Characterisation of the flavin-free oxygen-tolerant azoreductase from Xenophilus azovorans KF46F in comparison to flavin-containing azoreductases

Co-composting of dewatered sludge and wheat straw with newly isolated Xenophilus azovorans: Carbon dynamics, humification, and driving pathways

Composting is a biological reaction caused by microorganisms. Composting efficiency can be adequately increased by adding biochar and/or by inoculating with exogenous microorganisms. In this study, we looked at four methods for dewatered sludge waste (DSW) and wheat straw (WS) aerobic co-composting: T1 (no additive), T2 (5% biochar), T3 (5% of a newly isolated strain, Xenophilus azovorans (XPA)), and T4 (5% of biochar-immobilized XPA (BCI-XPA)). Throughout the course of the 42-day composting period, we looked into the carbon dynamics, humification, microbial community succession, and modifications to the driving pathways. Compared to T1 and T2, the addition of XPA (T3) and BCI-XPA (T4) extended the thermophilic phase of composting without negatively affecting compost maturation. Notably, T4 exhibited a higher seed germination index (132.14%). Different from T1 and T2 treatments, T3 and T4 treatments increased CO2 and CH4 emissions in the composting process, in which the cumulative CO2 emissions increased by 18.61-47.16%, and T3 and T4 treatments also promoted the formation of humic acid. Moreover, T4 treatment with BCI-XPA addition showed relatively higher activities of urease, polyphenol oxidase, and laccase, as well as a higher diversity of microorganisms compared to other processes. The Functional Annotation of Prokaryotic Taxa (FAPROTAX) analysis showed that microorganisms involved in the carbon cycle dominated the entire composting process in all treatments, with chemoheterotrophy and aerobic chemoheterotrophy being the main pathways of organic materials degradation. Moreover, the presence of XPA accelerated the breakdown of organic materials by catabolism of aromatic compounds and intracellular parasite pathways. On the other hand, the xylanolysis pathway was aided in the conversion of organic materials to dissolved organics by the addition of BCI-XPA. These findings indicate that XPA and BCI-XPA have potential as additives to improve the efficiency of dewatered sludge and wheat straw co-composting.

Revealing the degrading-possibility of methyl red by two azoreductases of Anoxybacillus sp. PDR2 based on molecular docking

Azo dyes, as the most widely used synthetic dyes, are considered to be one of the culprits of water resources and environmental pollution. Anoxybacillus sp. PDR2 is a thermophilic bacterium with the ability to degrade azo dyes, whose genome contains two genes encoding azoreductases (named AzoPDR2-1 and AzoPDR2-2). In this study, through response surface methodology (RSM), when the initial pH, inoculation volume and Mg2+ addition amount were 7.18, 10.72% and 0.1 g/L respectively, the decolorization rate of methyl red (MR) (200 mg/L) could reach its maximum (98.8%). The metabolites after biodegradation were detected by UV-Vis spectroscopy, Fourier transform infrared spectroscopy (FTIR), and liquid chromatography mass spectrometry (LC-MS/MS), indicating that MR was successfully decomposed into 4-aminobenzoic acid and other small substrates. In homologous modeling, it was found that both azoreductases were flavin-dependent azoreductases, and belonged to the α/β structure, using the Rossmann fold. In their docking results with the cofactor flavin mononucleotide (FMN), FMN bound to the surface of the protein dimer. Nicotinamide adenine dinucleotide (NADH) was superimposed on the plane of the pyrazine ring between FMN and the activity pocket of protein. Besides, both azoreductase complexes (azoreductase-FMN-NADH) exhibited a substrate preference for MR. Asn104 and Tyr74 played an important role in the combination of the azoreductase AzoPDR2-1 complex and the azoreductase AzoPDR2-2 complex with MR, respectively. This provided assistance for studying the mechanism of azoreductase biodegradation of azo dyes in thermophilic bacteria.

