Plant and Molecular Biology
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Item Morpho-molecular genetic diversity and population structure analysis to enrich core collections in tea [Camellia sinensis (L.) O. Kuntze] germplasm of Sri Lanka and India(Genetic Resources and Crop Evolution, 2023) Kottawa-Arachchi, J. D.; Ranatunga, M. A. B.; Sharma, R. K.; Chaudhary, H. K.; Attanayake, R. N.; Amarakoon, A. M. T.; Gunasekare, M. T. K.; Sharma, B.; Kumar, N.; Sood, V. K.Despite tea [Camellia sinensis (L.) O. Kuntze] is one of the top non-alcoholic beverages consumed around the world; its genetic and phenotypic diversity is less understood compared to other plantation crops. The study’s aims were to undertake phenotypic and genotypic characterization of Sri Lankan and Indian tea germplasm and to identify diverse accessions to accelerate tea breeding programmes in both countries. A total of 171 tea accessions, comprising 94 Sri Lankan and 77 Indian accessions were used. All the accessions were subjected to phenotyping and genotyping using 28 polymorphic simple sequence repeat (SSR) markers. Based on 16 morphological characters, the first three principal components explained 57.61% and 58.43% of the total variability of Sri Lankan and Indian accessions, respectively. Young shoot pubescence, young shoot pigmentation, serration of leaf margin, and mature leaf colour contributed positively to the grouping of accessions. Based on Neighbor-joining analysis, all Sri Lankan accessions grouped in a single cluster, whereas Indian accessions grouped in two distinct clusters. The Gower’s distance method was the most appropriate than other methods for developing core subsets. Among 21 Sri Lankan core accessions selected, 11 accessions belong to introductions, five TRI-developed cultivars and five estate selections. Among 18 Indian core accessions selected, 11 belong to China types, two Assam types and five Indian recommended cultivars. The current study is the first study to compare tea germplasm of both countries and the results are useful for tea crop improvement programme, conservation and utilization of tea germplasm in India and Sri Lanka in the future.Item Species identification and pollination biology of an economically important true halophyte, Salicornia brachiata Roxb.(Aquatic Botany, 2024) Siridewa, K.; De Silva, W.; Ratnayake, R.; Wijesundara, S.; Perera, D.; Attanayake, R. N.Members of the genus Salicornia have gained a global attraction due to their ability to thrive under high saline conditions and as potential candidates in saline agriculture. However, it has been a taxonomically challenging genus for decades since the members show plastic responses to extreme environmental conditions and due to incongruences between morphological and molecular identification methods. While only a handful of commercially grown Salicornia species are fully described, most of the species including S. brachiata, a native species in the Indian sub-continent, Myanmar, and Sri Lanka are poorly described. With the potentials in adapting S. brachiata in saline agriculture, the aim of this study was to establish a morphology and DNA barcodebased species delineation system and to study pollination biology for future crop improvement projects. Tentatively identified S. brachiata plant samples were collected from two populations in Sri Lanka and completely described. GenBank lacked authenticated barcode data for S. brachiata except for one chloroplast genome to which the matK sequence obtained in the present study matched with 100 % identity. For the first time, well defined sequences of three barcode regions, ITS, ETS and matK, of S. brachiata were made available for accurate species identification. Reproductive dynamics in different parts of the inflorescence was studied. A facultative xenogamous mating system was recorded for the first time in the genus and while the lower florets in the cladode showed a preference towards outcrossing, the upper florets displayed adaptations for selfing. Data could be effectively utilized in future Salicornia breeding programs.Item Efficacy of methanolic extract of Zingiber officinale against seed-born