Nur Adeela Yasid

Bio: Nur Adeela Yasid is an academic researcher from Universiti Putra Malaysia. The author has contributed to research in topics: Chemistry & Bioremediation. The author has an hindex of 10, co-authored 51 publications receiving 298 citations. Previous affiliations of Nur Adeela Yasid include University of Sheffield.

Rhizodegradation of Petroleum Oily Sludge-contaminated Soil Using Cajanus cajan Increases the Diversity of Soil Microbial Community

Abstract: Most components of petroleum oily sludge (POS) are toxic, mutagenic and cancer-causing. Often bioremediation using microorganisms is hindered by the toxicity of POS. Under this circumstance, phytoremediation is the main option as it can overcome the toxicity of POS. Cajanus cajan a legume plant, was evaluated as a phyto-remediating agent for petroleum oily sludge-spiked soil. Culture dependent and independent methods were used to determine the rhizosphere microorganisms’ composition. Degradation rates were estimated gravimetrically. The population of total heterotrophic bacteria (THRB) was significantly higher in the uncontaminated soil compared to the contaminated rhizosphere soil with C. cajan, but the population of hydrocarbon-utilizing bacteria (HUB) was higher in the contaminated rhizosphere soil. The results show that for 1 to 3% oily sludge concentrations, an increase in microbial counts for all treatments from day 0 to 90 d was observed with the contaminated rhizosphere CR showing the highest significant increase (p < 0.05) in microbial counts compared to other treatments. The metagenomic study focused on the POS of 3% (w/w) and based on the calculated bacterial community abundance indices showed an increase in the values for Ace, Cho, Shannon (Shannon-Weaver) and the Simpson’s (measured as InvSimpson) indices in CR3 compared to CN3. Both the Simpson’s and the Shannon values for CR3 were higher than CN3 indicating an increase in diversity upon the introduction of C. cajan into the contaminated soil. The PCoA plot revealed community-level differences between the contaminated non-rhizosphere control and contaminated rhizosphere microbiota. The PCoA differentiated the two treatments based on the presence or absence of plant. The composition and taxonomic analysis of microbiota-amplified sequences were categorized into eight phyla for the contaminated non-rhizosphere and ten phyla for the contaminated rhizosphere. The overall bacterial composition of the two treatments varied, as the distribution shows a similar variation between the two treatments in the phylum distribution. The percentage removal of total petroleum hydrocarbon (TPH) after 90 days of treatments with 1, 2, 3, 4, and 5% (w/w) of POS were 92, 90, 89, 68.3 and 47.3%, respectively, indicating removal inhibition at higher POS concentrations. As the search for more eco-friendly and sustainable remediating green plant continues, C. cajan shows great potential in reclaiming POS contaminated soil. Our findings will provide solutions to POS polluted soils and subsequent re-vegetation.

Biodeterioration of Untreated Polypropylene Microplastic Particles by Antarctic Bacteria.

Abstract: Microplastic pollution is globally recognised as a serious environmental threat due to its ubiquitous presence related primarily to improper dumping of plastic wastes. While most studies have focused on microplastic contamination in the marine ecosystem, microplastic pollution in the soil environment is generally little understood and often overlooked. The presence of microplastics affects the soil ecosystem by disrupting the soil fertility and quality, degrading the food web, and subsequently influencing both food security and human health. This study evaluates the growth and biodegradation potential of the Antarctic soil bacteria Pseudomonas sp. ADL15 and Rhodococcus sp. ADL36 on the polypropylene (PP) microplastics in Bushnell Haas (BH) medium for 40 days. The degradation was monitored based on the weight loss of PP microplastics, removal rate constant per day (K), and their half-life. The validity of the PP microplastics’ biodegradation was assessed through structural changes via Fourier transform infrared spectroscopy analyses. The weight loss percentage of the PP microplastics by ADL15 and ADL36 after 40 days was 17.3% and 7.3%, respectively. The optimal growth in the BH media infused with PP microplastics was on the 40th and 30th day for ADL15 and ADL36, respectively. The infrared spectroscopic analysis revealed significant changes in the PP microplastics’ functional groups following the incubation with Antarctic strains.