Bacterial oxidoreductive enzymes as molecular weapons for the degradation and metabolism of the toxic azo dyes in wastewater: a review

Azo dyes are extremely toxic and pose significant environmental and health risks. Consequently, mineralization and conversion to simple compounds are required to avoid their hazardous effects. A variety of enzymes from the bacterial system are thought to be involved in the degradation and metabolism of azo dyes. Bioremediation, a cost effective and eco-friendly biotechnology, involving bacteria is powered by bacterial enzymes. As mentioned, several enzymes from the bacterial system serve as molecular weapons in the degradation of these dyes. Among these enzymes, azoreductase, oxidoreductase, and laccase are of great interest for the degradation and decolorization of azo dyes. Combination of the oxidative and reductive enzymes is used for the removal of azo dyes from water. The aim of this review article is to provide information on the importance of bacterial enzymes. The review also discusses the genetically modified microorganisms in the biodegradation of azo dyes in polluted water.

Microbial Degradation of Azo Dyes: Approaches and Prospects for a Hazard-Free Conversion by Microorganisms

Azo dyes have become a staple in various industries, as colors play an important role in consumer choices. However, these dyes pose various health and environmental risks. Although different wastewater treatments are available, the search for more eco-friendly options persists. Bioremediation utilizing microorganisms has been of great interest to researchers and industries, as the transition toward greener solutions has become more in demand through the years. This review tackles the health and environmental repercussions of azo dyes and its metabolites, available biological approaches to eliminate such dyes from the environment with a focus on the use of different microorganisms, enzymes that are involved in the degradation of azo dyes, and recent trends that could be applied for the treatment of azo dyes.

Transcriptomic Analysis of Degradative Pathways for Azo Dye Acid Blue 113 in Sphingomonas melonis B-2 from the Dye Wastewater Treatment Process

Background: Acid Blue 113 (AB113) is a typical azo dye, and the resulting wastewater is toxic and difficult to remove. Methods: The experimental culture was set up for the biodegradation of the azo dye AB113, and the cell growth and dye decolorization were monitored. Transcriptome sequencing was performed in the presence and absence of AB113 treatment. The key pathways and enzymes involved in AB113 degradation were found through pathway analysis and enrichment software (GO, EggNog and KEGG). Results: S. melonis B-2 achieved more than 80% decolorization within 24 h (50 and 100 mg/L dye). There was a positive relationship between cell growth and the azo dye degradation rate. The expression level of enzymes involved in benzoate and naphthalene degradation pathways (NADH quinone oxidoreductase, N-acetyltransferase and aromatic ring-hydroxylating dioxygenase) increased significantly after the treatment of AB113. Conclusions: Benzoate and naphthalene degradation pathways were the key pathways for AB113 degradation. NADH quinone oxidoreductase, N-acetyltransferase, aromatic ring-hydroxylating dioxygenase and CYP450 were the key enzymes for AB113 degradation. This study provides evidence for the process of AB113 biodegradation at the molecular and biochemical level that will be useful in monitoring the dye wastewater treatment process at the full-scale treatment.

Structural diversity, functional aspects and future therapeutic applications of human gut microbiome

The research on human gut microbiome, regarded as the black box of the human body, is still at the stage of infancy as the functional properties of the complex gut microbiome have not yet been understood. Ongoing metagenomic studies have deciphered that the predominant microbial communities belong to eubacterial phyla Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria, Cyanobacteria, Verrucomicrobia and archaebacterial phylum Euryarchaeota. The indigenous commensal microbial flora prevents opportunistic pathogenic infection and play undeniable roles in digestion, metabolite and signaling molecule production and controlling host's cellular health, immunity and neuropsychiatric behavior. Besides maintaining intestinal health via short-chain fatty acid (SCFA) production, gut microbes also aid in neuro-immuno-endocrine modulatory molecule production, immune cell differentiation and glucose and lipid metabolism. Interdependence of diet and intestinal microbial diversity suggests the effectiveness of pre- and pro-biotics in maintenance of gut and systemic health. Several companies worldwide have started potentially exploiting the microbial contribution to human health and have translated their use in disease management and therapeutic applications. The present review discusses the vast diversity of microorganisms playing intricate roles in human metabolism. The contribution of the intestinal microbiota to regulate systemic activities including gut-brain-immunity crosstalk has been focused. To the best of our knowledge, this review is the first of its kind to collate and discuss the companies worldwide translating the multi-therapeutic potential of human intestinal microbiota, based on the multi-omics studies, i.e. metagenomics and metabolomics, as ready solutions for several metabolic and systemic disorders.