fungi(2023) Hansini, Navoda; Sooriyawansha, A.M.S.C.; Jayawardena, P.A.S.N.P.; Kumarathunga, P.G.J.D.; Dananjaya, P.D.H.; Edirisinghe, E.A.C.P.; Alwis, M.D.N.; Daranagama, D.A.; Dahanayake, J.N.; Kadigamuwa, C.C.This study is focused on determining the efficacy of natural compounds present in Zingiber officinale methanolic plant extraction in controlling seed-born fungal pathogens Aspergillus flavus and Rhizopus oryzae. The maximum percentage inhibition of 94.01% and 90.43% was reported against. A. flavus and R. oryzae respectively for the crude extract in the poison food agar method. These results were further confirmed by computational investigation. [4] gingerol, [6]-gingerol, [8]-gingerol, [10]-gingerol, and [6]-dehydroginger phytochemicals identified in the extract were docked to the active sites in chitin synthase from A. flavus and squalene epoxidase from A. flavus and R.oryzae, and to the RNA dependent RNA polymerase (RdRp) enzyme from R. oryzae. The highest binding energy (BE) (-8.12 kcal/mol) was noticed between the interactions of squalene epoxidase and [6]-dehydroginger, and this complex was subjected to Molecular Dynamic (MD) analysis. MD simulations were performed on protein-ligand complexes for 10 ns using CHARMM36 force field. The mean radius of gyration (Rg), root mean square deviation (RMSD), and root mean square fluctuation (RMSF) were calculated and hydrogen bond analysis (HBA) was also performed. Rg and RMSD results indicated the stability of the protein-ligand complex throughout the simulation time.Item Carbon stocks in mangrove ecosystems of Sri Lanka: Average contributions and determinants of sequestration potential(Elsevier, 2024) Perera, K.A. Roshan S.; de silva, Wasana; Amaransinghe, Mala D.Mangroves are crucial in carbon sequestration despite covering only a small percentage of the Earth's surface. Latitudinal gradient primarily determines the distribution of climatic zones of distinct sunlight, temperature, and precipitation patterns, which influence the community structure of the mangrove ecosystem. The tropical climate of Sri Lanka contributes to the island's lush mangrove forests. The present study estimated that the average island's carbon sequestration capacity of Sri Lankan mangrove ecosystems is 524.25 t/ha representing a substantial volume of carbon storage that contributes to offset greenhouse effect due to increasing atmospheric CO2. Our results substantiated that rainfall positively influences total carbon sequestration capacity of mangrove ecosystems. It was also revealed that a positive relationship exists between vegetation structural complexity and sediment organic carbon, highlighting the influence of vegetation structure, that is primarily dependent on climatic conditions, on production of organic matter and sediment carbon sequestration. Globally, the carbon sink function of mangrove ecosystems is reported to be highest in the tropical areas and it declines towards sub-tropical higher latitudes while those in the southern hemisphere perform better carbon sinks than those in the northern hemisphere. The vertical distribution of total organic matter content in mangrove sediments was revealed to be in a descending order, manifesting the weak tidal removal of surface organic matter under the microtidal conditions in Sri Lankan marine waters, thus qualifying mangrove ecosystems in microtidal coasts as effective carbon sinks.Item Unveiling the Probiotic Properties of Lactic Acid Bacteria Inhabiting Tender Coconut Water(, Centre for Research and Knowledge Dissemination (CRKD) of the Sabaragamuwa University of Sri Lanka, 2023) Pavalakumar, D.; Undugoda, L.J.S.; Manage, P.M.; Nugara, R.N.; Kannangara, S.This research delves into the unexplored potential of tender coconut water as a rich source of probiotics, with a focus on identifying promising probiotic lactic acid bacteria (LAB). By employing biochemical screening techniques, four potential LAB strains were isolated: Lactiplantibacillus plantarum CWJ3, Lacticaseibacillus paracasei CWKu14, Lacticaseibacillus rhamnosus CWKu12, and Lacticaseibacillus casei CWM15. These strains were comprehensively assessed to evaluate their resilience under various conditions: pH (2, 3, and 6.5), bile (0.3% and 0.5%), phenol (0.4% and 0.6%), salt (3% and 6%) concentrations, and