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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: Helminth fauna of Lutjanidae from Kedonganan, Bali, Indonesia ERICK ARRASHY RUDIANTO; DIAH PERMATA WIJAYANTI; DWI HARYANTI; ELIS INDRAYANTI
Biodiversitas Journal of Biological Diversity Vol. 25 No. 12 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d251236

Abstract

Abstract. Rudianto EA, Wijayanti DP, Haryanti D, Indrayanti E. 2024. Short Communication: Helminth fauna of Lutjanidae from Kedonganan, Bali. Biodiversitas 25: 4986-4993. The biodiversity of parasites in demersal reef fishes is immense but remains poorly understood and often overlooked. This is also hindered by the lack of survey of parasite communities in reef fishes, especially in Indonesia. Therefore, we surveyed endoparasites of reef-associated and demersal lutjanids in the Kedonganan fish market, Bali. A total of 25 individuals of six lutjanid species: Lutjanus erythropterus, Lutjanus russellii, Lutjanus sebae, Lutjanus timoriensis, Lutjanus vitta, and Pristipomoides multidens, were collected from the fish market. The parasites were collected using a modification of the gut wash method. Two individuals of Philometridae were recovered from L. vitta. Other recovered helminth fauna were Acanthocephala, Nematoda, and Digenea, mainly belonging to Siphoderina spp. and Hamacreadium sp. We also reported for the first time, endoparasites of L. erythropterus and P. multidens in Indonesian waters. This study highlighted the importance ichthyo-parasitological survey as a part of the biodiversity survey. More surveys and reports on endoparasites in demersal reef fishes in Indonesia are needed, especially on their biology, ecology, diversity, and impact on human health, considering that most of these demersal fishes are consumed by local people.
Diversity of fungal species and decomposition of Rhizophora mucronata leaf litter in the Deli Belawan River Estuary, North Sumatra, Indonesia YUNASFI YUNASFI; SRI RUSMAYANTI LUBIS; BUDI UTOMO; AFIFUDDIN DALIMUNTHE; VINANSIA M. SIHOTANG; SEPHIA SEMBIRING; GLOURY ARIZONA SITEPU; JON GANDA MARPAUNG PURBA; RICKSON SILALAHI; IPANNA ENGGAR SUSETYA; AMANATUL FADHILAH; ZULHERI NOER
Biodiversitas Journal of Biological Diversity Vol. 26 No. 4 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d260414

Abstract

Abstract. Yunasfi, Lubis SR, Utomo B, Dalimunthe A, Sihotang VM, Sembiring S, Sitepu GA, Purba JGM, Silalahi R, Susetya IE, Fadhilah A, Noer Z. 2025. Diversity of fungal species and decomposition of Rhizophora mucronata leaf litter in the Deli Belawan River Estuary, North Sumatra, Indonesia. Biodiversitas 26: 1631-1640. Rhizophora mucronata is one of the most widely known mangrove species, growing in coastal areas, such as along river estuaries, deltas, and lagoons. This species produces leaf litter that is useful for organisms living in mangrove water after decomposition. The decomposition of R. mucronata leaf litter is often affected by the presence of salinity in seawater including other environmental factors such as pH, humidity, rainfall, temperature, and river current speed. Fungi played an important role in the process of litter decomposition by facilitating the degradation of organic compounds such as cellulose and lignin which are components of leaf cell walls. The aim of this study was to determine the fungal species diversity and decomposition of R. mucronata leaf litter at salinity levels of 0-10 ppt in the Belawan Deli River. The study used 24 bags of 40 × 30 cm litter bags. Fungal isolation was carried out using the dilution method to calculate the number of fungal colonies in R. mucronata leaf litter. Furthermore, the analysis of carbohydrate and protein contents in R. mucronata leaf litter was carried out using the semi-micro method (01-2891-1992 SNI). The results of isolation showed that species of fungi were associated with R. mucronata leaf litter, namely Aspergillus sp.1, Aspergillus sp. 2, Aspergillus sp. 3, Penicillium sp., Trichoderma sp. The decomposition rate of R. mucronata leaf litter was 0.018/year. The average percentage of total carbohydrates and proteins was 9.33 and 5.54%, respectively. Based on the outcomes found in this research, the author suggested to conduct research on R. mucronata leaf litter at salinity levels of 11-20 ppt and 21-30 ppt to further observe the diversity of fungal species.
A comparative study of insect diversity and distribution across elevations at Denai Cadamba, UiTM Puncak Alam, Malaysia KHAIRUDIN NURUL FATHIAH; ISKANDAR MUDA DINDA PUTRI ALHAFIZA; IBRAHIM NUR AMIN; MD YUSOF NUR NADIAH; MOHD HATTA SITI KHAIRIYAH; ABD WAHAB NOOR AKMAL; MOHD ZAZI NORHAFIZAH
Biodiversitas Journal of Biological Diversity Vol. 25 No. 10 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d251009