Compositional variation of the human fecal microbiome in relation to azo-reducing activity: a pilot study

Background

Through an arsenal of microbial enzymes, the gut microbiota considerably contributes to human metabolic processes, affecting nutrients, drugs, and environmental poisons. Azoreductases are a predominant group of microbiota-derived enzymes involved in xenobiotic metabolism and drug activation, but little is known about how compositional changes in the gut microbiota correlate with its azo-reducing activity.

Results

To this end, we used high-throughput 16S rRNA amplicon sequencing, with Illumina MiSeq, to determine the microbial community composition of stool samples from 16 adults with different azo-reducing activity. High azo-reducing activity positively correlated with the relative abundance of phylum Firmicutes (especially genera Streptococcus and Coprococcus) but negatively with phylum Bacteroidetes (especially genus Bacteroides). Typical variations in the Firmicutes-to-Bacteroidetes and Prevotella-to-Bacteroides ratios were observed among samples. Multivariate analysis of the relative abundance of key microbial taxa and other diversity parameters confirmed the Firmicutes proportion as a major variable differentiating high and non-azo-reducers, while Bacteroidetes relative abundance was correlated with azo-reduction, sex, and BMI.

Conclusions

This pilot study showed that stool samples with higher azo-reducing activity were enriched in Firmicutes but with relatively fewer Bacteroidetes. More samples and studies from different geographical areas are needed to bolster this conclusion. Better characterization of different azoreductase-producing gut microbes will increase our knowledge about the fate and differential human responses to azodye-containing drugs or orally consumed chemicals, thus contributing to efforts towards implementing microbiome testing in precision medicine and toxicology.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13099-021-00454-0.

Mixed azo dyes degradation by an intracellular azoreductase enzyme from alkaliphilic Bacillus subtilis: a molecular docking study

The rise of pollution due to the dye industries and textile wastes are evolving rapidly every day. The dyes are used in different trade names by the textile industries. The actual chemistry of dye is vague and difficult to understand even today though we are equipped technically. The toxic effects of the dyes and the reasons behind the acute toxicity are also an undiscovered mystery; therefore, no effective measures can be employed to degrade dyes. Deploying physical or chemical methods to pre-treat the azo dyes are expensive, extremely energy-consuming, and are not environment friendly. Hence, the use of microbes for textile dye degradation will be eco-friendly and is probably a cost-effective alternative to physicochemical methods. The present study was conducted to investigate the degradation of azo dyes isolated from textile effluent contaminated soil by employing the bacterial strains for degradation. The bacterial strains could degrade the optimum concentration of mixed azo dyes (200 mg/L) with an incubation up to 5 days. The decolourization of the dyes was expressed in terms of percentage of decolourization, and was found that about 87.35% of degradation by Bacillus subtilis strain. The enzyme responsible was analyzed as intracellular azoreductase involved in the degradation of mixed azo dyes. The enzymatic pathway and 1-phenyl-2-4(4-methyl phenyl)-diazene 1-oxide was observed as the major metabolite by GC-MS analysis. The in silico study determined the binding of mixed azo dye with azoreductase and hypothesized that their linking could be the main reason for the degradation of mixed azo dye.

