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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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Fingerprinting sengon (Falcatria moluccana) accessions resistant to boktor pest and gall rust disease using microsatellite markers Ulfah Juniarti Siregar; DEWI RAHMAWATI; APRILIYA DAMAYANTI
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/d200935

Abstract

Abstract. Siregar UJ, Rahmawati D, Damayanti A. 2019. Fingerprinting sengon (Falcatria moluccana) accessions resistant to boktor pest and gall rust disease using microsatellite markers. Biodiversitas 20: 2698-2706. Sengon (Falcataria moluccana Miq.) is a multipurpose fast-growing tree species and widely planted as community forest in Indonesia. According to Indonesian Light Wood Association (ILWA) F. moluccana wood products coming from forest industries in Jawa worth US$ 244.46 million export to China alone. The wood dust also has high potential as source for biomass-based energy in the form of wood-pellet. Monoculture plantation however often suffers from stem borer pest, known as boktor (Xystrocera festiva) and a gall rust disease, caused by fungi Uromycladium falcatarium. This research was aimed to characterize accessions of resistant and susceptible sengon individuals to both gall rust disease as well as stem borer pest using microsatellite markers. Totally 50 accessions of resistant and of resistant to stem borer pest were collected from Sumedang, West Jawa Province, while 88 accessions of resistant and of resistant to gall rust disease were sampled from Kediri, East Jawa Province and Sukabumi, Indonesia. Eight microsatellite markers could amplify most of the accessions used in this study and produce polymorphic fragments. High genetic diversity was detected in all of F. moluccana populations, with He ranged from 0.431 to 0.650. AMOVA showed that most genetic variations come from within populations. A dendrogram based on Nei’s genetic distance (1972) clustered some resistant accessions to either stem borer pest or gall rust disease separately from susceptible ones.
Bacterial isolates from bryozoan Pleurocodonellina sp.: Diversity and antimicrobial potential against pathogenic bacteria Meezan Ardhanu Asagabaldan; Gilles Bedoux; Nathalie Bourgougnon; Rhesi Kristiana; Diah Ayuningrum; Agus Sabdono; Agus Trianto; Ocky Karna Radjasa
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/d200914

Abstract

Abstract. Asagabaldan MA, Bedoux G, Bourgougnon N, Kristiana R, Ayuningrum D, Sabdono A, Trianto A, Radjasa OK. 2019. Bacterial isolates from bryozoan Pleurocodonellina sp.: Diversity and antimicrobial potential against pathogenic bacteria. Biodiversitas 20: 2528-2535.  There is an urgent need to discover new compounds with antibacterial activity, which can be developed into lead structures for the treatment of human disease caused by multidrug-resistant (MDR) bacteria. In this study, we focussed on bryozoan-associated bacteria to screen them toward antibacterial activities, since the microbiome of these organisms can still be regarded as under-investigated. Most of the few publications about bryozoan-associated bacteria focused on taxonomy and the potential as producers of antibacterial natural products were neglected. Four specimens of bryozoan Pleurocodonellina sp. were collected from Teluk Awur, Jepara in Java Sea, Indonesia. Therefrom, 56 bacterial strains were isolated, and 17 displayed antibacterial activities against MDR bacteria Pseudomonas aruginosa, Klebsiella pneumoniae, Acinetobacter baumannii, Enterobacter cloacae, and methicillin-resistant Staphylococcus aureus (MRSA). Taxonomic identification of the bacteria by 16S rRNA gene sequencing revealed them belonging to the genera Virgibacillus, Pseudoalteromonas, Halomonas, and Bacillus. Most interestingly, the genus Virgibacillus was dominantly obtained from the Pleurocodonellina sp. specimens, i.e., 12 active isolates. Nevertheless, the best activities against MDR bacteria (both Gram-positive and Gram-negative) were contributed to isolates showing >99% identity to Pseudoalteromonas. The results further suggest adding the genus Virgibacillus as bacteria associated with bryozoan, since to the best of our knowledge there were no reports of this genus isolated from bryozoan.
Environmental DNA (eDNA) metabarcoding: Diversity study around the Pondok Dadap fish landing station, Malang, Indonesia Sapto Andriyono; MD. JOBAIDUL ALAM; HYUN-WOO KIM
Biodiversitas Journal of Biological Diversity Vol. 20 No. 12 (2019)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d201241

