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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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Feeding selectivity of Holothuria atra in different microhabitat in Panjang Island, Jepara (Java, Indonesia) Retno Hartati; AMBARIYANTO AMBARIYANTO; WIDIANINGSIH WIDIANINGSIH; MUHAMMAD ZAINURI
Biodiversitas Journal of Biological Diversity Vol. 21 No. 5 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210552

Abstract

Abstract. Hartati R, Zainuri M, Ambariyanto A, Widianingsih W. 2020. Feeding selectivity of Holothuria atra in different microhabitat in Panjang Island, Jepara (Java, Indonesia). Biodiversitas 21: 2233-2239. Particle selectivity by deposit feeder sea cucumber Holothuria atra was an important concept in its feeding ecology. This species utilized the organic matter that coated sediment and detrital particles as food. Thus, particle size, organic matter, and microalgal biomass had been proposed as variables food resources along which niche separation could occur in optimal foraging strategy. This study was conducted in five microhabitats of different coverage of seagrass bed (P1-P4) up to the rubble area (P5) over a tidally variable depth range of 0,5-5m in Panjang island, Jepara. Twenty samples of sea cucumber H. atra were taken from defined microhabitat, along with samples of sediment underneath the sea cucumber. Granulometry of the particles ingested by sea cucumbers, total organic matter, and microphytobenthic biomass (as chlorophyll-a) found throughout their digestive tract (alimentary canal) and in the sediments was analyzed. Comparison of the contents and the rates of organic matter assimilation of the digestive tract with those of the microhabitat sediment were carried out. The results showed that H. atra fed on sediment underneath their body and it was revealed that there were strong (?=0.833-0.876) to very strong (?=0.945) positive relationship between grain size in the sediment and in their alimentary canal which showed their feeding selectivity of the sediment. H. atra also found to have efficiency in feeding by taking advantage of the high TOM content and high abundance of microphytobenthic organisms (presented as chlorophyll-a) in their natural microhabitats.
Evaluation of antibacterial activity and molecular characterization of bacteria from Holothuria atra intestine collected from anthropogenic and non-anthropogenic region in Karimunjawa, Indonesia Bambang Sulardiono; NINIEK WIDYORINI; DJOKO SUPRAPTO; DIAH AYUNINGRUM; ARIF RAHMAN
Biodiversitas Journal of Biological Diversity Vol. 21 No. 7 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210736

Abstract

Abstract. Sulardiono B, Widyorini N, Suprapto D, Ayuningrum D, Rahman A. 2020. Evaluation of antibacterial activity and molecular characterization of bacteria from Holothuria atra intestine collected from anthropogenic and non-anthropogenic region in Karimunjawa, Indonesia. Biodiversitas 21: 3149-3155. Evaluation of antibacterial activity and molecular characterization of bacteria from the intestine of Holothuria atra is needed in the anthropogenic region of Menjangan Besar, Karimunjawa. The research aims to evaluate antibacterial activity and molecular characterization of bacteria from intestine of Holothuria atra collected from anthropogenic and non-anthropogenic regions in Karimunjawa, Indonesia. Sea cucumber samples were collected at Menjangan Besar waters as anthropogenic region (code of HM) and Alang-alang waters as non-anthropogenics region (code of HA), Karimunjawa National Park, Indonesia. The H. atra sample collection was using purposive sampling method. Examination of the bacteria from isolation until molecular characterisation was done at the Tropical Marine Biotechnology Laboratory, Uiversitas Diponegoro. The isolation process was conducted using spread plate method, followed by bacterial isolates purification using streak plate method. Screening of antibacterial activity using the agar plug method, as well as molecular identification was conducted by 16S rDNA PCR amplification. The results of this study indicated that a total of 26 bacterial strains were successfully isolated from sea cucumber intestine, consisted of eleven bacterial isolates from H. atra in Menjangan Besar waters and the rest fifteen isolates from H. atra in Alang-alang waters. The preliminary assay of antibacterial test showed H. atra in both waters have potential bacterial isolates. Those bacterial isolates with antibacterial activity were HM1.2 and HA1.1, which based on molecular identification, showed isolates HM1.2 and HA1.1 had the closest similarity with Bacillus paramcoides and Vibrio alginolyticus consecutively, with BLAST homology 98% and 99%. The accession number for both isolates were LC550090 and LC550089, respectively.
The effect of drying treatment to metabolite profile and cytotoxic potential of Rhizophora apiculata leaves Mada Triandala Sibero; ANGGUN PUSPITARINI SISWANTO; RUDHI PRIBADI; AGUS SABDONO; OCKY KARNA RADJASA; AGUS TRIANTO; EVAN HANSEL FREDERICK; ALDI PRATAMA WIJAYA; DWI HARYANTI; DESY WULAN TRININGSIH; SASTRA JENDRA HAYUNINGRAT; YASUHIRO IGARASHI
Biodiversitas Journal of Biological Diversity Vol. 21 No. 5 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210546

