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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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Cryptic diversity of mudskipper genus Boleophthalmus (Gobiiformes: Oxudercidae) from the north coast of East Java, Indonesia FAIZAH NUR SHABRINA; KUNTO WIBOWO; TUTY ARISURYANTI
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/d250148

Abstract

Abstract. Shabrina FN, Wibowo K, Arisuryanti T. 2024. Cryptic diversity of mudskipper genus Boleophthalmus (Gobiiformes: Oxudercidae) from the north coast of East Java, Indonesia. Biodiversitas 25: 412-420. Mudskippers of genus Boleophthalmus are commonly found in the Indo-Pacific area. This study aimed to examine the diversity of the genus Boleophthalmus from the north coast of East Java Province, Indonesia by employing the mitochondrial COI gene for DNA barcoding and morphological characterization. Ten individuals of this genus were analyzed. According to the similarity percentage evaluated using Basic Local Alignment Search Tool (BLAST) and Barcode of Life Data (BOLD) identification engines, all the individuals were identified as Boleophthalmus boddarti Pallas, 1770. However, phylogenetic analysis revealed that three of the individuals were identified as B. boddarti, and seven were identified as Boleophthalmus pectinirostris Linnaeus, 1758 originated from East Java, which is separated from the clade of B. pectinirostris from East Asia population. These results were supported by the genetic distance of 8.93%-13.81% and the morphological characteristics determined by principal component analysis (PCA). PCA revealed that B. boddarti and B. pectinirostris are primarily distinguished by the number of (longitudinal) scales (69-75 versus 113-123), length of second dorsal fin base (42.3-43.9 versus 38.1-49.0), and caudal fin length (18.1-22.4 versus 17.5-21.6). Further detailed studies are needed to clarify whether the seven individuals belonging to B. pectinirostris complex should be regarded as a new species or a new subspecies.
DNA barcoding of Burgo chicken from Bengkulu, Indonesia, based on the cytochrome oxidase gene sub unit I mitochondria DNA AHMAT FAKHRI UTAMA; JARULIS JARULIS; SIPRIYADI SIPRIYADI; IZUL MIFTAKHUL JANNAH
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/d241148

Abstract

Abstract. Utama AF, Jarulis, Sipriyadi, Jannah IM. 2023. DNA barcoding of Burgo chicken from Bengkulu, Indonesia, based on the cytochrome oxidase gene sub unit I mitochondria DNA. Biodiversitas 24: 6268-6275. The Burgo chicken provides a genetic source of one crossbreed chicken in Bengkulu Province. However, genetic information on Burgo chickens is not yet available, while the population of this chicken continues to decline. Research on DNA barcoding using the cytochrome oxidase subunit I mtDNA gene was conducted to obtain DNA barcodes and the relationship between Burgo chickens and other chicken species based on the COI mtDNA gene. Blood samples were obtained from Burgo chickens belonging to the Bengkulu Burgo chicken hobbyist community. Collected blood was isolated following the dneasy® blood and tissue kit protocol based on the spin-column protocol procedure, Qiagen. Amplification of genomic DNA using Polymerase Chain Reaction. The product was electrophoresed on a 1.2% agarose gel and visualized under UV light using Gel Documentation System, Axygen. Samples with bright DNA bands proceeded to the sequencing process. Sequencing results were analyzed using MEGA 11.0 software. The results showed that the target length of the Burgo chicken band was in accordance with the primer design used (752pb). SNPs were obtained at 10 specific sites in Burgo chickens and had a species barcode at site 746. The intraspecies genetic distance was 0.6%, interspecies 1.2%, and with the outgroup 14.5%, there were 12 haplotypes from all samples (n=15). Based on the result, we can conclude that the Burgo chicken is closely related to the red jungle fowl compared to other chicken species.
Plant species composition and diversity in traditional agroforestry landscapes on Siberut Island, West Sumatra, Indonesia GUSMARDI INDRA; ERIZAL MUKHTAR; SYAMSUARDI SYAMSUARDI; CHAIRUL CHAIRUL; MANSYURDIN MANSYURDIN
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/d250345

