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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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Morphology, molecular identification, and pathogenicity of Vibrio spp. on blood clam (Anadara granosa) in Yogyakarta, Indonesia tourism beach areas ANNA ROOSIANA DEVI; Ari Susilowati; RATNA SETYANINGSIH
Biodiversitas Journal of Biological Diversity Vol. 20 No. 10 (2019)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d201016

Abstract

Abstract. Devi AR, Susilowati A, Setyaningsih R. 2019. Morphology, molecular identification, and pathogenicity of Vibrio spp. on blood clam (Anadara granosa) in Yogyakarta, Indonesia tourism beach areas. Biodiversitas 20: 2890-2896. Seafood is very popular among Indonesian people, especially in coastal areas. In Bantul Yogyakarta, blood clams have become one of tourist's favorite, either cooked or raw. Blood clams are filter feeders that cause the clams to be vulnerable to contamination of pathogenic bacteria that can cause foodborne disease, including Escherichia, Pseudomonas, and Vibrio. The 10-20% cases of foodborne disease transmitted through seafood caused by Vibrio spp. Three species of Vibrio can cause foodborne disease in humans, i.e., V. cholerae, V. parahaemolyticus, and V. vulnificus. The purpose of this study was to determine the character of Vibrio using morphological and molecular identification and pathogenicity on blood clam (Anadara granosa). Blood clams samples were collected from Depok, Goa Cemara, and Kwaru beaches in Bantul, Yogyakarta, Indonesia. Isolation of Vibrio spp. from blood clams was done using selective differential Thiosulfate Citrate bile salts sucrose (TCBS) culture medium. The morphological characters of the isolate colonies were determined based on the color, shape, texture, and size of the colony. Hemolysis test was also performed to evaluate the pathogenicity by using blood agar media. Molecular identification of Vibrio species was made using 16S rRNA sequence. Phylogenetic analysis was performed using Neighbor-Joining method in Mega X software. Samples for the analysis came from DNA sequences of this study and those from the GenBank database. Of the total 15 isolates obtained, four isolates showed positive ?-hemolysis, namely, isolate P2S2 -1bH, P3S1-1aH, P2S1-1aK and P2S2-1aK, and one isolate had positive ?-hemolysis (P3S2-1aK). Seven species of Vibrio were identified as V. algynolyticus, V. parahaemolyticus, V. diabolicus, V neocaledonicus, V. azureus, V. natrigens, and V. cholerae.
Colony morphology and molecular identification of Vibrio spp. on green mussels (Perna viridis) in Yogyakarta, Indonesia tourism beach areas FARIDA HIKMAWATI; Ari Susilowati; RATNA SETYANINGSIH
Biodiversitas Journal of Biological Diversity Vol. 20 No. 10 (2019)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d201015

Abstract

Abstract. Hikmawati F, Susilowati A, Setyaningsih R. 2019. Colony morphology and molecular identification of Vibrio spp. on green mussels (Perna viridis) in Yogyakarta, Indonesia tourism beach areas. Biodiversitas 20: 2891-2899. Green mussels (Perna viridis) have filter feeder properties that allow pathogenic bacteria from the water environment to accumulate in relatively high levels. About 20% of foodborne diseases are caused by large quantities of seafood contaminated with bacteria. The purpose of this study is to determine the morphological characteristics, pathogenicity, identity, and the kinship of Vibrio species on green mussels in Yogyakarta coastal tourism areas. Vibrio spp. were grown on selective differential TCBS media. In this media, the suspected Vibrio spp. would produce yellow or green colonies. The ability of hemolysis of Vibrio was blood agar media, the species was molecularly identified using 16S rRNA gene sequence, and the phylogenetic relationship of the Vibrio spp., was analyzed using MEGA X Neighbor-Joining program. Based on morphological analysis, we obtained 23 bacterial isolates suspected to be Vibrio spp. Two Isolates (L1K2 6 and L2K2 13) were positive for ?-hemolysis activity and 4 isolates (L1K1 3, L2K1 8, L2K2 16, and L3K2 22) were positive for ?-hemolysis activity. The molecular analysis involved 18 Vibrio species, and 4 of them represented the Vibrio genus and 14 species represented 97-99% similarity species in accordance with the 16S rRNA sequence in database, namely: Vibrio alginolyticus, Vibrio parahaemolyticus, Vibrio cholerae, Vibrio neocaledonicus, Vibrio mimicus, Vibrio azureus, Vibrio diabolicus, Vibrio tapetis, Vibrio natriegens, and Vibrio owensii. The most dominant number of Vibrio isolates was V. alginolyticus, while the lowest was V. owensii. The highest number of Vibrio species in green mussels was found in Goa Cemara beach while the lowest was in Kwaru beach. Vibrio spp bacteria found in green clams in coastal tourism areas in Yogyakarta have close phylogenetic relationships with other Vibrio in seafood in Indonesian coastal waters.
Antimicrobial activities and phylogenetic study of bacteria associated with Cyperus rotundus rhizosphere from Cemoro Sewu Plateau, Indonesia AMBARWATI AMBARWATI; SUBAGUS WAHYUONO; SUKARTI MOELJOPAWIRO; LANGKAH SEMBIRING; TRIWIBOWO YUWONO
Biodiversitas Journal of Biological Diversity Vol. 20 No. 8 (2019)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d200814