Abstract

Abstract. Fathiah KN, Alhafiza IMDP, Amin IN, Khairiyah MHS, Akmal AWN, Norhafizah MZ. 2024. A comparative study of insect diversity and distribution across elevations at Denai Cadamba, UiTM Puncak Alam, Malaysia. Biodiversitas 25: 3473-3479. Insects play a significant role in shaping the ecosystem community and are beneficial to mankind in many ways. They are known for many roles such as pollinators, bioindicators, scavengers, and vectors for diseases. A study on the diversity and distribution of class Insecta was conducted using two Malaise traps at the hiking trail of Denai Cadamba, UiTM Puncak Alam, Malaysia as no study has been done here before. Two study sites with two different elevations were chosen: low elevation (70 meters above sea level/masl) and high elevation (110 masl). A total of 2476 individuals from 335 morphospecies belonging to 13 orders were collected. The orders identified were Diptera, Lepidoptera, Hymenoptera, Coleoptera, Hemiptera, Collembola, Thysanoptera, Orthoptera, Blattodea, Microcoryphia, Isoptera, Mantodea, and Psocoptera. Diptera was the most common order sampled, while Microcoryphia and Psocoptera recorded the least number, with only two individuals found each. The Shannon-Wiener Diversity Index (H?) showed that the higher elevation (trap 2) has a higher diversity with H?=1.362 compared to the lower elevation (trap 1) with H?=1.017. The Evenness Index (E?) and Margalef Richness Index (R?) were also higher for trap 2 with the values E?=0.300 and R?=1.635 respectively, while for trap 1, the values were E?=0.276 and the R?=1.315, respectively. Mann-Whitney test showed that there was a significant difference in the insect distribution between the low elevation and the high elevation with P<0.05. In general, this study found that the order distribution differs across the elevations. This might be due to the rainy season, sunlight exposure, warmer conditions, less human disturbance, and type of vegetation. The data obtained in this study can be used as a baseline for future research while serving as an educational purpose to create awareness among the public about insect conservation and management.
Floristic composition and carbon sequestration of traditional agroforestry on peatland in Rimbo Panjang, Kampar, Riau, Indonesia MAYTA NOVALIZA ISDA; SITI FATONAH; YULMINARTI YULMINARTI; NUR ZARAH OKTARINA; DEWI INDRIYANI ROSLIM
Biodiversitas Journal of Biological Diversity Vol. 26 No. 1 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d260146

