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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
 536   537   538   539   540 
Phylogeny of Wolbachia in Drosophila mutant from Bandung, Indonesia ENDANG SRIMURNI KUSMINTARSIH; PESONA GEMILANG; AGUS NURYANTO; HANAN HASSAN ALSHEIKH MAHMOUD; TRISNOWATI BUDI AMBARNINGRUM
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/d251226

Abstract

Abstract. Kusmintarsih ES, Gemilang P, Nuryanto A, Mahmoud HHA, Ambarningrum TB. 2024. Phylogeny of Wolbachia in Drosophila mutant from Bandung Indonesia. Biodiversitas 25: 4894-4899. Wolbachia is a microorganism known as an intracellular endosymbiont in arthropods that causes reproductive changes and most commonly cytoplasmic incompatibility. Wolbachia pipientis A has been divided into two major subgroups (A and B) and 17 subgroups. Therefore, the present study aims to determine the presence of Wolbachia subgroup in Drosophila mutants and to analyze the phylogeny, of Wolbachia in Drosophila mutants using Wolbachia surface protein (wsp) primer genes. The presence of Wolbachia was determined based on the DNA band pattern on the agarose gel. The phylogenetic relationship among Wolbachia in Drosophila mutants was inferred from a phylogenetic tree. Based on the neighbor-joining method, the phylogenetic tree reconstruction was done in MEGA X software. The result shows that Wolbachia from 7 types of Drosophila mutant samples (taxi, ebony, dumpy, miniature, sepia, white, eye missing, in one subgroup as Wolbachia sp. wMel isolate Yunnan outer surface protein precursor (wsp) gene, partial cds., while between samples and out-group is closely related to Wolbachia sp. in Diabrotica cristata 16S rRNA sub-group A. This result is the first systematic survey of Wolbachia in Drosophila mutants and the first survey classifying Wolbachia infections by subgroup. The research future is to explore Wolbachia in many more insects.
Whole genome sequencing of a siderophore-producing bacterium isolated from Simadu pineapple roots CUCU WIJAYANTI; PRAYOGA SURYADARMA; NISA RACHMANIA MUBARIK
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/d251222

Abstract

Abstract. Wijayanti C, Suryadarma P, Mubarik NR. 2024. Whole genome sequencing of a siderophore-producing bacterium isolated from Simadu pineapple roots. Biodiversitas 25: 4860-4869. Siderophores are organic compounds synthesized by bacteria that act as iron-chelating ligands, facilitating the solubilization and transport of iron into the cell. Siderophore-producing bacteria offer significant benefits across various fields of research and application. A recent study investigated a siderophore-producing bacterium, the M7 isolate, from Simadu pineapple roots in the Subang District of West Java, Indonesia. This study aimed to analyze the siderophore biosynthesis gene cluster (BGC) from the complete genome sequence of the M7 isolate through genome mining. Comparative genomic analysis with the strain Providencia manganoxydans LLDRA6 revealed that the M7 isolate has a similar guanine-cytosine (GC) content with a longer sequence length totaling 4,447,159 bp. Genome comparison using average nucleotide identity (ANI) calculations indicated that the M7 isolate had a genome similarity of 98.82% with strain P. manganoxydans LLDRA6. Additionally, the genome of the M7 isolate contains systems for iron acquisition and metabolism, which involve mechanisms for regulating iron. A specific region in the M7 isolate encodes the IucA/IucC family of siderophore biosynthesis proteins responsible for aerobactin biosynthesis through non-ribosomal peptide synthetase-independent siderophore (NIS) pathways. Regarding siderophore BGCs, this isolate showed the highest similarity to Providencia stuartii, with differences in genetic redundancy content. Additionally, pathogen prediction results for the M7 isolate indicate that it is not pathogenic to humans, unlike P. stuartii, which is known to be pathogenic. The new siderophore-producing bacterium, the M7 isolate, harbors a duplication of core biosynthesis genes, representing genetic redundancy that supports siderophore biosynthesis. This genetic feature may enable concurrent protein expression, potentially enhancing siderophore accumulation.
Teliospore morphology characterization of Uromycladium falcatariae in falcata plantations at different elevations in Mindanao Island, Philippines MHAR O. LOQUEZ; CAROLINA D. AMPER; ADRIAN M. TULOD; DENNIS M. GILBERO
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/d260129

