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  1. Fulltext Recent Understanding of Soil Acidobacteria and Their Ecological Significance: A Critical Review
    Kalam S, Basu A, Ahmad I, Sayyed RZ, El-Enshasy HA, Dailin DJ, et al.
    Front Microbiol, 2020;11:580024.
    PMID: 33193209 DOI: 10.3389/fmicb.2020.580024
    Acidobacteria represents an underrepresented soil bacterial phylum whose members are pervasive and copiously distributed across nearly all ecosystems. Acidobacterial sequences are abundant in soils and represent a significant fraction of soil microbial community. Being recalcitrant and difficult-to-cultivate under laboratory conditions, holistic, polyphasic approaches are required to study these refractive bacteria extensively. Acidobacteria possesses an inventory of genes involved in diverse metabolic pathways, as evidenced by their pan-genomic profiles. Because of their preponderance and ubiquity in the soil, speculations have been made regarding their dynamic roles in vital ecological processes viz., regulation of biogeochemical cycles, decomposition of biopolymers, exopolysaccharide secretion, and plant growth promotion. These bacteria are expected to have genes that might help in survival and competitive colonization in the rhizosphere, leading to the establishment of beneficial relationships with plants. Exploration of these genetic attributes and more in-depth insights into the belowground mechanics and dynamics would lead to a better understanding of the functions and ecological significance of this enigmatic phylum in the soil-plant environment. This review is an effort to provide a recent update into the diversity of genes in Acidobacteria useful for characterization, understanding ecological roles, and future biotechnological perspectives.
  2. Investigating the crude oil biodegradation performance in bioreactor by using a consortium of symbiotic bacteria
    Chuah LF, Nawaz A, Dailin DJ, Oloruntobi O, Habila MA, Tong WY, et al.
    Chemosphere, 2023 Oct;337:139293.
    PMID: 37369285 DOI: 10.1016/j.chemosphere.2023.139293
    Crude oil pollution is one of the most serious environmental issues today, and the clean-up procedure is perhaps the most difficult. Within one to three weeks, the vast majority of oil bacteria may degrade approximately 60% of the crude oil, leaving approximately 40% intact. The by-product metabolites produced during the breakdown of oil are essentially organic molecules in nature. These metabolites inhibit its enzymes, preventing the oil bacteria from further degrading the oil. By combining a variety of different oils with heterotrophic bacteria in a bioreactor, the rate of crude oil biodegradation was accelerated. In this study, two strains of oil-resistant, heterotrophic bacteria (OG1 and OG2-Erythrobacter citreus) and a bacterium that uses hydrocarbons (AR3-Pseudomonas pseudoalcaligenes) were used. Gas chromatography-mass spectroscopy was used to investigate the effectiveness of this consortium of symbiotic bacteria in the biodegradation of crude oil. According to gravimetric and gas chromatography analyses, the consortium bacteria digested 69.6% of the crude oil in the bioreactor, while the AR3 single strain was only able to destroy 61.9% of it. Under the same experimental conditions, consortium bacteria degraded approximately 84550.851 ppb (96.3%) of 16 aliphatic hydrocarbons and 9333.178 ppb (70.5%) of 16 aromatic hydrocarbons in the bioreactor. It may be inferred that the novel consortium of symbiotic bacteria accelerated the biodegradation process and had great potential for use in increasing the bioremediation of hydrocarbon-contaminated locations.
  3. Fulltext Tree bark scrape fungus: A potential source of laccase for application in bioremediation of non-textile dyes
    Sayyed RZ, Bhamare HM, Sapna, Marraiki N, Elgorban AM, Syed A, et al.
    PLoS One, 2020;15(6):e0229968.
