Molecular characterization and kinetics of isoprene degrading bacteria

Delineating acetaminophen biodegradation kinetics and metabolomics using bacterial community

Acetaminophen [N-(4-hydroxyphenyl) acetamide, APAP] is an extensively and frequently consumed over-the-counter analgesic and antiphlogistic medication. It is being regarded as an emerging pollutant due to its continuous increment in the environment instigating inimical impacts on humans and the ecosystem. Considering its wide prevalence in the environment, there is an immense need of appropriate methods for the removal of APAP. The present study indulged screening and isolation of APAP degrading bacterial strains from pharmaceuticals-contaminated sites, followed by their molecular characterization via 16S rRNA sequencing. The phylogenetic analyses assigned the isolates to the genera Pseudomonas, Bacillus, Paracoccus, Agrobacterium, Brucella, Escherichia, and Enterobacter based on genetic relatedness. The efficacy of these strains in batch cultures tested through High-performance Liquid Chromatography (HPLC) revealed Paracoccus sp. and Enterobacter sp. as the most promising bacterial isolates degrading up to 88.96 and 85.92%, respectively of 300 mg L-1 of APAP within 8 days of incubation. Michaelis-Menten kinetics model parameters also elucidated the high degradation potential of these isolates. The major metabolites identified through FTIR and GC-MS analyses were 4-aminophenol, hydroquinone, and 3-hydroxy-2,4-hexadienedioic. Therefore, the outcomes of this comprehensive investigation will be of paramount significance in formulating strategies for the bioremediation of acetaminophen-contaminated sites through a natural augmentation process via native bacterial strains.

Biodegradation of fipronil: molecular characterization, degradation kinetics, and metabolites

Fipronil (C12H4Cl2F6N4OS) is a commonly used insecticide effective against numerous insects and pests. Its immense application poses harmful effects on various non-target organisms as well. Therefore, searching the effective methods for the degradation of fipronil is imperative and logical. In this study, fipronil-degrading bacterial species are isolated and characterized from diverse environments using a culture-dependent method followed by 16S rRNA gene sequencing. Phylogenetic analysis showed the homology of organisms with Acinetobacter sp., Streptomyces sp., Pseudomonas sp., Agrobacterium sp., Rhodococcus sp., Kocuria sp., Priestia sp., Bacillus sp., Aeromonas sp., and Pantoea sp. The bacterial degradation potential for fipronil was analyzed through high-performance liquid chromatography (HPLC). Incubation-based degradation studies revealed that Pseudomonas sp. and Rhodococcus sp. were found to be the most potent isolates that degraded fipronil at 100 mg L-1 concentration, with removal efficiencies of 85.9 and 83.6%, respectively. Kinetic parameter studies, following the Michaelis-Menten model, also revealed the high degradation efficiency of these isolates. Gas chromatography-mass spectrometry (GC-MS) analysis revealed fipronil sulfide, benzaldehyde, (phenyl methylene) hydrazone, isomenthone, etc., as major metabolites of fipronil degradation. Overall investigation suggests that native bacterial species isolated from the contaminated environments could be efficiently utilized for the biodegradation of fipronil. The outcome derived from this study has immense significance in formulating an approach for bioremediation of fipronil-contaminated surroundings.

Genomic, Molecular, and Phenotypic Characterization of Arthrobacter sp. OVS8, an Endophytic Bacterium Isolated from and Contributing to the Bioactive Compound Content of the Essential Oil of the Medicinal Plant Origanum vulgare L

Medicinal plants play an important role in the discovery of new bioactive compounds with antimicrobial activity, thanks to their pharmacological properties. However, members of their microbiota can also synthesize bioactive molecules. Among these, strains belonging to the genera Arthrobacter are commonly found associated with the plant's microenvironments, showing plant growth-promoting (PGP) activity and bioremediation properties. However, their role as antimicrobial secondary metabolite producers has not been fully explored. The aim of this work was to characterize the Arthrobacter sp. OVS8 endophytic strain, isolated from the medicinal plant Origanum vulgare L., from molecular and phenotypic viewpoints to evaluate its adaptation and influence on the plant internal microenvironments and its potential as a producer of antibacterial volatile molecules (VOCs). Results obtained from the phenotypic and genomic characterization highlight its ability to produce volatile antimicrobials effective against multidrug-resistant (MDR) human pathogens and its putative PGP role as a producer of siderophores and degrader of organic and inorganic pollutants. The outcomes presented in this work identify Arthrobacter sp. OVS8 as an excellent starting point toward the exploitation of bacterial endophytes as antibiotics sources.