Abstract

Abstract. Loquez MO, Amper CD, Tulod AM, Gilbero DM. 2025. Teliospore morphology characterization of Uromycladium falcatariae in falcata plantations at different elevations in Mindanao Island, Philippines. Biodiversitas 26: 296-305. The fungus Uromycladium falcatariae causes gall rust disease in falcata (Falcataria falcata), with severe infections commonly observed at higher elevations (>400 masl). It produces teliospores that disperse through the air, contributing to its widespread prevalence. This study aimed to characterize the fungal teliospores across different elevations in Mindanao using Light Microscopy (LM) and Scanning Electron Microscopy (SEM). Mature galls with visible brown or rusty powder from falcata were collected from low (<400 masl), moderate (>400-800 masl), and high (>801 masl) elevations. Microphotographs of the teliospores were generated, examined, and compared for morpho-features and quantitative measurements across these elevations. This research provides the first SEM-based morphological characterization of U. falcatariae. The LM results revealed significant increases in teliospore length (P<0.05) and width (P<0.05) with elevation, with the largest dimensions observed at high elevations. SEM analysis demonstrated significant variation in the diameter of the germ pore (P<0.01) and the dorsal concave structure (P<0.05) across elevations, with the largest measurements recorded at high elevations. Detailed morphological features and quantitative measurements of teliospores were revealed from apical, dorsal, and equatorial orientations in SEM. Furthermore, this study provided morphological characteristics of teliospores across elevations, which can aid in the taxonomy and morphological classification of this rust fungus.
Diversity of Vachellia nilotica rhizosphere bacteria in the savanna of Baluran National Park, Indonesia and their potential for hydrolytic enzyme production NI’MATUZAHROH NI’MATUZAHROH; MOCH. AFFANDI; RICO RAMADHAN; FATIMAH FATIMAH; AGUS SUPRIYANTO; SALAMUN SALAMUN; TRI NURHARIYATI; ALMANDO GERALDI; JUNAIRIAH JUNAIRIAH; JOHAN SETIAWAN; BRIGITA NUR DIYAN AGUSTIANA; ARSY HABI PRIYATAMA; KIRANA ATMANINDYA; DELA DWI ALAWIYAH; ELVIS PERDANA PUTRA; ANA MARIATUL KHIFTIYAH; SILVIA KURNIA SARI; CHRISTOPHER CLEMENT
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/d260425

Abstract

Abstract. Ni’matuzahroh, Affandi M, Ramadhan R, Fatimah, Supriyanto A, Salamun, Nurhariyati T, Geraldi A, Junairiah, Setiawan J, Agustiana BND, Priyatama AH, Atmanindya K, Alawiyah DD, Putra EP, Khiftiyah AM, Sari SK, Clement C. 2025. Diversity of Vachellia nilotica rhizosphere bacteria in the savanna of Baluran National Park, Indonesia and their potential for hydrolytic enzyme production. Biodiversitas 26: 1754-1767. Vachellia nilotica, a leguminous plant introduced to Baluran National Park as a firebreak, is now causing environmental problems due to its invasiveness, which hinders the growth of native plants. Despite significant ecological changes, there is no data regarding the impact of this plant invasion on soil microorganisms. This study aimed to assess the bacterial diversity in the rhizosphere of V. nilotica and investigate the bacteria's ability to produce hydrolytic enzymes. The bacterial community was identified using Next-Generation Sequencing (NGS), and a conventional isolation technique. A total of 99,520 Operational Taxonomic Units (OTUs) were obtained, encompassing a rich diversity of 4,631 species. These species belonged to four phyla (i) Pseudomonadota; (ii) Actinomycetota; (iii) Bacillota; and (iv) Acidobacteriota. Additionally, 26 isolates were obtained through conventional isolation, and all of them can produce hydrolytic enzymes, including protease, lipase, amylase and cellulase. A total of 9 isolates showed highest proficiency in producing hydrolytic enzymes, of which 8 belonged to the Bacillota phylum and 1 isolate showed similar characteristic with Acidobacteriota phylum. The isolates SAV 2.NA.1.5.6 and SAV 2.NA.2.4.3 exhibited multiple enzyme activities and were classified as Bacillota. The findings indicate that the rhizosphere of V. nilotica contains a high diversity of bacteria, including those capable of producing hydrolytic enzymes. This information can serve as a foundation for managing V. nilotica and promoting sustainable development by leveraging the potential of rhizosphere bacteria in this plant. To our knowledge, no prior research has been conducted on this topic in the savanna area of BNP.
Assessment of morphological characteristics and quality of turfgrass Zoysia matrella accessions from Indonesia RAHAYU RAHAYU; AKTAVIA HERAWATI; GANJAR HERDIANSYAH; RADEN AJENG ALMA AZZAHRA KUSUMA PUTRI; ADNAN SOFYAN; QAMAL MUTTAQIN
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/d251232

