Genomic insights into waste valorized extracellular polymeric substances (EPS) produced by Bacillus sp. ISTL8

Deciphering the molecular interaction of extracellular polymeric substances of a marine bacterium Pseudomonas furukawaii PPS-19 with petroleum hydrocarbons and development of bioadsorbent

Petroleum hydrocarbon contamination is a serious hazard to marine environments, affecting ecosystems and marine life. However, extracellular polymeric substances (EPS) of marine bacteria constituting various hydrophilic and hydrophobic functional groups sequester petroleum hydrocarbons (PHs). In this study, interaction of EPS of Pseudomonas furukawaii PPS-19 with PHs such as crude oil, n-dodecane, and pyrene and its impact on PHs adsorption was investigated. Protein component of EPS was increased after treatment with PHs. Red shift of UV-Vis spectra implied change in molecular structure of EPS. Functional groups of proteins (CO, NH2) and polysaccharides (C-C, C-OH, C-O-C) predominantly interacted with PHs. Interaction with PHs affected secondary structure of EPS. Change in binding energies of corresponding functionalities of C 1s, O 1s, and N 1s confirmed the interaction. Disruption of crystalline peaks led to increased pore size in EPS primarily due to the increase in surface electronegativity. Static quenching mechanism unveils formation of complex between fulvic acid of EPS and PHs. Relative expression of alg8 gene was significantly increased in the presence of n-dodecane (6.31 fold) (P < 0.05; One way ANOVA). n-dodecane and pyrene adsorption capacity of Immobilized EPS was significantly higher (356.5 and 338.2 mg g-1, respectively) (P < 0.001; One way ANOVA) than control. Adsorption rate fits into the pseudo-second-order kinetic model. This study establishes that interaction of PHs causes structural and physical changes in EPS and EPS could be used as an adsorbent material for the sequestration of PHs pollution.

Little alginates synthesized in EPS: Evidences from high-throughput community and metagenes

As a significant structure in activated sludge, extracellular polymeric substances (EPS) hold considerable value regarding resource recovery and applications. The present study aimed to elucidate the relationship between the microbial community and the composition and properties of EPS. A biological nutrient removal (BNR) reactor was set up in the laboratory and controlled under different solid retention times (SRT), altering microbial species within the system. Then EPS was extracted from activated and analyzed by chemical and spectroscopic methods. High-throughput sequencing and metagenomic approaches were employed to investigate bacterial community and metabolic pathways. The results showed that lower SRT with a higher abundance of the family-level Proteobacteria (27.7%-53.5%) favored EPS synthesis, while another dominant group Bacteroidetes (20.0%-32.6%) may not significantly affect EPS synthesis. Furthermore, the abundance of alginates-producing bacteria including Pseudomonas spp. and Azotobacter vinelandii was only 2.53%-6.76% and 1.98%-6.34%, respectively. The alginate synthesis pathway genes Alg8 and Alg44 were also present at very low levels (0.05‱-0.11‱, 0.01‱-0.02‱, respectively). Another important gene related to alginates operons, AlgK, was absent across all the SRT-operated reactors. These findings suggest an impossible and incomplete alginate synthesis pathway within sludge. In light of these results, it can be concluded that EPS does not necessarily contain alginate components.

Genome analysis of a newly isolated Bacillus velezensis-YW01 for biodegrading acetaldehyde

Acetaldehyde (AL), a primary carcinogen, not only pollutes the environment, but also endangers human health after drinking alcohol. Here a promising bacterial strain was successfully isolated from a white wine cellar pool in the province of Shandong, China, and identified as Bacillus velezensis-YW01 with 16 S rDNA sequence. Using AL as sole carbon source, initial AL of 1 g/L could be completely biodegraded by YW01 within 84 h and the cell-free extracts of YW01 has also been detected to biodegrade the AL, which indicate that YW01 is a high-potential strain for the biodegradation of AL. The optimal culture conditions and the biodegradation of AL of YW01 are at pH 7.0 and 38 °C, respectively. To further analyze the biodegradation mechanism of AL, the whole genome of YW01 was sequenced. Genes ORF1040, ORF1814 and ORF0127 were revealed in KEGG, which encode for acetaldehyde dehydrogenase. Furthermore, ORF0881 and ORF052 encode for ethanol dehydrogenase. This work provides valuable information for exploring metabolic pathway of converting ethanol to AL and subsequently converting AL to carboxylic acid compounds, which opened up potential pathways for the development of microbial catalyst against AL.