Peering down the sink: A review of isoprene metabolism by bacteria

Isoprene (2-methyl-1,3-butadiene) is emitted to the atmosphere each year in sufficient quantities to rival methane (>500 Tg C yr^-1 ), primarily due to emission by trees and other plants. Chemical reactions of isoprene with other atmospheric compounds, such as hydroxyl radicals and inorganic nitrogen species (NO_x ), have implications for global warming and local air quality, respectively. For many years, it has been estimated that soil-dwelling bacteria consume a significant amount of isoprene (~20 Tg C yr^-1 ), but the mechanisms underlying the biological sink for isoprene have been poorly understood. Studies have indicated or confirmed the ability of diverse bacterial genera to degrade isoprene, whether by the canonical iso-type isoprene degradation pathway or through other less well-characterized mechanisms. Here, we review current knowledge of isoprene metabolism and highlight key areas for further research. In particular, examples of isoprene-degraders that do not utilize the isoprene monooxygenase have been identified in recent years. This has fascinating implications both for the mechanism of isoprene uptake by bacteria, and also for the ecology of isoprene-degraders in the environments.

Genome sequencing and in silico analysis of isoprene degrading monooxygenase enzymes of Sphingobium sp. BHU LFT2

The whole genome sequencing of a novel isoprene degrading strain of Sphingobium sp. BHU LFT2, its in silico analysis for identifying and characterizing enzymes, especially isoprene monooxygenases (IsoMO), which initiate the degradation process, and in vitro validation with cell extract of optimal temperature and pH and analysis for utilizing isoprene as the preferential substrate, were conducted. The most efficient monooxygenase was identified through comparative analyses using molecular docking followed by molecular dynamics simulation approach. The in silico results revealed high thermostability for most of the monooxygenases. Most potent monooxygenase with locus ID JQK15_20300 exhibiting high sequence similarity with known monooxygenases of isoprene-degrading Rhodococcus sp. LB1 and SC4 strains was identified. Interaction energy of -17.25 kJ/mol for JQK15_20300 with isoprene, was almost similar as that analysed for above-mentioned similar known counterparts, was exhibited by the molecular docking. Molecular dynamic simulation of 100 ns and free energy analysis of JQK15_20300 in the complex with isoprene gave persistent interaction of isoprene with JQK15_20300 during the simulation with high average binding energy of -47.13 kJ/mol thus proving higher affinity of JQK15_20300 for isoprene. The study revealed that the highly efficient isoprene degrading strain of Sphingobium sp. BHU LFT2 having effective monooxygenase could be utilized for large-scale applications including detoxification of air contaminated with isoprene in closed working systems.Communicated by Ramaswamy H. Sarma.

Biodegradation of imidacloprid: Molecular and kinetic analysis

Imidacloprid (C₉H₁₀ClN₅O₂) is the most widely used insecticide. Its persistence and toxic nature have caused a detrimental effect on living biota. Thus its removal from the contaminated environment has become imperative. The present study aimed to isolate bacterial species from pesticide-contaminated sites and assess their potential for biodegradation of imidacloprid. The 16S rRNA analysis revealed the genetic relatedness of isolates to Sphingobacterium sp., Agrobacterium sp., Pseudomonas sp., and Bacillus sp. Batch biodegradation studies showed that Sphingobacterium sp. and Agrobacterium sp. were the most promising isolates as they degraded 81.0% and 84.9%, respectively, of imidacloprid at the concentration of 95 mg/L via co-metabolism. Kinetic study (V_max/K_s ratio) also suggested the high degradation efficiency of these isolates. Imidacloprid-guanidine (C₉H₁₁ClN₄) was identified as the metabolite. This report highlights the potential of bacteria for imidacloprid degradation and could be utilized for the formulation of strategies for the remediation of imidacloprid contaminated environments.