Abstract

Abstract. Rahayu, Herawati A, Herdiansyah G, Putri RAAAK, Sofyan A, Muttaqin Q. 2024. Assessment of morphological characteristics and quality of turfgrass Zoysia matrella accessions from Indonesia. Biodiversitas 25: 4950-4960. Zoysia matrella is a popular turfgrass species suitable for tropical climates, including Indonesia. However, there are challenges related to the selection of accessions that produce the best quality. This research aimed to assess the morphological characteristics and visual and functional quality of turfgrass Z. matrella collected from various origins in Indonesia. The study combined exploratory surveys to collect Z. matrella accessions across Indonesia and was continued by laboratory experiments at Universitas Sebelas Maret, Central Java, using a Completely Randomized Design (CRD). We used 16 accessions of Z. matrella from 8 provinces in Indonesia to be compared with two commercials, imported accessions as controls. Results showed that Z. matrella accession from Sampit, Central Kalimantan showed the highest plant height of 10.22 cm, the longest root length of 15.72 cm, and the percentage of coverage was 94.06%. Conversely, accession from Marina Semarang had the shortest plant height of 8.35 cm with a percentage of cover of 72.75%. Some local accessions of Z. matrella had comparable visual and functional quality, growth, and morphology characteristics to the commercialized accessions, opening possibilities for the development of new, high-quality Z. matrella cultivars native to Indonesia.
Local and landscape effects on the abundance and diversity of soil arthropods in citrus orchards of Malang and Batu, East Java, Indonesia ITO FERNANDO; FAIZ NASHIRUDDIN MUHAMMAD; RAHMAT FURQONI; M. BAYU MARIO; RETNO DYAH PUSPITARINI; IRISA TRIANTI; MUHAMMAD AKHID SYIB’LI; AKHMAD RIZALI
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/d251052

Abstract

Abstract. Fernando I, Muhammad FN, Furqoni R, Mario MB, Puspitarini RD, Trianti I, Syib’li MA, Rizali A. 2024. Local and landscape effects on the abundance and diversity of soil arthropods in citrus orchards of Malang and Batu, East Java, Indonesia. Biodiversitas 25: 3920-3927. Soil arthropods are crucial for sustaining the balance and function of agroecosystems. This study aimed to assess the diversity and abundance of detritivorous and predatory soil arthropods across various citrus orchards that differ in agroecosystem management practices and landscape composition. The study was conducted in nine citrus orchards from November 2023 to January 2024, with soil arthropod samples collected using Berlese funnels. Analysis of Variance (ANOVA) was used to evaluate the effects of management practices (local effects) on soil arthropod diversity and abundance, while Generalized Linear Model (GLM) analysis was employed to assess the effects of landscape composition (landscape effects) on soil arthropod diversity and abundance. Meanwhile, Analysis of Similarity (ANOSIM) based on the Bray-Curtis index was used to evaluate differences in soil arthropod composition. A total of 1,562 individuals were collected, representing 16 families, 11 orders, and 3 classes. Among the predatory groups, the most abundant family was Laelapidae, while Entomobryidae was the most dominant among detritivores. The diversity of both predatory and detritivorous arthropods was not influenced by variations in management practices. However, the abundance and composition of predatory arthropods were influenced by the frequency of organic fertilizer application, while detritivores were affected by weeding treatments. At the landscape scale, predator abundance positively correlated with the number of natural habitat patches and the area of citrus orchards. In contrast, detritivores were not influenced by landscape variables. This study highlights the critical roles of land management practices and landscape composition in shaping the abundance and diversity of soil arthropods.
Amplicon metagenome comparison of Tandag River, Surigao del Sur, Philippines, based on high-throughput parallel DNA sequencing analysis of bacterial communities ROXAN G. EUPEÑA-CARAY; GISELLE B. RAMOS; JOCELYN B. PANDUYOS; LUZMINDA S. BACQUIAL; SHARON ROSE M. TABUGO
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/d251008

