DNA Fingerprinting Analysis Research Articles

Prevalence and Diversity of Plant Parasitic Nematodes in Irish Peatlands

The prevalence of plant parasitic nematodes (PPN) in the Irish peatlands was investigated in five different peatland habitats—raised bog, cutover scrub/woodlands, fens and peat grasslands, which were further sub-categorised into fourteen different sub-habitats. Within the raised bog habitat were healthy bog hummock (HBH), healthy bog lawn (HBL), degraded bog hummock (DBH) and degraded bog lawn (DBL) and the fen habitats were fen peat (FP) and rich fen peat (R-FP). Cutover scrub or woodland habitat included cutover scrub rewetted (C-RW), cutover scrub non-rewetted (C-NRW), woodlands rewetted (W-RW) and woodlands non-rewetted (W-NRW). Grassland included wasted peat (WP), rough grazing (RG-I) and improved fen peat grassland (IFPG-RW and IFPG-NRW). Soil samples from peatlands were all collected between July and December 2023 when the temperature ranged from 12 to 20 °C. One half of each sample was used for molecular nematode analysis and the other half for morphological identification of nematodes. For the morphological identification, a specific nematode extraction protocol was optimised for peatland soils, and the extracted nematodes were fixed onto slides to be studied under a high-power light microscope. Subsequently, the other part of the soil was processed to isolate total DNA, from which the 18S rRNA gene was sequenced for the identification of nematode taxa. The extracted DNA was also used for randomly amplified polymorphic DNA (RAPD) fingerprinting analysis to determine banding patterns that could classify different bog habitats based on PPN random primers. Compared to that in the climax habitats (HBH, HBL, DBH, DBL, FP, R-FP), PPN prevalence was recorded as being higher in grasslands (WP, RG-I, IFPG-RW and IFPG-NRW) and scrub/woodland ecosystems (C-RW, C-NRW, W-RW, W-NRW). The results indicate that nematode populations are different across the various bog habitats. Emerging and current quarantine PPN belonging to the families Pratylenchidae, Meloidogynidae, Anguinidae and Heteroderidae were noted to be above the threshold limits mentioned under EPPO guidelines, in grassland and wooded peatland habitats. Future actions for PPN management may need to be considered, along with the likelihood that these PPN might impact future paludiculture and other crops and trees growing in nearby agricultural lands.

Jackfruit Genotypes in Southern Nayarit: A Comparative Study of Morphological, Physiological, Physicochemical, Phytochemical, and Molecular Assessments

Jackfruit, primarily cultivated in Nayarit, Mexico, has four notable genotypes: “Agüitada”, “Rumina”, “Licenciada”, and “Karlita”, which require thorough characterization. This study aimed to provide a comprehensive characterization of these genotypes through an integration of morphological, physiological, physicochemical, phytochemical, and DNA fingerprinting analyses. Measurements were taken from physiological maturity to senescence. SSR and SRAP markers were employed for DNA fingerprinting, and a complete randomized design followed by multivariate analysis was used to observe variable relationships. The results revealed that “Rumina” had the largest leaf size, while “Karlita” had the largest fruit size and the highest respiration rate (117.27 mL of CO2·kg−1·h−1). “Licenciada” showed the highest ethylene production (265.45 µL·kg−1·h−1). “Agüitada” and “Licenciada” were associated with orange bulbs, whereas “Rumina” and “Karlita” were associated with yellow ones. Additionally, “Agüitada” demonstrated higher levels of soluble phenols and carotenoids, indicating greater antioxidant capacity. The Jaccard index suggested moderate genetic diversity among the genotypes, and the dendrogram revealed two genetic clusters. “Licenciada” emerged as a promising genotype, combining high genetic diversity with desirable physicochemical traits. This study highlights the need to broaden future genetic analyses to include a wider range of jackfruit genotypes from various regions, offering a more comprehensive understanding of genetic diversity.

