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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 6,315 Documents
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Fungal Basidiomycete Ceratobasidium theobromae DNA obtained directly from cocoa petioles Muhammad Junaid; David Guest; AGUS PURWANTARA
Biodiversitas Journal of Biological Diversity Vol. 22 No. 7 (2021)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d220734

Abstract

Abstract. Junaid M, Purwantara A, Guest G. 2021. Fungal Basidiomycete Ceratobasidium theobromae DNA obtained directly from cocoa petioles. Biodiversitas 22: 2838-2843. Understanding the biology of the fastidious Basidiomycete Ceratobasidium theobromae occupying host-tissue is essential for plant disease management. Direct pathogen DNA extraction from infected plant tissue avoids the need for isolation in artificial media. We report a modified DNA isolation protocol to obtain total plant DNA designed to overcome DNA extraction and isolation problems caused by infected petioles rich in polysaccharides and phenolic substances as a primary source of gummosis. This study examined and compared total plant DNA isolated from petioles high in polysaccharides and polyphenolic compounds using two methods: conventional CTAB lysis buffer and Kits (the standard method), and a new modified CTAB protocol to address these PCR inhibitors. The modified method resulted in higher quality and quantity of C. theobromae crude DNA and amplified PCR product. The modified method produced large quantities of clear, transparent, aqueous DNA-containing lysate (crude DNA) with a clear separation between the upper crude DNA and organic waste layers. Mean DNA absorbance was 1.80, and the lowest DNA yield was 836.6 ng/µl. With the standard method, the blurred, viscous lysate obtained showed signs of gummosis, with poor separation between layers of crude DNA, polysaccharides, protein, and organic waste layers and low yield. Gel electrophoresis indicated poor quality DNA extract. We conclude that this modified method will be valuable for genetic diversity and disease studies in a range of previously challenging plant tissues and their pathogens.
The dietary, productivity, and economic value of swiftlet (Aerodramus fuciphagus) farming in East Kalimantan, Indonesia Mursidah MURSIDAH; Abubakar M. Lahjie; MASJAYA MASJAYA; YAYA RAYADIN; YOSEP RUSLIM; MEIDI B. JUDINNUR; ANDY ANDY
Biodiversitas Journal of Biological Diversity Vol. 22 No. 6 (2021)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d220663

Abstract

Abstract. Mursidah, Lahjie AM, Masjaya, Rayadin Y, Ruslim Y, Judinnur MB, Andy. 2021. The dietary, productivity, and economic value of swiftlet (Aerodramus fuciphagus) farming in East Kalimantan, Indonesia. Biodiversitas 22: 2528-2537. Edible-nest swiftlets have many health benefits. The availability of edible-nest swiftlets from caves is decreasing, while the demand for edible-nest swiftlets is getting higher. Swiftlet farming is carried out to meet this demand. The location of swiftlet farming should be close to the feeding sources. Swiftlet is flying insectivorous animals. A financial feasibility assessment is carried out to determine the feasibility of the business. This study aims to determine the composition of land cover, determine the insect order of feed sources, and analyze the production and financial feasibility of swiftlet farming. The study was carried out from June to December 2019. The composition of land cover was determined using the supervised classification method, the order of insects was known using the insect determination key, while production and financial feasibility were analyzed using the Net B/C, NPV, IRR, and PP methods. The observed location and swiftlet farming were determined purposefully. The results of this study show that the land cover was dominated by shrubs (56.58%) and secondary forest (27.3%); both types of land cover are suitable for swiftlet farming locations. The dominant insects found in shrubs and wetland shrubs are Diptera (78.25%), in rice fields are Diptera (86.7%) and in oil palm plantations are Diptera (29.4%) and Hymenoptera (27.78%). Edible-nest swiftlets harvest begins in the third year, with a production period of between 17-34 years. From the financial feasibility, it can be concluded that swiftlet farming is feasible.
Evaluating the stomach content of Wild Scalloped Spiny Lobster (Panulirus homarus) MUHAMAD AMIN; ANIS FITRIA; AKHMAD T. MUKTI; ANDI BASO MANGUNTUNGI; SHAFWAN AMRULLAH; SAHRUL ALIM; MELISSA BEATA MARTIN
Biodiversitas Journal of Biological Diversity Vol. 23 No. 12 (2022)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d231237