A novel exopolysaccharide-producing bacterium, Pseudescherichia liriopis sp. nov. isolated from Liriope platyphylla, enhances the growth of Daucus carota subsp. sativus under drought and salinity stress

Biological and abiotic stresses in plant growth are associated with reduced crop yields. Therefore, improving plant stress resistance can be a crucial strategy to improve crop production. To overcome these problems, plant growth-promoting bacteria are emphasized as one of the alternative tools for sustainable agriculture. This study found a novel strain (L3T) of a plant growth-promoting bacterium in fermented Liriope platyphylla fruit. Strain L3T showed the ability to promote plant growth. The L3T strain promoted plant growth of D. carota subsp. sativus, increasing the length (increase rate compared to the control group, 36.98%), diameter (47.06%), and weight of carrots (81.5%), ultimately increasing the edible area. In addition, we confirmed that plant growth was improved even in situations that inhibited plant growth, such as salinity and drought stress. Strain L3T performed indole production, siderophore production, phosphate solubilization, and nitrogen fixation, all characteristics of a strain that promotes plant growth. Genome analysis revealed genes involved in the growth promotion effects of strain L3T. Additionally, the properties of exopolysaccharides were identified and characterized using FTIR, TGA, and UHPLC. Our results demonstrated that L3 isolated from fermented L. platyphylla fruit can be used to simultaneously alleviate drought and NaCl stress.

Exploring biosynthesis strategies to boost the yield of exopolysaccharide-protein blend from Bacillus arachidis SY8(T), an isolated native strain, as a potent adsorbent for heavy metals removal

This investigation centers on the synthesis of a polysaccharide-protein blend produced by an isolated native strain (99.12 % phylogenetic affinity with Bacillus arachidis SY8(T)). The primary objective was to investigate the production of extracellular polymeric substances (EPS) under diverse stress conditions, encompassing exposure to heavy metal ions, salt, and toxic agents. Additionally, the impact of environmental parameters, namely pH, inoculation percentage, and time, on the production was investigated. Subsequently, the study examined the biosorption potential of the EPS produced for Pb(II), Cu(II), and Mn(II). The EPS obtained was thoroughly characterized via various tests. Rheological evaluations of an EPS solution (2 wt%) confirmed its pseudo-plastic and non-Newtonian fluid properties, while TGA analysis demonstrated its thermal stability up to 600 °C. Additional analyses, including GPC, FTIR, and H-NMR, provide further insights into the produced EPS. The best conditions for EPS production are determined: 5 % NaCl salt, serving as an effective stress inducer, and 37 °C, pH 6, with a 5 % inoculation, over 96 h. EPS demonstrates remarkable removal efficiencies of 99.9, 99.4 and 78.9 % for Pb(II), Cu(II), and Mn(II), respectively. These findings highlight the potential of EPS as an effective agent for removing heavy metal ions.

Genome-based approach to evaluate the metabolic potentials and exopolysaccharides production of Bacillus paralicheniformis CamBx3 isolated from a Chilean hot spring

In the present study, a thermophilic strain designated CamBx3 was isolated from the Campanario hot spring, Chile. Based on 16S rRNA gene sequence, phylogenomic, and average nucleotide identity analysis the strain CamBx3 was identified as Bacillus paralicheniformis. Genome analysis of B. paralicheniformis CamBx3 revealed the presence of genes related to heat tolerance, exopolysaccharides (EPS), dissimilatory nitrate reduction, and assimilatory sulfate reduction. The pangenome analysis of strain CamBx3 with eight Bacillus spp. resulted in 26,562 gene clusters, 7,002 shell genes, and 19,484 cloud genes. The EPS produced by B. paralicheniformis CamBx3 was extracted, partially purified, and evaluated for its functional activities. B. paralicheniformis CamBx3 EPS with concentration 5 mg mL-1 showed an optimum 92 mM ferrous equivalent FRAP activity, while the same concentration showed a maximum 91% of Fe2+ chelating activity. B. paralicheniformis CamBx3 EPS (0.2 mg mL-1) demonstrated β-glucosidase inhibition. The EPS formed a viscoelastic gel at 45°C with a maximum instantaneous viscosity of 315 Pa.s at acidic pH 5. The present study suggests that B. paralicheniformis CamBx3 could be a valuable resource for biopolymers and bioactive molecules for industrial applications.