Draft genome sequence of Kocuria indica DP-K7, a methyl red degrading actinobacterium

In the present study, we report the draft genome of soil isolate DP-K7 that has the potential to degrade methyl red. The 16S rRNA gene sequencing and whole-genome analysis exposed that the bacterial strain DP-K7 belongs to the species Kocuria indica. The genome annotation of the strain DP-K7 through the bioinformatics tool “Prokka” showed that the genome contains 3,010,594 bp with 69.01% GC content. The genome comprises 57 contigs including 2 rRNA genes, 47 tRNA genes, and 2754 CDS. The plate and broth assay showed that the strain DP-K7 has the potential to utilize methyl red as the sole carbon source for growth. Indeed, the RP-HPLC analysis proved that the strain DP-K7 is capable of degrading methyl red. The genome BLAST against a characterized azoreductase (AzoB—Xenophilus azovorans KF46F) revealed the presence of two azoreductase-like genes (azoKi-1 and azoKi-2). The phylogenetic analysis of the primary amino acid sequence of characterized azoreductases suggested that AzoKi-1 and AzoKi-2 belong to members of the clade IV azoreductase, which are flavin-independent. The multiple sequence alignment of AzoKi-1 and AzoKi-2 with flavin-independent azoreductases showed the presence of NAD(P)H binding like motif (GxxGxxG). In addition, other genes coding for dye degrading enzymes (SodC, SodA, KatA, KatE, and DyP2) were also found in the genome supporting that the strain K. indica DP-K7 is a potential azo dye degrader.

Remarkable diversification of bacterial azoreductases: primary sequences, structures, substrates, physiological roles, and biotechnological applications

Azoreductases reductively cleave azo linkages by using NAD(P)H as an electron donor. The enzymes are widely found in bacteria and act on numerous azo dyes, which allow various unique applications. This review describes primary amino acid sequences, structures, substrates, physiological roles, and biotechnological applications of bacterial azoreductases to discuss their remarkable diversification. According to primary sequences, azoreductases were classified phylogenetically into four main clades. Most members of clades I-III are flavoproteins, whereas clade IV members include flavin-free azoreductases. Clades I and II prefer NADPH and NADH, respectively, as electron donors, whereas other members generally use both. Several enzymes formed no clades; moreover, some bacteria produce azoreductases with longer primary structures than those hitherto identified, which implies further diversification of bacterial azoreductases. The crystal structures commonly reveal the Rossmann folds; however, ternary structures are moderately varied with different quaternary conformation. Although physiological roles are obscure, several azoreductases have been shown to act on metabolites such as flavins, quinones, and metal ions more efficiently than on azo dyes. Considering that many homologs exclusively act on these metabolites, it is possible that azoreductases are actually side activities of versatile reductases that act on various substrates with different specificities. In parallel, this idea raises the possibility that homologous enzymes, even if these are already defined as other types of reductases, widely harbor azoreductase activities. Although azoreductases for which their genes have been identified are not abundant, it may be simple to identify azoreductases of biotechnological importance that have novel substrate specificities.

Complete genome sequence of the dissimilatory azo reducing thermophilic bacterium Novibacillus thermophiles SG-1

With the isolation and identification of efficient azo-dye degradation bacteria, bioaugmentation with specific microbial strains has now become an effective strategy to promote the bioremediation of azo dye. However, Azo dye wastewater discharged at high temperature restricted the extensive application of the known mesophilic azoreducing microorganisms. Here we present the complete genome sequence of a bacterium capable of reducing azo dye under thermophilic condition, Novibacillus thermophiles SG-1 (=KCTC 33118^T =CGMCC 1.12363^T). The complete genome of strain SG-1 contains a circular chromosome of 3,629,225 bp with a G + C content of 50.44%. Genome analysis revealed that strain SG-1 possessed genes encoding riboflavin biosynthesis protein that would secrete riboflavin, which could act as electron shuttles to transport the electrons to extracellular azo dye in decolorization process. HPLC analysis showed that the concentration of riboflavin increased from 0.01 μM to 0.255 μM with the growth of strain SG-1 under azo dye reduction. Quantitative real-time PCR analysis further demonstrated that the gene encoding riboflavin biosynthesis protein would be involved in the azo dye decolorization. The results from this study would be beneficial to research the mechanism of anaerobic reduction of azo dye under thermophilic conditions.