Abstract

Abstract. Amin M, Fitria A, Mukti AT, Manguntungi AB, Amrullah S, Alim S, Martin MB. 2022. Evaluating the stomach content of Wild Scalloped Spiny Lobster (Panulirus homarus). Biodiversitas 23: 6397-6403. The high demand for spiny lobster seeds has placed intense pressure on the lobsters’ wild stock in Indonesia. To address this issue, a hatchery was developed to produce scalloped spiny lobster larvae. However, the dietary requirements after the yolk sac has been depleted have proven to be a significant challenge. Thus, the present study aimed to identify the potential live diet of scalloped spiny lobster larvae by identifying the stomach contents of lobster larvae captured in the wild. Fifteen scalloped spiny lobsters at the post-larval stage were collected from three fishing grounds: Gerupuk Bay (Lombok Island), Tawang Bay (East Java), and Prigi Bay (East Java), Indonesia. The stomach of each scalloped spiny lobster was dissected under a dissecting microscope and its contents were observed under a binocular microscope for plankton identification and abundance. The stomach contents of scalloped spiny lobster resulted in five identified plankton species collected from Prigi Bay [Tintinnopsis sp. (37.5%), Grammatophora sp. (25%), Synedra sp. (18.8%), Phormidium sp. (4.3%), and Rhizisolenia sp. (4.3%)]; six plankton species collected from Tawang Bay [Ochromonas sp. (32.3%), Synedra sp. (20.6%), Tintinnopsis sp. (14.7%), Uronema sp. (14.7%), Coscinodiscuss sp. (2.9%), and Planktoniella sp. (2.9%)]; and six plankton species collected from Gerupuk Bay [Synedra sp. (33.3%), Chlorococcum sp. (33.0%), Phormidium sp. (13.3%), Gymnidinium sp. (6.6%), unidentified Cirripedia (3.3%), Rhizosolenia sp. (3.0%)]. Of these plankton, Synedra sp. and Rhizolenia sp. were the most common representatives in the stomach of all lobster samples. Thus, assessing these two plankton genera is highly recommended for future studies.
The anti-bacterial effect of phenolic compounds from three species of marine macroalgae ALIFAH EVI SCANIA; Abdul Razaq Chasani
Biodiversitas Journal of Biological Diversity Vol. 22 No. 6 (2021)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d220649

Abstract

Abstract. Scania AE, Chasani AR. 2021. The anti-bacterial effect of phenolic compounds from three species of marine macroalgae. Biodiversitas 22: 3412-3417. Bacterial infection is still a serious problem in human health due to many bacteria that are resistant to synthetic antibiotics. Natural antibiotics are needed for substituting synthetic antibiotics such as antibiotics derived from marine macroalgae. Marine macroalgae respond to extreme environmental conditions by producing secondary metabolites containing bioactive substances. Bioactive substances such as phenolic compounds in marine macroalgae may have an antibacterial effect on bacteria. Our research was aimed to detect the presence of phenolic compounds in three species of marine macroalgae (Ulva lactuca (Chlorophyta), Sargassum polycystum (Phaeophyta), Palmaria palmata (Rhodophyta)), and also to determine the most effective inhibition of phenols-contained extracts of marine macroalgae to the growth of Escherichia coli and Salmonella typhi. Our research was conducted through field sampling for collecting samples and laboratory work for identifying and extracting samples including qualitative testing of phenolic compounds, rejuvenating bacteria, preparing the tested bacteria, and determine the inhibition index of extracts against E.coli and S.typhi. Our results indicated that the extract of U. lactuca, S. polycystum, and P.palmata contained phenolic compounds. Phenols-contained extract of Sargassum polycystum is the most effective in inhibiting the growth of E. coli and S. typhi. The incubation temperature, the type of bacteria influence the antibacterial activity of marine macroalgae.
A spatial model of forest and land fire vulnerability level in the Dairi District, North Sumatra, Indonesia Achmad Siddik Thoha; Hesty Triani
Biodiversitas Journal of Biological Diversity Vol. 22 No. 8 (2021)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d220827

Abstract

Abstract. Thoha AS, Triani H. 2021. A spatial model of forest and land fire vulnerability level in the Dairi District, North Sumatra, Indonesia. Biodiversitas 22: 3319-3326. Fires often occur every dry season and have a significant impact on ecosystems and human activities. One of the important roles in reducing the risk of forest and land fires is the availability of updated vulnerability level maps in all vulnerable areas. The objective of this study was to determine the relationship between the driving factors for forest and land fires and hotspots and to obtain a spatial model of the distribution of vulnerability to forest and land fires in the Dairi District of North Sumatra Province. This study uses a composite mapping analysis method to obtain a spatial model and the distribution of vulnerable areas to forest and land fires. Six variables in the form of maps were used in building the model, including land cover, population density, distance from the road, distance from the river, and distance from the settlement. This study showed that the most important variable for vulnerability level model of forest and land fires was the distance from the settlement. This study also found that open land, the farthest distance to the road, the farthest distance to the river, the farthest distance to the settlement, and the densest population were the driving factors for increased fire activity. The spatial model of the vulnerability level to forest and land fires in Dairi District was Y = 0.022X1 + 0.214X2 + 0.113X3 + 0.482X4 + 0.169X5. Land cover having high-very high vulnerability level belonged to open land dominated by grass. The largest areas with a high-very high forest fire vulnerability level in Dairi District were spread over Tanah Pinem Sub-district.
Species composition, stand characteristics, aboveground biomass, and carbon stock of mangroves in Panabo Mangrove Park, Philippines JEMER A. ALIMBON; MARK RONALD S. MANSEGUIAO
Biodiversitas Journal of Biological Diversity Vol. 22 No. 6 (2021)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d220615

