Metagenomics-Based Discovery of Malachite Green-Degradation Gene Families and Enzymes From Mangrove Sediment

Novel small multidrug resistance protein Tmt endows the Escherichia coli with triphenylmethane dyes bioremediation capability

Dye contamination in printing and dyeing wastewater has long been a major concern due to its serious impact on both the environment and human health. In the quest for bioremediation of these hazardous dyes, biological resources such as biodegradation bacteria and enzymes have been investigated in severely polluted environments. In this context, the triphenylmethane transporter gene (tmt) was identified in six distinct clones from a metagenomic library of the printing and dyeing wastewater treatment system. Escherichia coli expressing tmt revealed 98.1% decolorization efficiency of triphenylmethane dye malachite green within 24 h under shaking culture condition. The tolerance to malachite green was improved over eightfold in the Tmt strain compared of the none-Tmt expressed strain. Similarly, the tolerance of Tmt strain to other triphenylmethane dyes like crystal violet and brilliant green, was improved by at least fourfold. Site-directed mutations, including A75G, A75S and V100G, were found to reinforce the tolerance of malachite green, and double mutations of these even further improve the tolerance. Therefore, the tmt has been demonstrated to be a specific efflux pump for triphenylmethane dyes, particularly the malachite green. By actively pumping out toxic triphenylmethane dyes, it significantly extends the cells tolerance in a triphenylmethane dye-rich environment, which may provide a promising strategy for bioremediation of triphenylmethane dye pollutants in the environments.

Metagenomic-based discovery and comparison of the lignin degrading potential of microbiomes in aquatic and terrestrial ecosystems via the LCdb database

Lignin, as an abundant organic carbon, plays a vital role in the global carbon cycle. However, our understanding of the global lignin-degrading microbiome remains elusive. The greatest barrier has been absence of a comprehensive and accurate functional gene database. Here, we first developed a curated functional gene database (LCdb) for metagenomic profiling of lignin degrading microbial consortia. Via the LCdb, we draw a clear picture describing the global biogeography of communities with lignin-degrading potential. They exhibit clear niche differentiation at the levels of taxonomy and functional traits. The terrestrial microbiomes showed the highest diversity, yet the lowest correlations. In particular, there were few correlations between genes involved in aerobic and anaerobic degradation pathways, showing a clear functional redundancy property. In contrast, enhanced correlations, especially closer inter-connections between anaerobic and aerobic groups, were observed in aquatic consortia in response to the lower diversity. Specifically, dypB and dypA, are widespread on Earth, indicating their essential roles in lignin depolymerization. Estuarine and marine consortia featured the laccase and mnsod genes, respectively. Notably, the roles of archaea in lignin degradation were revealed in marine ecosystems. Environmental factors strongly influenced functional traits, but weakly shaped taxonomic groups. Null mode analysis further verified that composition of functional traits was deterministic, while taxonomic composition was highly stochastic, demonstrating that the environment selects functional genes rather than taxonomic groups. Our study not only develops a useful tool to study lignin degrading microbial communities via metagenome sequencing but also advances our understanding of ecological traits of these global microbiomes.

Mechanistic insights on enzyme mediated-metabolite cascade during decolourization of Reactive Blue 13 using novel microbial consortium

Understanding the role of oxido-reductase enzymes followed by deciphering the functional genes and their corresponding proteins are crucial for the speculation of molecular mechanism for azo dye degradation. In the present study, decolourization efficiency of developed microbial consortium was tested using 100 mgL^-1 reactive blue 13 (RB13) and the results showed ∼92.67% decolourization of RB13 at 48 h of incubation. The fourier-transform infrared spectroscopy (FTIR), high-performance liquid chromatography (HPLC) and gas chromatography-mass spectrometry (GC-MS) analysis were performed to identify the metabolites formed during RB13 degradation, followed by hypothesizing the metabolic pathway. The GC-MS analysis showed formation of 1,4-dihydronaphthalen-1-ol and 1,3,5-triazin-2-amine as the final degraded compounds after enzymatic breakdown of RB13 dye. The activity of different oxido-reductase enzymes was determined, and the results showed that NADH DCIP reductase and azo reductase had higher activity than other enzymes. It clearly indicated the degradation was initiated with the enzymatic cleavage of azo bond of RB13. Further, the functional genes were annotated against the database of clusters of orthologous groups (COGs) and kyoto encyclopedia of genes and genomes (KEGG). It provided valuable information about the role of crucial functional genes and their corresponding proteins correlated with dominant bacterial species in degradation of RB13. Hence, the present research is the first systematic study that correlated the formation of degradation compounds with the functional genes/enzymes and their corresponding bacterial species responsible for RB13 degradation.