    PMID: 32497077 DOI: 10.1371/journal.pone.0229968
    Although laccase has been recognized as a wonder molecule and green enzyme, the use of low yielding fungal strains, poor production, purification, and low enzyme kinetics have hampered its large-scale application. Thus,this study aims to select high yielding fungal strains and optimize the production, purification, and kinetics of laccase of Aspergillus sp. HB_RZ4. The results obtained indicated that Aspergillus sp. HB_RZ4 produced a significantly large amount of laccase under meso-acidophilic shaking conditions in a medium containing glucose and yeast extract. A 25 μM CuSO4 was observed to enhance the enzyme yield. The enzyme was best purified on a Sephadex G-100 column. The purified enzyme resembled laccase of A. flavus. The kinetics of the purified enzyme revealed high substrate specificity and good velocity of reaction,using ABTS as a substrate. The enzyme was observed to be stable over various pH values and temperatures. The peptide structure of the purified enzyme was found to resemble laccase of A. kawachii IFO 4308. The fungus was observed to decolorize various dyes independent of the requirement of a laccase mediator system.Aspergillus sp. HB_RZ4 was observed to be a potent natural producer of laccase, and it decolorized the dyes even in the absence of a laccase mediator system. Thus, it can be used for bioremediation of effluent that contains non-textile dyes.
  4. Fulltext Bioprocess development for kefiran production by Lactobacillus kefiranofaciens in semi industrial scale bioreactor
    Dailin DJ, Elsayed EA, Othman NZ, Malek R, Phin HS, Aziz R, et al.
    Saudi J Biol Sci, 2016 Jul;23(4):495-502.
    PMID: 27298582 DOI: 10.1016/j.sjbs.2015.06.003
    Lactobacillus kefiranofaciens is non-pathogenic gram positive bacteria isolated from kefir grains and able to produce extracellular exopolysaccharides named kefiran. This polysaccharide contains approximately equal amounts of glucose and galactose. Kefiran has wide applications in pharmaceutical industries. Therefore, an approach has been extensively studied to increase kefiran production for pharmaceutical application in industrial scale. The present work aims to maximize kefiran production through the optimization of medium composition and production in semi industrial scale bioreactor. The composition of the optimal medium for kefiran production contained sucrose, yeast extract and K2HPO4 at 20.0, 6.0, 0.25 g L(-1), respectively. The optimized medium significantly increased both cell growth and kefiran production by about 170.56% and 58.02%, respectively, in comparison with the unoptimized medium. Furthermore, the kinetics of cell growth and kefiran production in batch culture of L. kefiranofaciens was investigated under un-controlled pH conditions in 16-L scale bioreactor. The maximal cell mass in bioreactor culture reached 2.76 g L(-1) concomitant with kefiran production of 1.91 g L(-1).
  5. Unleashing the potential of xanthan: a comprehensive exploration of biosynthesis, production, and diverse applications
    Rashidi AR, Azelee NIW, Zaidel DNA, Chuah LF, Bokhari A, El Enshasy HA, et al.
    Bioprocess Biosyst Eng, 2023 Apr 08.
    PMID: 37029808 DOI: 10.1007/s00449-023-02870-9
    Employing aerobic fermentation, Gram-negative bacteria belonging to the genus Xanthomonas produce the high molecular weight natural heteropolysaccharide known as xanthan. It has various amounts of O-acetyl and pyruvyl residues together with D-glucosyl, D-mannosyl, and D-glucuronyl acid residues in a molar ratio of 2:2:1. The unique structure of xanthan allowed its various applications in a wide range of industries such as the food industry, pharmacology, cosmetics and enhanced oil recovery primarily in petroleum. The cultivation medium used in the manufacture of this biopolymer is critical. Many attempts have been undertaken to generate xanthan gum from agro-based and food industry wastes since producing xanthan gum from synthetic media is expensive. Optimal composition and processing parameters must also be considered to achieve an economically viable manufacturing process. There have been several attempts to adjust the nutrient content and feeding method, temperature, pH, agitation and the use of antifoam in xanthan fermentations. Various modifications in technological approaches have been applied to enhance its physicochemical properties which showed significant improvement in the area studied. This review describes the biosynthesis production of xanthan with an emphasis on the importance of the upstream processes involving medium, processing parameters, and other factors that significantly contributed to the final application of this precious polysaccharide.