Abstract

Abstract. Sibero MT, Siswanto AP, Pribadi R, Sabdono A, Radjasa OK, Trianto A, Frederick EH, Wijaya AP, Haryanti D, Triningsih DW, Hayuningrat SJ, Igarashi Y. 2020. The effect of drying treatment to metabolite profile and cytotoxic potential of Rhizophora apiculata leaves. Biodiversitas 21: 2180-2187. Coastal communities in Indonesia have utilized Rhizophora spp. leaves as a traditional medicine for many years. The previous studies have succeeded in extracting bioactive compounds from this mangrove after drying treatment, but there is a possibility of the compound decomposition or breakdown. This study aimed to determine the effect of drying treatment on the metabolite profile of R. apiculata leaves which were taken from mangrove forests in Rembang, Central Java. The effect of pre-drying treatment was examined by comparing the metabolites profiles of fresh, oven-dried, and sun-dried leaves crude extracts. Extraction was carried out using maceration method with agitation (110 r.p.m.) for 24 hours in methanol. The metabolite profile was analyzed using high-performance liquid chromatography (HPLC) with diode array detector (DAD) and thin layer chromatography (TLC), while secondary metabolites were studied by phytochemical test. The phytochemical results showed that there were no differences in metabolites in dried and fresh R. apiculata leaves. Crude extract of fresh and oven-dried gave 10 spots on the TLC, while sun-dried crude extract had 9 spots. The one missing spot (Rf value of 0.79) in the sun-dried crude extract might have unstable compounds that are easily degraded or damaged by the sunlight. Moreover, HPLC chromatogram indicated the pre-drying treatment gave alteration to the R. apiculata metabolites that only detected at 400 nm. Cytotoxic assay against P388 murine leukemia cell indicated that oven-dried treatment gave the best anticancer activity with IC50 value of 0.0323 mg/mL. 
Antibacterial activity of CaO from blood cockle shells (Anadara granosa) calcination against Escherichia coli AMANDA FIRZA RUSDARYANTI; ULFAH AMALIA; SLAMET SUHARTO
Biodiversitas Journal of Biological Diversity Vol. 21 No. 6 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210660

Abstract

Abstract. Rusdaryanti AF, Amalia U, Suharto S. 2020. Antibacterial activity of CaO from blood cockle shells (Anadara granosa) calcination against Escherichia coli. Biodiversitas 21: 2826-2830. Calcium carbonate (CaCO3) in blood clamp shells (BCS) was able to be converted into calcium oxide (CaO) through a calcination process. Some research stated that CaO can be used in the food industries b, one of which is as an antibacterial agent. The purpose of this study was to determine the most optimal size of BCS's powder during calcination as an antibacterial agent and its effect on the activity of Escherichia coli. Data were analyzed using analysis of variance and Kruskal-Wallis test. The results showed that 200 mesh size of BCS’s powder produced the highest yield of CaO at about 98.68% compared to 120 and 230 mesh size. The best concentration of CaO powder as an antibacterial was 3.5% with a pH of 11.3 ± 0.17. CaO powder had antibacterial activity against E. coli with minimum inhibitory concentration’s value (MIC) of-0.115; a minimum bactericidal concentration’s value (MBC) of 0 CFU/mL; inhibition zone of 3.23 ± 0.2 mm. By the PCR method, DNA degradation has occurred in E. coli cells. The differences of CaO powder concentration had significant effect (P <0.05) on the inhibition zone of E. coli.
Forensic genetic case study: Species identification and traceability of sea turtle caught in illegal trade in Bali, Indonesia NI PUTU DIAN PERTIWI; MAULID DIO SUHENDRO; NI LUH ASTRIA YUSMALINDA; I NYOMAN GIRI PUTRA; I GUSTI RICCA MAHATMA PUTRI; ENEX YUNI ARTININGSIH; M. DANIE AL-MALIK; NI KADEK DITA CAHYANI; ANDRIANUS SEMBIRING
Biodiversitas Journal of Biological Diversity Vol. 21 No. 9 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210945