Screening and identification of azo dye decolorizers from mangrove rhizospheric soil

Removal of synthetic textile dyes poses a challenge to the textile industry and a threat to the environment's flora and fauna. These dyes are recalcitrant and not very amenable to physical and chemical techniques of degradation. Hence, several studies on alternative bioremediation methods involving plants, plant roots, single microbes, or a consortium of microbes for the decolorization of dyes have been carried out. In the present study, potent bacteria for dye decolorization were isolated from rhizospheric soil of mangrove plants collected from Kamothe, Navi Mumbai, India. Of the 20 isolates obtained after enrichment, seven isolates were used for further screening of efficient decolorization ability in minimal basal media containing 10% glucose, 2.5% trace metal solution, and 0.1% of Methyl Orange (MO) dye concentration. Physiological parameters to optimize the decolorization of dye at optimum pH, temperature, and incubation time were studied for all the seven isolates. UV-vis and Fourier transform infrared spectroscopy were used to investigate dye decolorization. The seven isolates were characterized morphologically, biochemically, and molecular identification of these bacterial isolates was performed by 16S rRNA sequence analysis. The isolates were identified as Bacillus paramycoides, Pseudomonas taiwanensis, Citrobacter murliniae, Acinetobacter pitti, Exiguobacterium acetylicum, Psychrobacter celer, and Aeromonas taiwanensis. Out of these, Aeromonas taiwanensis has shown exceptional capacity by ~ 100% decolorization of azo dye in minimum time.

Broad thermal spectrum metagenomic laccase with action for dye decolorization and fentin hydroxide treatment

Laccases are multicopper oxidases that act on various phenolic and non-phenolic compounds, enabling numerous applications including xenobiotic bioremediation, biofuel production, drug development, and cosmetic production, and they can be used as additives in the textile and food industries. This wide range of uses makes these enzymes extremely attractive for novel biotechnology applications. Here, we undertook the kinetic characterization of LacMeta, a predicted as homotrimeric (~ 107,93 kDa) small laccase, and demonstrated that this enzyme performs best at an acidic pH (pH 3–5) towards ABTS as substrate and has a broad thermal spectrum (10–60 °C), which can promote high plastic action potential through dynamic environmental temperature fluctuations. This enzyme showed following kinetic parameters: k_cat = 6.377 s⁻¹ ± 0.303, K_m = 4.219 mM, and V_max = 24.43 µM/min (against ABTS as substrate). LacMeta almost completely degraded malachite green (50 mg/mL) in only 2 h. Moreover, the enzyme was able to degrade seven dyes from four distinct classes and it respectively achieved 85% and 83% decolorization of methylene blue and trypan blue with ABTS as the mediator. In addition, LacMeta showed potential for the degradation of two thirds of an agricultural fungicide: fentin hydroxide, thus demonstrating its biotechnological aptitude for bioremediation. The results of this study suggest that LacMeta has potential in textile wastewater treatment and that it could help in the bioremediation of other human/environmental toxins such as pesticides and antibiotic compounds belonging to the same chemical classes as the degraded dyes.

LacMeta is a new two-domain laccase with activity over a wide temperature range

LacMeta maintained 50% activity after 5 months of storage at 4 °C.

Laccase was able to degrade in 2 h the Malachite Green dye, and had the potential to degrade fentin hydroxide

Direct extraction and detection of malachite green from marine sediments by magnetic nano-sized imprinted polymer coupled with spectrophotometric analysis

This research describes the application of magnetic molecularly imprinted nano-sized polymers (MMIPs) for the selective extraction and fast detection of malachite green (MG) from marine sediment samples followed by UV-Vis spectrophotometry. The novel material was prepared by surface imprinting using methacrylic acid as the functional monomer for fixing the template molecules. The polymers obtained at each step were thoroughly studied by transmission electron microscopy, FTIR spectroscopy and thermogravimetric analysis. Simultaneously, the adsorption performances of the resulting nanoparticles were analysed in detail and an excellent affinity with the MG was revealed. Further, the main parameters of magnetic molecular imprinted solid-phase extraction (MMIP-SPE) were screened via multivariate optimization methods. The magnetic nanoparticles were used as special adsorbents to directly extract MG from crude marine sediment extracts. The developed method exhibits satisfactory recoveries from the spiked samples, ranging from 80.40 to 92.96% with an RSD of less than 5.18% (n = 3).