temperatures (20°C, 37°C, 45°C, and 60°C). Further, resistance to lysozyme (100 mg L-1), artificial saliva juice (0.3% α-amylase, at pH 6.9), simulated gastric juice (0.3% pepsin, at pH 2), and simulated intestinal juice (0.3% Ox-gall and 0.1% pancreatin at pH 7) were determined. Their antibiotic susceptibility was tested against ten antibiotics at 100 ppm, and cell surface hydrophobicity, auto-aggregation, co-aggregation with selected pathogens, antibacterial activity, hemolytic activity, and DNase activity, also were evaluated. The statistical analysis demonstrated the survival of all four strains even in demanding circumstances, with Lactiplantibacillus plantarum CWJ3 displaying the greatest resilience. Optimum growth occurred at 37°C, while none of the strains survived at 60°C. A pH of 6.5 was optimal for their growth, and Lactiplantibacillus plantarum CWJ3 stood out as the only strain capable of withstanding pH 2 after 2 hours. Lacticaseibacillus rhamnosus CWKu12 and Lacticaseibacillus casei CWM15 showed the highest percentage of auto-aggregation and co-aggregation while Lacticaseibacillus rhamnosus CWKu12 and Lactiplantibacillus plantarum CWJ3 exhibited high cell surface hydrophobicity. The strains displayed susceptibility to Clarithromycin, Erythromycin, and Azithromycin, but resistance to Cefuroxime and Streptomycin antibiotics. All four strains inhibited various food-borne pathogens, showcasing their potential as probiotics. Moreover, they displayed no hemolytic or DNase activity. Remarkably, Lactiplantibacillus plantarum CWJ3 excelled in challenging environments, making it a noteworthy contender for a probiotic role.Item The mycoremediation potential of phyllosphere fungi in urban ornamental plants in Sri Lanka with mathematical models for PAH degradation(2024) Dharmasiri, Nadeema; Kannangara, Sagarika; Undugoda, Lanka; Munasinghe, Jayantha; Madushika, Ruvini; Thambugala, Kasun M.; Gunathunga, Chathuri; Pavalakumar, DayaniCurrently, phylloremediation has emerged as a highly effective method for eliminating air pollutants, particularly polyaromatic hydrocarbons (PAHs). When PAHs accumulate on the phyllosphere, they significantly impact the fungal communities residing on leaf surfaces. This study aimed to investigate how pollution distribution patterns affect the diversity and PAHdegrading abilities of phyllosphere fungi, alongside identifying suitable mathematical models for PAH degradation. Leaf samples from two locations, Maradana and Sapugaskanda, were identified as having the highest PAH concentrations through principal component analysis. The fungal diversity in these highly contaminated regions was varied, with dominant species exhibiting greater PAH-degrading capabilities than those in less polluted areas. Thirty-five morphologically different epiphytic fungal strains were isolated on Potato Dextrose Agar (PDA) medium using the sample leaf wash. Two different fungal strains were selected as the best PAH degraders among those 35 different strains. These fungal strains were identified as Trichoderma harzianum P4M-16, and Fusarium solani P11M-46 based on ITS sequence data. Notably, these fungal species were more prevalent in highly polluted urban areas compared to less contaminated sites. High-Performance Liquid Chromatography (HPLC) analysis revealed that these two fungal species degrade PAHs more efficiently than others. Their kinetics assays demonstrated alignment with four degradation models when breaking down phenanthrene, naphthalene, pyrene, and anthracene. Scanning electron microscopy images showed that these fungi function as endophytes, extending their mycelium into the core leaf tissue layers beyond the epidermis. Gas Chromatography-Mass Spectrometry (GCMS) analysis indicatedItem Evaluating the Probiotic Profile, Antioxidant Properties, and Safety of Indigenous Lactobacillus spp. Inhabiting Fermented Green Tender Coconut Water(2024) Pavalakumar, Dayani; Undugoda, Lanka Jeewanie Samarakoon; Gunathunga, Chathuri Jayamalie; Manage, Pathmalal Marakkale; Ruwani, Nilushi Nugara; Kannangara, Sagarika Dilpushpi; Lankasena, Bentotage Nalaka SamanthaThis study isolated and characterized four indigenous lactic acid bacterial strains from naturally fermented green