Abstract

Abstract. Pertiwi NPD, Suhendro MD, Yusmalinda NLA, Putra ING, Putri IGRM, Artinigsih EY, Al Malik MD, Cahyani NKD, Sembiring A. 2020. Forensic genetic case study: Species identification and traceability of sea turtle caught in illegal trade in Bali, Indonesia. Biodiversitas 21: 4276-4283. Although known as protected endangered species, sea turtle trade is still occurring, especially in Indonesia. Understanding the species and population origin of sea turtle being sold in the illegal market is crucial for its conservation, where it will reveal the traceability of sea turtle trade to its population origin in the management unit areas. Thus, genetic forensic has been used as a key investigating tool to help with this problem. In this research, we aim to identify the species and population origin of the sea turtle caught and traded in the illegal market in Bali. Of the 20 samples collected from confiscated sea turtle during illegal trade, by-catch, and a traditional restaurant serving sea turtle meat, 17 samples were successfully analyzed and identified using PCR (polymerase chain reaction) methods. The result identified 15 samples as a green sea turtle (Chelonia mydas), while two samples were olive ridley sea turtle (Lepidochelys olivacea). Mixed Stock Analysis (MSA) with Bayesian indicated that the green sea turtle caught in illegal trade in Bali is originated mostly from the rookeries populations in Berau (29.98%), Terengganu (17.84%), Sarawak (14.84%), and Ashmore Reef (11.85%). Meanwhile, 18 other locations only showed the MSA value below 2%, including the locations of Penang and Perak, Vietnam, Perhentian, Redang, Pahang, Mersing, Sabah Turtle Island Park (TIP), Sipadan, Coral Sea, western New Caledonia, Commonwealth of the Northern Mariana Island and Guam, northern New Guinea, Gulf of Carpenteria, Scott Reef, West Java, North West Self, Cobourg Peninsula, Cocos Keeling Island. Therefore, the exploitation of sea turtle in Bali will impact the decline in the genetic diversity of sea turtles population Indonesia and adjacent locations. Monitoring and protection of sea turtle species in Bali have to be a high priority because Bali is known as the hub for sea turtle illegal trade, and the exploitation of sea turtle in Bali will have an impact on the sea turtle population in other locations.
Estimation of aboveground biomass using aerial photogrammetry from unmanned aerial vehicle in teak (Tectona grandis) plantation in Thailand SASIWIMOL RINNAMANG; KAMPANART SIRIRUEANG; SORAVIS SUPAVETCH; PONTHEP MEUNPONG
Biodiversitas Journal of Biological Diversity Vol. 21 No. 6 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210605