Abstract

Abstract. Isda MN, Fatonah S, Yulminarti, Oktarina NZ, Roslim DI. 2025. Floristic composition and carbon sequestration of traditional agroforestry on peatland in Rimbo Panjang, Kampar, Riau, Indonesia. Biodiversitas 26: 470-479. Trees in agroforestry systems contribute to long-term carbon sequestration, helping to mitigate climate change. Traditional agroforestry is characterized by multifunctionality through the use a variety of native trees to maintain ecological balance and support local livelihoods. This study aimed to determine the plant composition of traditional agroforestry in Rimbo Panjang Village, Kampar, Riau, Indonesia, its utilization, and its role in carbon sequestration. Observations were made in two hamlets, namely Dusun 1 and Dusun 2, where both hamlets have traditional agroforestry systems. Observation on floristic composition was conducted by counting the number of individuals of each species and the diameter at breast height of each individual plant. Carbon sequestration was calculated based on the above-ground biomass determined using an allometric formula accounting for trunk diameter and wood density. The results showed that traditional agroforestry in Dusun 2 had a higher number of plant species, with a total of 17 species, compared to Dusun 1, which had 11 species. The dominant species in Dusun 1 was Cocos nucifera, while in Dusun 2 was Durio zibethinus. Plants in this agroforestry system have a variety of benefits, both for self-consumption and being marketed for domestic uses and as industrial raw materials. The average carbon sequestration in Rimbo Panjang Village was 508.65 tons/ha CO2 equivalent (CO2e), with carbon sequestration in Dusun 2 (618,3 tons/ha CO2e) higher than that of Dusun 1 (399 tons/ha CO2e). The high plant diversity in this agroforestry system supports community livelihoods and plays an important role in climate change mitigation through its role in carbon sequestration. These benefits highlight the need to support and develop sustainable agroforestry practices as a sustainable land use strategy, especially in Riau's extensively degraded peatlands.
Exploring the diversity of cellulolytic microorganisms from tea factory waste and evaluating their potential in breaking down tea waste MARIANI SEMBIRING; MUKHLIS MUKHLIS; RAZALI RAZALI; BENNY HIDAYAT
Biodiversitas Journal of Biological Diversity Vol. 26 No. 1 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d260137

Abstract

Abstract. Sembiring M, Mukhlis, Razali, Hidayat B. 2025. Exploring the diversity of cellulolytic microorganisms from tea factory waste and evaluating their potential in breaking down tea waste. Biodiversitas 26: 377-385. The rate at which organic materials decompose is influenced by their cellulose, lignin, and hemicellulose content. To accelerate the decomposition process, cellulolytic microorganisms can be employed, which can be isolated from organic materials. Tea plants, as a significant plantation commodity, produce various types of waste during processing, including solid, liquid, and gas wastes. Solid waste from tea factories is produced in large quantities year-round and has substantial potential as a source of organic material. This research aimed to find cellulolytic microbes that were sourced from tea waste and have superior potential in the decomposition of organic matter, especially tea waste. The research involved several stages: isolating microbes from semi-processed waste from the Bah Butong tea factory, purifying the microbes to obtain pure isolates, testing the semi-qualitative potency of these isolates on CMC (Carboxyl methyl cellulase) media, and assessing the degradation potential of the superior isolates on raw tea factory waste. The research findings revealed the presence of five bacteria and two fungi from tea factory waste that have potential as decomposer microbes: Enterobacter oligotrophicus (AS), Stenotrophomonas maltophilia H05 (BS), S. maltophilia (CS), Priestia megaterium (DS), Methylophilus methylotrophus (ES) and cellulolytic fungi Aspergillus fumigatus (J1) and Aspergillus corrugatus (J2). Overall, the use of these cellulolytic bacteria and fungi can accelerate the decomposition of tea factory waste, with compost nitrogen content increasing by 102%. The application of Aspergillus corrugatus (J2) and Methylophilus methylotrophus (ES) is the best treatment with the lowest C/N ratios and the highest total nitrogen content.
The effect of planting distance engineering treatment on the morphophysiology and yield of soybean varieties integrated with oil palm WAGINO WAGINO; ABDUL RAUF; CHAIRANI HANUM; RAHMANTA RAHMANTA
Biodiversitas Journal of Biological Diversity Vol. 25 No. 10 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d251051

Abstract

Abstract. Wagino, Rauf A, Hanum C, Rahmanta. 2024. The effect of planting distance engineering treatment on the morphophysiology and yield of soybean varieties integrated with oil palm. Biodiversitas 25: 3909-3919. The use of inter-land in oil palm plantations of immature plants is commonly studied, and the use in productive oil palm plantations distance has not been investigated. The research aimed to evaluate the productivity, environmental characteristics, and economic value of oil palm and soybean integration. A Split-Plot Design was used with the main plot consisted oil palm planting, the sub-plot was soybean planting repeated three times. The results that light intensity unmodified oil palm planting distance system decreased by 28% compared to the modified. The treatment of oil palm planting distance modification had a significant effect on the amount of leaf chlorophyll, seed weight per plant (11.49 g), weight of 100 seeds (18.29 g), production per-plot (993.55 g), and Dena 1 (692.90 g). The Land Equivalency Ratio (LER) was >1 (1.06) integration of Dena 1 soybean variety with oil palm planting distance engineering and an R/C value of 1.79, providing greater benefits compared to the monoculture planting system. The system also provided improvements to the environment by an increase in nitrogen (N) nutrient levels and soil organic carbon (C) levels. The oil palm planting distance engineering model could be a solution to increase sustainable soybean production in Indonesia.
Exploring the microbial diversity and functional potential of Domas Crater of Mount Tangkuban Perahu, Indonesia, through shotgun metagenomics HARYONO BUDI SANTOSO; ANTONIUS SUWANTO; RAHADIAN PRATAMA
Biodiversitas Journal of Biological Diversity Vol. 25 No. 11 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d251160