Abstract

Abstract. Eupeña-Caray RG, Ramos GB, Panduyos JB, Bacquial LS, Tabugo SRM. 2024. Amplicon metagenome comparison of Tandag River, Surigao del Sur, Philippines, based on high-throughput parallel DNA sequencing analysis of bacterial communities. Biodiversitas 25: 3464-3472. Rivers serve as a vital freshwater reservoir for the environment and human consumption. Biomonitoring based on eDNA is essential for aquatic ecosystems. The present study investigates the bacterial taxonomic diversity of this ecosystem using the V1-V3 16S rRNA regions obtained from paired-end Illumina MiSeq reads. A total of nine amplicon libraries (U1, U2, U3, M1, M2, M3, D1, D2, D3) were constructed corresponding to the sites (U-upstream, M-midstream, D-downstream) of the Tandag River. After post-quality control and processing, there were 608,099 amplicon sequence variants (ASVs), representing 1194 families and 2090 genera. Results showed that the most abundant ASVs were affiliated with genera Bacillus, Pseudomonas, Ralstonia, Alcaligenes, and Pseudarcicella, along with unclassified bacteria derived from Gammaproteobacteria, Alphaproteobacteria, Verrucomicrobia subdivision, Flavobacteria, and Pseudomonadaceae. The bacterial alpha diversity was ranked upstream>midstream>downstream. An increase in the abundance of Bacillus (Firmicutes) and Gammaproteobacteria in an urbanized zone indicated a high level of human activity and an important threat to public health. Noteworthy is that the alkaline environment characterized by increased pH levels favors the occurrence of alkaliphilic bacteria. Microbial community structure was influenced by anthropogenic interference and selective pressure from loads of urban discharge in the area. The functional prediction of bacterial communities by Parallel-Meta Suite (PMS) using the PICRUSt algorithm suggests functions related to metabolism and environment information processing. The presence of xenobiotic biodegradation bacteria highlights future possible applications. Findings contribute to understanding microbial communities in response to rapid urbanization. This is the first account of high-throughput sequencing analysis of bacterial communities in an urban river under anthropogenic stress in the Philippines.
The metabolomic fingerprinting of four duku (Lansium domesticum) cultivars from Central Java, Indonesia based on unique metabolites and prospects for future breeding ENDANG DEWI MURRINIE; FAZAT FAIRUZIA; NINDYA ARINI; HENY ALPANDARI; INGGIT MAHARANI
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/d251043

Abstract

Abstract. Murrinie ED, Fairuzia F, Arni N, Alpandari H, Maharini I. 2024. The metabolomic fingerprinting of four duku (Lansium domesticum) cultivars from Central Java, Indonesia based on unique metabolites and prospects for future breeding. Biodiversitas 25: 3816-3839. This research aims to map the genetic identity of Central Java (Indonesia) duku cultivars, Sumber, Woro, Matesih, and Kalikajar, through a metabolomic analysis approach using the Gas Chromatography-Mass Spectrophotometer (GC-MS) method from duku fruit peel and flesh. Heatmap and principal component analysis (PCA) of volatile organic compound (VOC) metabolites identified from duku fruit peel grouped Sumber, Woro, and Matesih as one group, with Sumber and Woro being more similar, while Kalikajar was in a different group. The identified metabolites of duku fruit flesh show that Woro and Matesih cultivars are in the same cluster, followed by Kalikajar, which is closer to the Woro and Matesih metabolites. Sumber mostly has different metabolites. VOC metabolites successfully identified primary and secondary metabolites defined as common metabolites in four cultivars, which have a myriad of functions for plant growth and development, nutritional value, plant defense against biotic stress and environmental stress tolerance, and physiological plant phenotypes. The successful identification of these metabolites not only enhances our understanding of the duku cultivars but also reassures the accuracy and reliability of future breeding for superior duku plants that are resistant to biotic and abiotic stress based on the VOC metabolites in the Sumber, Woro, Matesih, and Kalikajar cultivars, particularly the unique metabolites that distinguish these cultivars.
Species diversity, mosquito behavior, and microfilariae detection in vectors and reservoirs in filariasis-endemic areas of Bengkulu, Indonesia DERI KERMELITA; UPIK KESUMAWATI HADI; SUSI SOVIANA; RISA TIURIA; DIMAS NOVIANTO
Biodiversitas Journal of Biological Diversity Vol. 25 No. 9 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d250934