  6. Development of sodium alginate-pectin biodegradable active food packaging film containing cinnamic acid
    Tong WY, Ahmad Rafiee AR, Leong CR, Tan WN, Dailin DJ, Almarhoon ZM, et al.
    Chemosphere, 2023 Sep;336:139212.
    PMID: 37315854 DOI: 10.1016/j.chemosphere.2023.139212
    Plastics are still the most popular food packaging material and many of them end up in the environment for a long period. Due to packaging material's inability to inhibit microbial growth, beef often contains microorganisms that affect its aroma, colour and texture. Cinnamic acid is categorized as generally recognised as safe and is permitted for use in food. The development of biodegradable food packaging film with cinnamic acid has never been conducted before. This present study was aimed to develop a biodegradable active packaging material for fresh beef using sodium alginate and pectin. The film was successfully developed with solution casting method. The films' thickness, colour, moisture level, dissolution, water vapour permeability, bending strength and elongation at break were comparable to those of polyethylene plastic film in terms of these attributes. The developed film also showed the degradability in soil of 43.26% in a duration of 15 days. Fourier Transform Infrared (FTIR) spectra showed that cinnamic acid was successfully incorporated with the film. The developed film showed significant inhibitory activity on all test foodborne bacteria. On Hohenstein challenge test, a 51.28-70.45% reduction on bacterial growth was also observed. The antibacterial efficacy of the established film by using fresh beef as food model. The meats wrapped with the film showed significant reduction in bacterial load throughout the experimental period by 84.09%. The colour of the beef also showed significant different between control film and edible film during 5 days test. Beef with control film turned into dark brownish and beef with cinnamic acid turn into light brownish. Sodium alginate and pectin film with cinnamic acid showed good biodegradability and antibacterial activity. Further studies can be conducted to investigate the scalability and commercial viability of this environmental-friendly food packaging materials.
  7. Fulltext The Effect of Some Wild Grown Plant Extracts and Essential Oils on Pectobacterium betavasculorum: The Causative Agent of Bacterial Soft Rot and Vascular Wilt of Sugar Beet
    Rastgou M, Rezaee Danesh Y, Ercisli S, Sayyed RZ, El Enshasy HA, Dailin DJ, et al.
    Plants (Basel), 2022 Apr 25;11(9).
    PMID: 35567156 DOI: 10.3390/plants11091155
    The bacterial soft rot and vascular wilt of sugar beet are the major diseases of sugar crops globally induced by Pectobacterium betavasculorum and P. carotovorum subsp. carotovorum (Pcc). The control of this bacterial disease is a severe problem, and only a few copper-based chemical bactericides are available for this disease. Because of the limitations of chemicals to control plant bacterial pathogens, the essential oils and extracts have been considered one of the best alternative strategies for their control. In this study, twenty-seven essential oils and twenty-nine plant extracts were extracted and evaluated for their antibacterial activities against Pectobacterium betavasculorum isolate C3, using the agar diffusion method at 0.01%, 0.1%, and 100% (v/v). Pure Pimpinella anisum L. oil exhibited the most anti-bacterial activity among three different concentrations of essential oils and extracts, followed by Thymus vulgaris L. oil and Rosa multiflora Thunb. extract. The efficacy of effective essential oils and extracts on Ic1 cultivar of sugar beet seeds germination and seedling growth in vivo also were tested. The seed germination of the Ic1 cultivar was inhibited at all the concentrations of essential oils used. Only extracts of Rosa multiflora Thunb., Brassica oleracea L., Lactuca serriola L., Salvia rosmarinus Spenn., Syzygium aromaticum (L.) Merr. and L.M.Perry, Eucalyptus globulus Labill., and essential oils of Ocmium basilicum L., Pimpinella anisum L., and Mentha× piperita L.L. in 0.1% concentration had no inhibition on seed germination and could improve seedling growth. This is the first report of the antibacterial activity of essential oils and extracts on Pectobacterium betavasculorum.