tender coco-nut water: Lactiplantibacillus plantarum CWJ3, Lacticaseibacillus casei CWM15, Lacticaseibacillus paracasei CWKu14, and Lacticaseibacillus rhamnosus CWKu-12. Notably, among the isolates, Lact. plantarum CWJ3 showed exceptional acid tolerance, with the highest survival rate of 37.34% at pH 2.0 after 1 h, indicating its higher resistance against acidic gastric conditions. However, all strains exhibited robust resistance to bile salts, phenols, and NaCl, with survival rates exceeding 80% at given concentrations. Their optimal growth at 37 °C and survival at 20 °C and 45 °C underscored adaptability to diverse environmental conditions. Additionally, all strains showed sustainable survival rates in artifcial saliva and simulated gastrointestinal juices, with Lact. plantarum CWJ3 exhibiting signifcantly higher survival rate (70.66%) in simulated gastric juice compared to other strains. Adherence properties were particularly noteworthy, especially in Lact. rhamnosus CWKu-12, which demonstrated the highest hydrophobicity, coaggregation with pathogens and autoaggregation, among the strains. The production of exopolysaccharides, particularly by Lact. plantarum CWJ3, enhanced their potential for gut colonization and bioflm formation. Various in vitro antioxidative assays using spectrophotometric methods revealed the signifcant activity of Lact. plantarum CWJ3, while antimicrobial testing highlighted its efcacy against selected foodborne pathogens. Safety assessments confrmed the absence of biogenic amine production, hemolytic, DNase, and gelatinase activities, as well as the ability to hydrolase the bile salt. Furthermore, these non-dairy probiotics exhibited characteristics comparable to dairy derived probiotics, demonstrating their potential suitability in developing novel probiotic-rich foods and functional products.Item An analysis of regional variations in the physicochemical properties of Cocos nucifera L. var. nana across Sri Lanka(2024) Pavalakumar, Dayani; Undugoda, Lanka Jeewanie Samarakoon; Thambugala, Kasun Madhusanka; Manage, Pathmalal Marakkale; Ruwani, Nilushi Nugara; Kannangara, Sagarika Dilpushpi; Rajapaksha, Suranga M.This study explores the intriguing regional disparities in the characteristics of green dwarf tender coconut water (Cocos nucifera L. var. nana) in Sri Lanka. Physicochemical parameters of coconut water subjected to a comprehensive analysis following standard AOAC methods. The prevalent sugar types in the samples were identifed as fructose and glucose, with a minute amount of sucrose using High-Performance Liquid Chromatography (HPLC). Notably, regional diferences in sugar profles were observed during the analysis. Kurunegala samples exhibited signifcantly higher levels of total soluble solids (5.98±0.12°Brix), along with elevated total sugar (70.13±5.06 mg mL−1), total reducing sugar (68.53±5.57 mg mL−1), glucose (39.65±6.10 mg mL−1), and fructose (37.65±7.12 mg mL−1), while Colombo samples demonstrated the least values. Regarding pH values, Colombo samples exhibited a signifcantly lower value (4.87±0.10). Furthermore, a significant quantity of macro minerals such as calcium, sodium, potassium, and magnesium, along with trace minerals like iron and zinc, were identifed. Fourier-transform infrared spectroscopy analysis indicated the presence of functional groups from simple sugars and phenolic compounds as major chemical bonds for all regions. Principal Component Analysis was performed considering the Electronic Nose (E-nose) data, revealing distinctive volatile profle clusters for Kurunegala and Colombo samples. Moreover, sensory evaluations confrmed Kurunegala as the most preferred, while Colombo was ranked as the least preferred in terms of organoleptic characteristics. These fndings underscore the critical importance of regional variations in the nutritional content and sensory attributes of coconut water, which play a pivotal role in infuencing customer preferences.Item Quorum sensing capability of wine microbial consortium involved in spontaneous fermentation of regional wine production(2023) Thivijan, Sathivel; Undugoda, Lanka Jeewanie Samarakoon; Nugara, Ruwani Nilushi; Manage, Pathmalal Marakkale; Thambulugala, Kasun Madhusanka; Kannangara, Sagarika