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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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Short Communication: DNA barcodes and phylogenetic of striped snakehead and ocellated snakehead fish from South Sumatra, Indonesia MOCHAMAD SYAIFUDIN; MARINI WIJAYANTI; SEFTI HEZA DWINANTI; MUSLIM MUSLIM; MUHAMMAD MAHENDRA; SHELY MARLIANA
Biodiversitas Journal of Biological Diversity Vol. 21 No. 3 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210350

Abstract

Abstract. Syaifudin M, Wijayanti M, Dwinanti SH, Muslim, Mahendra M, Marliana S. 2020. DNA barcodes and phylogenetic of striped snakehead and ocellated snakehead fish from South Sumatra, Indonesia. Biodiversitas 21: 1227-1235. This research aimed to identify the sequences of cytochrome c oxidase subunit I gene mitochondrial DNA (COI mtDNA), to construct a phylogenetic tree of striped snakehead (Channa striata) and ocellated snakehead (Channa pleuropthalma), and to measure water quality of Kelekar River, Indralaya, Ogan Ilir District and Danau Burung Besar River, Penukal Abab Lematang Ilir (PALI) District in South Sumatra, Indonesia. The research procedures consisted of DNA isolation, amplification by PCR (Polymerase Chain Reaction) and sequencing of fragment COI mtDNA. The length of nucleotide was 604 bp for striped snakehead and 587-604 bp for ocellated snakehead. Optimum annealing temperature was 500C for 15 seconds with 30 cycles. The result of BLAST analysis showed that striped snakehead from Kelekar and Danau Burung Besar River had 100% identity to striped snakehead from Java-Bali and furthest (97%) with striped snakehead from India. Ocellated snakehead had 100% similarity with the same species from Musi Banyuasin and Banjarmasin; and furthest (83%) with Channa limbata from Myanmar. Water quality in Kelekar River were temperature 31-31.60C, pH 4.76-4.96, dissolved oxygen 2.7-3.0 mg/L, ammonia <0.009 mg/L, total alkalinity 20 mg/L, and turbidity 62.5-63 cm. Meanwhile in Danau Burung Besar River showed temperature (29.3-30.70C), pH (3.6-6.7), dissolved oxygen (1.31-3.76 mg/L), ammonia (0.17-0.20 mg/L), and turbidity (50-90 cm).
Diversity and distribution of microalgae in coastal areas of East Java, Indonesia UMI ZAKIYAH; MULYANTO; LUCIA TRI SUWANTI; MOCHAMAD DONNY KOERNIAWAN; EKO AGUS SUYONO; ARIEF BUDIMAN; Ulfah Juniarti Siregar
Biodiversitas Journal of Biological Diversity Vol. 21 No. 3 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210340

Abstract

Abstract. Zakiyah U, Mulyanto, Suwanti LT, Koerniawan MD, Suyono EA, Budiman A, Siregar UJ. 2020. Diversity and distribution of microalgae in coastal areas of East Java, Indonesia. Biodiversitas 21: 1149-1159. Indonesia is well known as one of hotspot for biodiversity, including marine resources. However, Indonesia biodiversity has declined rapidly due to the changes in the aquatic environmental quality as the consequence of human activities. Biodiversity loss has been well studied in larger organisms, however, less is known for microorganisms, such as microalgae. Microalgae have received much attention recently due to its potential as renewable energy sources. This study aimed at describing biodiversity and distribution of microalgae in coastal areas of East Java and Madura, Indonesia. Six sites, i.e. Trenggalek and Sendangbiru representing south coast, Banyuwangi and Situbondo representing north coast of East Java, Pasongsongan and Pamekasan representing Madura north and south coast, respectively were sampled, which representing different background of anthropogenic development in these areas. Results showed that seawater condition in all sites is still good, with average pH 8.0 despite intense human activities, such as ecotourism, fishing and boat harbor, as well as residential area that has the potential to produce a lot of waste. Totally, there were 35 genera from all locations with varying abundance in each location and diversity index ranging from 1.105-3.312. Although most genera belonged to Bacyllariophyta, domination indices showed that there was not any single specific domination in all locations. Morisita indices showed that most distribution gave positive values indicating clumped dispersion of microalgae in all locations. Higher Shannon-Weaver indices characterized the south coast of East Java and Madura compared to the north coast of East Java area, which corresponded with lower dominancy indices.
Molecular characterization of lactic acid bacteria producing edible biofilm isolated from kimchi FADILLA SAPALINA; Endah Retnaningrum
Biodiversitas Journal of Biological Diversity Vol. 21 No. 3 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210315

