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The green-lipped mussel Perna viridis’ sensitive nature and characteristic as a benthos organism that filters the sediment in its environment make it one of the possible bioindicators for pollution in the aquatic ecosystem. The present study aimed to determine the percentages of total shell deformities in comparison to the past data in the coastal waters of Peninsular Malaysia. It was found that several types of discontinuous, continuous, and unexplained shell abnormalities contributed to the overall range of shell deformities of 15.8–87.5%, which was greater in comparison to that (0.0–36.8%). The present study showed that the highest overall proportion of shell abnormalities occurred in Teluk Jawa, whereas the lowest percentages were found in Kampung (Kg.) Pasir Puteh. The regulative mechanisms at the well-known polluted sites at Kg. Pasir Puteh could be the explanation. Further research should be conducted to determine the degree of heavy metal that may be the source of these malformations in the mussel shells.

The ecological and children’s Health Risk Assessments (HRA) of Copper (Cu) in aquatic bodies ranging from rivers, mangrove, estuaries, and offshore areas were studied using the Cited Cu Data in The Sediments (CCDITS) from 125 randomly selected papers published from 1980 to 2022. The ecological and children’s HRA were assessed in all CCDITS. Generally, local point Cu sources (8%) and lithogenic sources were the main controlling factors of Cu concentrations. The present review revealed three interesting points. First, there were 11 papers (8%) documenting Cu levels of more than 500 mg/kg dw while China was the country with the highest number (26%) of papers published between 1980 and 2022, out of 37 countries. Second, with the Cu data cited from the literature not normally distributed, the maximum Cu level was higher than all the established guidelines. However, the median Cu concentration was lower than most of the established guidelines. The median values of the geoaccumulation index (Igeo) indicated a status of ‘unpolluted‘ and ‘moderate contamination’ for the contamination factor (CF), and ‘low potential ecological risk’ for the ecological risk (ER) of Cu. However, the Cu ER could be based at present on the above mentioned 8% of the literature in the present study. Third, the calculated hazard index (HI) values were found to be below 1, indicating no potential chance of Cu non–carcinogenic effects in both adults and children, except for children’s HI values from Lake Pamvotis of Greece, and Victoria Harbor in Hong Kong. Thus, regular monitoring (every 2 years), depending upon the available resources, is recommended to assess the ecological–health risk of Cu pollution in aquatic bodies to abate the risk of Cu exposure to children’s health and avoid injurious impacts on the biota. It can be concluded that there is always a need for the mitigation and management of a Cu exposure risk assessment that can be used successfully for screening purposes to detect important human health exposure routes. Consequently, any sediments contaminated with Cu require rapid sediment remediation techniques.

Microbially induced carbonate precipitation by ureolysis is a biomineralization process that has been adapted by various microorganisms in different natural environments. This widespread natural phenomenon can be employed in numerous civil engineering and soil stabilization applications. In the present study, the potential of indigenous soil urease-producing bacteria as potential agents for soil stabilization methods was investigated. Assessment of the eight active urease-producing bacterial species isolated from the farm soil samples has demonstrated that all the isolates were Gram-positive rod-shaped bacteria with promising characteristics such as the formation of endospore which is essential for bacterial survival in harsh conditions within the soil environment. The pH profile and growth profile of the isolates were studied and urease activity was measured by the phenol hypochlorite assay method. Two isolates designated isolate O6w and isolate O3a were selected based on the highest urease activity recorded at 665 U/mL and 620 U/mL, respectively, and they were able to increase and sustain alkaline culture condition (pH 8.71 ± 0.01 and 8.55 ± 0.01) which was suitable for CaCO3 precipitation. The isolates were identified based on 16S ribosomal RNA sequencing to be Bacillus cereus (O6w) and Bacillus paramycoides (O3a). This current study suggested that indigenous soil ureolytic bacteria are potential raw material for the biotreatment of soils stability.

The present study investigated the antioxidant enzyme activities (AEA) of ascorbate peroxidase (APX), catalase (CAT), guaiacol peroxidase (GPX), and superoxide dismutase (SOD) as biomarkers of Cu and Pb stress by using Centella asiatica grown in an experimental hydroponic condition. The results showed (i) higher accumulations of Cu and Pb in the roots of C. asiatica than those in the leaves, (ii) synergistic effects of Cu and Pb stress at higher metal-level exposures, and (iii) Cu and Pb stress triggered the increment of APX, CAT, GPX, and SOD levels in both the leaves and roots of C. asiatica. The increment of four AEA indicated that C. asiatica underwent oxidative stress caused by the production of reactive oxygen species when the plant was exposed to Cu and Pb. In order to prevent damages caused by Cu and Pb stress, the AEA system was heightened in C. asiatica, in which APX, CAT, GPX, and SOD can be used as biomarkers of Pb and Cu stress in the plant.