Abstract

Abstract. Santoso HB, Suwanto A, Pratama R. 2024. Exploring the microbial diversity and functional potential of Domas Crater of Mount Tangkuban Perahu, Indonesia, through Shotgun Metagenomics. Biodiversitas 25: 4613-4626. Domas Crater, an extreme environment in Indonesia, is known for high temperatures and acidic conditions, providing a unique habitat for specialized microbial communities. These extreme conditions increase the possibility of discovering thermophilic enzymes with valuable biotechnological applications. Therefore, this study aimed to explore the microbial diversity in Domas Crater using shotgun metagenomics to analyze both previously reported microbes and novel microorganisms comprehensively. Shotgun metagenomics is particularly advantageous in identifying microbial species that cannot be cultured using conventional methods, enabling the exploration of microorganisms with considerable potential. The application of next-generation sequencing technologies and bioinformatics tools allowed the successful reconstruction of eight high-quality Metagenome-Assembled Genomes (MAGs), a testament to the technical proficiency of the study. The genomes were further characterized based on the functional genes, including the enzymes in carbohydrate metabolism or Carbohydrate-active enzymes (CAZyme), biosynthetic gene clusters for secondary metabolite (BGCs), and genes associated with micronutrient metabolism. The results showed that the microbial community was dominated by Hydrogenobaculum and Sulfurisphaera, both known for adaptation to extreme environments. Moreover, the first Hydrogenobaculum and Thermocladium were recorded in Indonesia as the novel discoveries of the study. These findings highlight the significance of Domas Crater as a reservoir for novel microbial species, particularly in terms of thermophilic microorganisms with unique enzymatic properties.
Genetic diversity and phylogenetic reconstruction of horseshoe crabs from East Java, Indonesia based on DNA barcode COI DWI ANGGOROWATI RAHAYU; RENI AMBARWATI; ULFI FAIZAH; ENDIK DENI NUGROHO; RUSDIANTO RUSDIANTO; PURITY SABILA AJININGRUM; NOORHIDAYAH BINTI MAMAT
Biodiversitas Journal of Biological Diversity Vol. 25 No. 10 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d251041

Abstract

Abstract. Rahayu DA, Amarwati R, Faizah U, Nugroho ED, Rusdianto, Ajiningrum PS, Mamat NB. 2024. Genetic diversity and phylogenetic reconstruction of horseshoe crabs from East Java, Indonesia based on DNA barcode COI. Biodiversitas 25: 3789-3802. Horseshoe crabs or mimi mintuna (Indonesian) are an ancient arthropod with 4 species, but there are limited studies on the species from East Java. This indicates the need for the collection of more accurate genetic resources as an important step for its conservation. Therefore, this study aims to examine genetic diversity and phylogenetic reconstruction of horseshoe crabs from East Java using DNA barcode COI. A total of 20 samples were obtained from Beejay Bakau Resort, Probolinggo, Kenjeran Beach, Surabaya, Batah Timur Beach, Madura, and Lekok Beach, Pasuruan. The 621 bp CO1 gene sequence was used for genetic diversity analysis and phylogenetic tree reconstruction. Subsequently, muscle samples were preserved in pure-grade ethanol and subjected to DNA extraction, polymerase chain reaction (PCR), sequencing, and sequence analysis. The sequence data were analyzed using bioinformatics tools, Barcode of Life Data Systems (BOLD) Systems, the Automatic Barcode Gap Discovery (ABGD) web application, and haplotype network. Phenetic taxonomy was further applied using Ntysc to enhance the robustness of the genetic analysis. The results showed that the high haplotype diversity (Hd) of 0.957, 16 haplotypes, and nucleotide diversity (?) of 0.00097 indicated a wide range of genetic variations. The frequency of parsimony informative sites was 26.48%, with 19 polymorphic sites and an overall ts/tv ratio of 2.32. In addition, the phylogenetic trees showed a clear and unambiguous branching pattern for cluster Carcinoscorpius rotundicauda Latreille 1802 and Tachypleus gigas O.F.Müller 1785. This finding is a matter of concern for managing and conserving horseshoe crab species in East Java waters.
Diurnal activity patterns of painted storks (Mycteria leucocephala) in an urban artificial wetland in Malaysia NURFARAH AIN LIMIN; MUHAMMAD ZULFADLI ZAINAL ABIDIN; NURUL NABILAH SHAMSHUL KAMAR; MUHAMMAD AL AMIN AMRAN; NUR NADIAH MD YUSOF
Biodiversitas Journal of Biological Diversity Vol. 25 No. 12 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d251224