Unlocking Mysteries: A Multidisciplinary Approach to Forensic Science

Abstract: “Unlocking Mysteries: A Multidisciplinary Approach to Forensic Science” delves into the collaborative landscape of forensic investigations, where biology, chemistry, physics, psychology, and law converge to shed light on criminal mysteries. By exploring foundational principles, techniques, and challenges, the chapter emphasizes the importance of multidisciplinary collaboration in deciphering clues left at crime scenes. It outlines seven foundational principles guiding forensic investigations, from the Law of Individuality to the Principle of Analysis. The chapter discusses various forensic analysis techniques, including DNA analysis, fingerprint analysis, toxicology analysis, ballistics analysis, forensic anthropology, forensic chemistry, digital forensics, and trace evidence analysis. DNA analysis, as a cornerstone, aids in individual identification and resolving disputes. Forensic entomology and anthropology provide insights into post-mortem intervals and victim identification. Chemistry techniques like spectroscopy and chromatography aid in identifying substances. Trace evidence analysis offers valuable insights into crime circumstances. The integration of biology into forensic science enhances accuracy and provides closure to victims’ families. The chapter concludes by emphasizing the indispensable role of multidisciplinary collaboration, innovative technologies, and ethical standards in pursuing truth and justice in forensic science. Keywords: forensic science, multidisciplinary collaboration, forensic analysis techniques, DNA analysis, forensic entomology, forensic anthropology, chemistry techniques, trace evidence analysis

Power of Forensic Evidence in Solving Crimes

Forensic laws and evidence are important part of modern crime investigation. The remains of criminals or the pieces of evidence collected at crime scenes by investigators help in identifying the criminals and solving cases. This article holds the importance of forensics and forensic investigation to help the investigators reach the point with 100% verifications. Forensic evidence covers DNA Analysis, fingerprint analysis, and other various forms of digital analysis. This article along with its importance also highlights the limitations of forensic analysis during investigations and by taking the improvement steps for criminal identification.

Exploration of genetic variability in Garcinia [<i>Garcinia gummi-gutta</i> L.(Robson)] germplasm based on growth, yield and quality traits

Eleven Garcinia germplasm along with local check of Pechiparai were evaluated and underwent principal component analysis to assess genetic divergence and variation patterns during 2019 to 2022. The first two principal components, contributing significant Eigen values, explained 71.20% of the total variability. The Acc. Gg 9 was the top performer, exhibiting favourable yield and growth traits with lower pest and disease incidence, high biochemical compounds viz., hydroxy citric acid and tartaric acid compared to local check. Cluster analysis revealed four major clusters, offering diversity for breeding programs. Correlation studies highlighted traits such as number of fruits per tree, rind thickness, and tartaric acid showing significant positive correlations with yield per tree. Selection based on identified key traits was deemed crucial for enhancing effectiveness. Additionally, DNA fingerprinting analysis indicated the potential use of RAPD markers (OPA03570) for differentiating Kudampuli cultivar PPI (K) 1 from the local check. Overall, the present investigation provides insights into optimizing Garcinia breeding programs, emphasizing trait-based selection and DNA fingerprinting for varietal differentiation.

The seeds of invasion: a comparison of endophytic seed bacteria of Acacia longifolia between its native and invasive ranges

Acacia longifolia is an aggressive invader in Mediterranean-type ecosystems severely impacting biodiversity and ecosystem functions. The species’ invasiveness has been linked to its ability to thrive in nutrient poor soils, high seed production, and quick establishment after fire. In this study, we identify and compare the bacterial endophytes of A. longifolia seeds collected from populations in the species’ native (Australia) and invasive (Portugal) ranges. For this, we characterised the morphology (length, width, and weight) of seeds from two sites in each range and isolated and cultivated bacteria from seeds. DNA fingerprinting and cluster analyses revealed slightly higher, and distinct, bacterial diversity associated with seeds collected from native range populations in comparison to those collected from invasive populations. Sequencing of the 16S rDNA gene identified 119 bacterial isolates from 15 genera, with Curtobacterium strains being common in both ranges. Several differences in bacterial genera were found among ranges and sites: Dermacoccus, Frigoribacterium, Kocuria, Pantoea and Phyllobacterium taxa were each unique to seeds from the native populations, while Brevundimonas, Microbacterium, Rhizobium and Sphingomonas taxa were only found in the invasive seeds. The genus Paraburkholderia occurred in all invasive-range seeds but was not isolated from the native-range. Bacillus and Paenibacillus co-occurred in seeds collected from all invaded sites, but the simultaneous presence of both taxa was not found in native-range seeds. We propose that the bacterial endophytes present in invasive-range seeds may be important players for the invasiveness of A. longifolia, due to their role as plant growth promoters, providing extra capabilities helping acacia expansion.