Abstract

Abstract. Rinnamang S, Sirirueang K, Supavetch S, Meunpong P. 2020. Estimation of aboveground biomass using aerial photogrammetry from unmanned aerial vehicles in teak (Tectona grandis) plantation in Thailand. Biodiversitas 21: 2369-2376. Thailand is one of the best teak planting locations in the world. Teak is one of the most species planting and a significant source of high-value timber in Thailand. For plantation management, biomass is one of the important factors while determining the production of a plantation and also for sustainable forest management. Unmanned Aerial Vehicles (UAV) have the ability to produce 3D RGB digital images which can be used to study the plantation characteristics. This study aimed to use aerial images and photogrammetry techniques derived from unmanned aerial vehicles (UAV) to estimate teak biomass in Thong Pha Phum plantation, Kanchanaburi Province, Thailand. We conducted our study on 15-and 36-year-old teak stands, and compared the tree dimension between data obtained from field measurement and that from aerial images and photogrammetry techniques. In the 15-year-old stand, the average tree height estimated from the UAV and ground-truthing were 12.34 and 13.06 m, respectively. In the 36-year-old stand, the average tree height from the UAV and ground-truthing were 28.87 and 29.39 m, respectively. We found that in both stands, the difference between data generated from the UAV and ground-truthing data was not significant (p-value = 0.07 and 0.306, respectively). There was also a strong correspondence between tree height estimated from the UAV and that measured on the ground which is indicated by the high R2 (i.e. 0.70 and 0.64 for the 15-and 36-year-old stands, respectively). Using UAV generated data, the total biomass of 15-and 36-year-old stands was estimated to be around 42.07 t ha-1 and 67.13 t ha-1, respectively. The overall results suggest that UAV can be used as an effective tool to survey and monitor stand’s productivity in teak plantation.
Short Communication: Genetic structure of Longtail Tuna Thunnus tonggol (Bleeker, 1851) in Java Sea, Indonesia M. DANIE AL MALIK; NI PUTU DIAN PERTIWI; ANDRIANUS SEMBIRING; NI LUH ASTRIA YUSMALINDA; ENEX YUNIARTI NINGSIH; IDA AYU ASTARINI
Biodiversitas Journal of Biological Diversity Vol. 21 No. 8 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210828

Abstract

Abstract. Al Malik MD, Pertiwi NPD, Sembiring A, Yusmalinda NLA, Ningsing EY, Astarini IA. 2020. Short Communication: Genetic structure of Longtail Tuna Thunnus tonggol (Bleeker, 1851) in Java Sea, Indonesia. Biodiversitas 21: 3637-3643. Thunnus tonggol (Longtail Tuna) is an economically important fish found in Indonesia waters, however, the information regarding this fish is lacking. Known to be a neritic fish and found in shallow water, Java Sea is one of the ideal habitats for T. tonggol species. Due to high fishing rates activities in Java Sea, a better management plan to ensure the conservation and fisheries sustainability around this area is needed, especially to protect T. tonggol population. In order to complete the Indonesian tuna data, we aim to study the diversity and genetic structure of T. tonggol in Java Sea at three different locations; i.e. Semarang, Banjarmasin, and Jakarta. In this study, population genetic methods with the marker of mitochondrial DNA (mtDNA) control region were used in population structure analysis. A total of 115 specimens were collected from the fish market around the area of study locations and amplified using polymerase chain reaction (PCR) and sequenced using Sanger methods. The result showed genetic diversity (Hd) value of 0.99366, and nucleotide diversity (?) value of 0.01906. Both of these values indicated high genetic diversity. Population analyses using Analysis of Molecular Variance (AMOVA) showed nonsignificant differences between the three populations of study (mixing population), with the ?ST value of 0,00375 (p-value > 0.05). Based on this result, the fisheries management for T. tonggol in Java Sea needs to be managed as one single population management.
The density and diversity of plant-parasitic nematodes associated with maize rhizosphere in Malakaji Highland, South Sulawesi, Indonesia Hishar Mirsam; AMRAN MUIS; NURNINA NONCI
Biodiversitas Journal of Biological Diversity Vol. 21 No. 6 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210637

Abstract

Abstract. Mirsam H, Muis A, Nonci N. 2020. The density and diversity of plant-parasitic nematodes associated with maize rhizosphere in Malakaji Highland, South Sulawesi, Indonesia. Biodiversitas 21: 2654-2661. Plant-parasitic nematodes (PPNs) are one of the important pathogens, especially in tropical countries, including Indonesia. Nematodes can cause high yield losses and economic damage if not managed properly. This study aims to analyze PPN density in the vegetative phase of maize in the Malakaji Highland Gowa Regency, South Sulawesi. The sampling method was a diagonal sampling technique, done by taking samples at points along a diagonal line, which were the middle and fourth corners of the maize crop. Nematode extraction was done by the modified Baerman method. The density of parasitic nematode communities counted was absolute community density, relative community density, absolute frequency, relative frequency, frequency of all nematodes, and dominance values. Nematode identification was based on morphological characters. The highest PPNs density was found in two weeks old of maize planted area where the absolute community density reaching 618 and the dominance value of 61.80%. Age of maize plants is negatively correlated with PPNs community with a regression coefficient of (-3.85). So that it can be assumed that the older the age of maize plants, the lower the amount of PPNs. Five genera of plant-parasitic nematodes associated with the rhizosphere of maize plants were found, namely Helicotylenchus, Pratylenchus, Haplolaimus, Longidorus, and Xiphinema. In addition to parasitic nematodes, non-parasitic nematodes were also identified as having no stylet, namely Campydoroides, Mononchus, and Rhabditis.
Soil properties and sulfur-oxidizing bacterial diversity in response to different planting patterns of shallot (Allium ascalonicum) Muhammad Juwanda; SAKHIDIN; SAPARSO; KHARISUN
Biodiversitas Journal of Biological Diversity Vol. 21 No. 6 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210661