The current study assessed the ecological–health risks of potentially toxic arsenic (As) and antimony (Sb) in the vegetable Centella asiatica, topsoils, and mangrove sediments sampled from Peninsular Malaysia. The As concentrations ranged from 0.21 to 4.33, 0.18 to 1.83, and 1.32 to 20.8 mg/kg dry weight, for the leaves, stems, and roots of the vegetable, respectively. The ranges of Sb concentrations were 0.31–0.62, 0.12–0.35, and 0.64–1.61 mg/kg dry weight, for leaves, stems, and roots of the vegetable, respectively. The children’s target hazard quotient (THQ) values indicated no non-carcinogenic risks of As and Sb in both leaves and stems, although children’s THQ values were higher than those in adults. The calculated values of estimated weekly intake were lower than established provisional tolerable weekly intake of As and Sb for both children and adult consumers. The carcinogenic risk (CR) values of As for children’s intake of leaves and stems of vegetables showed more public concern than those of adults. The levels of Sb and As in the topsoils were generally higher (although not significantly) than those in the mangrove sediments, resulting in a higher geoaccumulation index, contamination factor and ecological risk, hazard index, THQ, and CR values. This indicated that the anthropogenic sources of Sb and As originated from the land-based activities before reaching the mangrove near the coast. The CR of As signifies a dire need for comprehensive ecological–health risks exposure studies, as dietary intake involves more than just vegetable consumption. Therefore, risk management for As and Sb in Malaysia is highly recommended. The present findings of the ecological–health risks of As and Sb based on 2010–2012 samples can be used as an important baseline for future reference and comparison.

As an attempt to examine the causes of forest disturbance and degradation of the orchid community, a comparative study on diversity and ecology in eight undisturbed and ten disturbed forests in Peninsular Malaysia was conducted that varied in areas, elevations, vegetation types, and disturbance regimes. Density and individual-based rarefaction curves were used to describe the abundance. Univariate and multivariate analyses were also performed to explore the associations of species abundance with biotic and abiotic factors. The study reported 239 orchid species belonging to 65 genera. Species richness, abundance, density, and diversity of orchids varied by locality. Higher density of orchids (2.433 plants/km2) occurred in the undisturbed forests than in the disturbed forests (0.228 plants/km2). As with the character of undisturbed forests, the temperature was between 27.8 ± 0.3 °C and 31.2 ± 0.2 °C, humid (77.1 ± 1.2%–89.6 ± 0.9%), and with low light intensity (23.8 ± 3.3 μmol m−2s−1–171.7 ± 18.8 μmol m−2s−1), thus supporting the high density of the plants. Disturbed forests had higher diversity (H = 4.934 and 1-D = 0.990) and abundance (183 species of 57 genera) but were determined to be highly influenced by the higher abundance of epiphytic orchids on the fallen trees and ease of accessibility in the logged forests. Terrestrial and mycoheterotroph orchids were much lower in density and abundance in the disturbed habitat indicating a gradual reduction in their niche availability following the disturbance. Additionally, the ecology data show that the microclimate conditions of the canopy-covered forest was influenced by proximity to the logged area which had eventually reduced the orchids’ habitat quality. Furthermore, the results show that the abundance of epiphytic orchid communities was associated with the host plant characteristics. Host types and bark texture preference were apparent for the epiphytic orchid species, with certain types and textures hosting more orchid species than others. Overall results show that extreme temperature, humidity, and light intensity caused by the canopy opening inflicted damages to the habitat conditions and bark textures of the host plants and limits recolonisation of the orchids in the disturbed forests. The species diversity and density patterns of orchids in undisturbed and disturbed forests revealed in this study provide a baseline for conservationists, policy makers, and forest authorities in expanding the understanding of the forest ecology and vegetation along the disturbance gradient, forest regeneration, and criteria for plant selection for forest restoration in Peninsular Malaysia.

Paphiopedilum exul, Calanthe chrysoglossoides, and Luisia brachystachys are reported here as new records for Malaysia, whereas Bryobium cordiferum subsp. borneense, Habenaria rostellifera, and Taeniophyllum rugulosum are three rare orchid species recollected from Sarawak, Perlis, and Perak, respectively. This paper highlights brief descriptions and photographic illustrations of each species for easy identification. Besides, notes on morphological comparisons with the closely related species and artificial taxonomic keys are included as well.