Isolation and characterization of the aspartame-degrading strain Pseudarthrobacter sp. AS-1

Aspartame is one of the main varieties of artificial sweeteners. Although it has been approved as a food additive, the environmental hazards and ecological risks posed by aspartame are attracting more and more attention. In the present study, strain Pseudarthrobacter sp. AS-1 was isolated and characterized as an efficient aspartame degrader. Strain AS-1 was capable of degrading 200 mg L-1 aspartame within 10 h under conditions optimized at 30 °C and pH 8.0. At the same time, it was found that enzymes degrading aspartame in strain AS-1 were induced and secreted extracellularly. Degradation of aspartame in Pseudarthrobacter sp. AS-1 was identified as following: it was first demethylated to aspartyl-phenylalanine, then degraded to phenylalanine and aspartate, and finally the two amino acids were further degraded. In addition, strain AS-1 was able to remove more than 85% of aspartame in soil and river water. It is the first time that pure bacterial cultures were reported to have the capability of aspartame degradation. These findings add to our knowledge of the microbial metabolic mechanisms of aspartame.

Mechanism of Cr(VI) reduction by an indigenous Rhizobium pusense CR02 isolated from chromite mining quarry water (CMQW) at Sukinda Valley, India

Toxicological assessment of CMQW generated due to chromite mining activities at Sukinda Valley has revealed high chromium contamination along with Zn and Fe. The present study focused on the mechanism of chromate reduction by an indigenous multi-metal tolerant bacterium, Rhizobium pusense CR02, isolated from CMQW. The isolated strain has shown resistance up to 520 mg/L of Cr(VI) with an IC50 value of 385.4 mg/L. The highest reduction rate 8.6 × 10^-2/h was recorded with 20 mg/L of initial concentration of Cr(VI). Extracellular (3.06 ± 0.012 U/mL), intracellular (3.60 ± 0.13 U/mL), and membrane (1.89 ± 0.01 U/mL) associated chromate reductases were found to be involved for reduction. The extracellular polymeric substances (EPS) produced by the isolate also enhanced reduction activity of 46.32 ± 1.69 mg/L after 72 h with an initial concentration of 50 mg/L. FTIR analysis revealed the involvement of functional groups -OH, -CO, and -NH for Cr(VI) biosorption whereas P=O, -CO-NH- and -COOH interacted with Cr(III). Zeta potential with less negative surface charge favored reduction of Cr(VI). Treatment of CMQW by bacterial isolate detoxified Cr(VI) minimizing chromosomal aberrations in root cells of Allium cepa L., suggesting the role of Rhizobium pusense CR02 as a promising bio-agent for Cr(VI) detoxification.

Phytochemical Profiling of Tupistra nutans Wall. ex Lindl. Inflorescence Extract and Evaluation of Its Antioxidant Activity and Toxicity in Hepatocarcinoma (HepG2) and Fibroblast (F111) Cells

Tupistra nutans Wall. ex Lindl. is a medicinal plant found in the Eastern Himalayan region. Besides being used as a folk medicine for pain and high blood sugar, its inflorescence is consumed as a vegetable. However, its medicinal properties have not been proven in vitro and in vivo till now. Therefore, in this study, we reported the phytochemicals present in the methanolic extract of Tupistra nutans Wall. ex Lindl. inflorescence (METNI) and its comparative effect in liver carcinoma HepG2 cells against non-cancerous murine fibroblast F111 cells. Phytochemical profiling by gas chromatography-mass spectrometry (GC-MS) analysis showed that METNI was rich in unsaturated fatty acids, vitamin E, and anticancer compounds like diosgenin, linoleic acid, and palmitoleic acid. METNI was found to have in vitro antioxidant property as determined by DPPH and pyrogallol methods, and UV protection property as investigated by fluorescence-based and spectrophotometric methods. MTT assay revealed METNI caused significantly more cell proliferation inhibition in HepG2 (IC₅₀ = 138 µg/ml) compared to F111 (IC₅₀ = 347 µg/ml) cells. Although in both HepG2 and F111 cells METNI showed significant antioxidant activity, it led to intracellular ROS generation and cell cycle alteration at higher exposure. The obtained results suggest that Tupistra nutans can be a promising application for anticancer drug and skin care product development, but can be harmful if overconsumed.