Abstract

Abstract. Juwanda M, Sakhidin, Saparso, Kharisun. 2020. Soil properties and sulfur-oxidizing bacterial diversity in response to different planting patterns of shallot (Allium ascalonicum). Biodiversitas 21: 2832-2839. Sulfur is one of the primary elements required by plants for growth and development. Sulfur-oxidizing bacteria (SOB) can oxidize sulfur to sulfate, which is directly taken up by plant roots. This study aims to evaluate the soil properties and SOB diversity in various shallot planting patterns, i.e. PP1 (shallot-dry season-shallot-shallot), PP2 (shallot-dry season-shallot-rice), and PP3 (shallot-pulses-shallot-rice). Soil samples were collected from the rhizosphere of the shallot plant and analyzed for the soil properties based on the standard methods. Bacteria isolation was cultured on Starkey broth and Starkey agar. Bacteria isolate was identified based on the 16S rRNA gene sequence and compared to the GenBank database. The results showed that shallot planting patterns influence soil properties and SOB diversity. The highest content of sulfate (41.31 ppm), organic C (0.957 %), organic matter (1.650%), C/N ratio (9.57), and SOB diversity was obtained in PP3 planting pattern. Three bacterial strains have been successfully isolated i.e. A-3245D, B-3246F, and C-3247C with their closest related to Burkholderia cepacia, Klebsiella variicola, and Klebsiella aerogenes, respectively. The highest diversity and population density of SOB was in the PP3 planting patterns, i.e Burkholderia cepacia (7.45 x 105 CFU/mL); Klebsiella variicola (1.79 x 107 CFU/mL; Klebsiella aerogenes: 3.9 x 106 CFU/mL). K. variicola can be found in three planting patterns of shallot.
The diversity of entomopathogenic fungi collected from leaves and rhizospheres of rice implementing integrated pest management Aminudin Afandhi; Elyka Putri Pertiwi; Dicky Prejeki Purba; Tita Widjayanti; Amin Setyo Leksono
Biodiversitas Journal of Biological Diversity Vol. 21 No. 6 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210642

Abstract

Abstract. Afandhi A, Pertiwi EP, Purba DP, Widjayanti T, Leksono AS. 2020. The diversity of entomopathogenic fungi collected from leaves and rhizospheres of rice implementing integrated pest management. Biodiversitas 21: 2690-2695. Rice is an important food source for most of the world’s population. However, its production often faces pest and disease problems. This study aimed to determine the diversity of entomopathogenic fungi from the leaves and rhizospheres of rice plants, implementing applied integrated pest management (IPM), and to test the pathogenicity of insect fungi species against Spodoptera litura and Tenebrio molitor larvae collection. Entomopathogenic fungi were collected from the leaves and rhizospheres of two rice fields: a field in which IPM is implemented and a conventional field. A total of 24 species were collected from the leaves and rhizospheres in three locations. Pathogenicity test against S. litura larvae was conducted using the Beauveria sp. isolate, whereas pathogenicity test against T. molitor was conducted using the other isolates. Paddy fields in which IPM has been implemented have higher diversity and species richness compared with a conventional field. Location 1 (3 years of IPM implementation) has the highest diversity (2.04 of leaf collection and 1.65 of rhizosphere collection), location 2 has the lowest fungi diversity collected from rhizosphere, whereas location 3 (conventional implementation) has the lowest diversity of leaf collection (1.68). Laboratory testing of Beauveria spp. against S. litura revealed that all species were effective for pest control. Entomopathogenic fungi collected from leaves (Paecilomyces sp.) increased T. molitor mortality by 60%, whereas those isolated from rhizospheres had no effective control of the pest.

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