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Biodiversitas Journal of Biological Diversity
Published by Universitas Sebelas Maret
ISSN : 1412033X     EISSN : 20854722     DOI : https://doi.org/10.13057/biodiv/d230231
Core Subject : Science, Agriculture,
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology
The Biodiversitas Journal was first published in 2000 by the Department of Biology, FMNS, Universitas Sebelas Maret, Surakarta, Indonesia, then in 2006 it was co-published by the Society for Indonesian Biodiversity and that department; since 2017 it was also hosted by Smujo. From 2003-2012 it was accredited by DGHE, Ministry of Education, R.I., since 2014 was indexed by Scopus, where DOAJ and Google Scholar was indexed first.
Arjuna Subject : Biokimia, Genetika dan Biologi Molekuler - Biokimia, Genetika dan Biologi Molekuler (Lain-Lain)
Articles 6,269 Documents
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Morphological study and DNA fingerprint pattern of Goniothalamus tapis and G. umbrosus (Annonaceae) using M13 marker and its taxonomic implication IMAM MAHADI; FATHURRAHMAN FATHURRAHMAN; NERY SOFIYANTI; AGUS SUSATYA
Biodiversitas Journal of Biological Diversity Vol. 24 No. 11 (2023)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d241152

Abstract

Abstract. Mahadi I, Fathurrahman F, Sofiyanti N, Susatya A. 2023. Morphological study and DNA fingerprint pattern of Goniothalamus tapis and G. umbrosus (Annonaceae) using M13 marker and its taxonomic implication. Biodiversitas 24: 6299-6306. The species of Goniothalamus (Blume) JD Hooker & Thomson (Annonaceae) is widely considered a source of traditional medicine and containsoniothalamin, which is used for anti-cancer and anti-bacterial drugs. Goniothalamus tapis and G. umbrosus are traditional medicines in Sumatra, Indonesia, and Malaysia Peninsula, respectively. The community uses this plant as a source of traditional medicinal ingredients. Clinically, Goniothalamus contains the compound goniothalamin, an anti-cancer and anti-bacterial drug. The existence of this plant is gradually maintained. G. tapis is often used as a traditional medicine for the Malay community in Sumatra, and G. umbrosus is widely used by the Malay community in the Peninsular Malaysia. These two plants are morphologically similar, but the two species are different. Some researchers consider these plants to be the same. For this reason, it needs to be studied by combining two methods, both molecular and morphological. G. tapis and G. umbrosus are species of the Goniothalamus distributed in Sumatra and Peninsular Malaysia. Their taxonomic status needs to be clarified due to the morphological character similarity. This study aimed to study the morphological characters of G. tapis and G. umbrosus as well as their DNA fingerprint pattern using M13 Marker. The morphological examination showed that G. tapis and G. umbrosus characters are distinguished by leaf, flower, and fruit. This result is supported by a DNA fingerprint pattern using an M13 marker. The results show that these two species are different both in terms of morphology and fingerprints. So, it can be concluded that these two species are different.
Segregation analysis and floral phenotype of T2 transgenic yellow cosmos (Cosmos sulphureus Cav.) carrying neomycin phosphotransferase II gene in second generation MUHAMMAD GHAUTS AL AZAM MUCHYIDDIN; WIDHI DYAH SAWITRI; MUHAMMAD BURHANUDDIN IRSYADI; TANTRI SWANDARI; AZIZ PURWANTORO
Biodiversitas Journal of Biological Diversity Vol. 25 No. 4 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d250441

Abstract

Abstract. Muchyiddin MGAA, Sawitri WD, Irsyadi MB, Swandari T, Purwantoro A. 2024. Segregation analysis and floral phenotype of T2 transgenic yellow cosmos (Cosmos sulphureus Cav.) carrying neomycin phosphotransferase II gene in second generation. Biodiversitas 25: 1711-1717. The seed of transgenic yellow cosmos (Cosmos sulphureus Cav.) lines harbouring neomycin phosphotranferase II (nptII) gene have been obtained from our previous studies. The nptII selectable marker gene is commonly used for developing a method to estimate the number of targeted gene integrated into the genome. In order to produce successful clones, it is important to ensure that transgenes are inherited sexually as the dominant trait in T2 progeny. This study aimed to obtain the segregation patterns of nptII gene in two populations derived from open- and self-pollinated and evaluated floral phenotypic of T2 transgenic yellow cosmos. The molecular analysis of transgenic yellow cosmos was conducted by PCR and the obtained data was analyzed using a Chi-Square test. The results showed that transgenes were inherited in 1:1 for transgenic and wild-type in both self- and open-pollinated populations. Therefore, it indicated that T2 transgenic plants were still unstable and evolved continuously to segregate independently in the over generation. Surprisingly, the morphological changes were detected in transgenic plants. The mixture of ligulate and tubular types in ray floret was found in some of the flower types in T2 yellow cosmos. In this case, nptII gene may diverge in apparently random genome insertion. This insertion would induce morphological changes in the ray floret type of flower since recombination estimates varied among transformation events.
Molecular characterization of pathogenic Aeromonas jandaei bacteria isolated from cultured walking catfish (Clarias sp.) DINI SISWANI MULIA; NOERHALIZA RAHMAN DWI; SUWARSITO SUWARSITO; BOBY MUSLIMIN
Biodiversitas Journal of Biological Diversity Vol. 25 No. 3 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d250334