Binding characteristics of Hg(II) with extracellular polymeric substances: implications for Hg(II) reactivity within periphyton

Periphyton contains extracellular polymeric substances (EPS), yet little is known about how periphyton EPS affect the speciation and mobility of mercury (Hg(II)) in aquatic systems. This study extracted and characterized EPS from periphyton in Florida Everglades, and explored its role in Hg(II) binding and speciation using multiple approaches. Results from Fourier transform infrared spectroscopy (FTIR) revealed that colloidal and capsular EPS were primarily comprised of proteins, polysaccharides, phospholipids, and nucleic acids. Ultrafiltration experiments demonstrated that 77 ± 7.7% and 65 ± 5.5% of Hg(II) in EPS solution could be transformed into colloidal and capsular EPS-bound forms. Three-dimensional excitation emission fluorescence spectra (3D-EEMs) showed that the binding constants (K_b) between colloidal/capsular EPS and Hg(II) were 3.47×10³ and 2.62×10³ L·mol^-1. Together with 3D-EEMs and FTIR, it was found that the protein-like and polysaccharide-like substances in EPS contributed to Hg(II) binding. For colloidal EPS, COO- was the most preferred Hg(II) binding group, while C-N, C-O-C, and C-OH were the most preferred ones in capsular EPS. Using the stannous-reducible Hg approach, it was found that EPS significantly decreased the reactive Hg(II). Overall, this study demonstrated that EPS from periphyton are important organic ligands for Hg(II) complexation, which may further affect the migration and reactivity of Hg(II) in aquatic environment. These observations could improve our understanding of Hg(II) methylation and accumulation within periphyton in aquatic systems.

Genomic analysis, simultaneous production, and process optimization of extracellular polymeric substances and polyhydroxyalkanoates by Methylobacterium sp. ISTM1 by utilizing molasses

In the current study, the isolated Methylobacterium sp. ISTM1 simultaneously produced both extracellular polymeric substances (EPS) and polyhydroxyalkanoates (PHA) in a single-step process. The yield of biopolymers (EPS and PHA) was enhanced by optimizing the process parameters of EPS and PHA production. Methylobacterium sp. ISTM1 was able to produce 7.18 ± 0.04 g L^-1 EPS and 1.41 ± 0.04 g L^-1 PHA simultaneously at optimized culture conditions i.e., 9% molasses and pH 7. The genomic analysis of the strain has identified the involved genes and pathways in the production of EPS and PHA. Both the biopolymers were found non-toxic according to the cytotoxicity analysis. The results of the current study present the potential of the bacterium Methylobacterium sp. ISTM1 produces non-toxic biopolymers by utilizing agro-industrial waste (molasses) that can be harnessed sustainably for various applications.

Degradation of dimethachlon by a newly isolated bacterium Paenarthrobacter sp. strain JH-1 relieves its toxicity against Chlorella ellipsoidea

Dimethachlon, a broad-spectrum dicarboximide fungicide, poses a hazard to the safety of human and ecosystem due to its residue in the environment. A high-efficient dimethachlon degrading bacteria JH-1 belonging to Paenarthrobacter sp. was isolated and characterized. Strain JH-1 can utilize high concentration of dimethachlon as sole carbon source for growth and degrade 98.53% of 300 mg·L^-1 dimethachlon within 72 h. Crude enzyme of strain JH-1 could degrade 99.76% of 100 mg·L^-1 dimethachlon within 2 h. The optimum degradation condition of dimethachlon by strain JH-1 was at 35 °C and pH 7.0. Dimethachlon was degraded in Paenarthrobacter sp. JH-1 as following: it was firstly converted to 4-(3,5-dichloroanilino)-4-oxobutanoic acid and then subjected to the hydrolysis to 3,5-dichloroaniline and succinic acid, the latter was further degraded. Dimethachlon inhibited the growth of Chlorella ellipsoidea, while Paenarthrobacter sp. JH-1 could degrade dimethachlon to relieve its toxicity. This work facilitates our knowledge of the degradation mechanism of dimethachlon and offers potential resource of microbial strains for the bioremediation of dimethachlon-contaminated environments in the future.

Biogeochemical profiling and taxonomic characterization of municipal landfill site by metagenomic sequencing

Most of the discarded waste material paves their way to the utmost common dumping grounds, Landfills. Despite their widespread use, the landfill microbiomes are still not well characterized. Metagenomics approach provides insight into the identification of operational parameters influencing the microbiome composition and their biodegradation competencies. The metagenomic DNA was prepared to explore taxonomical community structure, phylogenetic relationships, and functional profile at the same time. A total of 100,021,052 high-quality filtered reads were acquired with a GC abundance of 62.59%. Taxonomical abundance revealed the dominance of phylum Proteobacteria and genes involved in biomolecules metabolism, aromatic compound degradation, stress tolerance, xenobiotic biodegradation etc. were revealed functionally. The intricate heterogeneous environment of landfill revealed well flourished biogeochemical metabolic profiles including nitrogen metabolism. This is the first study for the generated metagenome of Ghazipur landfill and the obtained results propose that microbial communities in landfill settings are far more intricate than expected. It remain mostly unexplored which demands the usage of multiple platforms for a better understanding.