(Bio)transformation of 2,4-dinitroanisole (DNAN) in soils

Recent studies have begun to assess the environmental fate and toxicity of 2,4-dinitroanisole (DNAN), an insensitive munition compound of interest to defense agencies. Aerobic and anaerobic DNAN biotransformation in soils was evaluated in this study. Under aerobic conditions, there was little evidence of transformation; most observed removal was attributed to adsorption and subsequent slow chemical reactions. Under anaerobic conditions, DNAN was reductively (bio)transformed and the rate of the transformation was positively correlated with soil organic carbon (OC) up to a threshold of 2.07% OC. H2 addition enhanced the nitroreduction rate compared to endogenous treatments lacking H2. Heat-killed treatments provided rates similar to the endogenous treatment, suggesting that abiotic factors play a role in DNAN reduction. Ten (bio)transformation products were detected by high-resolution mass spectrometry. The proposed transformation pathway involves reduction of DNAN to aromatic amines, with putative reactive nitroso-intermediates coupling with the amines to form azo dimers. Secondary reactions include N-alkyl substitution, O-demethylation (sometimes followed by dehydroxylation), and removal of an N-containing group. Globally, our results suggest that the main reaction DNAN undergoes in anaerobic soils is nitroreduction to 2-methoxy-5-nitroaniline (MENA) and 2,4-diaminoanisole (DAAN), followed by anaerobic coupling reactions yielding azo-dimers. The dimers were subsequently subject to further (bio)transformations.

Intracellular azo decolorization is coupled with aerobic respiration by a Klebsiella oxytoca strain

Reduction of azo dye methyl red coupled with aerobic respiration by growing cultures of Klebsiella oxytoca GS-4-08 was investigated. In liquid media containing dye and 0.6 % glucose in a mineral salts base, 100 mg l(-1) of the dye are completely removed in 3 h under shaking conditions. The dye cannot be aerobically decolorized by strain GS-4-08 without extra carbon sources, indicating a co-metabolism process. Higher initial dye concentration prolonged the lag phase of the cell growth, but final cell concentrations of each batches reached a same level with range from 6.3 to 7.6 mg l(-1) after the dye adaption period. This strain showed stronger dye tolerance and decolorization ability than many reported strains. Furthermore, a new intracellular oxygen-insensitive azoreductase was isolated from this strain, and the specific activity of enzyme was 0.846 and 0.633 U mg(-1) protein in the presence of NADH and NADPH, respectively. N,N dimethyl-p-phenylenediamine and anthranilic acid were stoichiometrically released from MR dye, indicating the breakage of azo bonds accounts for the intracellular decolorization. Combining the characteristics of azoreductase, the stoichiometry of EMP, and TCA cycle, the electron transfer chain theory of aerobic respiration, and the possible mechanism of aerobic respiration coupled with azo reduction by K. oxytoca GS-4-08 are proposed. This study is expected to provide a sound theoretical basis for the development of the K. oxytoca strain in aerobic process for azo dye containing wastewaters.

Differential expression of peroxidase and ABC transporter as the key regulatory components for degradation of azo dyes by Penicillium oxalicum SAR-3

Fungal species are potential dye decomposers since these secrete spectra of extracellular enzymes involved in catabolism. However, cellular mechanisms underlying azo dye catalysis and detoxification are incompletely understood and obscure. A potential strain designated as Penicillium oxalicum SAR-3 demonstrated broad-spectrum catabolic ability of different azo dyes. A forward suppression subtractive hybridization (SSH) cDNA library of P. oxalicum SAR-3 constructed in presence and absence of azo dye Acid Red 183 resulted in identification of 183 unique expressed sequence tags (ESTs) which were functionally classified into 12 functional categories. A number of novel genes that affect specifically organic azo dye degradation were discovered. Although the ABC transporters and peroxidases emerged as prominent hot spot for azo dye detoxification, we also identified a number of proteins that are more proximally related to stress-responsive gene expression. Majority of the ESTs (29.5%) were grouped as hypothetical/unknown indicating the presence of putatively novel genes. Analysis of few ESTs through quantitative real-time reverse transcription polymerase chain reaction revealed their possible role in AR183 degradation. The ESTs identified in the SSH library provide a novel insight on the transcripts that are expressed in P. oxalicum strain SAR-3 in response to AR183.