Abstract

Biofilm is a community of microorganisms that interrelated and covered by an extracellular polymer matrix. This biofilm can be produced by Lactic acid bacteria (LAB) which was edible for human and animal.  Therefore, it possible to be applied in the food and health industry. One source of LAB is kimchi, as fermented food from Korea and it has good benefits for health. This research aimed to obtain LAB from kimchi that can produce edible biofilms and to identify LAB producing edible biofilms based on the 16S rRNA gene. Isolation of lactic acid bacteria from kimchi cultured in MRS agar medium containing 1% CaCO3, biofilm production test with biofilm assay method and zeolite as a substrate to adherent cells. For amplification of 16S rRNA gene used primer 27F and 1492R. The isolate of KA2, KA5, KB1, and KC4 isolated from kimchi and could produce biofilms with the highest biofilm formation at 48 hours incubation time. Based on molecular identification with 16S rRNA gene sequencing, the four isolates identified as Lactobacillus brevis species.
DNA barcoding of razor clam Solen spp. (Solinidae, Bivalva) in Indonesian beaches ninis trisyani margono; DWI ANGGOROWATI RAHAYU
Biodiversitas Journal of Biological Diversity Vol. 21 No. 2 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210207

Abstract

Abstract. Trisyani N, Rahayu DA. 2020. DNA barcoding of razor clam Solen spp. (Solinidae, Bivalva) in Indonesian beaches. Biodiversitas 21: 478-484. Solen spp. are shells with various morphological characteristics with a wide distribution of tropical and subtropical beaches, including Indonesia. The identification of Solen spp. is generally based on its morphological characteristics. This method is very problematic due to specimens share similarity in morphology and color. This study was using DNA barcode as a molecular identification tool. The bivalve COI sequence was amplified using PCR and molecular phylogenetic analysis using the Neighbor-Joining method. The amplified COI gene has a length of about 665 bp. The purpose of this study was to evaluate genetic variation and compare the phylogenetic Solen spp. in Indonesian waters. The composition of the nucleotide bases of Solen spp. the comparative species are A = 26.79%, C = 23.16%, G = 19.17% and T = 30.93%. The total nucleotide base A + T was 57.72%, while G + C was 42.33%. The results of phylogenetic analysis showed that Solen spp. Cirebon and Jambi are in one clade with Solen regularis with genetic distance 0.000 - 0.002. Solen spp. Surabaya, Bangkalan, Pamekasan, and Sumenep are in separate clades and are related to Solen grandis, Solen stricus and Solen lamarckii with genetic distance from 0.146 - 0.156. The diversity of nucleotide was 0.9780 and was divided into 12 haplotypes.
Population structure, vegetation composition and economic potentials of Parkia timoriana in Meru Betiri National Park, East Java, Indonesia Anik Nur Hidayati; ERVIZAL A.M. ZUHUD; NURI ANDARWULAN
Biodiversitas Journal of Biological Diversity Vol. 21 No. 1 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210126

Abstract

Abstract. Hidayati AN, Zuhud EAM, Andarwulan N. 2020. Population structure, vegetation composition and economic potentials of Parkia timoriana in Meru Betiri National Park, East Java, Indonesia. Biodiversitas 21: 203-210. Kedawung (Parkia timoriana (DC.) Merr.) is one of rare medicinal plant species because it is only found in a small part of Indonesia. P. timoriana has high ecological and economic potential because it contains various active compounds such as anticancer. This study was aimed to investigate the population structure, vegetation community composition, and distribution, as well as the potential production and economic values of P. timoriana in rehabilitation zone in Meru Betiri National Park, East Java, Indonesia. The methods used were vegetation analysis, direct observation, and in-depth interviews with selected respondents using purposive sampling. We found that P. timoriana population at the study sites was only at tree and pole stages, while no sapling and seedling was found. This condition implies that regeneration of P. timoriana at the study sites was not happening which can threaten its sustainability in the future. P. timoriana dominated the vegetation at the studied sites which were indicated by the highest importance value index. Utilization of P. timoriana by the local community was by selling the seeds to medicinal industries or used as herbal medicine. While having conservation values, the management of P. timoriana stands in Andongrejo Resort also had the potential to generate economic values up to 17.6 billion rupiahs. Considering the great economic potential of P. timoriana and to ensure sustainability, so that nursery, breeding and regeneration of P. timoriana should be made in order to obtain the best quality seeds.
Molecular identification of amylase-producing thermophilic bacteria isolated from Bukit Gadang Hot Spring, West Sumatra, Indonesia Aulia Ardhi; Arina Nadenggan Sidauruk; Nabella Suraya; Nova Wahyu Pratiwi; Usman Pato; Saryono
Biodiversitas Journal of Biological Diversity Vol. 21 No. 3 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210319