Abstract

Abstract. Ambarwati A, Wahyuono S, Moeljopawiro S, Sembiring L, Yuwono T. 2019. Antimicrobial activities and phylogenetic study of bacteria associated with Cyperus rotundus rhizosphere from Cemoro Sewu Plateau, Indonesia. Biodiversitas 20: 2206-2212. A study has been conducted to investigate the activity of bacteria isolated from the rhizosphere of Purple Nut Sedge (Cyperus rotundus) from Cemoro Sewu Plateu, Indonesia as antimicrobial agent and the molecular relatedness between the isolates with other bacteria based on phylogenetic tree analysis. A total of six bacteria were obtained and tested for their capability to inhibit the growth of test organisms using agar block method and characterized molecularly using 16S rDNA sequence analysis. It was observed that the six isolates demonstrated the ability to inhibit at least one of four test microorganisms growth, with a diameter of inhibition zone ranging from 8-35 mm. The CRC32 isolate was the best isolate in inhibiting Staphylococcus aureus ATCC 25923 with a diameter inhibition zone of 26 mm (strong), while isolate CRA8 was the best anti-Candida (showing 35 mm of inhibition zone). The phylogenetic tree analysis resulted in two genera, four isolates belonging to Bacillus, while the other two isolates were known related to Paenibacillus genus. BLAST analysis on the CRC 32 isolate revealed that it is closely related with Paenibacillus peroriae strain 3763 with 99% sequence similarities and CRA8 isolates demonstrated the highest similarity with Paenibacillus sonchi strain X19-5 (97%). The results of this study demonstrated that the bacterial isolates from plant rhizosphere of Cemoro Sewu Plateau were the members of the Bacillus and Paenibacillus genera and demonstrated the potential as antimicrobial agent.
Screening for amylolytic activity and characterization of thermophilic Actinobacteria isolated from a Geothermal Area in West Java, Indonesia WINDA AYU SYAFITRI; FITRIA NINGSIH; PUTRI PRATIWI SETYANINGSIH; MAZYTHA KINANTI RACHMANIA; DHIAN CHITRA AYU FITRIA SARI; SHUHEI YABE; AKIRA YOKOTA; ARIYANTI OETARI; WELLYZAR SJAMSURIDZAL
Biodiversitas Journal of Biological Diversity Vol. 20 No. 7 (2019)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d200720