  8. Evaluation on microalgae for the production of bio-chemicals and electricity
    Khairuddin F, Zaharah Mohd Fuzi SF, Ahmad A, Oon LK, Bokhari A, Dailin DJ, et al.
    Chemosphere, 2024 Feb;350:141007.
    PMID: 38141667 DOI: 10.1016/j.chemosphere.2023.141007
    Recent advancement in biophotovoltaic systems using microalgae, coupled with biorefinery approach, would improve economy-feasibility in production. The major concern is its commercial strength in terms of scalability, strain selection and extraction procedure cost. It must compete with conventional feedstocks such as fossil fuels. This project proposes to enhance the economic feasibility of microalgae-based biorefinery by evaluating their performance for bio-electricity, bio-diesel and carotenoids production in a single cycle. The first part of the study was to construct and select a Bio-bottle Voltaic (BBV) device that would allow microalgae to grow and produce bioproducts, as well as generate the maximum current output reading derived from the microalgae's photosynthesis process. The second phase consisted of a 25-day investigation into the biorefinery performance of six different microalgal species in producing bio-electricity, bio-diesel and carotenoid in a prototype BBV device. The prototype BBV device with aluminium foil and pencil lead as its anode and cathode produced the highest carotenoid and biodiesel component production from the two microalgae tested, according to the results of the first phase of the experiment. In the second portion of the study, Scenedesmus dimorphus and Chlorella vulgaris were identified as the two microalgae most capable of maintaining their growth throughout the experiment. The maximum current reading observed for C. vulgaris was 653 mV. High Performance Liquid Chromatography analysis showed four major carotenoid compounds found which were Neoxanthin, Cantaxanthin, Astaxanthin and 9-cis antheraxanthin, and the highest carotenoid producer was C. vulgaris which recorded at 1.73 μg/mL. C. vulgaris recorded as the most alkanes producer with 22 compounds detected and Heptacosane and Heneicosane as the two major biodiesel compounds found in the extracts. Evaluation of C. vulgaris data showed that it has enormous potential for microalgal biorefinery candidates. Further ongoing research and development efforts for C. vulgaris will improve the economic viability of microalgae-based industries and reduce reliance on depleted fossil fuels.
  9. Antifungal Mechanism of Rhodotorula mucilaginosa and Aureobasidium sp. nov. Isolated from Cerbera manghas L. against the Growth of Destructive Molds in Post Harvested Apples
    Sukmawati D, Shabrina A, Indrayanti R, Kurniati TH, Nurjayadi M, Hidayat I, et al.
    Recent Pat Food Nutr Agric, 2020;11(3):219-228.
    PMID: 32324527 DOI: 10.2174/2212798411666200423101159
    BACKGROUND: Apples often experience postharvest damage due to being attacked by mold organisms. Several groups of molds such as Aspergillus sp., Penicilium expansum, Botrytis cinerea, and Venturia sp. can cause a serious postharvest disease exhibited as watery regions where areas of blue-green tufts of spores develop. Current methods using fungicides to control pathogenic fungi can cause resistance if applied in the long term. An alternative procedure using yeast as a biological agent has been found.

    OBJECTIVE: The aim of this study is to screen potential yeast, which has the ability to inhibit the growth of Aspergillus brasielensis (isolate A1) and Aspergillus flavus section flavi (isolate A17) isolated from apple fruits.

    METHODS: Antagonism test using YMA dual culture medium using in vitro assays and ITS rDNA identification were performed.