Biodegradation of phenol by cold-adapted bacteria from Antarctic soils

Abstract: Phenol is an important pollutant widely discharged as a component of hydrocarbon fuels, but its degradation in cold regions is a great challenge due to the harsh environmental conditions. To date, there is little information available concerning the biodegradation of phenol by indigenous Antarctic bacteria. This study addresses the isolation of three phenol-degrading bacterial strains from King George Island, Antarctica. Based on preliminary screening, three isolates (AQ5-05, AQ5-06 and AQ5-07) capable of completely degrading 0.5 g/L phenol within 120 h at 10 °C were selected for detailed study. Two were identified as Arthrobacter spp., and one Rhodococcus sp., based on 16S rRNA sequences. All strains were non-motile, Gram positive, oxidase negative and catalase positive. A study on the effects of parameters including temperature, pH, salinity and nitrogen source was conducted to optimise the conditions for phenol degradation. This revealed that the three isolates were psychrotolerant with the optimum temperature for phenol degradation between 10 and 15 °C. This study suggests the potential use of cold-adapted bacteria in the bioremediation of phenol over a wide range of low temperatures.

Toxic effects of copper on liver and cholinesterase of Clarias gariepinus

Abstract: The release of pollutants, especially heavy metals, into the aquatic environment is known to have detrimental effects on such an environment and on living organisms including humans when those pollutants are allowed to enter the food chain. The aim of this study is to analyse the damage to Clarias gariepinus' liver caused by exposure to different concentrations of copper. In the present study, samples of C. gariepinus were exposed to sub-lethal copper sulphate (CuSO4) concentrations (from 0.2 to 20.0 mg/L) for 96 h. Physiological and behavioural alterations were observed with respect to their swimming pattern, mucus secretion and skin colour. Mortality was also observed at high concentrations of copper. Histopathological alterations of the liver were analysed under light, transmission and scanning electron microscopies. The liver of the untreated group showed normal tissue structures, while histopathological abnormalities were observed in the treated fish under light and electron microscopes with increased copper concentrations. Histopathological abnormalities include necrosis, melanomacrophage, hepatic fibrosis and congested blood vessels. In addition, the enzyme activity of liver cholinesterase (ChE) was also found to be affected by copper sulphate, as 100% of cholinesterase activity was inhibited at 20.0 mg/L. Thus, liver enzyme activity and histopathological changes are proven to be alternative sources for biomarkers of metal toxicity.

Isolation and characterisation of glyphosate-degrading bacteria isolated from local soils in Malaysia

Abstract: Glyphosate (N-(phosphonomethyl)glycine) is a herbicide that is used to kill broadleaf weeds and grass, which was developed by the Monsanto company in the early 1970s. However, excessive usage of glyphosate in the agricultural field has led to soil accumulation of the pesticides causing various adverse effects. Due to the concern on its toxicity, an alternative way to ease its effect is through bioremediation, which exploits the ability of microorganisms to degrade harmful toxic substances into less toxic forms. Seven different microbial strains were isolated from glyphosate-contaminated sites in Malaysia. These strains were able to grow in a medium containing glyphosate as the sole phosphorus source. None of the strains were able to grow when glyphosate was introduced as a sole carbon source. Two microbial strains: AQ5–12 and AQ5–13, were found to be the best degraders among them as they were able to withstand up to 12 ml/L of the Roundup® glyphosate formulation and 200 ppm of analytical grade glyphosate. Based on 16s rRNA and biochemical tests, AQ5–12 was identified as Burkholderia vietnamiensis, whereas AQ5–13 was identified as Burkholderia sp. AQ5–12, with the latter possessing better degradation capability compared to AQ5–13 with utilisation of 91 and 74% of 50 ppm glyphosate, respectively. The best optimum degradation conditions were seen at the temperature of 30 °C and a pH of 6 for both strains. Based on these results, both strains displayed their potential to be used in the bioremediation of glyphosate-contaminated environment.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