Abstract

Abstract. Syafitri WA, Ningsih F, Setyaningsih PP, Rachmania MK, Sari DCAF, Yabe S, Yokota A, Oetari A, Sjamsuridzal W. 2019. Screening for amylolytic activity and characterization of thermophilic Actinobacteria isolated from a geothermal area in West Java, Indonesia. Biodiversitas 20: 1929-1938. In this study, we describe the screening for amylolytic activity of 17 thermophilic Actinobacteria isolates obtained from the soil of Cisolok geysers, a geothermal area in West Java, Indonesia. All isolates were screened for amylolytic activity by the starch-agar plate method at various temperatures. The results showed that all of isolates were able to grow at 45oC. The growth abilities of the isolates grown in ISP 1 medium varied at temperatures from 45 to 60oC. Fifteen of the 17 isolates showed amylolytic activity at 45oC, 13 showed such activity at 50oC, and four showed activity at 55oC. Only three isolates, designated SL1-2-R-2, SL1-2-R-3, and SL1-2-R-4, showed growth and amylolytic activity at 60oC. These three isolates were selected for molecular identification. The nearly full-length of 16S rRNA gene sequences data showed that these three isolates have a similarity of 99.93-100% with Actinomadura keratinilytica WCC-2265T and of 98.74-98.91% with A. miaoliensis BC 44T-5T. Phylogenetic tree shows that all three isolates are clustered together in a monophyletic group with the type strain of A. keratinilytica WCC-2265T as their most closely related species, with 100% bootstrap support. Based on sequencing of the 16S rRNA gene, phylogenetic comparison, and phenotypic characterization, the three isolates were identified as A. keratinilytica.
Phylogenetic of sago palm (Metroxylon sagu) and others monocotyledon based on mitochondrial nad2 gene markers Barahima Abbas; IHWAN TJOLLI; MUHAMMAD DAILAMI; MUNARTI
Biodiversitas Journal of Biological Diversity Vol. 20 No. 8 (2019)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d200820

Abstract

Abstract. Abbas B, Tjolli I, Dailami M, Munarti. 2019. Phylogenetic of sago palm (Metroxylon sagu) and others monocotyledon based on mitochondrial nad2 gene markers. Biodiversitas 20: 2249-2256. Sago palm forest and sago palm semi cultivated are found in the Papua islands as well as Ambon and Seram islands. The diversity center of sago palm is found in the Papua Islands. The objectives of this study are revealed sequence DNA mitochondrial associated with nad2 genes in sago palm accessions and molecular phylogenetic of sago palm and other monocotyledon plants. Plant materials used in the studies were derived from Sago Research Center (SRC) and sequencing and other monocotyledon were retrieved from the GenBank, NCBI accessions. Young fresh leaflets were derived from the experimental field of SRC and DNA extraction by following the procedure of Plant Genomic DNA Mini Kit and then PCR performed by using nad2 primer sets. Thereafter, DNA PCR product was sequenced by Macrogen Inc., Seoul, Korea. Sequences of nad2 genes in sago palm accessions from Papua, Indonesia were registered by GenBank NCBI for further used in the future as biological authenticity from the certain location. Mitochondrial DNA sequences associated with nad2 genes in the genome of sago palm were shown no differences among sago palm accessions. Molecular phylogenetic of sago palm and others monocotyledon based on nad2 gene markers showed the sago palm and others monocotyledon incorporated into two major clades and five subclades. Sago palm, coconut, and date palm were described as close related and being in the same subclades.
Biological activity of sponge-associated fungi from Karimunjawa Islands, Indonesia against pathogenic Streptococcus pneumoniae: Biological Activity of Sponge-associated Fungi Olvi Cristianawati; Aninditia Sabdaningsih; Leontine Elisabeth Becking; Miftahudin Majid Khoeri; Handung Nuryadi; Agus Sabdono; AGUS TRIANTO; OCKY KARNA RADJASA
Biodiversitas Journal of Biological Diversity Vol. 20 No. 8 (2019)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d200807

