Draft Genome Sequence of the Carbofuran-Mineralizing Novosphingobium sp. Strain KN65.2

Coupling pathway prediction and fluorescence spectroscopy to assess the impact of auxiliary substrates on micropollutant biodegradation

Some bacteria can degrade organic micropollutants (OMPs) as primary carbon sources. Due to typically low OMP concentrations, these bacteria may benefit from supplemental assimilation of natural substrates present in the pool of dissolved organic matter (DOM). The biodegradability of such auxiliary substrates and the impacts on OMP removal are tightly linked to biotransformation pathways. Here, we aimed to elucidate the biodegradability and effect of different DOM constituents for the carbofuran degrader Novosphingobium sp. KN65.2, using a novel approach that combines pathway prediction, laboratory experiments, and fluorescence spectroscopy. Pathway prediction suggested that ring hydroxylation reactions catalysed by Rieske-type dioxygenases and flavin-dependent monooxygenases determine the transformability of the 11 aromatic compounds used as model DOM constituents. Our approach further identified two groups with distinct transformation mechanisms amongst the four growth-supporting compounds selected for mixed substrate biodegradation experiments with the pesticide carbofuran (Group 1: 4-hydroxybenzoic acid, 4-hydroxybenzaldehyde; Group 2: p-coumaric acid, ferulic acid). Carbofuran biodegradation kinetics were stable in the presence of both Group 1 and Group 2 auxiliary substrates. However, Group 2 substrates would be preferable for bioremediation processes, as they showed constant biodegradation kinetics under different experimental conditions (pre-growing KN65.2 on carbofuran vs. DOM constituent). Furthermore, Group 2 substrates were utilisable by KN65.2 in the presence of a competitor (Pseudomonas fluorescens sp. P17). Our study thus presents a simple and cost-efficient approach that reveals mechanistic insights into OMP-DOM biodegradation.

Bacterial redox response factors in the management of environmental oxidative stress

Bacteria evolved to survive in the available environmental chemosphere via several cellular mechanisms. A rich pool of antioxidants and stress regulators plays a significant role in the survival of bacteria in unfavorable environmental conditions. Most of the microbes exhibit resistant phenomena in toxic environment niches. Naturally, bacteria possess efficient thioredoxin reductase, glutaredoxin, and peroxiredoxin redox systems to handle environmental oxidative stress. Further, an array of transcriptional regulators senses the oxidative stress conditions. Transcription regulators, such as OxyR, SoxRS, PerR, UspA, SsrB, MarA, OhrR, SarZ, etc., sense and transduce bacterial oxidative stress responses. The redox-sensitive transcription regulators continuously recycle the utilized antioxidant enzymes during oxidative stress. These regulators promote the expression of antioxidant enzymes such as superoxide dismutase, catalase, and peroxides that overcome oxidative insults. Therefore, the transcriptional regulations maintain steady-state activities of antioxidant enzymes representing the resistance against host cell/environmental oxidative insults. Further, the redox system provides reducing equivalents to synthesize biomolecules, thereby contributing to cellular repair mechanisms. The inactive transcriptional regulators in the undisturbed cells are activated by oxidative stress. The oxidized transcriptional regulators modulate the expression of antioxidant and cellular repair enzymes to survive in extreme environmental conditions. Therefore, targeting these antioxidant systems and response regulators could alter cellular redox homeostasis. This review presents the mechanisms of different redox systems that favor bacterial survival in extreme environmental oxidative stress conditions.