Abstract

Abstract. Andriyono S, Jobaidul Alam Md, Kim HW. 2019. Environmental DNA (eDNA) metabarcoding: Diversity study around the Pondok Dadap fish landing station, Malang, Indonesia. Biodiversitas 20: 3772-3781. Molecular identification of species is now fast growing and currently widely applied method in the diversity estimation of aquatic biota; even though morphological identification is still carried out. The molecular approach is beneficial complementing on regular surveys, e.g. use of nets, traps, fishing rods, and even with poisons. In this study, the eDNA metabarcoding was applied to water samples around the Pondok Dadap fish landing station, Indonesia to determine the diversity of fish around the waters and also to identify marine fish landed in this area. Molecular identification was carried out on fish samples obtained from the fish market improved GenBank database on COI and ITS. While, seawater samples were carried out by using the next-generation sequencing (NGS) platform to obtain the eDNA metabarcoding data for the first time. Molecular identification obtained 34 species (68 sequences of COI and ITS regions) belonging to 28 genera, 18 families, 4 orders, while the eDNA metabarcoding approach identified 53 marine fish species by using the MiFish pipeline representing 38 genera, 27 families, and 7 orders. From the present study, we can able to estimated fish diversity by eDNA metabarcoding, and this finding will be helpful for baseline data preparation for future effective management of resources in this area.
Species diversity and prey items of amphibians in Yoddom Wildlife Sanctuary, northeastern Thailand Prapaiporn Thongproh; PRATEEP DUENGKAE; PRAMOTE RATREE; EKACHAI PHETCHARAT; WASSANA KINGWONGSA; WEEYAWAT JAITRONG; YODCHAIY CHUAYNKERN; CHANTIP CHUAYNKERN
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/d200937

Abstract

Abstract. Thongproh P, Duengkae P, Ratree P, Phetcharat E, Kingwongsa W, Jaitrong W, Chuaynkern Y, Chuaynkern C. 2019. Species diversity and prey items of amphibians in Yoddom Wildlife Sanctuary, northeastern Thailand. Biodiversitas 20: 2718-2732.  Amphibian occurrence within Yoddom Wildlife Sanctuary, which is located along the border region among Thailand, Cambodia, and Laos, is poorly understood. To determine amphibian diversity within the sanctuary, we conducted daytime and nocturnal surveys from 2014 to 2017 within six management units. We recorded 26 amphibian species and two additional unidentified taxa from two orders (Anura and Gymnophiona) and six families. Four of the encountered species are new records for Ubon Ratchathani, (Kalophrynus interlineatus, Microhyla berdmorei, Micryletta inornata, and Chiromantis nongkhorensis). In addition to observational surveys, we investigated amphibian prey items via fecal pellet analyses. Prey items comprised mainly animals (85% from class Insecta), but 9% of species consumed both plants and animals. Among insects, Coleoptera and Hymenoptera were the most abundant prey (35% and 31%, respectively). In addition, we observed one case of Ichthyophis kohtaoensis consuming an earthworm and an incident of cannibalism in Sylvirana mortenseni. Finally, due to illegal logging activities and active landmines, surveys were limited to the secure regions within the sanctuary. Thus, we noted that further species might remain unidentified within Yoddom Wildlife Sanctuary due to this limitation.
Genetic variations among selected wild Asian elephant populations in Peninsular Malaysia based on mitochondrial D-loop region DNA sequences KAYAL VIZI KARUPPANNAN; NOR AIFAT RAHMAN; KHAIRUL AMIRIN MOHAMED; NURUL FARAH DIYANA AHMAD TAHIR; FATIN MARDHIAH NORDIN; SALMAH YAAKOP; JESÚS E MALDONADO; BADRUL MUNIR MD ZAIN
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/d200910

