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Biodiversitas Journal of Biological Diversity
Published by Universitas Sebelas Maret
ISSN : 1412033X     EISSN : 20854722     DOI : https://doi.org/10.13057/biodiv/d230231
Core Subject : Science, Agriculture,
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology
The Biodiversitas Journal was first published in 2000 by the Department of Biology, FMNS, Universitas Sebelas Maret, Surakarta, Indonesia, then in 2006 it was co-published by the Society for Indonesian Biodiversity and that department; since 2017 it was also hosted by Smujo. From 2003-2012 it was accredited by DGHE, Ministry of Education, R.I., since 2014 was indexed by Scopus, where DOAJ and Google Scholar was indexed first.
Arjuna Subject : Biokimia, Genetika dan Biologi Molekuler - Biokimia, Genetika dan Biologi Molekuler (Lain-Lain)
Articles 6,269 Documents
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Short Communication: Phylogenetic analysis of mango (Mangifera) in Northern Sumatra based on gene sequences of cpDNA trnL-F intergenic spacer FITMAWATI FITMAWATI; SANDI PRATIWI HARAHAP; NERY SOFIYANTI
Biodiversitas Journal of Biological Diversity Vol. 18 No. 2 (2017)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d180239

Abstract

Harahap SP, Fitmawati, Sofiyanti N. 2017. Short Communication: Phylogenetic analysis of mango (Mangifera) in Northern Sumatra based on gene sequences of cpDNA trnL-F intergenic spacer. Biodiversitas 18: 715-719. Northern Sumatra is an area with geographical variation. The environmental factors are affected on character plasticity such as found in Anacardiaceae family especially Mangifera genus. The character plasticity of Mangifera members raises a problem in determining clear boundaries between species based on morphological character. Therefore, a molecular approach is necessary to provide a specific character among Mangifera species. This study aimed to reconstruct the phylogeny among Mangifera members in Northern Sumatra based on the sequences of trnLF intergenic spacer. All of the sequences were aligned by using Clustal W and Cladogram was reconstructed by using PAUP by Maximum Parsimony (MP) and Neighbour-Joining (NJ) methods. The MP cladogram produced two in groups i.e., clade I consist of M. odorata1, M. odorata2, M. laurina1, M. laurina2, M. indica, M. zeylanica, M. quadrifida and Mangifera sp. and clade II consisted of M. foetida1 and M. foetida2. Based on the NJ method, it was obtained M. laurina2 which had the highest genetic distance among other members of Mangifera. The trnL-F intergenic spacer with a low sequences variation indicated that this region was highly conserved and had a low evolution rate in Mangifera.
Study of climatic factors on the population dynamics of Pyricularia oryzae on some varieties of paddy rice (Oryza sativa) SOPIALENA SOPIALENA; PRATIWI JATI PALUPI
Biodiversitas Journal of Biological Diversity Vol. 18 No. 2 (2017)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d180237

Abstract

Sopialena, Palupi PJ. 2017. Study of climatic factors on the population dynamics of Pyricularia oryzae on some varieties of paddy rice (Oryza sativa). Biodiversitas 18: 701-708. The occurrence of plant diseases is influenced by three factors: pathogen, environment, and host. Environment playing important role in the development of the disease is the climatic factor, whereas the resistance of plants also influences the development of disease. The research was conducted during five months from April to August 2016 and the location of the research was in paddy fields in Tanah Merah, North Samarinda, East Kalimantan, Indonesia. The study aims to determine the climatic factors (temperature and humidity) which are most dominant to the rate of spot width, the infection rate of pathogen attack intensity on Pyricularia oryzae and the development of P. oryzae spores in several varieties of paddy rice (Inpari 7, Ciherang and Cibogo). The parameters in the study are climate factors namely humidity and temperature, the width rate of spot blast disease, the attack intensity of pathogenic P. oryzae and the spores number of P. oryzae. Research shows that the population of P. oryzae is strongly influenced by temperature. Low temperature is the most dominant factor affecting the rate of infection of blast disease. The number of pathogen population also affects the attack intensity of the disease. A higher population of P. oryzae led to higher intensity of blast disease in rice plants. Moreover, varieties of rice plants also affect P. oryzae attack. The more vulnerable the plants, the higher level of P. oryzae attack on the plant. The lowest intensity attack of the disease is found in Ciherang, then Cibogo and the most vulnerable is Inpari 7.
Agroforestry system biodiversity of Arabica coffee cultivation in North Toraja District, South Sulawesi, Indonesia ANDI LISNAWATI; ABUBAKAR M. LAHJIE; B.D.A.S. SIMARANGKIR; SYAHRIR YUSUF; YOSEP RUSLIM
Biodiversitas Journal of Biological Diversity Vol. 18 No. 2 (2017)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d180243