Biotechnological tools to elucidate the mechanism of pesticide degradation in the environment

Pesticides are widely used in agriculture, households, and industries; however, they have caused severe negative effects on the environment and human health. To clean up pesticide contaminated sites, various technological strategies, i.e. physicochemical and biological, are currently being used throughout the world. Biological approaches have proven to be a viable method for decontaminating pesticide-contaminated soils and water environments. The biological process eliminates contaminants by utilizing microorganisms' catabolic ability. Pesticide degradation rates are influenced by a variety of factors, including the pesticide's structure, concentration, solubility in water, soil type, land use pattern, and microbial activity in the soil. There is currently a knowledge gap in this field of study because researchers are unable to gather collective information on the factors affecting microbial growth, metabolic pathways, optimal conditions for degradation, and genomic, transcriptomic, and proteomic changes caused by pesticide stress on the microbial communities. The use of advanced tools and omics technology in research can bridge the existing gap in our knowledge regarding the bioremediation of pesticides. This review provides new insights on the research gaps and offers potential solutions for pesticide removal from the environment through the use of various microbe-mediated technologies.

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.

Carbofuran toxicity and its microbial degradation in contaminated environments

Carbofuran is one of the most toxic broad-spectrum and systemic N-methyl carbamate pesticide, which is extensively applied as insecticide, nematicide and acaricide for agricultural, domestic and industrial purposes. It is extremely lethal to mammals, birds, fish and wildlife due to its anticholinesterase activity, which inhibits acetyl-cholinesterase and butyrylcholinesterse activity. In humans, carbofuran is associated with endocrine disrupting activity, reproductive disorders, cytotoxic and genotoxic abnormalities. Therefore, cleanup of carbofuran-contaminated environments is of utmost concern and urgently needs an adequate, advanced and effective remedial technology. Microbial technology (bacterial, fugal and algal species) is a very potent, pragmatic and ecofriendly approach for the removal of carbofuran. Microbial enzymes and their catabolic genes exhibit an exceptional potential for bioremediation strategies. To understand the specific mechanism of carbofuran degradation and involvement of carbofuran hydrolase enzymes and genes, highly efficient genomic approaches are required to provide reliable information and unfold metabolic pathways. This review briefly discusses the carbofuran toxicity and its toxicological impact into the environment, in-depth understanding of carbofuran degradation mechanism with microbial strains, metabolic pathways, molecular mechanisms and genetic basis involved in degradation.

Comparative Genomics of Degradative Novosphingobium Strains With Special Reference to Microcystin-Degrading Novosphingobium sp. THN1

Bacteria in genus Novosphingobium associated with biodegradation of substrates are prevalent in environments such as lakes, soil, sea, wood and sediments. To better understand the characteristics linked to their wide distribution and metabolic versatility, we report the whole genome sequence of Novosphingobium sp. THN1, a microcystin-degrading strain previously isolated by Jiang et al. (2011) from cyanobacteria-blooming water samples from Lake Taihu, China. We performed a genomic comparison analysis of Novosphingobium sp. THN1 with 21 other degradative Novosphingobium strains downloaded from GenBank. Phylogenetic trees were constructed using 16S rRNA genes, core genes, protein-coding sequences, and average nucleotide identity of whole genomes. Orthologous protein analysis showed that the 22 genomes contained 674 core genes and each strain contained a high proportion of distributed genes that are shared by a subset of strains. Inspection of their genomic plasticity revealed a high number of insertion sequence elements and genomic islands that were distributed on both chromosomes and plasmids. We also compared the predicted functional profiles of the Novosphingobium protein-coding genes. The flexible genes and all protein-coding genes produced the same heatmap clusters. The COG annotations were used to generate a dendrogram correlated with the compounds degraded. Furthermore, the metabolic profiles predicted from KEGG pathways showed that the majority of genes involved in central carbon metabolism, nitrogen, phosphate, sulfate metabolism, energy metabolism and cell mobility (above 62.5%) are located on chromosomes. Whereas, a great many of genes involved in degradation pathways (21-50%) are located on plasmids. The abundance and distribution of aromatics-degradative mono- and dioxygenases varied among 22 Novosphingoibum strains. Comparative analysis of the microcystin-degrading mlr gene cluster provided evidence for horizontal acquisition of this cluster. The Novosphingobium sp. THN1 genome sequence contained all the functional genes crucial for microcystin degradation and the mlr gene cluster shared high sequence similarity (≥85%) with the sequences of other microcystin-degrading genera isolated from cyanobacteria-blooming water. Our results indicate that Novosphingobium species have high genomic and functional plasticity, rearranging their genomes according to environment variations and shaping their metabolic profiles by the substrates they are exposed to, to better adapt to their environments.