Genetic discrimination of button mushroom Agaricus bisporus by DNA fingerprinting using RAPD marker

The investigation was conducted for DNA fingerprinting and genetic diversity analysis of five button mushroom strains (Agaricus bisporus-6, Agaricus bisporus-2, Agaricus bisporus-3, Agaricus bisporus-8 and Agaricus bisporus-5) using eight decamer RAPD primers (OPA01, OPA02, OPA03, OPA04, OPA07, OPB17, OPB12 and OPA10). A modified CTAB technique was used to isolate DNA. RAPD analysis resolved 152 scorable bands, 89 bands were monomorphic and 63 bands were polymorphic. The primer OPB17 amplified the highest number of band (30) and OPA01 amplified the lowest number of bands (09). The primer OPA04 produced the 8 polymorphic bands. Thus, it showed higher level of polymorphism (80%). Dendrogram based on linkage distance using Unweighted Pair Group Method of Arithmetic Means (UPGMA) indicated segregated of five button mushroom strains into two main clusters. Only Agaricus bisporus-6 (V1) grouped in cluster 1 (C1) while the major cluster C2 included all other strains, as well as V2 (Agaricus bisporus-2), V3 (Agaricus bisporus-3), V4 (Agaricus bisporus-8) and V5 (Agaricus bisporus-5). At the linkage distance of 50.5, the major cluster C2 formed sub-cluster C2A (Agaricus bisporus-3) and C2B (Agaricus bisporus-2, A. bisporus-8 & A. bisporus-5). Overall results from the dendrogram indicated that the V1 (Agaricus bisporus-6) button mushroom was shown to be outliers in the dendrogram, that is different from other strains because of its unique genetic makeup and high yields of this starin. The present work revealed that the DNA fingerprinting of five button mushroom strains based on RAPD showed significant different among the strains.

Genomic insights into virulence, antimicrobial resistance, and adaptation acumen of Escherichia coli isolated from an urban environment.

Evolutionary patterns of E. coli bacteria convey that they evolve into highly pathogenic forms by acquiring fitness advantages, such as AMR, and various virulence factors through the horizontal gene transfer (HGT)-mediated acquisition of MGEs. However, limited research on the genetic profiles of environmental E. coli, particularly from India, hinders our understanding of their transition to pathogenic forms and impedes the adoption of a comprehensive approach to address the connection between environmentally dwelling E. coli populations and human and veterinary public health. This study focuses on high-resolution genomic analysis of the environmental E. coli isolates aiming to understand the genetic similarities and differences among isolates from different environmental niches and uncover the survival strategies employed by these bacteria to thrive in their surroundings. Our approach involved molecular characterization of environmental samples using PCR-based DNA fingerprinting and subsequent WGS analysis. This multidisciplinary approach is likely to provide valuable insights into the understanding of any potential spill-over to human and animal populations and locales. Investigating these environmental isolates has significant potential for developing epidemiological strategies against transmission and understanding niche-specific evolutionary patterns.

A customizable series of microbiology lab activities exploring a foodborne outbreak to enhance student recruitment to a biology program.