Abstract

Abstract. Cristianawati O, Sabdaningsih A, Becking LE, Khoeri MM, Nuryadi H, Sabdono A, Trianto A, Radjasa OK. 2019. Biological activity of sponge-associated fungi from Karimunjawa Islands, Indonesia against pathogenic Streptococcus pneumoniae. Biodiversitas 20: 2143-2150. Threats of drug-resistant Streptococcus pneumoniae and the urgent need for new antibiotics require prompt and sustained action for discovering bioactive compounds. This study aimed to isolate sponge-associated fungi as a candidate for sources of drugs. The sponge-associated fungi were screened against the MDR S. pneumoniae. The Deoxyribonucleic Acid (DNA) of fungal isolates that showed the most active was generated by using universal primers ITS1 and ITS4. While the sponge host was identified based on the molecular and by slide section. Out of twenty-nine fungal isolates from 13 marine sponges, S.06.2 isolate produced secondary metabolite that inhibiting the growth of MDR S. pneumoniae. Molecular identification based on the ITS region revealed that the active fungal isolate was closely related to Curvularia lunata, with a 99% similarity. The C. lunata S.06.2 was isolated from sponge Cinachyrella australiensis. Thus, C. lunata S.06.2_ LC315806 can serve as a fruitful strategy for the discovery of novel antibiotics for the treatment of MDR S. pneumoniae.
Methylene blue decolorization fungi from crude oil contaminated soils Irvan Permana; AMIR AWALUDDIN; SARYONO
Biodiversitas Journal of Biological Diversity Vol. 20 No. 9 (2019)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d200934

Abstract

Abstract. Permana I, Awaluddin A, Saryono. 2019. Methylene blue decolorization fungi from crude oil-contaminated soils. Biodiversitas 20: 2693-2697. One of the world problems is the treatment to remove dyes in textile wastewater. Nowadays, the most effective and compatible method to the environment is decolorization by microorganisms. Therefore, the objective of this study is to find out the best fungi to decolorize synthetic dye methylene blue (MB). Total eight fungi that isolated from crude oil-contaminated soil were analyzed to study the effect of various parameters such as pH, the concentration of dyes, contact times and agitation on their rate of reaction. The initial screening showed that Penicillium sp. FTM7 had greater potential in biodegradation the MB. The optimum decolorization of MB by Penicillium sp. was found after 8 days incubation with agitation 150 rpm and concentration of MB is 40 ppm and unadjusted pH (95.45%). The decolorization of MB was found to follow first-order reactions.
Traditional ecological knowledge and biodiversity conservation: the medicinal plants of the Dayak Krayan people in Kayan Mentarang National Park, Indonesia Rina Susanti; Ervizal A.M. Zuhud
Biodiversitas Journal of Biological Diversity Vol. 20 No. 9 (2019)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d200943

Abstract

Abstract. Susanti R, Zuhud EAM. 2019. Traditional ecological knowledge and biodiversity conservation: the medicinal plants of the Dayak Krayan people in Kayan Mentarang National Park, Indonesia. Biodiversitas 20: 2764-2779. Traditional ecological knowledge and biodiversity conservation can support one another for management of national parks in Indonesia as some such areas established in customary areas. This quantitative ethnobotany study aims to find the correlation of traditional ecological knowledge of medicinal plants of the Dayak Krayan people to biodiversity conservation in Kayan Mentarang National Park (KMNP), North Kalimantan, Indonesia. The research method used key informant interviews, transect walks, and questionnaire interviews. There were about 51 and 42 medicinal plants in Wa’ Yagung and Pa’ Padi respectively, which most used in life form of herb and tree, and to treat digestive system and infestations. Moreover, the important species are trees Alstonia scholaris and Cinnamomum cuspidatum, and vine Aristolochia sp. which grow in primary forest, while shrub Melastoma malabathricum in young secondary forest. There were significant differences in knowledge and use regarding age and gender groups, which older groups tend to possess higher values. The linking concept is proposed by using a review of three stimuli NUR (Natural-Usefulness-Religious) pro-conservation tool of traditional ecological knowledge and biodiversity conservation. The authorities’ stakeholders in KMNP will have to emphasize the traditional ecological knowledge in short or long-term management plan to achieve the objective of collaborative management in this national park.
Short Communication: Intraspecific genetic diversity and population subdivision of rabbitfish (Siganidae: Siganus canaliculatus) in urbanized reefs of Jakarta Bay, Indonesia Hawis Madduppa; MUTIARA KRISTINA MARGARETHA; ADITYA BRAMANDITO; TRI PRARTONO; BEGINER SUBHAN; DONDY ARAFAT; NURLITA PUTRI ANGGRAINI
Biodiversitas Journal of Biological Diversity Vol. 20 No. 10 (2019)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d201017