Abstract

Lisnawati A, Lahjie AM, Simarangkir BDAS, Yusuf S, Ruslim Y. 2017. Agroforestry system biodiversity of Arabica coffee cultivation in North Toraja District, South Sulawesi, Indonesia. Biodiversitas 18: 741-751. Sustainable coffee plantation emphasizes the concept that is able to provide services that can improve the quality of the environment and the ecosystem as a conservation efforts. Arabica coffee plants do not need full sunlight that they are planted according to agroforestry system which covers simple mix system to complex system such as forest. Shade tree has a very big role in sustainable coffee agro-ecosystem and become one of the conditions in the world's coffee certification. This study aimed to analyze the role of shade trees lamtoro types (Leucaena glauca), and calliandra (Calliandra calothyrsus) used by companies as an agroforestry systems on coffee cultivation in North Toraja located at an altitude between 1050-1250 m above sea level, this study was conducted from January to December 2016. Result of the study suggests that the shade trees lamtoro and calliandra influence the amount of sunlight intensity that reaches coffee plant. The shaded and unshaded coffee plants received different sunlight intensity of every minute with a coefficient of determination R2 = 0.98 for unshaded and R2 = 0.89 for under the shade of calliandra, with a diameter growth increased 7.8% year-1, increase growth (riap) diameter decreased 2% year-1. Cherry increased growth of 13.5% year-1 with an average weight of 3.81 g beans-1,while for the effect of lamtoro, the coefficient of determination is R2 = 0.98 for unshaded and R2 = 0.91 for under the shade. The percentage of light intensity outside and under the shade obtained from a 17 year coffee plant is on average of 58% for the types of tree of calliandra, while for lamtoro the average is of 72.5%, diameter growth of coffee tree in under shade lamtoro by 7.4% year-1 and increase of growth (riap) diameter decreased by 2.5% year-1, cherry growth increased by 13.3% year-1 with an average weight of 3.92 g beans-1. In addition to that, shading also affect the surrounding nutrient soil and maximum production of coffee is achieved at the age 17 years i.e. an average of 1.50 kg tree-1 for a shaded tree calliandra species and 1.35 kg tree-1 for lamtoro species.
Effect of seed coating with biological agents on seed quality of rice TANTRI PALUPI; SATRIYAS ILYAS; MUHAMMAD MACHMUD; ENY WIDAJATI
Biodiversitas Journal of Biological Diversity Vol. 18 No. 2 (2017)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d180241