Abstract

Abstract. Limin NA, Abidin MZZ, Kamar NNS, Amran MAA, Yusof NNM. 2024. Diurnal activity patterns of painted storks (Mycteria leucocephala) in an urban artificial wetland in Malaysia. Biodiversitas 25: 4878-4885. The increasing population of painted storks (Mycteria leucocephala) in Malaysia poses potential risks to native waterbird species, such as the milky stork. Despite their growing presence in urban artificial lakes, such as those in Putrajaya and Selangor, our understanding of their activity patterns remains limited, highlighting the importance of this research. Therefore, this study closely investigated the diurnal activity patterns of painted storks in an urban artificial wetland in Malaysia. Stork behavior was observed using instantaneous scanning and focal sampling methods for over 20 days. Results indicated that preening was the most common activity (30%), followed by foraging (24%), vigilance (23%), walking (15%), and other behaviors (8%). Storks displayed significantly more preening in the morning, though the durations were shorter compared to the afternoon and late afternoon. They also spent more time foraging and being vigilant in the morning than at other times. Furthermore, during all sessions, the number of individuals observed in the grassy areas was much higher than in the lake or on nearby rooftops. This study provides valuable insights into the behavior of painted storks, which could inform management strategies for waterbird species in urban artificial wetlands.
Isolation and identification of salt-tolerant, phosphorus-solubilizing bacterial strains from rice soil in rice-shrimp farming systems in Tien Giang Province, Vietnam TRUONG QUOC TAT
Biodiversitas Journal of Biological Diversity Vol. 25 No. 10 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d251047

Abstract

Abstract. Tat TQ. 2024. Isolation and identification of salt-tolerant, phosphorus-solubilizing bacterial strains from rice soil in rice-shrimp farming systems in Tien Giang Province, Vietnam. Biodiversitas 25: 3868-3875. This study aimed to isolate, select, and identify the phosphate-soluble bacterial (PSB) pathogens from eight salt-affected soil samples collected from paddy rice fields in the Go Cong Dong and Tan Phu Dong districts of Tien Giang Province, Vietnam. Bacteria were isolated on Pikovskaya’s agar media supplemented with 1% NaCl, and the amount of phosphorus dissolved in liquid NBRIP was supplemented with various concentrations of NaCl via molybdate coloration to evaluate the salt tolerance and phosphorus solubility of the isolated bacterial strains. The result showed that from 8 saline soil samples, a total of 15 strains of phosphorus solubilizing bacteria were isolated and 2 (code 1.7 and 6.1) of them showed good phosphorus solubilization. In addition, isolates 1.7 and 6.1 exhibited good growth and phosphorus solubilization in liquid NBRIP media supplemented with NaCl at concentrations ranging from 1.0% to 5.0%. Molecular analysis results showed that strains 1.7 and 6.1 were identified as Burkholderia vietnamiensis 1.7 and Priestia aryabhattai 6.1, respectively. These results show that B. vietnamiensis 1.7 and P. aryabhattai 6.1 can be used as biofertilizers for rice cultivation in salty soils in Tien Giang Province, reducing the cost and use of chemical fertilizers.

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