Gallic acid and catechin are the most abundant phenolic and flavonoid contents found in all plant extracts. The contents and the bioassay-guided fractionating substances of the Sclerocarya birrea (A. Rich) Hochst (Anacardiaceae) fraction played vital roles. The goals of the study were to determine the contents of some useful medicinal plants and the bioassay-guided fractionation substances of S. birrea fraction compounds capable of acting against Salmonella isolate using LC-MS/LC-HRMS (Dionex ultimate 3000 RS UPLC with Thermo Scientific Q Exactive Orbitrap Hybrid Tandem Mass Spectrometer). The Folin–Ciocalteu reagent procedure and flavonoid content determination were conducted spectrophotometrically. Bioassay-guided fractionation, chronological partitioning, and screening of the antibacterial action against Salmonella typhi were performed. The ethyl acetate fraction extracts of S. birrea stem (bark) extract were analyzed using LC-MS/LC-HRMS. The gallic acid content increased tremendously in Vachellia nilotica (L.) P.J.H. Hurter and Mabb (Fabaceae) pod extracts with curve fitting (R2 = 0.9958). Catechin content increase was significantly increased in S. birrea stem (bark) extracts followed by that of V. nilotica pod extracts with curve fitting (R2 = 0.9993); they were all significantly different in the Guiera senegalensis J.F. Gmel. and the Leptadenia lanceolata (Poir.) Goyder leaves extracts at p value

Abstract Background Vibriosis is an important bacterial disease of cultured marine fishes worldwide. However, information on the virulence and antibiotic resistance of Vibrio spp. isolated from fish are scarce. This study investigates the distribution of virulence associated genes and antibiotic resistance patterns of Vibrio spp. isolated from cage-cultured marine fishes in Malaysia. Results A total of 63 Vibrio spp. isolated from 62 cultured marine fishes in various geographical regions in Peninsular Malaysia were analysed. Forty-two of the isolates (66.7%) were positive for all chiA, luxR and vhpA, the virulence genes produced by pathogenic V. harveyi. A total of 62 Vibrio isolates (98%) had tlh gene of V. parahaemolyticus, while flaC gene of V. anguillarum was detected in 43 of isolates (68%). Other virulence genes, including tdh, trh, hlyA and toxR vc were absent from any of the isolates. Multiple antibiotic resistance (MAR) was exhibited in all strains of Harveyi clade, particularly against ampicillin, penicillin, polypeptides, cephems and streptomycin. The MAR index ranged between 0.06 and 0.56, and 75% of the isolates have MAR index of higher than 0.20. Host species and geographical origin showed no correlation with the presence of virulence genes and the antibiotic resistance patterns of Vibrio spp. Conclusions The study indicates that majority of Vibrio spp. isolated from cultured marine fishes possess virulence genes, but were not associated with human pathogen. However, the antibiotics resistance is a real concern and warrants ongoing surveillance. These findings represent an updated knowledge on the risk of Vibrio spp. to human health, and also provides valuable insight on alternative approaches to combat vibriosis in cultured fish.

Polycyclic aromatic hydrocarbons (PAHs) comprised of many dangerous organic pollutants which affect human cell. The choice of phenanthrene and pyrene as model substrates was based on their classification among the most hazardous PAHs group by the US EPA where they belonged to low and high molecular weights PAHs respectively. Biodegradation of these PAHs is the best strategy that completely removes such pollutants in an environmentally friendly manner. However, the bacteria involved are challenged degradation difficulties as a result of PAHs inhibitory effects to the organisms. This research is aimed at formulating phenanthrene and pyrene degrading consortium that effectively perform best even in complex mixture with hazardous heavy metals. Different bacteria consortia were formulated using the compatibility testing and mathematical permutation approach and the best consortium selected. This selected consortium was then subjected to the degradation of both phenanthrene and pyrene separately in a combined mixture with the selected heavy metals from the inductively coupled plasma optical emission spectrophotometer (ICP-OES) analysis. Consortium composition of C. sakazakii MM045 (2%, v/v) and Enterobacter sp. MM087 (2%, v/v) were found to be much effective during phenanthrene (500 mg/L) and pyrene (250 mg/L) degradation. This consortium also resisted more than 6 mg/L each of Nickel (Ni), Cadmium (Cd), Vanadium (V) and Lead (Pb) in such complex degradation which was found to be more than the concentration in the natural habitat the consortium exists prior to isolation. Such performance makes the selected consortium to be an extremely efficient tool for the PAHs degradation application as many biodegradation agents were reported to be less effective when significant concentration of Ni, Cd, V and Pb are present.