Abstract

Palupi T, Ilyas S, Machmud M, Widajati E. 2017. Effect of seed coating with biological agents on seed quality of rice. Biodiversitas 18: 727-732. The research that consisted of two activities was performed at the Laboratory. Experiment 1 the aim to obtain biological agents that have high antagonistic potential against Xanthomonas oryzae pv. oryzae (Xoo) and two biological agents that are compatible to one another. Experiments 2 to determine the effect of rice (Oryza sativa L.) seeds coated with biological agents to improve seed quality and reduce levels of Xoo infection. In the first experiment, four isolates of bacterial antagonists, i.e: isolate Pseudomonas diminuta A6; isolate P. aeruginosa A54; isolate Bacillus subtilis 11/C, and isolate B. subtilis 5/B, were tested for their antagonism activities against Xoo on PSA plates using the method of growth inhibition zone with filter paper. Furthermore, the four antagonists were tested for their compatibility with each other on PSA plates. In the second experiment used a completely randomized design with a single factor (seed coating) consisting of seven levels, namely: negative control, healthy seed; positive control, the seeds contaminated with Xoo; P. diminuta A6 and B. subtilis 5/B; alginate 3% + 1% peat + P. diminuta A6 and B. subtilis % 5/B; arabic gum 3% + 1% gypsum + P. diminuta A6 and B. subtilis 5/B; CMC 1.5% + 1% talc + P. diminuta A6 and B. subtilis 5/B, and bactericide streptomycin sulfate 20%. Results of Experiment 1 showed that isolates P. diminuta A6 has the highest antagonistic potential against Xoo based on the diameter of inhibition zone on Xoo, followed by isolate B. subtilis 5/B. Isolate P. diminuta A6 and B. subtilis 5/B had a good growth compatibility with no antagonism. Therefore, isolates P. diminuta A6 and B. subtilis 5/B were selected and used as biocontrol agents in further studies. Results of Experiment 2 showed that treatment with P. diminuta A6 + B. subtilis 5/B gave the best of the increase of seed vigor, and the decrease of Xoo infection level in the seeds.
Growth and mortality rate of the Napan-Yaur Coral Trout, Plectropomus leopardus (Pisces: Serranidae), Cenderawasih Bay National Park, Indonesia RONI BAWOLE; MUDJI RAHAYU; UNSTAIN N.W.J. REMBET; ARNOLDUS S. ANANTA; FERAWATI RUNTUBOI; RIDWAN SALA
Biodiversitas Journal of Biological Diversity Vol. 18 No. 2 (2017)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d180245

Abstract

Bawole R, Rahayu M, Rembet UNWJ, Ananta AS, Runtuboi F, Sala R. 2017. Growth and mortality rate of the Napan-Yaur Coral Trout, Plectropomus leopardus (Pisces: Serranidae), Cenderawasih Bay National Park, Indonesia. Biodiversitas 18: 758-764. Coral trout, Plectropomus leopardus, is one of the important fishery resources in Cenderawasih Bay National Park, Papua, Indonesia. The catch production of this species has declined since 2015. This study aims to assess growth, mortality, and exploitation rate parameters of P. leopardus taken from Napan Yaur water, Cenderawasih Bay National Park (CBNP), Indonesia. The data were collected during periods of February to March 2016. Growth and mortality parameters were analyzed using von Bertalanffy method. Some fish samples used in this study was 123 individuals, with the average length of 32.34 ± 5.13 cm, the maximum length of 48.00 cm and minimum length of 24.5 cm. The von Bertalanffy analysis showed that the growth coefficient (K) was 0.34 year-1, L∞ was 47.78 cm and t0 was-0.09 year-1. The estimation of total mortality (Z) was 1.61 year-1, natural mortality (M) was 0,75year-1 for fishing mortality (F) was 0.86 year-1, and exploitation rate (E) was 0.53 year-1. The results indicated that most P. leopardus caught were at the pre-maturity size (age) and have been exploited at slightly above its optimum exploitation level. Nevertheless, P. leopardus is categorized as fast growing and long-lived fish species. These findings are important to fisheries management and conservation authorities to fish exploitation in the future.
Endophytic bacteria producing antibacterial against methicillinresistant Staphylococcus aureus (MRSA) in seagrass from Rote Ndao, East Nusa Tenggara, Indonesia DIAN SAGITA FITRI; ARTINI PANGASTUTI; ARI SUSILOWATI; SUTARNO SUTARNO
Biodiversitas Journal of Biological Diversity Vol. 18 No. 2 (2017)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d180242