Abstract

Abstract. Alimbon JA, Manseguiao MRS. 2021. Species composition, stand characteristics, aboveground biomass, and carbon stock of mangroves in Panabo Mangrove Park, Philippines. Biodiversitas 22: 3130-3137. Mangrove ecosystems have been recognized for their roles in climate change mitigation through their carbon sequestration capacity. However, information on the ecology and carbon stock of mangroves is limited. Thus, this study assessed the species composition, stand characteristics, aboveground biomass, and carbon stock of mangroves in Panabo Mangrove Park, Panabo City, Davao del Norte, Philippines. Data for vegetation analysis and biodiversity assessment were collected using transect line plots method. Meanwhile, aboveground biomass estimation was conducted using nondestructive method. Twenty plots with size of 10 m x 10 m each were established to account for the stand characteristics and aboveground biomass of mangroves. Species composition data identified five species from four families. Avicennia marina was the most important species with an importance value of 153.33%. Stand structure analysis revealed a basal area of 14.65 m² ha?¹ and a mean density of 11835 stems ha?¹. Biodiversity indices indicated very low species diversity (H’ = 1.027), low species richness (R = 0.5148) and less even distribution of species (J = 0.6383). Using allometric equation, the aboveground biomass was 77.45 Mg ha?¹ with an estimated stored carbon of 37.18 Mg ha?¹ and sequestration potential of 136.44 Mg CO?ha?¹. These baseline data demonstrate that the area can store and sequester potential amounts of carbon and carbon dioxide, respectively, despite the low diversity.
Evaluation of Toraja (Indonesia) local aromatic rice mutant developed using heavy-ion beam irradiation Andi Muliarni Okasa; Rinaldi Sjahril; Muhammad Riadi; Meta Mahendradatta; Tadashi Sato; Kinya Toriyama; Kotaro Ishii; Yoriko Hayashi; Tomoko Abe
Biodiversitas Journal of Biological Diversity Vol. 22 No. 8 (2021)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d220846

Abstract

Abstract. Okasa AM, Sjahril R, Riadi M, Mahendradatta M, Sato T, Toriyama K, Ishii K, Hayashi Y, Abe T. 2021. Evaluation of Toraja (Indonesia) local aromatic rice mutant developed using heavy-ion beam irradiation. Biodiversitas 22: 3474-3481. The aromatic local Toraja rice "Pare Bau" has a good grain quality and aroma. However, it has some disadvantages, including a late heading and low yield for a modern farming system. This study aims to evaluate and select early heading as well as high yield mutant lines induced by heavy-ion beam irradiation. Furthermore, dry seeds of Pare Bau were irradiated with Argon-ion (300 keV/?m) and Carbon-ion (30 keV/?m) at RI-beam factory, RIKEN Nishina Center, Japan. The germination percentages of the M1 seeds were 49% for Pare Bau irradiated with Argon-ion (PB-A), 53% for Pare Bau irradiated with Carbon-ion (PB-C), and 70% for the Control. The 13 PB-A and 13 PB-C M1 plants were selected, and the seeds were sampled in the paddy field of Hasanuddin University (20 m asl.), Makassar. During the following planting season, the M2 generation plant was examined in Enrekang District (650 m asl.), South Sulawesi, Indonesia. Based on the early heading and a larger number of panicles, the 18 PB-A and one PB-C M3 line were selected from a total of 404 M2 survival plants. The selected lines and control were grouped into seven clusters based on the quantitative phenotypic traits, indicating the existence of genetic variability. The plant yield was significantly correlated with plant height, the number of tillers, the number of panicles, as well as grain weight per panicle, which showed that these traits are good criteria for selection.
Population genetics analysis of Phytophthora nicotianae associated with heart rot in pineapple revealed geneflow between population Auliana Afandi; Siti Subandiyah; Arif Wibowo; Ayaka Hieno; Afandi AFANDI; Supriyono Loekito; Haruhisa Suga; Koji Kageyama
Biodiversitas Journal of Biological Diversity Vol. 22 No. 8 (2021)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d220830