Abstract

Abstract. Mulia DS, Dwi NR, Suwarsito, Muslimin B. 2024. Molecular characterization of pathogenic Aeromonas jandaei bacteria isolated from cultured walking catfish (Clarias sp.). Biodiversitas 25: 1185-1193. Aeromonas spp. is pathogenic bacteria capable of causing fish disease, including walking catfish (Clarias sp.). In bacteria, virulence genes play a significant role in determining pathogenicity, while resistance genes influence resistivity. Therefore, this study aimed to determine molecular characterization of pathogenic Aeromonas jandaei bacteria isolated from walking catfish. The purposive sampling method was used to obtain diseased walking catfish from aquaculture ponds in Banyumas District, Central Java Province, Indonesia. The identification of bacteria was molecularly carried out based on 16S rDNA, followed by the detection of virulence genes on aer/haem, alt, ast, flaA, lafA, and fstA, as well as resistance genes on tet-A, strA-strB, and qnrA. The results of molecular analysis showed that three isolates from Singasari, namely BmSL-02, BmSL-04, and BmSL-07, were closely related to A. jandaei strain CDC0787-80 with a similarity rate and query coverage of 99.86% and 99%, respectively. Meanwhile, isolates from Cikawung, including BmCL-02, BmCL-05, and BmCL-07 were closely related to A. jandaei strain ATCC 49568. A total of six A. jandaei isolates had aer/haem virulence genes while alt, ast, and fstA were not found. BmSL-04 and BmCL-07 isolates had flaA gene, while four isolates including BmSL-02, BmSL-04, BmSL-07, and BmCL-07 had lafA gene. Additionally, BmCL-05 had tetA resistance gene, while the strA-strB and qnrA genes were not detected in all isolates. A. jandaei isolates were resistant to bacitracin, tetracycline, and gentamycin, but BmSL-04, BmSL-07, BmCL-02, and BmCL-05 were sensitive to chloramphenicol. This study provided valuable information on molecular characteristics of A. jandaei, serving as guidance in effective control and monitoring of isolates from Indonesia, specifically Banyumas, Central Java.
Study of Curcuma diversity from Central Java, Indonesia for sunscreen and antioxidant activity based on quantitative phytochemical analysis HENNY NURHASNAWATI; REKSI SUNDU; ANITA SUKMAWATI
Biodiversitas Journal of Biological Diversity Vol. 24 No. 12 (2023)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d241249

Abstract

Abstract. Nurhasnawati H, Sundu R, Sukmawati A. 2023. Study of Curcuma diversity from Central Java, Indonesia for sunscreen and antioxidant activity based on quantitative phytochemical analysis. Biodiversitas 24: 6880-6887. Indonesia is home to various plants, including those of the genus Curcuma. This study aimed to determine the effect of total phenolic and flavonoid content of Curcuma on antioxidant activity and SPF values. It is known that this rhizome contains secondary metabolites such as flavonoids and phenols, which are known to have antioxidant potential and are believed to act as natural ingredients for sun protection products. The samples used in this study were rhizomes of five Curcuma species from Central Java, namely C. aeruginosa, C. longa, C. mango, C. xanthorrhiza, and C. zedoaria. Alkaloids, flavonoids and tannins are present in all samples. UV-Vis spectrophotometry was used with the following results: the flavonoid total content ranged from 0.94-243.5 mg QE/g, while the total phenolic from 11.27-109.23 mg GAE/g. The DPPH and ABTS test for antioxidant activity showed that C. longa had the highest activity with an IC50 of 78.79 and 0.4273 ppm. The highest SPF values in C. longa were 31.55-36.97 (high protection). The results of the data analysis using the Spearman correlation test revealed a significant correlation between the antioxidant activity and SPF with the flavonoid and phenolic content of the Curcuma extracts.
Sound management strategies in swiftlet ranching from Southern Thailand NANTACHAI PONGPATTANANURAK; SANGSAN PHUMSATHAN; TANIT SOMLEEWONG; PHRUT RASRI
Biodiversitas Journal of Biological Diversity Vol. 24 No. 11 (2023)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d241144