Abstract

Abstract. Ardhi A, Sidauruk AN, Suraya N, Pratiwi NW, Pato U, Saryono. 2020. Molecular identification of amylase-producing thermophilic bacteria isolated from Bukit Gadang Hot Spring, West Sumatra, Indonesia. Biodiversitas 21: 994-1000.  Amylase is one of the hydrolytic enzymes that is widely used in a wide number of industrial processes such as food, fermentation, textile, paper, detergent, and pharmaceutical industries. Amylase produced by thermophilic bacteria may be thermostable, which is very beneficial in several applications requiring high temperature, for example, the process of gelatinization, liquefaction, and saccharification are performed in high temperature involved in the starch processing. In this study, the amylase-producing ability of thermophilic bacteria isolated from Bukit Gadang hot spring, West Sumatra, Indonesia, was checked and followed by molecular identification. Thirteen isolates that were successfully isolated from the hot springs were microscopically and macroscopically characterized, biochemically tested, and determined their amylase enzyme activity both qualitatively and quantitatively. The isolate that performed the best amylase activity was identified using the molecular technique. The DNA sequencing was carried out in 16S rRNA and continued with BLAST search for species identification. The result of molecular identification showed that the isolate with the best amylase activity was identified as Bacillus licheniformis. The optimum amylase production  (231.33 U/ml)  and the best enzyme-specific activity  (101.79 U/mg) were obtained at the incubation time of 36 hours.
Short communication: Effects of the various source areas of Indonesian bay leaves (Syzygium polyanthum) on chemical content and antidiabetic activity Indah Dewijanti; WIBOWO MANGUNWARDOYO; ASTARI DWIRANTI; MUHAMMAD HANAFI; NINA ARTANTI
Biodiversitas Journal of Biological Diversity Vol. 21 No. 3 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210345

Abstract

Abstract. Dewijanti ID, Mangunwardoyo W, Dwiranti A, Hanafi M, Artanti N. 2020. Short communication: Effects of the various source areas of Indonesian bay leaves (Syzygium polyanthum) on chemical content and antidiabetic activity. Biodiversitas 21: 1190-1195. Bay leaves (Syzygium polyanthum (Wight) Walp) are from an Indonesian plant species belonging to the Myrtaceae family. The Indonesian name for this plant is salam; it is found in Sumatra, Kalimantan, and the Java Islands. Its leaves are the part of the plant commonly used. Salam leaves are usually consumed by people as a food flavoring, but are also used as a traditional antidiabetic medicine. The purpose of this study was to discover the effects of salam leaves’ origins on their chemical content and antidiabetic activity. For this reason, salam leaf samples were collected from three different provinces in Java (West Java, Central Java, and East Java). The samples were extracted by boiling in water. Phytochemical screening, chemical analysis using TLC, HPLC, LC-MSMS, and FTIR, and antidiabetic in vitro testing using alpha-glucosidase inhibition methods were conducted on the salam leaves’ water extracts. The results showed that salam leaf extracts from all three provinces contained quercetin. However, the salam originating from East Java also contained coniferin, the salam from Central Java contained juncusol, and the salam from West Java contained retucine. The salam leaves originating from East Java showed the lowest antidiabetic activity, whereas salam leaf extract showed significantly higher antidiabetic activity. As conclusion, a plant’s growth origin affects its chemical content and antidiabetic activity.
Genetic variation and phylogenetic relationships of Thelymitra javanica (Orchidaceae: Orchidoideae) in East and Central Java, Indonesia I Made Saka Wijaya; Budi Setiadi Daryono; Purnomo
Biodiversitas Journal of Biological Diversity Vol. 21 No. 3 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210343