As educators at a small university, we are constantly trying to find new and innovative ways of getting high school students interested in a degree in Biology at our school. Thus, we designed an outreach program to draw interested high school students to our campus and participate in a day-long outbreak investigation. The investigation is composed of six distinct activities, each taking between 15 min and 1 h of active time. These activities can be used in conjunction or individually to engage students with basic epidemiology and microbiology. The modules included in this recruitment event are outbreak interviews, DNA fingerprinting analysis, Gram staining, examination of microbial diagnostic tests, use of high-performance liquid chromatography to analyze toxins, and examination of potential food preparation contamination. Our first event was a success, with all participants reporting that they enjoyed their time at the University and found the faculty and staff helpful. One of the students even said, "I wish all school was like this." The goal of this event was to increase potential student interest and enrollment in our program. We hope that in sharing our experience here we can provide other instructors with a menu from which to pick and choose inexpensive, easy, and engaging activities for high school and introductory college students.

Comparison of Different DNA Isolation Protocols in Old and New Insect Samples

Insects belong to the Arthropoda phylum and are the most numerous animal group in the world, with more than 1.000.000 species. Insects ensure the sustainability of life on earth by pollinating plants, improving soil texture by decomposing organic materials, and providing nutrients to humans. DNA isolation is a necessity for performing analyses such as Sanger sequencing, DNA fingerprinting, and gene-genome analysis. Isolated insect DNA samples can be used to carry out studies such as species identification, taxonomic relations, comparison of insect-plant and –microfauna relations, revealing genomic, population, and genetic diversity, bio-geography determination, combating agricultural pests, etc. In this study, it is aimed to compare three different isolation methods in terms of time and quality for obtaining genetic material from museum samples (old) and new samples of insects. The samples used in this investigation belong to the same insect species of Cerambycidae family (Coleoptera). Samples collected at most 9-12 months ago are considered as “new specimen”, whereas “old specimens” consist samples of 7-28 years old. Three DNA isolation protocols: Phenol-Chloroform, Salting Out and DArT seq, are compared in this study. Considering quality gel images and A260/280 and A260/230 values in newly collected samples, the best results in terms of quality were obtained with the phenol-chloroform method. When A260/280 values were examined alone, DArT seq protocol appears to be the most appropriate protocol in terms of purity in both old and new insect samples. In terms of time, the Phenol-chloroform method was found to be the shortest protocol lasting for about 2 h. Accordingly, the phenol-chloroform method was deduced to be the better choice for both old and new insect samples. After concentration adjustments, the obtained DNAs can be used for the next experimental stages or stored as stock material at -20 ºC. Determining the appropriate protocol to obtain high-quality DNA in a short time is important for the continuation of the studies. Our findings are important in terms of accelerating the studies for identification and determining systematic status and especially in examining the taxonomic relationships of the insect species. Using molecular taxonomy in addition to classical taxonomy allows the identification of insects on a species basis. These types of studies will generate useful information for researchers who study insect molecular biology.

DNA Fingerprinting and Genetic Diversity Analysis in Advanced Clones of Sugarcane (Saccharum sp. complex) Using STMS Markers

DNA Fingerprinting and Genetic Diversity Analysis in Advanced Clones of Sugarcane (Saccharum sp. complex) Using STMS Markers

Erroneous Patient Tissue Contaminants in 1574 Surgical Pathology Slides: Impact on Diagnostic Error and a Novel Framework for Floater Management.

Tissue contaminants on histology slides represent a serious risk of diagnostic error. Despite their pervasive presence, published peer-reviewed criteria defining contaminants are lacking. The absence of a standardized diagnostic workup algorithm for contaminants contributes to variation in management, including investigation and reporting by pathologists. To study the frequency and type of tissue contaminants on microscopic slides using standardized criteria. Using these data, we propose a taxonomy and algorithm for pathologists on "floater" management, including identification, workup, and reporting, with an eye on patient safety. A retrospective study arm of 1574 histologic glass slides as well as a prospective study arm of 50 slide contamination events was performed. Using these data we propose a structured classification taxonomy and guidelines for the workup and resolution of tissue contamination events. In the retrospective arm of the study, we identified reasonably sized benign tissue contaminants on 52 of 1574 slides (3.3%). We found size to be an important parameter for evaluation, among other visual features including location on the slide, folding, ink, and tissue of origin. The prospective arm of the study suggested that overall, pathologists tend to use similar features when determining management of potentially actionable contaminants. We also report successfully used case-based ancillary testing strategies, including fluorescence in situ hybridization analysis of chromosomes and DNA fingerprinting. Tissue contamination events are underreported and represent a patient safety risk. Use of a reproducible classification taxonomy and a standardized algorithm for contaminant workup, management, and reporting may aid pathologists in understanding and reducing risk.