Abstract

Abstract. Pongpattananurak N, Phumsathan S, Somleewong T, Rasri P. 2023. Sound management strategies in swiftlet ranching: An experiment from Southern Thailand. Biodiversitas 24: 6218-6228. Edible-nest swiftlets are well-known for the medicinal properties of their nests. With the global demand, swiftlet ranching has emerged as a vital industry. Swiftlet houses employ acoustic stimuli to entice wild swiftlets. However, the use of loud acoustic stimuli in swiftlet houses has inadvertently led to sound pollution in urban areas. This study investigates the interplay of acoustic stimuli, loudness, and environmental factors in attracting swiftlets while reducing noise. Our findings highlight the critical role of sound management in swiftlet ranching. Higher loudness, especially around 80-90 dB, significantly increases swiftlet activity and maximizes daily counts. Furthermore, optimizing loudness levels, particularly at around 80 dB, extends the swiftlet presence duration, offering valuable ranching benefits. Strategic loudness management is recommended to balance attraction and noise control. Timing acoustic stimulation during mornings and late afternoons aligns with swiftlets' natural behavior. Lowering loudness to under 70 dB during midday minimizes disturbances, especially in populated areas. Weather conditions, including outdoor absolute humidity and temperature, also influence swiftlet attraction. The study finally provides guidance for complying with environmental noise regulations, demonstrating that sound levels of 70-80 dB effectively control noise. These insights support swiftlet ranching while respecting urban communities and coexisting harmoniously.
Parasitoid of coffee berry borer, Hypothenemus hampei Ferrari (Coleoptera: Curculionidae) at Bogor District, West Java, Indonesia HIKSA MAULANA SAPUTRA; NINA MARYANA; PUDJIANTO PUDJIANTO
Biodiversitas Journal of Biological Diversity Vol. 24 No. 12 (2023)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d241206

Abstract

Abstract. Saputra HM, Maryana N, Pudjianto. 2023. Parasitoid of coffee berry borer, Hypothenemus hampei Ferrari (Coleoptera: Curculionidae) at Bogor District, West Java, Indonesia. Biodiversitas 24: 6447-6453. The coffee berry borer (CBB), Hypothenemus hampei Ferrari (Coleoptera: Curculionidae), is an essential pest of coffee plants that can cause loss and decrease in the quality of coffee berries. Parasitoids were expected to affect the presence of coffee berry borer in the ecosystem as one of its natural enemies. This study aimed to identify and describe the parasitoid of CBB in Bogor District, West Java, Indonesia. The study was conducted from June 2022 to January 2023 on three coffee cultivation located in three sub-districts in Bogor District, i.e., Cijeruk, Dramaga, and Sukamakmur. This study collected attacked coffee berries by CBB from coffee cultivation that kept the coffee berry until the parasitoids emerged and the parasitoids were identified; the morphological characters and descriptions of parasitoids CBB were presented. Ten species of Hymenopteran parasitoids belonging to five families were found. These parasitoids were Microgastrinae, Mendesellinae (Braconidae), Trissolcus sp. (Scelionidae), Anagyrus sp., Marxella sp., Procheiloneurus sp., Pararhopella sp., Parablastothrix sp. (Encyrtidae), Pronotalia sp. (Eulophidae), and Pteromalus sp. (Pteromalidae). The parasitoids of CBB in Bogor District were quite diverse, but their abundance was low.
Population dynamics of Variola albimarginata Baissac, 1953 and Variola louti Fabricius, 1775 (Perciformes: Serranidae) in Sulawesi Sea, Indonesia DEWI SHINTA ACHMAD; MUH. SALEH NURDIN; APRIS ARA TILOME; ABIGAIL M. MOORE
Biodiversitas Journal of Biological Diversity Vol. 25 No. 3 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d250310