DilpushpiQuorum sensing (QS) is an intercellular communication process in which wine microbial consortium collectively adapts their metabolism by secreting quorum sensing molecules (QSM) into their environment. These QSMs continuously diffuse into the medium until approaching the threshold level, which stimulates the microbial cell population. Moreover, these molecules bind with their target sensory proteins and stimulate the transcription and translation of genes responsible for aromatic alcohol production. The research findings revealed that ARO genes regulate the synthesis of quorum sensing molecules like tyrosol, 2-phenylethanol, and tryptophol. For instance, ARO8, ARO9, and ARO10 present in Saccharomyces cerevisiae are the significant genes regulating the above QSMs and other aromatic alcohols, which determine the organoleptic qualities of wine. Another essential gene that affects the quality of wine is FLO11. Hence, different grape cultivars harbor different types of wine fermenting microbes with unique quorum sensing systems, leading to the unique organoleptic qualities in regional wine. Since we could still find the quorum sensing system of S. cerevisiae, this may open avenues to conduct much research to discover the unique quorum sensing systems of different wine microbes. These findings will lead to novel wine starter cultures with many specific genes developed through recombinant DNA technology. Therefore, this review focuses on quorum sensing of wine microbial consortium involved in the fermentation process of spontaneous wine fermentation through the chemistry of QSMs and how these signaling processes are genetically manipulated. Furthermore, this focus reviews the organoleptic quality development of regional wine products due to different quorum sensing abilities.Item Assessing the antioxidative potential of lactic acid bacteria inhabiting tender coconut water(Faculty of Graduate Studies - University of Kelaniya, Sri Lanka, 2023) Pavalakumar, D.; Undugoda, L.J.S.; Manage, P.M.; Nugara, R.N.; Kannangara, S.Probiotics are renowned for their beneficial impact on human health, including their antioxidative properties. Lactic acid bacteria (LAB), which constitute a major group within probiotics, have been recognized for their ability to act as potent antioxidants, providing relief from oxidative stress in the host. This study aims to evaluate the antioxidative activity of probiotic LAB inhabiting the tender coconut water samples collected from different regions of Sri Lanka. In a previous study, analysis of the collected tender coconut samples resulted in the identification of four potential probiotic strains at the species level: Lactiplantibacillus plantarum CWJ3, Lacticaseibacillus rhamnosus CWKu12, Lacticaseibacillus paracasei CWKu14, and Lacticaseibacillus casei CWM15. The antioxidative activities of these strains were evaluated using four different chemical antioxidant assays: the 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay at 517 nm, the 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) assay at 734 nm, the ferric reducing antioxidant power (FRAP) assay at 593 nm, and the total phenolic content (TPC) assay at 765 nm through spectrophotometric method. Three different concentrations of each bacterial strain (107, 108, and 109 CFU mL-1) were prepared using overnight grown cultures in deMan, Rogosa, and Sharpe broth at 37 °C, included in the study. The results indicate a significant increase (p < 0.05) in antioxidative activity for all four strains across all analyzed methods with an increase in cell concentration. Lactiplantibacillus plantarum CWJ3 exhibited the highest antioxidative potential at 109 CFU mL-1, with 88.85±0.84% radical scavenging activity in the DPPH assay, 84.0±0.14% radical scavenging activity in the ABTS assay, 0.029±0.004 mg mL-1 ascorbic acid equivalent in the FRAP assay, and 0.0052±0.0006 mg mL-1 gallic acid equivalent in the TPC assay. Conversely, Lacticaseibacillus paracasei CWKu14 demonstrated the lowest values for all antioxidative activities. Continued research on the antioxidative properties of probiotic LAB derived from tender coconut water holds promising prospects for the development of functional beverages.