Isolation, Identification and Determination of Saccharomyces cerevisiae Yeast Species from The Wines Made by Spontaneous Fermentation Using Papazkarası Grapes from Thrace Region

Especially in large-scale commercial wine production, fermentation is usually carried out by using the species of Saccharomyces cerevisiae yeast cultures. Standard wine yeast starter cultures are brought from abroad and used in industrial winemaking in our country. Thus, in course of time, the wines of all producers began to show similar properties. Today, studies focus on terroir wines production with local characteristics by using the countries' own local wine yeasts as a starter. Within the scope of this study Papazkarası grapes were collected from 4 vineyards with different characteristics, such as viticulture practices, microclimatic conditions and locations in the borders of Edirne and Kırklareli. In addition, the grapes were also collected from the vineyard in Tekirdağ Viticulture Research Institute. Spontaneous fermentation was done by crushing the collected grapes in the laboratory. At the end of the fermentation, yeast isolations were made from the musts to YPD medium and a total of 66 isolates were obtained as a result of purification. Fermentation rate, H2S production amount, growth at high temperature, growth at high sugar concentration, resistance to high ethanol, ability to grow at low pH values, resistance to SO2, and volatile acid analysis were done to determine whether they meet the technological requirements for basic winemaking, together with two commercial wine yeasts. DNA sequencing analyzes were made by selecting 15 of the isolates that were found to have the necessary characteristics and it was determined that they belonged to the Saccharomyces cerevisiae species. DNA fingerprinting analysis was performed using delta 12-21 primers to determine the strain differences of the isolates determined to belong to the same species. By DNA fingerprint analysis, it was determined that 9 out of 15 isolates were different strains.

The Genues Trichoderma: Ecologicological Diversity, Taxonomic Classification and Its Agricultural, Human Health, Industrial and Environmental Applications

The genus Trichoderma is a diverse group of free-living fungi in the family Hypocreaceae (class Ascomycetes), that are living at different ecosystems in a wide range of climatic zones and that can be found all over the globe. The common ecological nich of the genus Trichoderma includes Natural soils, Decaying wood, Agricultural Habitats, Endophytes and mushroom related substrates. Trichoderma classified base on their morphological and cultural characteristics, conidiophore structure as well as the size of conidia. Now adays, molecularmethods including DNA fingerprinting and sequence analysis of multiple genes (ITS1- 5.8 rDNA-ITS2 and genes encoding translation-elongation factor 1-alpha (tef1) as well as some specific molecular databases have been used for taxonomic classification of this fungi. Trichodermahave been used agriculture biological control of plant diseases and as plant growth promoter, in industry as sources of cellulolytic and hemicellulolytic enzymes used in different industries, in human health producer of secondary metabolites that have clinical importance and in enviromt they are as a potential biodegrader of toxic compounds and soil bioremediation.Therefore, this review article presented the ecological diversiy, taxonomic classification and application of genus Trichoderma.

The effects of 21 cytological and nucleic acid binding dyes on autosomal and Y-chromosomal STR markers using new generation STR amplification kits

Before DNA fingerprinting analysis, many biochemical and histopathological testing are conducted on a forensic biological sample. The samples are exposed to cytological and nuclear binding dyes for their visualization under a microscope. The present study assessed the usability of these biological samples exposed to 21 routinely used histological and nuclear binding dyes for forensic DNA examination in a simulated experiment. Wright's stain, Hematoxylin, Coomassie Brilliant Blue, and Evan's Blue did not show any effect on the amplification of autosomal STR markers. Y-STRs showed higher robustness in presence of 10 dyes. Wright's stain showed the least effect on the generation of complete autosomal and Y-STR profiles. Mobility issues in capillary electrophoresis were observed in the presence of Eosin yellowish, Coomassie Brilliant Blue, and Hematoxylin for autosomal STRs and Wright's stain, Orcein, Malachite Green, Nigrosin, Bromophenol blue, and Fast green for Y STRs. Peak heights of the respective Y STR markers showed a mixed result in comparison to the positive control. In autosomal STR analysis, the peak heights showed a sharp decrease in comparison to the positive control.

