanisms with microbial strains, metabolic pathways, molecular mechanisms, and their genetic basis in degradation.

Bibliometric Analysis of Hydrocarbon Bioremediation in Cold Regions and a Review on Enhanced Soil Bioremediation

Simple Summary

Anthropogenic activities in cold regions require petroleum oils to support various purposes. With the increased demand of petroleum, accidental oil spills are generated during transportation or refuelling processes. Soil is one of the major victims in petroleum pollution, hence studies have been devoted to find solutions to remove these petroleum hydrocarbons. However, the remote and low-temperature conditions in cold regions hindered the implementation of physical and chemical removal treatments. On the other hand, biological treatments in general have been proposed as an innovative approach to attenuate these hydrocarbon pollutants in soils. To understand the relevancy of biological treatments for cold regions specifically, bibliometric analysis has been applied to systematically analyse studies focused on hydrocarbon removal treatment in a biological way. To expedite the understanding of this analysis, we have summarised these biological treatments and suggested other biological applications in the context of cold conditions.

Abstract

The increased usage of petroleum oils in cold regions has led to widespread oil pollutants in soils. The harsh environmental conditions in cold environments allow the persistence of these oil pollutants in soils for more than 20 years, raising adverse threats to the ecosystem. Microbial bioremediation was proposed and employed as a cost-effective tool to remediate petroleum hydrocarbons present in soils without significantly posing harmful side effects. However, the conventional hydrocarbon bioremediation requires a longer time to achieve the clean-up standard due to various environmental factors in cold regions. Recent biotechnological improvements using biostimulation and/or bioaugmentation strategies are reported and implemented to enhance the hydrocarbon removal efficiency under cold conditions. Thus, this review focuses on the enhanced bioremediation for hydrocarbon-polluted soils in cold regions, highlighting in situ and ex situ approaches and few potential enhancements via the exploitation of molecular and microbial technology in response to the cold condition. The bibliometric analysis of the hydrocarbon bioremediation research in cold regions is also presented.