Marine clay soils are problematic soils in the construction industry when they are subjected to construction loads. When these soils are loaded, they lose their structure. This leads to the soil being unable to withstand loads of any magnitude without exhibiting significant, permanent deformations. In order to stabilize the marine soil, new methods for soil improvement were built upon biogrouting by incorporating physical, biological and chemical treatments into the soil. However, the biggest challenge of this method is the bacteria migration through the soil medium. To overcome this issue, the electrokinetic phenomenon can be utilized alongside biogrouting to prevent the bacteria migration. In this regard, the present study applied electrobiogrouting stabilization to investigate the improvement of acidic marine clay soil with a pH of 3.69. To accomplish this, two large-scale physical models with dimensions of 500 × 300 × 1200 mm were fabricated to examine the influence of two different treated distances between the inlet and outlet—450 mm (D45) and 600 mm (D60)—on the stability of the treated soil. It was observed that the shear strength of the treated soil improved significantly. The shear strength at the D45 treated distance increased from 3.65 kPa (untreated soil) to 28.14 kPa (treated soil). However, the strength increased by increasing the treated distance. In addition, compressibility and soil electrical conductivity were reduced significantly, and the Atterberg limits were significantly enhanced from OH to OL. The reasons for the enhancement of treated soil were the formation of CaCO3, which filled the soil voids, and that the water content was reduced. To address issues with marine clay soil, this study aims to minimize the high cost of a special foundation system and the use of non-environmentally friendly materials such as calcium-based binders, aside from the reduction of deformations caused by loading. The findings of this study can be used for acidic soils and the improvement of soil’s geotechnical behavior in general.

Chitinase 42 kDa produced by Trichoderma harzianum has been proven as a prime compound to be excreted onto the hyphae of the pathogen causing localised cell wall lysis at the point of interaction. This finally initiate the process of the host cell becomes empty of cytoplasm, disintegrates and shows a rapid collapse. This study investigates the existence of N-glycan linked mannose in chitinase 42 kDa produced by the Malaysian T. harzianum strain BIO10671. The chitinase 42 kDa from T. harzianum BIO10671 was initially purified using anion exchange chromatography prior to a series of experiments such as immunoblotting against the chitinase 42 kDa antibody, lectin staining for detecting any terminal linked mannose, and galactofuranose detection to determine the presence of galatofuranose components in glycoproteins. The enzyme purification harvested about 12-fold of chitinase 42 kDa from T. harzianum BIO10671 with strong indication of the presence chitinase 42 kDa presence on SDS-Page. This was confirmed by immunoblotting with a strong response around 42 kDa after overnight incubation in chitinase 42 kDa antibody suggesting that the gene for chitinase 42 kDa was greatly expressed in this strain. There are no intervation of galatofuranose on any of the terminal mannose in chitinase 42 kDa as shown by negative results on samples treated with or without endoglycosidase-H and lectin staining. Therefore, it can be concludeed that glycosylation occurred in the chitinase 42 kDa from T. harzianum 42 kDa was not in the form of N-glycan linked mannose as expected.

Polycyclic Aromatic Hydrocarbons (PAHs) are complex and widely distributed environmental pollutants that can affect living ecosystems. This study was conducted to rapidly degrade phenanthrene and pyrene representing low and high molecular weight of PAHs, respectively. Cronobacter sakazakii MM045 (KT933253) was identified from used engine oil of contaminated soil. PAHs biodegradation was carried out using 2,6-dichlorophenol indophenol (DCPIP) assay. Biodegradation influencing factors including agitation, temperature, pH, inoculums volume and salinity were enhanced using Response Surface Methodology (RSM) by Central Composite Design (CCD). Phenanthrene and pyrene biodegrading metabolites were identified using gas chromatography mass spectrophotometer (GCMS). • Initial biodegradation indicated 75.2% and 54.3% phenanthrene and pyrene degraded by C. sakazakii MM045 within 24 h. After CCD optimisation, 100% degradation was achieved for each of the phenanthrene and pyrene, resulting in the formation of intermediate metabolites. • The identified phenanthrene metabolites were 3,4-dihydroxyphenathrene, phthalic acid, pyruvic acid, acetic acid and oxalic acid. Pyrene intermediates comprised pyrene cis-4,5-dihydrodiol, 3,4-dihydroxyphenanthrene, phthalic acid, pyruvic acid, acetic acid and lactic acid. • Cronbacter sakazakii MM045 was proven to be rapid and effective in degrading PAHs within 24 h despite the unavailability of existing literatures on PAHs biodegradation.