Phytoremediation : 植物による環境/土壌浄化

Abstract: In addition to the often-cited advantages of using Arabidopsis thaliana as a model system in plant biological research (1), Arabidopsis has many additional characteristics that make it an attractive experimental organism for studying lea d (Pb) accumulation and tolerance in plants. These include its fortuitous familial relationship to many known metal hyperaccumulators (Brassicaceae), as well as similar Pbaccumulation patterns to most other plants. Using nutrient-agar plates, hydroponic culture, and Pb-contaminated soils as growth media, we found significant variation in Arabidopsis thaliana ecotypes in accumulation and tolerance of Pb. In addition, we have found that Pb accumulation is not obligatorily linked with Pb tolerance, suggesti ng that different genetic factors control these two processes. We also screened ethyl methanesulfonate-mutagenized M2 populations and identified several Pb-accumulating mutants. Current characterization of these mutants indicates that their phenotypes are likely due to alteration of general metal ion uptake or translocation processes since these mutants also accumulate many other metals in shoots. We expect that further characterization of the ecotypes and mutants will shed light on the basic genetic and physiological underpinnings of plant-based Pb remediation. 7. Aromatic nitroreduction of acifluorfen in soils, rhizospheres, and pure cultures of rhizobacteria. Zablotowicz, R. M., Locke, M. A., and Hoagland, R. E. Phytoremediation of soil and water contaminants. Washington, DC : American Chemical Society, 1997. p. 38-53. NAL Call #: QD1.A45-no.664 Abstract: Reduction of nitroaromatic compounds to their corresponding amino derivatives is one of several pathways in the degradation of nitroxenobiotics. Our studies with the nitrodiphenyl ether herbicide acifluorfen showed rapid metabolism to am inoacifluorfen followed by incorporation into unextractable soil components in both soil and rhizosphere suspensions. Aminoacifluorfen was formed more rapidly in rhizospheres compared to soil, which can be attributed to higher microbial populations, espec ially of Gram-negative bacteria. We identified several strains of Pseudomonas fluorescens that possess nitroreductase activity capable of converting acifluorfen to aminoacifluorfen. Factors affecting acifluorfen nitroreductase activity in pure cultures an d cell-free extracts, and other catabolic transformations of acifluorfen, ether bond cleavage, are discussed. Plant rhizospheres should be conducive for aromatic nitroreduction. Nitroreduction by rhizobacteria is an important catabolic pathway for the ini tial degradation of various nitroherbicides and other nitroaromatic compounds in soils under Reduction of nitroaromatic compounds to their corresponding amino derivatives is one of several pathways in the degradation of nitroxenobiotics. Our studies with the nitrodiphenyl ether herbicide acifluorfen showed rapid metabolism to am inoacifluorfen followed by incorporation into unextractable soil components in both soil and rhizosphere suspensions. Aminoacifluorfen was formed more rapidly in rhizospheres compared to soil, which can be attributed to higher microbial populations, espec ially of Gram-negative bacteria. We identified several strains of Pseudomonas fluorescens that possess nitroreductase activity capable of converting acifluorfen to aminoacifluorfen. Factors affecting acifluorfen nitroreductase activity in pure cultures an d cell-free extracts, and other catabolic transformations of acifluorfen, ether bond cleavage, are discussed. Plant rhizospheres should be conducive for aromatic nitroreduction. Nitroreduction by rhizobacteria is an important catabolic pathway for the ini tial degradation of various nitroherbicides and other nitroaromatic compounds in soils under phytoremediation management. 8. Ascorbate: a biomarker of herbicide stress in wetland plants. Lytle, T. F. and Lytle, J. S. Phytoremediation of soil and water contaminants. Washington, DC : American Chemical Society, 1997. p. 106-113. NAL Call #: QD1.A45-no.664 Abstract: In laboratory exposures of wetland plants to low herbicide levels (<0.1 micrograms/mL), some plants showed increased total ascorbic acid suggesting a stimulatory effect on ascorbic acid synthesis occurred; at higher herbicide conce ntrations (greater than or equal to 0.1 micrograms/mL) a notable decline in total ascorbic acid and increase in the oxidized form, dehydroascorbic acid occurred. Vigna luteola and Sesbania vesicaria were exposed for 7 and 21 days respectively to atrazine (0.05 to 1 microgram/mL); Spartina alterniflora 28 days at 0.1 micrograms/mL trifluralin; Hibiscus moscheutos 14 days at 0.1 and 1 microgram/mL metolachlor in fresh and brackish water. The greatest increase following low dosage occurred with S. alterniflo ra, increasing from <600 micrograms/g wet wt. total ascorbic acid to >1000 micrograms/g. Ascorbic acid may be a promising biomarker of estuarine plants exposed to herbicide runoff; stimulation of ascorbic acid synthesis may enable some wetland plant s used in phytoremediation to cope with low levels of these compounds. In laboratory exposures of wetland plants to low herbicide levels (<0.1 micrograms/mL), some plants