Abstract

Abstract. Kermelita D, Hadi UK, Soviana S, Tiuria R, Novianto D. 2024. Species diversity, mosquito behavior, and microfilariae detection in vectors and reservoirs in filariasis-endemic areas of Bengkulu, Indonesia. Biodiversitas 25: 3125-3131. Filariasis, recognized by the WHO as a neglected tropical disease, remains a significant global health challenge, particularly in Southeast Asia. In Bengkulu Province, Indonesia, 66 cases of filariasis were reported between 2010 and 2020, with the highest prevalence found in Mukomuko and Seluma Districts. This study analyzed the vector behavior and detection of filariasis reservoirs in endemic areas of Bengkulu Province. Human landing and resting collections were employed for mosquito collection for 12 h (18:00-06:00), and blood sampling was performed on reservoir animals (Canis familiaris, Felis catus Linnaeus, 1758, and Macaca fascicularis (Raffles, 1821)). Mosquito diversity was analyzed using several diversity indices. Filaria larvae in mosquitoes were detected using Polymerase Chain Reaction (PCR) methods, and filaria in reservoir animals were detected using blood smears with Giemsa staining. The result showed that 17 mosquito species were captured in the filariasis-endemic regions of Bengkulu Province: Culex quinquefasciatus Say, 1823; Culex hutchinsoni Barraud, 1924; Culex gelidus Theobald, 1901; Culex pseudovishnui Colless, 1957; Culex vishnui Theobald, 1901; Armigeres subalbatus (Coquillett, 1898); Aedes aegypti (Linnaeus, 1762); Aedes albopictus (Skuse, 1894); Anopheles tessellatus Theobald, 1901; Anopheles vagus Döntiz, 1902; Anopheles minimus Theobald, 1901; Anopheles indefinitus (Ludlow, 1904); Anopheles sundaicus (Rodenwaldt, 1948); Anopheles barbirostris Wulp, 1884; Anopheles maculatus Theobald, 1901; Anopheles sp., and Mansonia annulata Leicester, 1908. Culex pseudovishnui exhibited the highest indoor density among the mosquito species, whereas C. quinquefasciatus exhibited the highest outdoor density. Filaria larvae were not detected in all mosquito sample pools based on the PCR results, whereas microfilariae of Dirofilaria immitis (Leidy, 1856) Railliet & Henry, 1911 were identified in the reservoir (Canine) blood samples. Thus, the presence of microfilariae in reservoir animals must be monitored because they can transmit filariasis to the community. Control strategies should be developed for endemic regions in Bengkulu Province.
Effects of long-term fire protection on Deciduous Dipterocarp Forest dynamics in Northeastern Thailand NATTAKARNDA DUANGON; CHONGRAK WACHRINRAT; CHATCHAI NGERNSAENGSARUAY; SATHID THINKAMPHEANG; SUTHEERA HERMHUK; JAKKAPHONG THONGSAWI; WONGSATORN PHUMPHUANG; ANUSORN KULLAWONG; ARERUT YARNVUDHI; DOKRAK MAROD
Biodiversitas Journal of Biological Diversity Vol. 25 No. 9 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d250936

Abstract

Abstract. Duangon N, Wachrinrat C, Ngernsaengsaruay C, Thinkampheang S, Hermhuk S, Thongsawi J, Phumphuang W, Kullawong A, Yarnvudhi A, Marod D. 2024. Effects of long-term fire protection on Deciduous Dipterocarp Forest dynamics in Northeastern Thailand. Biodiversitas 25: 3141-3153. Forest fires are a significant problem that is often unmanaged, particularly their effect on tree regeneration. We aimed to clarify the forest dynamics and effects of climbers on tree regeneration after fire protection in a Deciduous Dipterocarp Forest in Northeastern Thailand. In 2004, permanent plots of 4 ha were established, and all trees with a Diameter at Breast Height (DBH) larger than 4.5 cm were labeled, measured, and identified. Monitoring was conducted in 2017 and 2022 when all trees with a DBH of more than 2 and 1 cm, respectively, were included and measured. The 92 species comprised 72 genera and 35 families with low species diversity. Tree density and basal area (DBH?1 cm) were 22.01 m2 ha-1 and 1,740 stem ha-1, respectively. The average recruitment rate was higher than the mortality rate throughout the study period (9.43 and 0.51 % y-1, respectively). However, it varied between periods. Long fire protection from 2004 to 2017 promoted the highest tree recruitment (12.67 % y-1, about 60 times to mortality rate) and regeneration of climbers on tree stems. It induced slightly higher mortality rates from 2017-2022, and approximately 18.87% of dead trees were damaged by dense climber cover. Our findings can help evaluate forest sustainability and support the planning of forest fire management strategies preserving species diversity in other tropical dry forests.

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