Abstract

Abstract. Achmad DS, Nurdin MS, Tilome AA, Moore AM. 2024. Population dynamics of Variola albimarginata Baissac, 1953 and Variola louti Fabricius, 1775 (Perciformes: Serranidae) in Sulawesi Sea, Indonesia. Biodiversitas 25: 978-989. The lyretail groupers Variola louti Fabricius, 1775 and Variola albimarginata Baissac, 1953 (Epinephelinae) are valuable foodfishes. IUCN Red List assessments classified both species as Least Concern, while noting that some stocks are overfished. The purpose of this study on the population dynamics of Variola groupers in Kwandang Bay was to evaluate the exploitation level for both species in this important grouper fishing area of the Sulawesi Sea, Indonesia. Population dynamics parameters were calculated based on length-frequency data collected from October 2022 to September 2023 using the ELEFAN I response surface analysis option in FISAT II. The asymptotic length at infinity TL? was 54.90 cm for V. louti and 54.40 cm for V. albimarginata with von Bertalanffy growth function K values 0.54 and 0.55, respectively. Recruitment occurred throughout the year, with monthly percentages of 1.08-13.52 % and 1.61-14.99%, respectively. Natural and fishing mortality were M = 1.04/year-1 and F = 1.17/year-1 for V. louti and M = 1.05/year-1 and F= 2.56/year-1 for V. albimarginata giving F/M ratios of 1.13:1 and 2.44:1. Beverton and Holt yield per recruit analysis gave exploitation rates (E = 0.53/year-1 and E = 0.71/year-1) exceeding the maximum sustainable value Emax = 0.37/year-1, indicating overexploitation of both species. To achieve the optimum exploitation rate of E50 = 0.24, fishing effort needs to be reduced by 29% for V. louti and 47% for V. albimarginata. Management options include setting a minimum legal size with recommended values of 32-33 cm and temporary closures during the peak reproductive season in May-June.
Mangrove distribution to support biodiversity management in Teluk Bintuni District, West Papua, Indonesia PETRUS KASIHIW; RONI BAWOLE; JONNI MARWA; AGUSTINUS MURDJOKO; ALEXANDER WIHYAWARI; YUNO HEIPON; REINARDUS LIBORIUS CABUY; NITHANEL MIKAEL HENDRIK BENU; FRANCINE HEMATANG; NICOLAUS Y. LEFTUNGUN
Biodiversitas Journal of Biological Diversity Vol. 25 No. 2 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d250223

Abstract

Abstract. Kasihiw P, Bawole R, Marwa J, Murdjoko A, Wihyawari A, Heipon Y, Cabuy RL, Benu NMH, Hematang F, Leftungun NY. 2024. Mangrove distribution to support biodiversity management in Teluk Bintuni District, West Papua, Indonesia. Biodiversitas 25: 644-653. Mangroves play an important role in coastal ecosystems, but the areas of mangroves are decreasing globally. Understanding the ecological and geographical distribution of mangroves will be useful to develop sustainable management and policy. Thus, this study aimed to analyze the ecological and geographical distribution of mangroves in Teluk Bintuni, West Papua, Indonesia. The distribution of mangroves was investigated to see the relationships between elevation and the number of individual mangroves at the family level. Vegetation data were collected by setting 180 circular plots and geographical data were obtained from secondary sources. Our study revealed that Rhizophoraceae family was found in all plots with 97.78% presence, whereas Acanthaceae and Meliaceae families were found in half of the plots with 65% and 60.56% presence, respectively. Lythraceae, Primulaceae, Malvaceae, and Arecaceae were only found in 15% of the plots. Elevation affected significantly the presence of mangroves which there mainly occurred in elevation between 10-30 m asl, while they were lower in below 10 m asl and above 30 m asl. Species belonging to Acanthaceae and Lythraceae, such as those from the genera of Avicennia and Sonneratia, were found more abundant in the low elevation (seaward zone) than in the higher elevation (landward zone). In contrast, species belonging to Meliaceae and Rhizophoraceae were more abundant in the landward zone with the presence of genera Xylocarpus, Bruguiera, Ceriops, and Rhizophora. The distribution of Arecaceae, Malvaceae, and Primulaceae did not show a significant pattern where they appeared randomly in mangrove forests. Geographically, 12.43% area of Teluk Bintuni District was mangroves which mainly occurred in the eastern and southern parts. Based on forest status, 2.23%, 35.60%, 10.46%, and 51.71% of mangroves in Teluk Bintuni occur in non-forestry use areas (Area Penggunaan Lain/APL), conservation forest (Hutan Konservasi) in the form of nature reserve, protected forest (Hutan Lindung), and production forest (Hutan Produksi), respectively. As the mangrove ecosystem has been part of local people, the specific management to support biodiversity in mangrove forests must be put officially in the development program.
Diversity of the genus Chondrilla L. (Asteraceae) in Eastern Europe ALEXANDR S. KASHIN; ALENA S. PARKHOMENKO; ANNA O. KONDRATI; TATIANA A. KRITSKAYA; ARTEM V. BOGOSLOV; IRINA V. SHILOVA
Biodiversitas Journal of Biological Diversity Vol. 25 No. 5 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d250506