Abstract

Abstract. Karuppannan KV, Aifat NR, Mohamed KA,  Ahmad-Tahir NFD,  Nordin FM, Yaakop S, Maldonado JE, Md-Zain BM. 2019. Genetic variations among selected wild Asian elephant populations in Peninsular Malaysia based on mitochondrial D-loop region DNA sequences. Biodiversitas 20: 2494-2502. Asian elephant (Elephas maximus) is an important large mammal in Peninsular Malaysia and is completely protected by the Wildlife Conservation Act 2010 (Act 716). The conservation of this species requires strong information-based research, such as genetic evaluations. The aim of this study was to compare mitochondrial control region variation among selected elephants from the Taman Negara National Parks (TNNP) population with other selected populations in Peninsular Malaysia. DNA materials were extracted from fecal samples and amplified using partial mitochondrial D-loop region. Total 13 haplotypes with haplotype diversity (Hd) of 0.7524 were observed. A total of 34 base pair (bp) segregation sites were formed in 547 bp sequences. Both phylogenetic trees showed that a few individual elephants from the TNNP formed a clade together with individuals from other populations. The remaining individual elephants from TNNP formed a monophyletic clade supported by a high bootstrap value. Low genetic distance was detected among the tested populations, which proved that both individuals from the TNNP and other selected populations have similar genetic patterns. High gene flow among tested populations would impact on fitness and long-term resilience of the populations. This highly significant outcome provides strong baseline data for Department of Wildlife and National Parks (DWNP) in monitoring elephant populations in order to reduce number of human-elephant conflicts which indirectly minimize translocating conflict elephants to TNNP.
Analysis of nutlet morphological characteristics of some Iranian Ajuga L. taxa Sayed Mehdi Talebi; RAHELEH TABARIPOUR; MAJID ESKANDARI
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/d201008

Abstract

Abstract. Talebi SM, Tabaripour R, Eskandari M. 2019. Analysis of nutlet morphological characteristics of some Iranian Ajuga L. taxa. Biodiversitas 20: 2833-2840. Ajuga is one of the problematic Lamiaceae genera, which naturally grows in different parts of Iran. There are many discussions about infrageneric and infraspecific classifications of the genus and several synonyms were definite for its taxa. In the current study, we evaluated nutlet morphological characteristics from six Iranian taxa of the genus using Scanning Electron Microscopy (SEM) and Light microscopy (LM). In total, thirteen (four qualitative and nine quantitative) nutlet morphological variables were investigated, and the obtained data were analyzed using MVSP and SPSS software. Quantitative nutlet features varied among the studied taxa and ANOVA test revealed significant variations (P <0.01) for most of them. Moreover, PCA analysis showed some characteristics made more than 60% of variations. Some quantitative characteristics like nutlet and ventral sculpturing shapes were nearly stable among the taxa. But dorsal sculpturing shape and existence of exocarp cell indumentum highly varied among the taxa and could be used as distinguishing traits for identification of taxa. The studied taxa were divided into four groups in UPGMA dendrogram and also PCA and PCO plots of the nutlet features. CA. Joined plot revealed that each group had specific nutlet characteristic (s). Taxa arrangements were not similar to those have been definite for them in Flora Iranica and Flora of Iran. Furthermore, some infraspecific taxa must be redefinite. It is advised to use complementary molecular studies to better clearing species relationship, taxa position and rank in the genus.
Genetic variability of Indonesian eggplant (Solanum melongena) based on ISSR markers U.B. HUSNUDIN; B.S. DARYONO; Purnomo Purnomo
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/d201038