Agro-forestry waste management- A review

Agroforestry, an integration of farming system with woody perennials leads to the generation of potential agroforestry residues. The conventional treatment of agroforestry waste includes landfilling, thermal management, and decomposition which is accompanied with their own share of disadvantages. The ample amount of residues and products needs effective management to reap the economic and environmental benefits. The channel of waste collection, transportation, and recycle or valorization into products like biofuel, fertilizers, biochar, industrial chemicals is essential to maintain a circular sustainable bioeconomy. Global market value of biowaste to bioenergy (BtB) technology is roughly US $25.32 billion and is projected to enhance to US $40 billion by 2023. Employment of an appropriate pretreatment technology such as fermentation, hydrolysis, gasification etc. is going to elevate the degree of valorization along with surpassing the mobilization barrier. The sustainability assessment of the management process can be achieved with multiple models including technoeconomic analysis, life cycle assessment and multi criteria approach which are dependent on both hard and soft indices. Additionally, the loopholes of the agroforestry sectors would be managed by the introduction of appropriate policies which are undertaken globally by the Orlando and Lugo declarations, food and agriculture organization, Millennium Development Goals, Global Research Alliance and Guidelines for Sustainable Agriculture and Rural Development. The present review envisaged the agroforestry waste management strategy and its sustainability assessment primarily based upon Social, Economic and Environmental parameters without tormenting the future generations.

Unravelling the attributes of novel cyanobacteria Jacksonvillea sp. ISTCYN1 by draft genome sequencing

Filamentous cyanobacteria, Jacksonvillea sp. ISTCYN1 was isolated from agriculture field and cultured in BG-11 medium. This study, report the genome sequence of cyanobacteria Jacksonvillea thatto the best of our knowledgeis the firstgenome sequenceof thisgenus. The 5.7 MB draft genome sequence of this cyanobacterium contains 5134 protein-coding genes. The phylogenetic tree was constructed based on genome and Desertifilum sp. IPPAS B-1220 validated the closest relationship with Jacksonvillea sp. ISTCYN1. The growth of strain ISTCYN1 has been reported in the presence of different types of plastic when used as a sole carbon source. SEM analysis revealed biofilm formation by cyanobacterial strain ISTCYN1 on the surface of high and low-density polyethylene and polypropylene. In the presence of these plastics, EPS production has also been reported by this strain. Whole genome sequence analysis reveals the presence of many genes involved in biofilm formation. The presence of key enzymes responsible for plastic degradation laccase, esterase, lipase, thioesterase, and peroxidase have been predicted in the genome analysis. Genome analysis also provides insight into the genes involved in biotin biosynthetic pathways. Furthermore, the presence of many selenoproteins reveals the selenium acquisition by this cyanobacterium.

Production, characterization and bio-emulsifying application of exopolysaccharides from Rhodotorula mucilaginosa YMM19

Microbial exopolysaccharides (EPS) are high molecular weight polymers having different sugar residues. EPS have potential applications in different fields, such as medicine, food and environment. Therefore, there is a growing interest in production, characterization and application of EPS from different microorganisms. The present study designed to investigate the production and characterization of EPS from Rhodotorula mucilaginosa YMM19 isolated from Morus nigra L. fruits as well as to examine their potential emulsifying properties. Effect of NaCl concentration, incubation period and pH on the production of EPS was studied. The maximum EPS production by yeast was achieved at 10% NaCl (9741.84 mg/l). The best incubation time for production of EPS was 5 days. Production of EPS decreased under neutral condition and increased at acidic and alkaline condition. The structural feature of EPS was examined by FT-IR and NMR spectral analysis and confirmed the presence of glucose, glucopyranose and galactose. The isolated EPS showed higher emulsification capacity with emulsification activity of 71% and emulsifying index of 60%. The EPS gave strong emulsification for farnesol and was more effective than sodium dodecyl sulphate, a reference emulsifier, in enhancing the herbicidal activity of farnesol against Melilotus indicus under greenhouse condition. The results suggest that the EPS produced by YMM19 strain has a potential to be used as emulsifying agent in pesticide formulations.