Abstract

Abstract. Madduppa H, Margaretha MK, Bramandito A, Prartono T, Subhan B, Arafat D, Anggraini NP. 2019. Short Communication: Intraspecific genetic diversity and population subdivision of rabbitfish (Siganidae: Siganus canaliculatus) in urbanized reefs of Jakarta Bay, Indonesia. Biodiversitas 20: xxxx. Indonesian coral reefs and seagrass are heavily influenced by human activities through pollution and habitat loss, and sea-level rise or the increase of ocean temperature due to the global change. In the Jakarta Bay and Seribu Islands, marine communities have been impacted by an increase in eutrophication and sedimentation levels. As a result, these habitats became degraded and could affect their associated organisms such as rabbitfish. Genetic diversity and population structure can provide information about a long-term condition in an aquatic organism. The study was conducted to assess genetic diversity and population structure of rabbitfish (Siganus canaliculatus) across an environmental gradient in Jakarta Bay and Seribu Islands. A total of 31 individuals were collected using gillnet in study sites. A molecular marker mitochondrial Cytochrome oxidase 1 (CO1) was used to amplify DNA. The result of the phylogenetic tree formed two major clades, which generally separate northern and southern region of Seribu Islands populations. AMOVA analysis showed significant genetic differentiation between the population of Siganus canaliculatus in the north zone (National Park) and south zone Seribu Island (FST = 0.38, p<0.005). The highest haplotype diversity (Hd) of Siganus canaliculatus contained was observed in the north (Pulau Semak Daun) and south (Pulau Damar) in both as moderate (0.50). Nucleotide diversity ( ) of Siganus canaliculatus was categorized as low (0.076) to moderate (0.500). Environment and humans seem to affect the value of genetic diversity, and as the study suggests, a significant population subdivision makes this population vulnerable.  
Variation induction of Glycine max through low dose gamma irradiation produces genetic and physiological alteration as source of tolerant variants in waterlogging conditions triono bagus saputro; WIRDHATUL MUSLIHATIN; DWI KUSUMA WAHYUNI; TUTIK NURHIDAYATI; FILA OXI WARDHANI; ELENA ROSALIA
Biodiversitas Journal of Biological Diversity Vol. 20 No. 11 (2019)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d201124

Abstract

Abstract. Saputro TB, Muslihatin W, Wahyuni DK, Nurhidayati T, Wardhani FO, Rosalia E. 2019. Variation induction of Glycine max through low dose gamma irradiation produces genetic and physiological alteration as source of tolerant variants in waterlogging conditions. Biodiversitas 20: 3299-3308. Soybean (Glycine max L.) is the main food commodity that contains high proteins, oils, and carbohydrates. Waterlogging is considered as the dominant factor and major constraint responsible for the decrements of soybean production in Indonesia. The development of promising G.max that tolerates waterlogging is essentially needed. In this study, induction of variation was conducted by gamma rays irradiation with doses of 25Gy, 50Gy, 75Gy, and 100Gy. The mutant or variants lines were then selected under waterlogging conditions with 100%, 150%, 200%, and 250% of field capacity. The results showed that, in 250% waterlogging condition, plants irradiated with 25Gy shows the best performance in amount of roots, adventitious roots and number of pods parameters, while plants irradiated with 50Gy have the highest growth indicated by amount of root nodules, plant heights, dry weights, leaf area, and chlorophyll contents. The genotypes then were assayed by the Inter Simple Sequence Repeats (ISSR) to confirm that the mutants differ compared to its wild type. Out of 10 ISSR primers, seven primers showed polymorphic patterns. The best primer to differentiate the mutant lines and its wild type is primer ISSR1 [ (AC)8G] that able to generate the highest level of polymorphism with 44.0%. The comparison of protein profiles among the mutant lines showed that proteins with molecular weight 53,78 KDa; 43,12 KDa; and 20,62 Kda are all overexpressed for plants irradiated at 25Gy and treated with 250% waterlogging stress. All those three proteins are predicted as 1-amino cyclopropane-1-carboxylate synthase (ACS), Alcohol-dehydrogenase (ADH), and Superoxide dismutase (SOD) respectively.

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