Carbon source type can affect tetracycline removal by Pseudomonas sp. TC952 through regulation of extracellular polymeric substances composition and production

The objective of this work is to elucidate the mechanism of tetracycline (TC) removal by Pseudomonas sp. TC952. The TC removal characteristics of strain TC952 under various environmental conditions were studied. Results showed that the bio-removal efficiency was significantly affected by initial TC and peptone concentration, pH values, divalent metal ion (Zn²⁺) and carbon source, and the strain TC952 efficiently removed approximately 72.8% of TC within 6 days with 10 g/L peptone. The best conditions for strain TC952 to remove TC are as follows: initial TC concentration is 50 mg/L, solution initial pH is 7, Zn²⁺ concentration is 0.1 μg/L, carbon source is peptone. And through intra- and extracellular fractions assay and extracellular polymeric substances (EPS) component analysis, TC removal by strain TC952 was mainly attributed to the adsorption by bacterial EPS and bacterial cell. Furthermore, different carbon source affected the EPS production content and component of strain TC952, so EPS produced under peptone and serine conditions could bio-adsorb TC and formed a buffer area outside the cells, thus reducing or preventing TC from entering the bacteria cells. All the results obtained showed that secretion of EPS and adsorption of TC by EPS and bacterial cell wall may be a common way for bacteria to reduce TC in the environment, which brought novel insights for better management of TC contamination by functional bacteria and for understanding the natural removal process of antibiotics by microorganisms in the environment.

Biodegradation of isoprene by Arthrobacter sp. strain BHU FT2: Genomics-proteomics enabled novel insights

The bacterial degradation of isoprene is important for maintaining its atmospheric concentration in unpolluted environment. It may be possible to use natural isoprene degrading bacteria in engineered systems to eliminate or limit isoprene emissions from various sources. Biodegradation of isoprene by Arthrobacter sp. strain BHU FT2 was investigated. The genome was found to contain 4151545 bp long chromosome having 3747 coding genes, and coded potential isoprene degrading enzymes. The molecular docking of monooxygenases with isoprene displayed a higher binding energy (-4.59 kcal/mol) for WP_015938387.1 monooxygenase. Analysis of the identified monooxygenases with the known isoprene monooxygenases revealed 67% sequence identity of WP_015938387.1 (Locus tag JHV56_10705) monooxygenase of the considered strain with the OPX16961.1 monooxygenase of Gordonia sp. i37 isoprene degrading starin. These results provided a strong evidence for the high isoprene degrading potential of the Arthrobacter sp. BHU FT2 which could be efficiently exploited for isoprene degradation in large scale bio-filtration units.

The survival and removal mechanism of Sphingobacterium changzhouense TC931 under tetracycline stress and its' ecological safety after application

Sphingobacterium changzhouense TC931 was isolated as a novel TC (tetracycline) removal bacterium through adsorption on extracellular polymerase substances (EPS) and cellular surface and biodegradation. TC biodegradation efficiency by strain TC931 was affected by solution initial pH and carbon source. Polysaccharides and hydrocarbons in EPS and cellular surface were responsible for TC biosorption. Eight possible biodegradation products were identified and the biodegradation pathway was proposed. Strain TC931 was rich in antibiotic resistance genes, and tetX_-TC931 and antibiotics resistance genome island (GI) may be acquired via horizontal gene transfer in early evolutionary history. The GI was incomplete and may stable in strain TC931, but it could develop into an intact and transferability GI with help of other mobile genetic elements. This work offers a theoretical basis for understanding the survival and biodegradation mechanisms of S. changzhouense TC931 under TC stress, and offers an ecological safety assessment for its application in environmental bioremediation.