Abstract

Abstract. Wijaya IMS, Daryono BS, Purnomo. 2020. Genetic variation and phylogenetic relationships of Thelymitra javanica Blume (Orchidaceae: Orchidoideae) in East and Central Java, Indonesia. Biodiversitas 21: 1174-1181. Thelymitra J.R. Forst & G. Forst is a terrestrial orchid genera and mainly distributed in Australia as a center of its diversification. Moreover, Thelymitra javanica Blume is the only species of Thelymitra found in Asia, especially in Indonesia. In Australia and New Zealand, most of Thelymitra species easily found in lowland, whereas, T. javanica in Indonesia preferred to grows near the peaks of mountains around 2,000-3,000 m asl. The high altitude correlated with high light intensity and lower soil nutrients which require specific adaptation of plant to survive. The wide range of adaptation could be due to the presence of genetic variability among populations of Thelymitra. Therefore, this study was carried out to assess the genetic variability and phylogenetic relationships of T. javanica in East and Central Java. The genetic variability of Thelymitra was evaluated by molecular approaches, which is preferably utilized to determine the plant taxonomy to establish the taxonomic uncertainties. ITS-nrDNA is a popular DNA marker that widely used in phylogenetic study among various taxa. Sequences were analyses using Maximum Likelihood method with 11 in-group, 6 interspecies out-group of Thelymitra, and 2 intergeneric out-group of Thelymitrinae subtribe. The result showed that ITS-nrDNA sequences of T. javanica have no variation in nucleotide compositions and showing polytomy branch in cladogram. Thelymitra javanica also has a close relationship with Thelymitra longifolia J.R. Forst & G. Forst that are endemic to New Zealand.
Seed longevity of Buchanania siamensis in reclaiming salt-affected areas in Thailand Yongkriat KU-OR; NISA LEKSUNGNOEN; CHATCHAI NGERNSAENGSARUAY; TUSHAR ANDRIYAS
Biodiversitas Journal of Biological Diversity Vol. 21 No. 2 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210241

Abstract

Abstract. Ku-or Y, Leksungnoen N, Ngernsaengsaruay C, Andriyas T. 2020. Seed longevity of Buchanania siamensis Miq. in reclaiming salt-affected areas in Thailand. Biodiversitas 21: 743-747. Inland salinity is a grave threat to soil fertility as it causes loss of arable land. Salt-tolerant species, such as Buchanania siamensis Miq., can be used for the reclamation of land affected by salinity. We investigated the appropriate conditions to store the seeds of B. siamensis and the storage duration after which the seeds can still germinate. Storage methods included cooling at 4°C and storing at room temperature (between 25-30°C). Seeds kept at 4°C had low germination (6.75% ± 1.71), with longevity of only up to a week, compared to seeds stored at room temperature, which had germination of 94% ± 4.00 and could be stored for more than 200 days. Seed-longevity test was conducted at 14 levels (the number of storage days). Germination was reduced by 50% after 3.5 months, indicating that the seed could only be stored for the short term. The seeds were classified as having an intermediate behavior in which the germination increased exponentially with increasing seed moisture content. We recommend that seeds be stored at a temperature between 25 and 30°C, with sowing done within 3.5 months to obtain germination at or above 50%.
Coat protein gene of a PStV-Bm isolate from West Nusa Tenggara, Indonesia Nur Indah Julisaniah; SUHARJONO; RETNO MASTUTI; ESTRI LARAS ARUMINGTYAS
Biodiversitas Journal of Biological Diversity Vol. 21 No. 3 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210308

Abstract

Abstract. Julisaniah NI, Suharjono, Mastuti R, Arumingtyas EL. 2020. Coat protein gene of a PStV-Bm isolate from West Nusa Tenggara, Indonesia. Biodiversitas 21: 903-909. Peanut stripe virus (PStV) is a single-stranded positive-sense RNA virus capable of infecting peanut plants. An isolate of PStV (PStV-Bm) was collected from a peanut field in the Bima District, West Nusa Tenggara Province, Indonesia and the coat protein (CP) gene of this virus (CP-PStV) was extracted from the viral RNA and analyzed using reverse transcription-polymerase chain reaction methods. The CP-PStV gene of PStV-Bm was aligned with several PStV genes deposited in the Genbank (http://www.ncbi.nml.nih.gov). Based on the nucleotide sequence of the CP gene, PStV-Bm was grouped into a similar cluster with other PStVs that originated from Indonesia with a similar index, ranging from 96.8% to 98.9%. Genetic similarity (about 96.1%) was also observed between PStV-Bm and PStV from the USA. This genetic similarity indicated that viruses from adjacent regions have high genetic relationships. Some amino acid differences were observed in PStV-Bm that may be typical of this strain.

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