Bivalves have been utilised extensively as a biomonitoring agent for heavy metal pollution in the marine ecosystem. In the present study, heavy metal concentrations [e.g., copper (Cu), zinc (Zn), cadmium (Cd), and lead (Pb)] were determined in the soft tissues of bivalve Geloina expansa as well as sediment and water samples collected from the Sepang Besar River on the west coast of Peninsular Malaysia. Bioaccumulation factors, such as biota sediment accumulation factor (BSAF) and biota concentration factor (BCF), were used to estimate metal accumulation. The bivalve tissues were digested and analysed using an inductively coupled plasma optical emission spectrometer (ICP-OES). In sediment samples, the heavy metal concentration was Zn (67 mg/kg) > Cu (23 mg/kg) > Pb) (14 mg/kg), on a dry weight basis. Whereas in water samples, Zn (19.2 g/L) > Cu (1.9 g/L) > Pb (1.0 g/L). Meanwhile, the tissues of G. expansa accumulated heavy metals from the surroundings, with concentrations of Zn (56.63 mg/kg) > Cu (4.10 mg/kg), on dry weight basis. Cd was not detected in the samples. The findings of this study suggested that G. expansa serve as a macroconcentrator (BSAF > 2) for Zn, a deconcentrator (BSAF < 1) for Cu, and a bioaccumulator' (BCF < 5000) of Zn and Cu. [ABSTRACT FROM AUTHOR]

Abstract Phenanthrene and pyrene are low and high molecular weights polycyclic aromatic hydrocarbons (PAHs) being classified as priority organic pollutants in the environment. This study was aimed to optimizing PAHs biodegradation conditions and then identifying intermediate metabolites using effective Enterobacter sp. MM087 (KT933254). Biodegradation quantitative experiments were carried out using colorimetric assay and the intermediate metabolites were identified based on gas chromatography mass spectrophotometer (GC–MS). Enterobacter sp. MM087 initially degraded 80.2% phenanthrene (500 mg/L) and 59.7% pyrene (250 mg/L) within 24 h. Further enhancement of the culture conditions involving agitation, temperature, pH, inoculums volume and salinity was carried out using response surface methodology (RSM) based on central composite design (CCD). The CCD optimizations allowed the interactions among the culture conditions which eventually resulted in 100% degradation in each of the phenanthrene and pyrene thereby released non-hazardous metabolites. Correlation between the predicted and actual results further validated the CCD optimization. The phenanthrene metabolites identified were 3,4-dihydroxyphenathrene, phthalate, pyruvic acid and acetic acid. Pyrene metabolites identified involved pyrene cis -4,5-dihydrodiol, 3,4-dihydroxyphenathrene, phthalate, pyruvic acid, acetic acid and formic acid. The biodegradation experiments were finally validated using numerical optimizations. Enterobacter sp. MM087 was found to rapidly degrade 500 mg/L phenanthrene and 250 mg/L pyrene within 24 h which makes it a very efficient and rapid PAHs degrader. [ABSTRACT FROM AUTHOR]

Shrimp shells generally contain natural astaxanthin which is lost to the environment industrial food processing as the shrimp shells are discarded as wastes. An approach to recover astaxanthin was developed utilising Aeromonas hydrophila in single factor optimisation method to screen several physio-chemical sources using response surface methodology. The central composite design determined the optimised culture media-conditions to be pH 7.0, monosodium glutamate 3% (w/v), glucose (1% w/v) and 30 °C. In addition, the optimised media increased astaxanthin recovery by 38% in comparison to the unoptimised media as under optimal conditions, A. hydrophila degraded shrimp shell waste more efficiently to recover more astaxanthin. This study contributes to the application of A. hydrophila and provides an alternative route for the recovery of astaxanthin from shrimp shell wastes. • Aeromonas hydrophila is capable of recovering astaxanthin from shrimp shell waste. • Optimisation of culture media enhances the recovery of astaxanthin. • This study shows the utilisation of application of Aeromonas hydrophila. • Providing an alternative method in aerobic fermentation and astaxanthin recovery. • Enhancing the management of shrimp shell wastes using a common pathogen on shrimps. [ABSTRACT FROM AUTHOR]