Isoprene-Degrading Bacteria from Soils Associated with Tropical Economic Crops and Framework Forest Trees

Isoprene, a volatile hydrocarbon emitted largely by plants, plays an important role in regulating the climate in diverse ways, such as reacting with free radicals in the atmosphere to produce greenhouse gases and pollutants. Isoprene is both deposited and formed in soil, where it can be consumed by some soil microbes, although much remains to be understood about isoprene consumption in tropical soils. In this study, isoprene-degrading bacteria from soils associated with tropical plants were investigated by cultivation and cultivation-independent approaches. Soil samples were taken from beneath selected framework forest trees and economic crops at different seasons, and isoprene degradation in soil microcosms was measured after 96 h of incubation. Isoprene losses were 4-31% and 15-52% in soils subjected to a lower (7.2 × 10⁵ ppbv) and a higher (7.2 × 10⁶ ppbv) concentration of isoprene, respectively. Sequencing of 16S rRNA genes revealed that bacterial communities in soil varied significantly across plant categories (framework trees versus economic crops) and the presence of isoprene, but not with isoprene concentration or season. Eight isoprene-degrading bacterial strains were isolated from the soils and, among these, four belong to the genera Ochrobactrum, Friedmanniella, Isoptericola and Cellulosimicrobium, which have not been previously shown to degrade isoprene.

Molecular Ecology of Isoprene-Degrading Bacteria

Isoprene is a highly abundant biogenic volatile organic compound (BVOC) that is emitted to the atmosphere in amounts approximating to those of methane. The effects that isoprene has on Earth's climate are both significant and complex, however, unlike methane, very little is known about the biological degradation of this environmentally important trace gas. Here, we review the mechanisms by which bacteria catabolise isoprene, what is known about the diversity of isoprene degraders in the environment, and the molecular tools currently available to study their ecology. Specifically, we focus on the use of probes based on the gene encoding the α-subunit of isoprene monooxygenase, isoA, and DNA stable-isotope probing (DNA-SIP) alone or in combination with other cultivation-independent techniques to determine the abundance, diversity, and activity of isoprene degraders in the environment. These parameters are essential in order to evaluate how microbes might mitigate the effects of this important but neglected climate-active gas. We also suggest key aspects of isoprene metabolism that require further investigation in order to better understand the global isoprene biogeochemical cycle.

Microbial metabolism of isoprene: a much-neglected climate-active gas

The climate-active gas isoprene is the major volatile produced by a variety of trees and is released into the atmosphere in enormous quantities, on a par with global emissions of methane. While isoprene production in plants and its effect on atmospheric chemistry have received considerable attention, research into the biological isoprene sink has been neglected until recently. Here, we review current knowledge on the sources and sinks of isoprene and outline its environmental effects. Focusing on degradation by microbes, many of which are able to use isoprene as the sole source of carbon and energy, we review recent studies characterizing novel isoprene degraders isolated from soils, marine sediments and in association with plants. We describe the development and use of molecular methods to identify, quantify and genetically characterize isoprene-degrading strains in environmental samples. Finally, this review identifies research imperatives for the further study of the environmental impact, ecology, regulation and biochemistry of this interesting group of microbes.

Isoprene Oxidation by the Gram-Negative Model bacterium Variovorax sp. WS11

Plant-produced isoprene (2-methyl-1,3-butadiene) represents a significant portion of global volatile organic compound production, equaled only by methane. A metabolic pathway for the degradation of isoprene was first described for the Gram-positive bacterium Rhodococcus sp. AD45, and an alternative model organism has yet to be characterised. Here, we report the characterisation of a novel Gram-negative isoprene-degrading bacterium, Variovorax sp. WS11. Isoprene metabolism in this bacterium involves a plasmid-encoded iso metabolic gene cluster which differs from that found in Rhodococcus sp. AD45 in terms of organisation and regulation. Expression of iso metabolic genes is significantly upregulated by both isoprene and epoxyisoprene. The enzyme responsible for the initial oxidation of isoprene, isoprene monooxygenase, oxidises a wide range of alkene substrates in a manner which is strongly influenced by the presence of alkyl side-chains and differs from other well-characterised soluble diiron monooxygenases according to its response to alkyne inhibitors. This study presents Variovorax sp. WS11 as both a comparative and contrasting model organism for the study of isoprene metabolism in bacteria, aiding our understanding of the conservation of this biochemical pathway across diverse ecological niches.