Abstract

Abstract. Indra G, Mukhtar E, Syamsuardi, Chairul, Mansyurdin. 2024. Plant species composition and diversity in traditional agroforestry landscapes on Siberut Island, West Sumatra, Indonesia. Biodiversitas 25: 1286-1296. The research conducted on Siberut Island, situated in the western part of Sumatra, focuses on traditional communities practicing an agroforestry land management system. This study aimed to identify the plant species within agroforestry land, their respective uses, and techniques for adapting these species to the landscape in two villages, Matotonan in South Siberut District and Bojakan in North Siberut District, Mentawai Islands. Data collection involved direct observation, unstructured interviews for plant species utilization, and transects with a 10m width along contour lines for landscape data. The findings revealed that Siberut's traditional agroforestry land, known as "Pomunean," is divided into Tinugglu and Mone categories based on land slope, proximity to riverbanks, and planted species. Plant species in agroforestry land served nine primary purposes, including staple and additional food, construction, furniture, medicine, firewood, traditional rituals, and commercial activities. Tinugglu land exhibited a higher Landscape Utilization Value Index (LUVI) at 57% compared to Mone land (43%). Regarding specific plant types, Metroxylon sago (Bojakan) and Durio zybethinus (Matotonan) had the highest LUVI values. These findings shed light on the vital role that traditional ecological knowledge and sustainable land management play in maintaining the delicate balance between human livelihoods and the preservation of natural ecosystems.
The role of local pigs for economic and socio-cultural in East Flores District, East Nusa Tenggara, Indonesia Arkadius Suban Keray; Rini Widiati; Tri Anggraeni Kusumastuti
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/d250124

Abstract

Abstract. Keray AS, Widiati R, Kusumastuti TA. 2024. The role of local pigs for economic and socio-cultural in East Flores District, East Nusa Tenggara, Indonesia. Biodiversitas 25: 214-222. This study was conducted to identify the cultural activities related to swine rearing in East Flores District and analyze the decision making in choosing the types of rearing practice. Based on the survey using questionnaires from 120 pig farmers, which was conducted purposive, were those who had at least three sows for breeding, fattening with five heads of pigs, and combined with sows and sires. To identify the role of local pigs, as many as 3 informants consist of traditional leaders, farmers, and Agriculture Extension Officers, and analyzed by multinomial logistic regression model. The results showed that the traditional rituals that required the sacrifice of pigs included the ceremonies marking the start of building residential and traditional community buildings and dowry (belis)  presentation in a wedding ceremony. The decision-making in choosing the rearing practice was influenced by pig ownership, care system (P<0.01), and income (P<0.05). Farmers who have small scale will choose extensive and fattening systems to reduce feed costs. Those practicing breeding are still maintaining local breeds because traditional rituals require it. Further efforts are needed to increase the populations of local breeds as well as cross-bred pigs to maintain the ceremonies in traditional rituals and income generation.
Morphological and molecular identifications of ectoparasites infesting the gills of scalloped spiny lobster Panulirus homarus Linnaeus, 1758 KISMIYATI KISMIYATI; YUSUF TAUFIK HIDAYAT; MUHAMAD AMIN
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/d250143

Abstract

Abstract. Kismiyati, Hidayat YT, Amin M. 2024. Morphological and molecular identifications of ectoparasites infesting the gills of scalloped spiny lobster Panulirus homarus Linnaeus, 1758. Biodiversitas 25: 372-378. Ectoparasite infestation has been reported to cause stress, weaken the immune system, and disturb respiratory systems, which lead to death in cultured spiny lobsters. Many lobster farmers have reported an infestation of ectoparasites in cultured scalloped spiny lobsters in West Nusa Tenggara, Indonesia. However, fewer studies have been conducted to identify the ectoparasite-infesting scalloped spiny lobster cultured in West-Nusa Tenggara Province. Thus, using morphological and molecular approaches, the present study aimed to identify ectoparasites infesting scalloped spiny lobsters (Panulirus homarus Linnaeus, 1758). A total of 30 scalloped spiny lobsters were collected from lobster farmers at Ekas, East Lombok, West Nusa Tenggara, Indonesia, and ectoparasites were observed and identified morphologically under a microscope as well as confirmed using CO1 gene sequences. The results showed that the ectoparasites were morphologically identified as Octolasmis angulata Aurivillius, 1894 and Octolasmis lowei Darwin, 1852. Similarly, based on the mtDNA sequence of the COI region (~721 bp length), the ectoparasite was also referred to O. angulata (95.65% similarity) and Octolasmis lowei (~683 bp length) with a similarity of 98.75%. These results suggest that ectoparasite has become one potential disturbance in lobster aquaculture; therefore, preventing or curing strategies should be developed.
Short Communication: Evaluation of antibacterial activities and phytochemical composition of ethanolic extract of Diplazium esculentum FESKAHARNY ALAMSJAH; SASQIA FANDINI; MILDAWATI MILDAWATI
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/d250304