    RESULTS: The result showed that 3 out of 19 yeast isolated from Cerbera manghas L, T1, T3 and T4, demonstrated the potential ability as a biocontrol agent. ITS rDNA identification demonstrated that T1 has a similarity to Rhodotorula mucilaginosa while T3 and T4 were identified as Aureobasidium sp. nov. The 3 isolates exhibited the ability to reduce the growth of A. brasiliensis sensu lato better than dithane 0.3% with a Disease Incidence (DI) of 100% and a Disease Severity (DS) value of 45%. Only isolate T1 and T3 were able to reduce decay symptoms in apples inoculated with A. flavus sensu lato (with DO and DS were 100% and 25%, respectively) compared to dithane pesticides 0.3%.

    CONCLUSION: This study indicated that competition between nutrients occurs between pathogenic molds and under-yeast in vitro and in vivo conditions. However, further studies in the future might be able to elucidate the 'killer' activity and interaction with the pathogen cells and the bio-product production using Rhodotorula mucilaginosa and Aureoubasidium namibiae strains to control postharvest diseases.

  10. Fulltext Multifarious Indigenous Diazotrophic Rhizobacteria of Rice (Oryza sativa L.) Rhizosphere and Their Effect on Plant Growth Promotion
    Mir MI, Hameeda B, Quadriya H, Kumar BK, Ilyas N, Kee Zuan AT, et al.
    Front Nutr, 2021;8:781764.
    PMID: 35096930 DOI: 10.3389/fnut.2021.781764
    A diverse group of rhizobacteria persists in the rhizospheric soil, on the surface of roots, or in association with rice plants. These bacteria colonize plant root systems, enhance plant growth and crop yield. Indigenous rhizobacteria are known to promote soil health, grain production quality and serve as sustainable bioinoculant. The present study was aimed to isolate, identify and characterize indigenous plant growth promoting (PGP) diazotrophic bacteria associated with the rhizosphere of rice fields from different areas of Jammu and Kashmir, India. A total of 15 bacteria were isolated and evaluated for various PGP traits, antagonistic activity against phytopathogens, production of hydrolytic enzymes and biofilm formation under in-vitro conditions. The majority of the isolated bacteria were Gram-negative. Out of 15 bacterial isolates, nine isolates produced IAA (12.24 ± 2.86 to 250.3 ± 1.15 μg/ml), 6 isolates exhibited phosphate solubilization activity (36.69 ± 1.63 to 312.4 ± 1.15 μg/ml), 7 isolates exhibited rock phosphate solubilization while 5 isolates solubilized zinc (10-18 mm), 7 isolates showed siderophore production, 8 isolates exhibited HCN production, 6 isolates exhibited aminocyclopropane-1-carboxylate (ACC) deaminase activity, 13 isolates exhibited cellulase activity, nine isolates exhibited amylase and lipase activity and six isolates exhibited chitinase activity. In addition, 5 isolates showed amplification with the nifH gene and showed a significant amount of nitrogenase activity in a range of 0.127-4.39 μmol C2H4/mg protein/h. Five isolates viz., IHK-1, IHK-3, IHK-13, IHK-15 and IHK-25 exhibited most PGP attributes and successfully limited the mycelial growth of Rhizoctonia solani and Fusarium oxysporum in-vitro. All the five bacterial isolates were identified based on morphological, biochemical and 16S rDNA gene sequencing study, as Stenotrophomonas maltophilia, Enterobacter sp., Bacillus sp., Ochrobactrum haematophilum and Pseudomonas aeruginosa. Rice plants developed from seeds inoculated with these PGP strains individually had considerably higher germination percentage, seed vigor index and total dry biomass when compared to control. These findings strongly imply that the PGP diazotrophic bacteria identified in this work could be employed as plant growth stimulators in rice.
  11. Nanoparticle-laden contact lens for controlled release of vancomycin with enhanced antibiotic efficacy
    Tong WY, Tan WN, Kamarul Azizi MA, Leong CR, El Azab IH, Lim JW, et al.