Hydrolase CehA and Monooxygenase CfdC Are Responsible for Carbofuran Degradation in Sphingomonas sp. Strain CDS-1

Carbofuran, a broad-spectrum systemic insecticide, has been extensively used for approximately 50 years. Diverse carbofuran-degrading bacteria have been described, among which sphingomonads have exhibited an extraordinary ability to catabolize carbofuran; other bacteria can only convert carbofuran to carbofuran phenol, while all carbofuran-degrading sphingomonads can degrade both carbofuran and carbofuran phenol. However, the genetic basis of carbofuran catabolism in sphingomonads has not been well elucidated. In this work, we sequenced the draft genome of Sphingomonas sp. strain CDS-1 that can transform both carbofuran and carbofuran phenol but fails to grow on them. On the basis of the hypothesis that the genes involved in carbofuran catabolism are highly conserved among carbofuran-degrading sphingomonads, two such genes, cehA_CDS-1 and cfdC_CDS-1, were predicted from the 84 open reading frames (ORFs) that share ≥95% nucleic acid similarities between strain CDS-1 and another sphingomonad Novosphingobium sp. strain KN65.2 that is able to mineralize the benzene ring of carbofuran. The results of the gene knockout, genetic complementation, heterologous expression, and enzymatic experiments reveal that cehA_CDS-1 and cfdC_CDS-1 are responsible for the conversion of carbofuran and carbofuran phenol, respectively, in strain CDS-1. CehA_CDS-1 hydrolyzes carbofuran to carbofuran phenol. CfdC_CDS-1, a reduced flavin mononucleotide (FMNH₂)- or reduced flavin adenine dinucleotide (FADH₂)-dependent monooxygenase, hydroxylates carbofuran phenol at the benzene ring in the presence of NADH, FMN/FAD, and the reductase CfdX. It is worth noting that we found that carbaryl hydrolase CehA_AC100, which was previously demonstrated to have no activity toward carbofuran, can actually convert carbofuran to carbofuran phenol, albeit with very low activity.IMPORTANCE Due to the extensive use of carbofuran over the past 50 years, bacteria have evolved catabolic pathways to mineralize this insecticide, which plays an important role in eliminating carbofuran residue in the environment. This study revealed the genetic determinants of carbofuran degradation in Sphingomonas sp. strain CDS-1. We speculate that the close homologues cehA and cfdC are highly conserved among other carbofuran-degrading sphingomonads and play the same roles as those described here. These findings deepen our understanding of the microbial degradation mechanism of carbofuran and lay a foundation for the better use of microbes to remediate carbofuran contamination.

Comparative Genomic Analysis Reveals Habitat-Specific Genes and Regulatory Hubs within the Genus Novosphingobium

This study highlights the significant role of the genetic repertoire of a microorganism in the similarity between Novosphingobium strains. The results suggest that the phylogenetic relationships were mostly influenced by metabolic trait enrichment, which is possibly governed by the microenvironment of each microbe’s respective niche. Using core genome analysis, the enrichment of a certain set of genes specific to a particular habitat was determined, which provided insights on the influence of habitat on the distribution of metabolic traits for Novosphingobium strains. We also identified habitat-specific protein hubs, which suggested delineation of Novosphingobium strains based on their habitat. Examining the available genomes of ecologically diverse bacterial species and analyzing the habitat-specific genes are useful for understanding the distribution and evolution of functional and phylogenetic diversity in the genus Novosphingobium.