showed increased total ascorbic acid suggesting a stimulatory effect on ascorbic acid synthesis occurred; at higher herbicide conce ntrations (greater than or equal to 0.1 micrograms/mL) a notable decline in total ascorbic acid and increase in the oxidized form, dehydroascorbic acid occurred. Vigna luteola and Sesbania vesicaria were exposed for 7 and 21 days respectively to atrazine (0.05 to 1 microgram/mL); Spartina alterniflora 28 days at 0.1 micrograms/mL trifluralin; Hibiscus moscheutos 14 days at 0.1 and 1 microgram/mL metolachlor in fresh and brackish water. The greatest increase following low dosage occurred with S. alterniflo ra, increasing from <600 micrograms/g wet wt. total ascorbic acid to >1000 micrograms/g. Ascorbic acid may be a promising biomarker of estuarine plants exposed to herbicide runoff; stimulation of ascorbic acid synthesis may enable some wetland plant s used in phytoremediation to cope with low levels of these compounds. 9. Atmospheric nitrogenous compounds and ozone--is NO(x) fixation by plants a possible solution. Wellburn, A. R. New phytol. 139: 1 pp. 5-9. (May 1998). NAL Call #: 450-N42 Descriptors: ozoneair-pollution nitrogen-dioxide nitric-oxide air-quality tolerancebioremediationacclimatizationnutrient-sources nutrient-uptake plantscultivarsgenetic-variation literature-reviews 10. Atrazine degradation in pesticide-contaminated soils: phytoremediation potential. Kruger, E. L., Anhalt, J. C., Sorenson, D., Nelson, B., Chouhy, A. L., Anderson, T. A., and Coats, J. R. Phytoremediation of soil and water contaminants. Washington, DC : American Chemical Society, 1997. p. 54-64. NAL Call #: QD1.A45-no. 664 Abstract: Studies were conducted in the laboratory to determine the fate of atrazine in pesticide-contaminated soils from agrochemical dealer sites. No significant differences in atrazine concentrations occurred in soils treated with atrazine i ndividually or combinations with metolachlor and trifluralin. In a screening study carried out in soils from four agrochemical dealer sites, rapid mineralization of atrazine occurred in three out of eight soils tested, with the greatest amount occurring i n Bravo rhizosphere soil (35% of the applied atrazine after 9 weeks). Suppression of atrazine mineralization in the Bravo rhizosphere soil did not occur with the addition of high concentrations of herbicide mixtures, but instead was increased. Plants had a positive impact on dissipation of aged Studies were conducted in the laboratory to determine the fate of atrazine in pesticide-contaminated soils from agrochemical dealer sites. No significant differences in atrazine concentrations occurred in soils treated with atrazine i ndividually or combinations with metolachlor and trifluralin. In a screening study carried out in soils from four agrochemical dealer sites, rapid mineralization of atrazine occurred in three out of eight soils tested, with the greatest amount occurring i n Bravo rhizosphere soil (35% of the applied atrazine after 9 weeks). Suppression of atrazine mineralization in the Bravo rhizosphere soil did not occur with the addition of high concentrations of herbicide mixtures, but instead was increased. Plants had a positive impact on dissipation of aged atrazine in soil, with significantly less atrazine extractable from Kochia-vegetated soils than from nonvegetated soils. 11. Bacterial inoculants of forage grasses that enhance degradation of 2-chlorobenzoic acid in soil. Siciliano, S. D. and Germida, J. J. Environ toxicol chem. 16: 6 pp. 1098-1104. (June 1997). NAL Call #: QH545.A1E58 Descriptors: polluted-soils bioremediationAbstract: Biological remediation of contaminated soil is an effective method of reducing risk to human and ecosystem health. Bacteria and plants might be used to enhance remediation of soil pollutants in situ. This study assessed the potential of bacteria (12 isolates), plants (16 forage grasses), and plant-bacteria associations (selected pairings) to remediate 2-chlorobenzoic acid (2CBA)-contaminated soil. Initially, grass viability was assessed in 2CBA-contaminated soil. Soil was contaminated wi th 2CBA, forage grasses were grown under growth chamber conditions for 42 or 60 d, and the 2CBA concentration in soil was determined by gas chromatography. Only five of 16 forage grasses grew in 2CBA-treated (816 mg/kg) soil. Growth of Bromus inermis had no effect on 2CBA concentration, whereas Agropyron intermedium, B. biebersteinii, A. riparum, and Elymus dauricus decreased 2CBA relative to nonplanted control soil by 32 to 42%. The 12 bacteria isolates were screened for their ability to promote the germ ination of the five grasses in 2CBA-contaminated soil. Inoculation of A. riparum with Pseudomonas aeruginos

Glyphosate: Its Environmental Persistence and Impact on Crop Health and Nutrition

Abstract: Glyphosate-based herbicide products are the most widely used broad-spectrum herbicides in the world for postemergent weed control. There are ever-increasing concerns that glyphosate, if not used judiciously, may cause adverse nontarget impacts in agroecosystems. The purpose of this brief review is to present and discuss the state of knowledge with respect to its persistence in the environment, possible effects on crop health, and impacts on crop nutrition.