Abstract

Abstract. Afandi A, Subandiyah S, Wibowo A, Hieno A, Afandi, Loekito S, Suga H, Kageyama K. 2021. Population genetics analysis of Phytophthora nicotianae associated with heart rot in pineapple revealed gene flow between populations. Biodiversitas 22: 3342-3348.  Phytophthora nicotianae has caused heart rot in pineapple. This study identified the population genetic diversity of P. nicotianae, collecting 90 isolates of P. nicotianae from the pineapple plantation sites in three provinces of Indonesia and, as comparisons, seven isolates from non-pineapple sites. Six polymorphic microsatellite markers amplified the non-coding region was used to characterize the population diversity. The phylogenetic tree constructed by MEGA revealed three major clades; the first and second clades were dominated by the isolates from pineapple plantation sites, and the third clade contained isolates from the non-pineapple sites. The allelic pattern analysis using Genalex software revealed the local alleles specific to Lampung and Blitar populations. The AMOVA of microsatellite genotypes data showed that the isolates had a low diversity among the population (6%) but high diversity within individual. Conclusively, P. nicotianae population associated with heart rot in pineapple showed geneflow between populations.
Nematode diversity indices application to determine the soil health status of Lembo Agroecosystem in West Kutai, East Kalimantan Province, Indonesia Suyadi SUYADI; SURYA SILA; JEMI SAMUEL
Biodiversitas Journal of Biological Diversity Vol. 22 No. 7 (2021)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d220737

Abstract

Abstract. Suyadi, Sila S, Samuel J. 2021. Nematode diversity indices application to determine the soil health status of Lembo agroecosystem in West Kutai, East Kalimantan Province, Indonesia. Biodiversitas 22: 2861-2869. Lembo is a typical agroecosystem developed by the people of East Kalimantan, especially in the West Kutai District. Lembo agroecosystems (LA) are generally built on the former of sifting cultivation rice fields. The fertile condition of tropical rainforest land in East Kalimantan, if converted to a rice field agroecosystem, its fertility decreases drastically. However, Lembo is an agroecosystem similar to the forest, and its soil health status in this study was determined by using nematode diversity indices as the indicator. Nematode diversity indices are very useful as indicators because nematodes occupy all positions of the micro food web in the rhizosphere. They can support the increase in soil fertility or pose risks as a pest. This study was aimed to determine the health status of LA soil by using evaluation indicators: (i) nematode absolute abundance, (ii) nematode diversity indices [Shannon-Wiener index (H'), genera richness index (GR), and dominance index (?)], and (iii) nematode maturity indices (?MI, MI, MI2-5, PPI, and the PPI/MI-ratio), and using the oil palm plantation (OPP) as the comparison agroecosystem. Based on nematode maturity indices, LA soil health status was categorized as good with MI value > 2.6, the community abundance of nematode genera in the colonizers' group (c-p2) ? 50%, and community abundance of nematode genera in the persisters group (c-p4) > 10%. Then based on the nematode diversity indices (H', GR, and ?), the LA soil health status was higher than the OPP soil health status, in LA the values of H', GR, and ? were 30%-43%, 60%-91%, and 12%-88%, respectively higher than OPP. The pest status of plant-parasitic nematodes in both agroecosystems is relatively light because their presence is counterbalanced by predatory, carnivore, and omnivore nematodes.
Diversity of endophytic bacteria and microfungi in Syzygium cumini fruit from West Java, Indonesia IDA INDRAWATI; NIA ROSSIANA; Muhammad Faizal Fathurrohim
Biodiversitas Journal of Biological Diversity Vol. 22 No. 9 (2021)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d220941

Abstract

Abstract. Rossiana N, Fathurrohim MF, Indrawati I. 2021. Diversity of endophytic bacteria and microfungi in Syzygium cumini fruit from West Java, Indonesia. Biodiversitas 22: 3943-3948. Syzygium cumini L. Skells is a native evergreen tropical tree in Southeast Asia belong to the Myrtaceae family, known as the Java plum, jambul, jambolan, jamblang, or jamun. The bacterial and fungal endophytes associated with fruit have not been determined and functionally characterized. The endophytic microbes live inside the surface-sterilized fruits and have no visibly harmful effects on the plants. The purposes of the study were to isolate, characterize, and determine the diversity of endophytic bacteria and fungi in S. cumini fruit. The endophytes from S. cumini fruit were observed morphologically for identification. The result of isolation and identification showed there are four bacterial isolate endophytes (B. cereus, B. subtilis, B. megaterium, and Bacillus sp.) and four fungal endophytes (Candida guilliermondii, Penicillium sp., Mycelia sterilia, and Aspergillus sp.) isolated from S. cumini fruit.   Keywords:Biodiversity, Bacterial endophyte, Fungi endophyte, Jamblang

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