Abstract

Fitri DS, Pangastuti A, Susilowati A, Sutarno. 2017. Endophytic bacteria producing antibacterial against methicillin-resistant Staphylococcus aureus (MRSA) in seagrass from Rote Ndao, East Nusa Tenggara, Indonesia. Biodiversitas 18: 733-740. Methicillinresistant Staphylococcus aureus (MRSA) are bacteria that resistant to the various type of antibiotics and yet cannot be handled comprehensively. The discovery of new antibiotic from endophytic bacteria in seagrass of Rote Island is an option to overcome the resistance. The aims of this research were to screen endophytic bacteria inhibit MRSA from seagrass, to determine the species of the endophytic bacteria and the genetic relationship. Isolation of endophytic bacteria has carried out by inoculating surface sterilization seagrass leaves on Marine Agar (MA) medium. Selection of potential endophytic bacteria-producing anti-MRSA has done using overlay method against MRSA, gram-positive Bacillus subtilis, and gram-negative Escherichia coli. Identification of the endophytic bacteria based on the sequence of 16S rRNA encoding gene. The results showed that there were eight isolates of endophytic bacteria which have antibacterial activity against MRSA of seagrass Enhalus acoroides, Thalassia hemprichii, and Cymodocea rotundata in the Litianak and Oeseli Beaches, Rote Ndao. The diameter of inhibition zone was between 0.65-18.27 mm with narrow spectrum with broad spectrum antibacterial activity. The eight potential endophytic bacteria identity were Bacillaceae E2M1, Bacillaceae E2M3, Bacillus E2M4, Bacillus E2M7, Bacillaceae E2M8, Pseudomonadaceae C1M7, Shewanellaceae C2M3, and Rhodobacteraceae T1M3. Most of the isolates can be said to be a new species as the percent similarity of 16S rRNA gene sequence was less than 95% and promising to produce new antibacterial compounds. Phylogenetic relationship showed some isolates clustering in different groups that present the diverse groups of endophytic bacteria were found.
Short Communication: Fish fauna of Lake Lauik Tawar and Lake Laulo, Simeulue Island, Indonesia ZAINAL A. MUCHLISIN; NURFADILLAH NURFADILLAH; IKO IMELDA ARISA; ALVI RAHMAH; DEDI F. PUTRA; MUHAMMAD NAZIR; ARMEN ZULHAM
Biodiversitas Journal of Biological Diversity Vol. 18 No. 2 (2017)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d180244

Abstract

Muchlisin ZA, Nurfadillah N, Arisa II, Rahmah A, Putra DF, Nazir M, Zulham A. 2017. Short Communication: Fish fauna of Lake Lauik Tawar and Lake Laulo, Simeulue Island, Indonesia. Biodiversitas 18: 752-757. The objectives of the present study were to evaluate the species composition and diversity index of fishes in Lake Lauik Tawar and Lake Laulo, Simeulue Island, Aceh Province, Indonesia. The survey was conducted from 17th to 21st of November 2015. The fishes were sampled using gillnets with mesh size 1-3 inches. The representative of each species was photographed and then preserved in 10% formalin and transported for taxonomic identification in the Laboratory of Ichthyology, Syiah Kuala University, Banda Aceh, Indonesia. The study showed that there were 11 species of fish recorded during the survey; where eight species were found in Lake Lauik Tawar and six species were found in Lake Laulo. Two species of alien fish were recorded in Lake Lauik Tawar, i.e. Osphronemus gouramy and Oreochromis niloticus and one species in Lake Laulo i.e. O. niloticus. In addition, Ambassis miops and Clarias batrachus were predominant species in Lake Lauik Tawar and Lake Laulo, respectively. In general, the two lakes were categorized as a low degree of fish diversity.
Seagrass community structure of Tayando-Tam Island, Southeast Moluccas, Indonesia TYANI FITRIAN; AGUS KUSNADI; ROSMI NUSLAH PERSILETTE
Biodiversitas Journal of Biological Diversity Vol. 18 No. 2 (2017)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d180250