Integrated metagenomic and metaproteomic analyses reveal potential degradation mechanism of azo dye-Direct Black G by thermophilic microflora

Direct Black G (DBG) is a typical toxic azo dye with extensive applications but it poses a serious threat to the aquatic ecosystem and humans. It is necessary to efficiently and safely remove DBG from environments by the application of various treatment technologies. A thermophilic microflora previously isolated from the soil can effectively metabolize DBG. However, the molecular basis of DBG degradation by this thermophilic microflora remains unknown. In this study, metagenomic sequencing technology and qRT-PCR have been used to elucidate the functional potential of genes and their modes of action on DBG. A quantitative metaproteomic method was further utilized to identify the relative functional proteins involved. Subsequently, the possible co-metabolic molecular mechanisms of DBG degradation by candidate genes and functional proteins of the thermophilic microflora were illustrated. The combination of metagenomics and metaproteomics to investigate the degradation of DBG by a microflora was reported for the first time in recent literature; this can further provide a deep insight into the molecular degradation mechanism of dye pollutants by natural microflora.

Co-metabolic degradation of refractory dye: A metagenomic and metaproteomic study

Fructose was utilized as an additional co-substrate to systematically investigate the molecular mechanism of its boosting effect for the degradation of refractory dye reactive black 5 (RB5) by a natural bacterial flora DDMZ1. A decolorizing rate of 98% was measured for sample YE + FRU(200) (with 3 g/L fructose additionally to yeast extract medium, 10% (v/v) inoculation size of flora DDMZ1, 200 mg/L RB5) after 48 h. This result was 21% and 77%, respectively, higher than those of samples with only yeast extract or only fructose. Fructose was found to significantly stimulated both intracellular and extracellular azoreductase secretion causing enhanced activity. Metagenomic sequencing technology was used to analyze the functional potential of genes. A label-free quantitative proteomic approach further confirmed the encoding of functional proteins by the candidate genes. Subsequently, the molecular mechanism of RB5 degradation by candidate genes and functional proteins of the dominant species were proposed. This study provides important perspectives to the molecular mechanism of co-metabolic degradation of refractory pollutants by a natural bacterial flora.

Biodegradation of Malachite Green in Milkfish Pond Sediments

Malachite green (MG) is usually applied as a biocide in aquaculture worldwide. The microbial degradation of MG and changes in the microbial community composition of milkfish (Chanos chanos) culture pond sediments were assessed in this study. Three MG-degrading bacteria strains—M6, M10, and M12—were isolated, identified, and characterized. Strains M6, M10, and M12 are closely related to Zhouia amylolytica, Tenacibaculum mesophilum, and Enterobacter cloacae, respectively. The bacterial strains M10 and M12 showed good ability to degrade MG in the sediment. The MG degradation rate was increased after adding MG three more times. The microbial community in the sediment changes with different treatments. The bacterial strains M10 and M12 provide a potential solution for the treatment of sediment of saline aquaculture ponds with MG contamination.

Heterologous expression of Stlac2, a laccase isozyme of Setosphearia turcica, and the ability of decolorization of malachite green

The active laccases of ascomycetous fungus Setosphaeria turcica were identified by Native-PAGE and ESI-MS/MS, and one of these isozymes Stlac2 was heterologous expressed to investigate the decolorization of malachite green. Setosphaeria turcica produced three active laccase isozymes: Stlac1, Stlac2, and Stlac6. Stlac2 was heterologously expressed in both eukaryotic and prokaryotic expression systems. The eukaryotic recombinant Stlac2 expressed in Pichia pastoris was inactive, and also showed a higher molecular weight than predicted because of glycosylation. The depression of laccase activity was attributable to the incorrect glycosylation at Asn97. Stlac2 expressed in Escherichia coli and the recombinant Stlac2 exhibited activity of 28.23 U/mg with 2,2-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) as the substrate. The highest activity was observed at pH of 4.5 and the temperature of 60 °C. The activity of recombinant Stlac2 was inhibited by 10 mM Na⁺, Mg²⁺, Ca²⁺, Mn²⁺, and increased by 10 mM of Fe³⁺ with a relatively activity of 315% compared with no addition. Cu²⁺ did not affect enzyme activity. Recombinant Stlac2 was capable of decolorizing 67.08% of 20 mg/L malachite green in 15 min without any mediators. CONCLUSIONS: Generally, recombinant protein of fungal laccase Stlac2 was active without glycosylation and decolorize malachite green efficiently, which has potential industrial applications.