Identification of NAD(P)H quinone oxidoreductase activity in azoreductases from P. aeruginosa: azoreductases and NAD(P)H quinone oxidoreductases belong to the same FMN-dependent superfamily of enzymes

Water soluble quinones are a group of cytotoxic anti-bacterial compounds that are secreted by many species of plants, invertebrates, fungi and bacteria. Studies in a number of species have shown the importance of quinones in response to pathogenic bacteria of the genus Pseudomonas. Two electron reduction is an important mechanism of quinone detoxification as it generates the less toxic quinol. In most organisms this reaction is carried out by a group of flavoenzymes known as NAD(P)H quinone oxidoreductases. Azoreductases have previously been separate from this group, however using azoreductases from Pseudomonas aeruginosa we show that they can rapidly reduce quinones. Azoreductases from the same organism are also shown to have distinct substrate specificity profiles allowing them to reduce a wide range of quinones. The azoreductase family is also shown to be more extensive than originally thought, due to the large sequence divergence amongst its members. As both NAD(P)H quinone oxidoreductases and azoreductases have related reaction mechanisms it is proposed that they form an enzyme superfamily. The ubiquitous and diverse nature of azoreductases alongside their broad substrate specificity, indicates they play a wide role in cellular survival under adverse conditions.

Characterization of a new oxygen-insensitive azoreductase from Brevibacillus laterosporus TISTR1911: toward dye decolorization using a packed-bed metal affinity reactor

This study reports the identification of a new bacterial azoreductase from Brevibacillus laterosporus TISTR1911, its heterologous production in Escherichia coli, the biochemical characterization and immobilization for use in dye biodegradation processes. The recombinant azoreductase (BrAzo) is a monomeric FMN oxygen-insensitive enzyme with a molecular mass of 23 kDa showing a broad specificity for the reduction of synthetic azo dyes. Double hexahistidine-tagged BrAzo was immobilized onto a nickel chelating column and methyl orange was used to assess its degradation potential using a packed-bed reactor. The dye degradation is described by an exponential model in a downstream batchwise continuous flow mode operated with recycling. The complete degradation of methyl orange (170 μM at 600 mL/h) was achieved in 3 h and continued over 9 cycles. Coupling the immobilized BrAzo with glucose dehydrogenase for NADH regeneration yielded a shorter 1.5 h-degradation period that was maintained throughout 16 cycles.

Characterization of an efficient catalytic and organic solvent-tolerant azoreductase toward methyl red from Shewanella oneidensis MR-1

The acyl carrier protein (ACP) phosphodiesterase gene (SO 4396) of Shewanella oneidensis MR-1 which was analyzed to have azoreductase activity was heterologously expressed in Escherichia coli. The ACP phosphodiesterase was found to reach maximum enzyme velocity 220.59 U/mg, named azoreductase in this study. The azoreductase had highest specific activity (153.16 U/mg) at pH 6.5, which showed a preference for nicotinamide adenine dinucleotide (NADH) as electron donor. The phylogenetic tree analysis indicated that the azoreductase had preference for NADH and dependence for flavin mononucleotide (FMN). However, the azoreductase from S. oneidensis MR-1 still had high enzyme activity in the absence of FMN. The Mg(2+) had a positive influence on the enzyme activity with 25 mM concentration, whereas Cr(3+), Cd(2+) usually had significantly negative effect on enzyme activity. The purified azoreductase retained nearly 100 % activity after incubating in 30 % dimethyl sulfoxide (DMSO), 30 % acetone, 30 % methanol, 20 % ethanol, 20 % isopropanol, and 10 % propanol.

The microbial degradation of azo dyes: minireview

The removal of dyes in wastewater treatment plants still involves physical or chemical processes. Yet numerous studies currently exist on degradation based on the use of microbes-which is a well-studied field. However progress in the use of biological methods to deal with this environmentally noxious waste is currently lacking. This review focuses on the largest dye class, that is azo dyes and their biodegradation. We summarize the bacteria identified thus far which have been implicated in dye decolorization and discuss the enzymes involved and mechanisms by which these colorants are broken down.