Development of SLAF-Sequence and Multiplex SNaPshot Panels for Population Genetic Diversity Analysis and Construction of DNA Fingerprints for Sugarcane.

A genetic diversity analysis and identification of plant germplasms and varieties are important and necessary for plant breeding. Deoxyribonucleotide (DNA) fingerprints based on genomic molecular markers play an important role in accurate germplasm identification. In this study, Specific-Locus Amplified Fragment Sequencing (SLAF-seq) was conducted for a sugarcane population with 103 cultivated and wild accessions. In total, 105,325 genomic single nucleotide polymorphisms (SNPs) were called successfully to analyze population components and genetic diversity. The genetic diversity of the population was complex and clustered into two major subpopulations. A principal component analysis (PCA) showed that these accessions could not be completely classified based on geographical origin. After filtration, screening, and comparison, 192 uniformly-distributed SNP loci were selected for the 32 chromosomes of sugarcane. An SNP complex genotyping detection system was established using the SNaPshot typing method and used for the precise genotyping and identification of 180 sugarcane germplasm samples. According to the stability and polymorphism of the SNPs, 32 high-quality SNP markers were obtained and successfully used to construct the first SNP fingerprinting and quick response codes (QR codes) for sugarcane. The results provide new insights for genotyping, classifying, and identifying germplasm and resources for sugarcane breeding

Use of SSR Markers for the Exploration of Genetic Diversity and DNA Finger-Printing in Early-Maturing Upland Cotton (Gossypium hirsutum L.) for Future Breeding Program

DNA fingerprinting and genetic diversity analysis of 79 early-maturing upland cotton (Gossypium hirsutum L.) cultivars were performed using Simple Sequence Repeat (SSR) molecular markers. Out of 126 pairs of SSR primers, we selected 71 pairs that gave good polymorphisms and clear bands, had good stability, and showed even distribution on the cotton chromosomes, and 142 polymorphic genotypes were amplified. The average number of alleles amplified with the SSR primers was 2.01. The polymorphism information content (PIC) of the markers ranged from 0.1841 to 0.9043, with an average of 0.6494. The results of fingerprint analysis showed that nine varieties had characteristic bands, and at least six primer pairs could be used to completely distinguish all 79 cotton accessions. Using NTSYS-pc 2.11 cluster analysis, the genetic similarity coefficients between the cotton genotypes ranged from 0.3310 to 0.8705, with an average of 0.5861. All cotton accessions were grouped into five categories at a similarity coefficient of 0.57, which was consistent with the pedigree sources. At the same time, the average genetic similarity coefficients of early-maturing upland cotton varieties in China showed a low-high-low pattern of variation over time, revealing the development history of early-maturing upland cotton varieties from the 1980s to the present. This also indirectly reflects that in recent years, China’s cotton breeders have focused on innovation and have continuously broadened the genetic resources for early-maturing upland cotton.