Abstract

Abstract. Husnudin UB, Daryono BS, Purnomo. 2019. Genetic variability of Indonesian Eggplant (Solanum melongena) based on ISSR markers. Biodiversitas 20: 3049-3055. Eggplant (Solanum melongena L.) is one of important vegetable in Indonesia and this country has a variety of eggplant germplasm, whereas molecular data of Indonesian eggplant is limited. This study describes an analysis of genetic variation based on ISSR markers to determine the diversity and phenetic relationship of Indonesian eggplants. 23 samples were collected from the Indonesian Center for Agricultural Biotechnology Research and Development (ICABIOGRAD) and some commercial cultivars. Data were analyzed by ISSR analysis using UBC 809, UBC 880, UBC 888, UBC 892 and UBC 895 primers. Similarity index was counted by Jaccard Coefficient formula based on molecular scoring. Cluster analysis was conducted by Unweighted Pair Group Methods using Arithmetic averages (UPGMA) method to create a dendrogram with Multivariate Statistical Program (MVSP) v.3.1 software. The results showed that ISSR markers were effective in the estimation of the genetic variability of eggplant accessions characterized by different level of polymorphism. Five ISSR primers generated 40 polymorphic bands (64.5% of the total). The dendrogram divided 23 eggplant accessions into 2 main clusters and one accession ("terong jawa"/K18) located outside from the main cluster. Results suggested that all accessions were grouped randomly into some clusters not in accordance with the locations of sample collection.
RAPD based genetic diversity, agronomic characters, and nutrition content of Timor Leste kidney bean (Phaseolus vulgaris) genotypes MARCOS CORREIA VIDAL; Asep Setiawan; YUDIWANTI WAHYU
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/d200925

Abstract

Abstract. Vidal MC, Setiawan A, Wahyu Y. 2019. RAPD based genetic diversity, agronomic characters, and nutrition content of Timor Leste kidney bean (Phaseolus vulgaris) genotypes. Biodiversitas 20: 2612-2619. The productivity of kidney beans (Phaseolus vulgaris L.) in Timor Leste is relatively low and needs to be improved. The increase in kidney bean yield through plant breeding, however, can only be obtained if information the genetic diversity of breeding materials is available. This study aimed to characterize agronomic characters, to assess genetic diversity and nutrient content of kidney bean in Timor Leste. The materials used in this study were 13 Timor Leste and 2 Indonesian genotypes as controls. The experimental design for the field trial was a complete randomized block design with three replications. The treatment was 13 kidney bean genotypes. The results showed that there were significant variations in agronomic characters among the genotypes tested. Result from phylogenetic trees based on the Random Amplified Polymorphic DNA (RAPD) indicated that the genetic material understudied can be grouped into three main groups. The Indonesian genotype belongs to a different group from Timor Leste genotypes. Direct selection based on seed yields produced the best eight East Timor genotypes, TL-RO3, TL-LUN, TL-LM, TL-R10, TL-LL, TL-RW, TL-LB, TL-LB, and TL-Umabano. The nutritional content of the kidney bean genotype from Timor Leste was similar to that of the Indonesian genotype. The carbohydrate content of the Timor Leste genotype was considered high (average = 59.95%), while the average fat content is low (1.71%) and the average protein content was quite moderate (18.08%).  
Genetic heterogeneity of proteolytic bacteria isolated from sediments mangrove areas based on repetitive sequence-based polymerase chain reaction and 16S-rRNA gene sequences wilis ari setyati; ERNI MARTANI; TRIYANTO; MUHAMMAD ZAINUDDIN; MAYA PUSPITA; CHRISNA ADI SURYONO; SUBAGYO; delianis pringgenies
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/d201118