    Chemosphere, 2023 Oct;338:139492.
    PMID: 37451643 DOI: 10.1016/j.chemosphere.2023.139492
    Vancomycin is the last resort antibiotic for the treatment of severe bacterial keratitis. Its clinical application is limited due to its hydrophilicity and high molecular weight. To overcome this, this study aims to develop nanoparticles-laden contact lens for controlled ocular delivery of vancomycin. Polyvinyl alcohol (PVA) was used as encapsulant material. The nanoparticles had a negative surface charge and an average size of 147.6 nm. A satisfactory encapsulation efficiency (61.24%) was obtained. The release profile was observed to be slow and sustained, with a release rate of 1.29 μL mg-1 h-1 for 48 h. Five out of 6 test bacteria were suppressed by vancomycin nanoparticles-laden contact lens. Vancomycin is generally ineffective against Gram-negative bacteria and unable to pass through the outer membrane barrier. In this study, vancomycin inhibited Proteus mirabilis and Pseudomonas aeruginosa. Nano-encapsulation enables vancomycin to penetrate the Gram-negative cell wall and further destroy the bacterial cells. On Hohenstein challenge test, all test bacteria exhibited significant reduction in growth when exposed to vancomycin nanoparticles-laden contact lens. This study created an effective and long-lasting vancomycin delivery system via silicone hydrogel contact lenses, by using PVA as encapsulant. The antibiotic efficacy and vancomycin release should be further studied using ocular in vivo models.
  12. Physicochemical and thermal characteristics of choline chloride-based deep eutectic solvents
    Sazali AL, AlMasoud N, Amran SK, Alomar TS, Pa'ee KF, El-Bahy ZM, et al.
    Chemosphere, 2023 Oct;338:139485.
    PMID: 37442394 DOI: 10.1016/j.chemosphere.2023.139485
    It is essential to investigate the physicochemical and thermal properties of choline chloride (ChCl)-based deep eutectic solvents (DESs) as hydrogen bond acceptor (HBA) with various hydrogen bond donor (HBD) functional groups, such as α-hydroxy acid (lactic acid) or polyol (glycerol). It is important to consider how molar ratios impact these properties, as they may be altered for particular applications. This study aimed to examine the physicochemical and thermal properties of ChCl-based DESs with lactic acid (LA) or glycerol (Gly) at different molar ratios (1:2-1:10). The pH of ChCl:LA (0-1.0) is lower than that of ChCl:Gly (4.0-5.0) because of the hydrogen bonds between ChCl and LA. A higher amount of LA/Gly resulted in higher densities of ChCl:Gly (1.20-1.22 g cm-3) and ChCl:LA (1.16-1.19 g cm-3) due to the stronger hydrogen bonds and tighter packing of the molecules. The refractive index of ChCl:Gly (1.47-1.48) was higher than ChCl:LA (1.44-1.46), with a trend similar to density. The viscosities of ChCl:Gly (0.235-0.453 Pa s) and ChCl:LA (0.04-0.06 Pa s) increased with increasing LA/Gly molar ratio but decreased with temperature due to the high kinetic energy from heating, lowering the attractive forces between molecules. The activation energy for ChCl:LA (15.29-15.55 kJ mol-1) is greater than for ChCl:Gly (7.77-8.78 kJ mol-1), indicating that ChCl:LA has a greater viscosity-temperature dependence than ChCl:Gly. The DESs decomposition temperatures are 179.73-192.14 °C for ChCl:LA and 189.69-197.41 °C for ChCl:Gly. Freezing temperatures are correlated with the molecular weight of HBDs, with lower values causing a larger decrease in freezing temperatures. The interactions of polyols with anions were stronger than those of α-hydroxy acids with anions. The variations in HBA to HBD molar ratios affected DESs properties, providing a fundamental understanding of the properties critical for their diverse applications.
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