GENETIC VARIABILITY OF ARROWROOT (MARANTA ARUNDINACEA L.) IN YOGYAKARTA PROVINCE, INDONESIA BASED ON ISSR ANALYSIS

The cultivation of arrowroot (Maranta arundinacea L.) in Indonesia, particularly in Yogyakarta Province has a great potential to be developed. This study aims to determine the genetic variability and analyze the intraspecific relation of arrowroot using Inter Simple Sequence Repeats (ISSR) markers as basic informations for considerations in the character selection of arrowroot cultivation in Yogyakarta. Exploratory survey method was occured in Gunungkidul, Kulon Progo, Sleman, and Bantul Districts to collect cultivar accessions. Accessions were replanted in Sawitsari Research Station. DNA isolation from the leaves of 7 moths old accessions was done using CTAB buffer solution. The DNA fingerprinting analysis was carried out using the result of DNA amplification with 4 ISSR markers. The polymorphism data then used for phenetic analysis using UPGMA algorithm and Baroni-Urbani Busser similarity coefficient to form dendrogram. Total of 5 local cultivars were found, identified as ‘Sili’, ‘Sembowo’,’ Sugo’, ‘Kebo’, and ‘Teropng’, each showed distinct rhizome morphological characters. The ISSR-PCR analysis resulted high polymorphism with 68,17% polymorphism mean and mean of polymorphic band was 6,75. Dendrogram resulted 4 clusters in 80% similarity index. Cluster A, B.I., and B.II.b consisted of ‘Sili’, ‘Teropong’, and ‘Kebo’ cultivars, respectively, while the cluster B.II.a gathered ‘Sugo’and ‘Sembowo’ cultivars.

Rhizospheric and endophytic Pseudomonas aeruginosa in edible vegetable plants share molecular and metabolic traits with clinical isolates.

Pseudomonas aeruginosa, a leading opportunistic pathogen causing hospital-acquired infections, is also commonly found in agricultural settings. However, there are minimal attempts to examine the molecular and functional attributes shared by agricultural and clinical strains of P. aeruginosa. This study investigates the presence of P. aeruginosa in edible vegetable plants (including salad vegetables) and analyses the evolutionary and metabolic relatedness of the agricultural and clinical strains. Eighteen rhizospheric and endophytic P. aeruginosa strains were isolated from cucumber, tomato, eggplant, and chili directly from the farms. The identity of these strains was confirmed using biochemical and molecular assays. The genetic and metabolic traits of these plant-associated P. aeruginosa isolates were compared with clinical strains. DNA fingerprinting and 16S rDNA-based phylogenetic analyses revealed that the plant- and human-associated strains are evolutionarily related. Both agricultural and clinical isolates possessed plant-beneficial properties, including mineral solubilization to release essential nutrients (phosphorous, potassium, and zinc), ammonification, and the ability to release extracellular pyocyanin, siderophore, and indole-3 acetic acid. These findings suggest that rhizospheric and endophytic P. aeruginosa strains are genetically and functionally analogous to the clinical isolates. In addition, the genotypic and phenotypic traits do not correlate with plant sources or ecosystems. This study reconfirms that edible plants are the potential source for human and animal transmission of P. aeruginosa.

Diversity of Gyrinops versteegii from several agarwood plantation on Lombok Island (Indonesia) as raw material of Gyrinops tea

Abstract. Wangiyana IGAS, Supriadi, Nikmatullah A, Sunarpi, Triandini IGAAH. 2021. Diversity of Gyrinops versteegii from several agarwood plantation on Lombok Island (Indonesia) as raw material of Gyrinops tea. Biodiversitas 23: 178-186. The purpose of this research is to examine the diversity of Gyrinops versteegii as a raw material of agarwood Gyrinops tea based on morphology, phytochemical, and molecular characters. G. versteegii samples were taken from 5 agarwood plantation on Lombok Island: Lingsar, Rarung, Mataram, Kekait, and Pejaring. Variation of G. versteegii stem, leaves, and fruit was the morphology character observed in this study. Qualitative phytochemical screening, quantitative tannin concentration, and the hedonic score of Gyrinops tea were the essential phytochemical character in this study. DNA fingerprinting and RAPD analysis were the molecular characters of this study. All of those characters were used in numeric-phenetics analysis to construct a dendrogram. MVSP program with UPGMA algorithm as clustering method and Simple Matching Coefficient for similarity analysis was used to construct dendrogram. The result has shown variation topology of dendrogram based on morphology, phytochemical, molecular, and combination character. However, all dendrograms had the same number of clusters and cluster members. G. versteegii kekait and G. versteegii Pejaring were grouped to cluster 1 while G. versteegii Rarung and G. versteegii Mataram were grouped to cluster 2. G. versteegii Lingsar was grouped later on the node after cluster 1 or 2. It could be concluded that G. versteegii from Lombok Island Plantation could be divided into three different cluster groups based on the variation of morphology, chemical, and molecular characters.