Abstract

Abstract. Alamsjah F, Fandini S, Mildawati M. 2024. Short Communication: Evaluation of antibacterial activities and phytochemical composition of ethanolic extract of Diplazium esculentum. Biodiversitas 25: 937-941. Antibacterial agents are crucial in fighting infections by stopping or inhibiting pathogenic bacteria growth. Diplazium esculentum (Retz.) Sw., is a natural resource with great potential in traditional medicine. This study aimed to investigate the antibacterial effectiveness of ethanol extract of D. esculentum against two common bacteria, Pseudomonas aeruginosa and Staphylococcus epidermidis. This research was done using disc diffusion technique with comprehensive phytochemical screening. The results revealed antibacterial properties of the ethanolic extract of D. esculentum against P. aeruginosa and S. epidermidis. The most potent antibacterial activity was observed at 80 and 60% concentrations against P. aeruginosa, resulting in inhibition zones with 5.90 mm and 5.47 mm diameters. A similar pattern was also observed against S. epidermidis, where 80% concentration showed significant efficacy, with an inhibition zone of 5.69 mm diameter. Phytochemical analysis result revealed the presence of various secondary metabolites, including alkaloids, steroids, polyphenols, tannins, flavonoids, and saponins. These phytochemical compounds contribute antibacterial properties and have promising potential for further research to develop natural antibacterial agents.
The impact of Saccharomyces cerevisiae stimulation on various physiological indicators of oats (Avena sativa) exposed to salinity HIBA FOUAD ABDULFATAH; ENAS FAHD NAJI
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/d241238

Abstract

Abstract. Abdulfatah HF, Naji EF. 2023. The impact of Saccharomyces cerevisiae stimulation on various physiological indicators of oats (Avena sativa) exposed to salinity. Biodiversitas 24: 6753-6760. The objective of the current study is to examine the effects of different levels of salinity, specifically 0, 2.5, and 4.5 ds m-1(S1, S2, S3), on diverse physiological parameters in two principal oat cultivars (Avena sativa L.), Pimula (A1), and Genzania (A2), priming with Saccharomyces cerevisiae for 24 hours at a concentration of 0 and 6 g.L-1. The study employed a completely randomized design with three repetitions for each treatment and was conducted at the laboratory of the College of Science, University of Anbar. The Genzania cultivar that was not stimulated with yeast demonstrated the highest percentage of total chlorophyll content (2.28 mg. g. plant-1), statistically significant (P?0.05) compared to the lowest rate recorded by the Pimula cultivar (1.94 mg. g. plant-1). While no significant differences appeared between both cultivars stimulated with yeast under the influence of the salinity concentrations, the S2 treatment had the highest rate and significantly more than the S3 treatment. This demonstrates increased tolerance of the yeast priming cultivars to salinity treatment. The A2 cultivar was characterized by the highest rate of proline in plants stimulated and not stimulated with yeast, with significant differences from the A1 cultivar. However, the S3 treatment had the highest rate of proline (20.96?mole g plant-1) in the stimulated plants, with a higher significance than treatment S2. There was a statistically significant in the electrolyte leakage rate between the non-stimulated cultivars. In contrast, no significant differences appeared for the plants stimulated with yeast, indicating an increase in their tolerance to salinity. Priming seeds with yeast extract has been shown to improve important physiological characteristics in plants, such as total chlorophyll content, proline content, and electrolyte leakage, indicating the effectiveness of yeast in increasing plant resilience to salt stress.
Vegetation diversity and habitat suitability modeling of the invasive plant Bellucia pentamera in conservation forests of West Sumatra, Indonesia SOLFIYENI SOLFIYENI; ADLI FADHLAN; AL AZIZ; GITO SYAHPUTRA; ANISA AZZAHRA; MILDAWATI MILDAWATI
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/d250238