Abstract

Abstract. Kashin AS, Parkhomenko AS, Kondratieva AO, Kritskaya TA, Bogoslov AV, Shilova IV. 2024. Diversity of the genus Chondrilla L. (Asteraceae) in Eastern Europe. Biodiversitas 25: 1901-1910. The genus Chondrilla (Asteraceae) has a complex taxonomic structure due to widespread apomictic reproduction. This study aimed to identify the variability and clarify the status of Chondrilla species growing in Eastern Europe (European Russia and Western Kazakhstan). The study of morphological variability in Chondrilla species was assessed using 28 morphometric parameters. Moreover, 840 specimens from 28 populations of 8 Chondrilla species from Eastern Europe were analyzed. Principal Component Analysis (PCA), Nonmetric Multi-Dimensional Scaling (NMDS), recursive decomposition, and random forest algorithm were used for analysis. The ordination methods divided the studied samples into two groups: the first group included samples of C. ambigua and C. pauciflora, and the second group included all remaining samples. Following the resulting binary trees, obtained by recursive decomposition method and the random forest algorithm, a determination key was compiled for the Chondrilla species of Eastern Europe. The high level of morphological variation in Chondrilla and its distribution characteristics revealed in this study by numerical taxonomy and recursive decomposition methods, along with our previous studies results, show that only C. ambigua is a morphologically and genetically well-separated species, including C. pauciflora as a triploid cytotype; C. canescens, C. graminea, C. latifolia and C. juncea are synonyms with the priority name C. juncea and should be considered as subspecies; and C. brevirostris and C. laticoronata are hybrids with C. ambigua as maternal parent.
Systematic assessment of salt tolerance based on morpho-physiological traits and genes related in inbred rice lines at the seedling stage RENY HERAWATI; MARULAK SIMARMATA; MASDAR MASDAR; BAMBANG S. PURWOKO; MISWATI MISWATI
Biodiversitas Journal of Biological Diversity Vol. 25 No. 1 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d250102

Abstract

Abstract. Herawati R, Simarmata M, Masdar, Purwoko BS, Miswati. 2023. Systematic assessment of salt tolerance based on morpho-physiological traits and genes related in inbred rice lines at the seedling stage. Biodiversitas 24: 6256-6267. Salinity stress is an abiotic constraint that limits rice productivity. Salinity-tolerant traits are very complex and involve many genes. Therefore, it is difficult to conclude how rice plants respond to salinity stress. This study aimed to investigate the genetic potential of 19 rice genotypes for salt tolerance as well as the quantitative impacts of varying salinity stress levels on a subset of the genotypes. Salinity tolerance is identified in two stages: assessing salinity stress in nutrient solutions using 0, 5,000 (EC 7.8 dS.m-1), and 10,000 ppm (EC 15.62 dS.m-1). Gene expression analysis detected genes controlling salinity stress tolerance using two pairs of specific primers: DST (Drought Salt Tolerance) and OsAPX (ascorbate peroxidase). The results showed that all lines could survive high salinity stress up to EC 7.8 dS.m-1. Biplot is reflected in K-means grouping the 21 rice genotypes into three major groups, namely salt-sensitive (1 genotype, 4.75%), moderately salt-tolerant (2 genotypes, 9.5%), and salt-tolerant-very tolerant (18 genotypes, 85.7%). The DST and OsAPX1 genes showed both genes were expressed under salinity stress, although some lines showed smears or even did not appear at all, namely in G3 and G7. This result is consistent with the PCA analysis, where genotypes G3 and G7 are categorized as moderately tolerant. This study reveals that screening at the seedling stage combined with marker-assisted selection can identify tolerant genotypes. Furthermore, conducting field trials on soil salinity with EC > 4 dS.m-1 is recommended to obtain salinity-tolerant lines as potential new varieties.

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