Abstract

Abstract. Setyati WA, Martani E, Triyanto, Zainuddin M, Puspita M, Suryono CA, Subagyo, Pringgenies D. 2019. Genetic heterogeneity of proteolytic bacteria isolated from sediments mangrove areas based on repetitive sequence-based polymerase chain reaction and 16S-rRNA gene sequences. Biodiversitas 20: 3256-3261. Intensive shrimp farming has organic waste that results in pollution. Such waste needs to be bio-remediated for liquid waste. This study aimed to discover bacteria isolated from mangrove sediments that can degrade organic matter and apply them for bioremediation of polluted shrimp farms. The study consisted of bacterial isolation, bioassay of enzymatic activity, and isolates identification through cluster analysis. Bacterial isolates were collected from mangrove ecosystems in Rembang (R), Cilacap (C), Banyuwangi (B), and Karimunjawa (K). Enzymatic activity test consists of proteolytic, amylolytic, cellulolytic, lipolytic, and ligninolytic activity. Identification analysis was conducted with 16S-rRNA gene sequences followed by cluster analysis using the results of Rep-PCR. There were 19 isolates derived from proteolytic mangrove area represented in five clusters (groups). Group 1 consisted of 5 isolates; isolates 14.C, 22.R, 28.K, 15.C and 19.R. Group 2 consisted of 5 isolates; 30.K, 33.K, 34.K, 39.K and 40.B. Group 3 consisted of 3 isolates of bacteria; 13.C, 2.C and 32.C. Group 4 consisted of 5 isolates; isolates 36.K, 35.K, 37.K, 38.K and 48.B. Group 5 consisted of 1 isolate was isolate 26.R. The results of the sequences analysis of the 16S-rRNA gene indicated that the isolate 13C of the Group 3 had 97% sequence homology with Bacillus oceanisediminis strain H2. Isolate 14.C of the Group 1 had 96% sequence homology with Halomonas aquamarina strain DSM 30161. Isolate 26.R of the Group 5 had 98% sequence homology with Acinetobacter pitti strain ATCC 19004. Isolate 30.K of the Group 2 had 93% sequence homology with Salinicola salarius strain M27. Isolate 36.K of the Group 4 had 97% sequence homology with Bacillus aquimaris strain TF-12. Please write here your concluding remarks based on your results obtained.
The population, utilization and local management of Elaeodendron transvaalense in the Blouberg Municipality, Limpopo Province, South Africa Marula Triumph Rasethe; Sebua Silus Semenya
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/d201028

Abstract

Abstract. Rasethe MT, Semenya SS. 2019. The population, utilization and local management of Elaeodendron transvaalense in the Blouberg Municipality, Limpopo Province, South Africa. Biodiversitas 20: 2978-2985. Elaeodendron transvaalense is highly harvested by rural communities of the Limpopo Province (South Africa) to meet various livelihoods. However, its information on the population, uses, harvesting practices, threatening factors and local management is still not investigated and documented in many parts of this province. The current study therefore, provides a base-line data of E. transvaalense occurring in two villages of the Blouberg Municipality, Limpopo Province. Data on the population locations, utilization and local management strategies of this species was collected from community members, traditional healers and leaders via semi-structured questionnaires, supplemented by field observations on harvesting practices, threats, area of occupancy, population size, density and demographic structure and population health. Two populations, referred in this study as Sebotlana and Makgabeng covering an area of 25252.17 m2 and 45099.79 m2, respectively, were located in the two villages of the Blouberg Municipality. Both populations were characterized by a mixture of healthy seedlings, sapling, juvenile, middle trees, adult trees, and senescent trees, with Makgabeng population having the highest plant density. Various morphological parts such as bark and roots were mainly used by respondents as common ingredients in traditional medicines, mainly for cough, fever, diarrhoea, symptoms of AIDS and as blood purifier. Evidence of harvesting was only observed on Sebotlana population, which was also highly impacted by rural settlement expansion. Overall, there were no local management strategies meant specifically for the identified E. transvaalense around the Blouberg area.

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