Abstract

Fitrian T, Kusnadi A, Persilette RN. 2017. Seagrass community structure of Tayando-Tam Island, Southeast Moluccas, Indonesia. Biodiversitas 18: 788-794. Seagrass bed is one of the marine ecosystem that having the highest productivity that could sustain coastal resources. The research purposes of this paper is to determine the community structure of seagrass at Tayando-Tam Island, Southeast Moluccas, Indonesia. The method of observation of seagrass bed using a line transect, transect ran perpendicular to the shore line for 100 meters. The field of observations include identification of seagrass species, counting the number of shoots and percentage (%) of seagrass cover. Seven species of seagrass had been found in Tayando-Tam island, i.e. Enhalus acoroides, Thalassia hemprichii, Cymodocea serrulata, Cymodocea rotundata, Halodule pinifolia, Halophila ovalis, Syringodium isoetifolium. Halodule pinifolia had the highest density in Tam Island with the number of 684.18 shoots/m2. The coverage in this area was between 4.64-43.1 %. Based on the number of species, diversity index and dominance index Tam Island had the most stable seagrass communities, with moderate value of diversity index (H'=1.26), high evenness Index (E=1.63), and low value of dominance index (D=0.34). Seagrass resources in the Tayando-Tam islands is good and the potential for biota the association, which is supported by the quality of water is good for the growth of seagrass.
The dominant species of herpetofauna in the coal mining area at East Kalimantan, Indonesia TEGUH MUSLIM; ULFAH KARMILA SARI; ISHAK YASSIR
Biodiversitas Journal of Biological Diversity Vol. 18 No. 2 (2017)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d180247

Abstract

Muslim T, Sari UK, Yassir I. 2017. The dominant species of herpetofauna in the coal mining area at East Kalimantan, Indonesia. Biodiversitas 18: 773-779. Changing of habitat condition influences the variety of species including Herpetofauna. Herpetofauna is one of the components in the ecosystem that plays an important role, both from the ecological and economical aspect. From the ecological aspect, it has a specific role in the food chain, and it can also be used as a bio-indicator of the environment’s condition. Furthermore, herpetofauna found in reclamation area of coal mining not only stabilizes the ecosystem in the food chain, but also it can be used as a bioindicator of environment changes and the success rate of reclamation. The aim of this research was to find out the community of herpetofauna comprising and dominating the coal mining reclamation area, especially the wet and dry areas. The research location was located at PT. Singlurus Pratama Kalimantan Timur. The methods used in this research were visual encounter survey and patch sampling. This research found 10 species from 5 families of reptiles and 11 species from 6 families of amphibians. The highest dominant index score for reptile was 0.71, found in the fragmented forests. Meanwhile, the dominant reptile species were Eutropis multifasciata (20 individuals), Enhydris enhydris (4 individuals), and Dendrelaphis pictus (4 individuals). The highest dominant index score for amphibian was 1, found in the settling pond. Moreover, the dominant amphibian species were Polypedates leucomystax (42 individuals) and Fejervarya cancrivora (41 individuals). These two species were the ones able to survive in the degraded areas and they were easily found in the areas with disrupted habitats.
Short Communication: Investigation of Diphtheria in Indonesia: dtxR and tox genes analysis of Corynebacterium diphtheriae collected from outbreaks YUANITA MULYASTUTI; SIWIPENI I. RAHAYU; SUNARNO SUNARNO; EDDY B. WASITO
Biodiversitas Journal of Biological Diversity Vol. 18 No. 2 (2017)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d180249

Abstract

Mulyastuti Y, Rahayu SI, Sunarno S, Santoso S, Wasito EB. 2017. Short Communication: Investigation of Diphtheria in Indonesia: dtxR and tox genes analysis of Corynebacterium diphtheriae collected from outbreaks. Biodiversitas 18: 784-787. Diphtheria outbreaks have sporadically occurred in Indonesia recently. It is suspected that toxin profile changes play an important role in vaccine efficacy and the occurrence of outbreaks. This study aimed to investigate the genetic changes of dtxR and tox genes in Corynebacterium diphtheria in Indonesia. Four C. diphtheriae toxigenic isolates circulating in current outbreak area were analyzed by comparing DNA sequences of their dtxR and tox genes to those of the PW8 vaccine strain. Among the four isolates, three point mutations were detected in dtxR gene while three other point mutations were detected in the tox gene. All six were silent mutations, suggesting that the diphtheria toxin is highly conserved at the amino acid sequence level, and indirectly indicating that the vaccine remains appropriate. Genetic variation in dtxR and tox genes of C. diphtheriae isolates from the recent outbreaks in Indonesia was detected.

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