Species belonging to the genus Novosphingobium are found in many different habitats and have been identified as metabolically versatile. Through comparative genomic analysis, we identified habitat-specific genes and regulatory hubs that could determine habitat selection for Novosphingobium spp. Genomes from 27 Novosphingobium strains isolated from diverse habitats such as rhizosphere soil, plant surfaces, heavily contaminated soils, and marine and freshwater environments were analyzed. Genome size and coding potential were widely variable, differing significantly between habitats. Phylogenetic relationships between strains were less likely to describe functional genotype similarity than the habitat from which they were isolated. In this study, strains (19 out of 27) with a recorded habitat of isolation, and at least 3 representative strains per habitat, comprised four ecological groups—rhizosphere, contaminated soil, marine, and freshwater. Sulfur acquisition and metabolism were the only core genomic traits to differ significantly in proportion between these ecological groups; for example, alkane sulfonate (ssuABCD) assimilation was found exclusively in all of the rhizospheric isolates. When we examined osmolytic regulation in Novosphingobium spp. through ectoine biosynthesis, which was assumed to be marine habitat specific, we found that it was also present in isolates from contaminated soil, suggesting its relevance beyond the marine system. Novosphingobium strains were also found to harbor a wide variety of mono- and dioxygenases, responsible for the metabolism of several aromatic compounds, suggesting their potential to act as degraders of a variety of xenobiotic compounds. Protein-protein interaction analysis revealed β-barrel outer membrane proteins as habitat-specific hubs in each of the four habitats—freshwater (Saro_1868), marine water (PP1Y_AT17644), rhizosphere (PMI02_00367), and soil (V474_17210). These outer membrane proteins could play a key role in habitat demarcation and extend our understanding of the metabolic versatility of the Novosphingobium species.

IMPORTANCE This study highlights the significant role of a microorganism’s genetic repertoire in structuring the similarity between Novosphingobium strains. The results suggest that the phylogenetic relationships were mostly influenced by metabolic trait enrichment, which is possibly governed by the microenvironment of each microbe’s respective niche. Using core genome analysis, the enrichment of a certain set of genes specific to a particular habitat was determined, which provided insights on the influence of habitat on the distribution of metabolic traits in Novosphingobium strains. We also identified habitat-specific protein hubs, which suggested delineation of Novosphingobium strains based on their habitat. Examining the available genomes of ecologically diverse bacterial species and analyzing the habitat-specific genes are useful for understanding the distribution and evolution of functional and phylogenetic diversity in the genus Novosphingobium.

Expanded insecticide catabolic activity gained by a single nucleotide substitution in a bacterial carbamate hydrolase gene

Carbofuran-mineralizing strain Novosphingobium sp. KN65.2 produces the CfdJ enzyme that converts the N-methylcarbamate insecticide to carbofuran phenol. Purified CfdJ shows a remarkably low K_M towards carbofuran. Together with the carbaryl hydrolase CehA of Rhizobium sp. strain AC100, CfdJ represents a new protein family with several uncharacterized bacterial members outside the proteobacteria. Although both enzymes differ by only four amino acids, CehA does not recognize carbofuran as a substrate whereas CfdJ also hydrolyzes carbaryl. None of the CfdJ amino acids that differ from CehA were shown to be silent regarding carbofuran hydrolytic activity but one particular amino acid substitution, i.e., L152 to F152, proved crucial. CfdJ is more efficient in degrading methylcarbamate pesticides with an aromatic side chain whereas CehA is more efficient in degrading the oxime carbamate nematicide oxamyl. The presence of common flanking sequences suggest that the cfdJ gene is located on a remnant of the mobile genetic element Tnceh carrying cehA. Our results suggest that these enzymes can be acquired through horizontal gene transfer and can evolve to degrade new carbamate substrates by limited amino acid substitutions. We demonstrate that a carbaryl hydrolase can gain the additional capacity to degrade carbofuran by a single nucleotide transversion.