Abstract

Abstract. Solfiyeni S, Fadhlan A, Aziz A, Syahputra G, Azzahra A, Mildawati M. 2024. Vegetation diversity and habitat suitability modeling of the invasive plant Bellucia pentamera in Conservation Forests of West Sumatra, Indonesia. Biodiversitas 25: 781-791. The invasive plant Bellucia pentamera has spread to several regions in Indonesia, including the province of West Sumatra. Mapping the distribution of this invasive plant needs to be done to facilitate its management. offers a comprehensive approach to delineate the potential ecological range of a species and assess habitat suitability. This study aimed to evaluate the impact of B. pentamera invasion on vegetation diversity, conduct potential distribution mapping, and assess B. pentamera habitat suitability in West Sumatra conservation forests. The study utilized observational methods to determine coordinate points for B. pentamera presence and conducted vegetation analysis. The results from the vegetation analysis revealed disparities in composition and structure across three study areas, with diversity indices ranging from 2.60 to 3.84. The similarity index between study areas was relatively low, below 50%. The MaxEnt analysis delineated suitable locations for B. pentamera using the ROC curve (AUC) model, yielding values of 0.947 for training data and 0.923 for testing data. MaxEnt modeling identified suitable habitat for B. pentamera concentrated at Lima Puluh Kota, Tanah Datar, Padang, Solok and South Solok districts. This study's findings indicate a broad distribution of this species, with over 5% of the habitat deemed suitable for B. pentamera.
Wood decomposers on six community timber species in two different locations MARLINA WIDYA NURHADI; ARINANA ARINANA; ANINDYA INTAN RAHMAWATI; ELIS NINA HERLIYANA; RIKI ANDIKA; SETIAWAN KHOIRUL HIMMI
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/d241225

Abstract

Abstract. Nurhadi MW, Arinana A, Rahmawati AI, Herliyana EN, Andika R, Himmi SK. 2023. Wood decomposers on six community timber species in two different locations. Biodiversitas 24: 6629-6640. Wood has a close relationship with termites and fungi as decomposers. Decomposers are important as dead organic matter is broken down into elements and returned to the soil. This study aims to analyze the amount of wood attacked by termites and fungi on six types of community timber during six months of testing at two different locations, analyze the degree of damage, and identify the species of termites and fungi that attack them. The research was conducted in two locations: the Arboretum of the Faculty of Forestry and Environment of IPB and a residential area in Bogor Asri, Cibinong Sub-district, Bogor District. The wood tested were Acacia mangium, Falcataria moluccana, Anthocephalus cadamba, Maesopsis eminii, Pinus merkusii, and Hevea brasiliensis. Tests were conducted based on ASTM D 1758-06. Infested wood increased with the time tested, and infestation was higher in the arboretum (75%) than in the residential area (39.4%). The highest level of wood damage in the arboretum was Hevea brasiliensis (35.4 g); in residential, it was Pinus merkusii (18.9 g). The subterranean termite types found during the six months of testing are Macrotermes sp., Microtermes sp., Schedorhinotermes sp., and Odontotermes sp. The weathering fungi types found during the six months of testing were  Aspergillus sp., Mucor sp., Trichoderma sp., Gliocladium sp., Mycelia sterilia, and red fungus. Soil type, moisture, and ambient temperature also strongly favored the development of decomposer life found in the two research sites.
Cloning and expression of Rubisco Like Protein (RLP) from halophilic bacterium Chromohalobacter salexigens BKL 5 IRWAN SUDARMANTO; LINCE SITOHANG; SAIFUR ROHMAN; WAYAN TUNAS ARTAMA
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/d250429

Abstract

Abstract. Sudarmanto I, Sitohang L, Rohman S, Artama WT. 2024. Cloning and expression of Rubisco Like Protein (RLP) from halophilic bacterium Chromohalobacter salexigens BKL 5. Biodiversitas 25: 1605-1614. This research seeks to identify and determine the Rubisco-like protein characteristics from Chromohalobacter salexigens BKL 5 tested using a recombinant method approach. C. salexigens BKL 5 is a halophilic bacterium found in Bledug Kuwu Mud, Central Java. The Open Reading Frame (ORF) gene encoding Rubisco-like protein from that bacterium was successfully amplified using the polymerase chain reaction method using the primers we designed. Cloning of that gene on the pCold plasmid was carried out using the double digest method with the restriction enzymes NdeI and EcoRI. The results of plasmid transformation in Escherichia coli BL 21 were successful, indicating that the bacterial culture was grown in Luria Bertoni agar media containing the antibiotic ampicillin. Overexpression protein of the transformed Escherichia coli BL 21 shows that the effective temperature that produces maximum results is 16°C. The results of sequencing and phylogenetic analysis showed that the protein belongs to the Rubisco family, namely Rubisco-like protein with a residue of 429 amino acids and a weight of 46 kDa. Prediction of 3D structures using the Alphafold tool gives an accuracy above 90%. Observation of the 3D structure shows that glutamic acid is more distributed on the surface of the protein which is important for protein solubility. Tests with SOPMA showed that this protein was dominated by random coil structure of 41.96% which was identical to that found in bacterial species in extreme habitats. The dynamic molecular analysis using Yasara at 10 ns showed that the protein had a tendency to undergo considerable deformation but remained stable.

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