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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
 549   550   551   552   553 
Analysis of the factors contributing to the degradation of coral reefs and marine biota at Pasir Putih Beach, Prigi Bay, Trenggalek District, East Java, Indonesia RAHMANTA SETIAHADI; MARHENY LUKITASARI; NURUL KUSUMA DEWI; SUMANI SUMANI; CATUR RETNANINGDYAH; MUKHTASOR MUKHTASOR
Biodiversitas Journal of Biological Diversity Vol. 26 No. 3 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d260339

Abstract

Abstract. Setiahadi R, Lukitasari M, Dewi NK, Sumani, Retnaningdyah C, Mukhtasor. 2025. Analysis of the factors contributing to the degradation of coral reefs and marine biota at Pasir Putih Beach, Prigi Bay, Trenggalek District, East Java, Indonesia. Biodiversitas 26: 1384-1394. The deterioration of coral reefs and marine ecosystems poses a significant challenge that needs to be addressed to maintain sustainable marine ecotourism management. Both natural processes and human activities contribute to the decline of coral reef ecosystems. This study seeks to examine the factors causing damage to coral reefs and marine life along the Karanggongso Coast, East Java Province, Indonesia. The research utilized a survey method combined with a descriptive analytical approach. Coral reef surveys were conducted using the Line Intersept Transect (LIT) technique, while sedimentation and land cover changes were assessed using grab samplers, Google Earth maps, and Rupa Bumi Indonesia (RBI) maps. Beach physical condition observations provided material for descriptive analysis, and coral reef and sedimentation data were used to create indicative maps. The overlay of indicative maps and descriptive analysis results were employed in the spatial analysis of factors destroying coastal ecosystems. The study findings revealed the Physical Condition of the Waters, with indicators including temperature (28.7oC), salinity (35%), dissolved oxygen (13.2 Ppm), pH (7.73), and brightness (4.5m). While these conditions remain favorable, extensive sedimentation has reduced the Percentage of Coral Reef Cover to below 24.9%. Analysis of sedimentation from land use change indicates that significant areas of forest and shrubland have been converted to agricultural land, settlements, tourist facilities, and several shrimp ponds, leading to erosion and sedimentation. The size of the sediment grains in the water reflects the predominant sand content at each station, with values ranging from 99.19% to 99.63%.
Diversity of epilithic diatoms from coral reef ecosystem of Bawean Island, Indonesia OKTIYAS MUZAKY LUTHFI; YENNY RISJANI; NAGARAJ SUBRAMANI; MATEUSZ RYBAK; JINSOON PARK; MAŁGORZATA BĄK; ANDRZEJ WITKOWSKI
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/d251202

Abstract

Abstract. Luthfi OM, Risjani Y, Subramani N, Rybak M, Park J, B?k M, Witkowski A. 2024. Diversity of epilithic diatoms from coral reef ecosystem of Bawean Island, Indonesia. Biodiversitas 25: 4642-4663. This study investigates the diversity and community structure of epilithic diatoms in the coral reef ecosystems of Bawean Island, Indonesia. A total of 137 taxa from 49 genera were identified from coral rubble habitats across four distinct locations. The Shannon-Wiener Diversity Index (H') and Dominance Index (C) were used to assess species diversity and dominance, revealing that Station 4 exhibited the highest diversity (H' = 3.88) and lowest dominance (C = 0.03), while Station 2 had the lowest diversity (H' = 2.55) and highest dominance (C = 0.09). Evenness values (E = 0.9) were consistent across all sites, indicating a uniform distribution of species. The findings suggest that coral rubble provides unique microhabitats conducive to diatom diversity, challenging the conventional understanding that habitat diversity correlates positively with species diversity. The study also compares Bawean Island's diatom diversity with other regions, noting its intermediate diversity level, which may be influenced by its geographical position between Kalimantan and Java. The presence of dominant species like Diploneis crabro, Petroneis marina, Halamphora coffeiformis, and Trachyneis aspera underscores the ecological significance of these diatoms in coral reef ecosystems. This research fills a significant gap in our understanding of the marine biodiversity and ecological dynamics of Bawean Island, highlighting the importance of diatoms in maintaining the health and stability of coral reef ecosystems and its potential implications for future research and conservation efforts.
Effects of different media and solvents on biological activities and secondary metabolites profiles of a coral-derived Streptomyces sp. RC4 RIZKY RIZKY; RISA NOFIANI; RUDIYANSYAH RUDIYANSYAH; CANTIKA DYLANI PUTRI; ARIE SETIAWAN; DES SAPUTRO WIBOWO; FITRI SETIYONINGRUM
Biodiversitas Journal of Biological Diversity Vol. 26 No. 2 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d260222

Abstract

Abstract. Rizky, Nofiani R, Rudiyansyah, Putri CD, Setiawan A, Wibowo DS, Setiyoningrum F. 2025. Effects of different media and solvents on biological activities and secondary metabolites profiles of a coral-derived Streptomyces sp. RC4. Biodiversitas 26: 739-747.  Streptomyces sp. RC4 demonstrates a potential source of secondary metabolites with various biological activities. Culture media and solvents for culture media influence the production of the metabolites. This study investigated the effect of different culture media and solvents on the biological activities and secondary metabolite profiles of Streptomyces sp. RC4. Seven different media, i.e.,  International Streptomyces Project (ISP) 1, ISP2, ISP4, A1, Starch Casein Broth (SCB), Potato Dextrose Broth (PDB), and PC-1, were used as growth media. Three different solvents, i.e., distilled water, 2.5% NaCl solution, and artificial seawater (ASW), were used to prepare each medium. The cultures were then shaken at 200 rpm for seven days, after which secondary metabolites were extracted with ethyl acetate. Each extract was tested for antibacterial activity and cytotoxicity using brine shrimp lethality assays (BSLT). The result showed that 11 of 21 extracts exhibited antimicrobial activity with varying levels of effectiveness. ISP2 extract (ISP2 dissolved in distilled water) demonstrated the largest inhibition zones, while SCB NaCl extract (SCB dissolved in 2.5% NaCl solution) inhibited the highest number of test microbes. Three extracts (ISP2, PC-1 ASW, and SCB NaCl extracts) were classified as highly toxic based on Clarkson’s toxicity category (LC50 < 100 µg/mL). The most toxic extract was PC-1 ASW extract (PC-1 dissolved in ASW) with an LC50 value of 40 ?g/mL. Metabolomic analysis revealed distinct chemical profiles for each extract, with secondary metabolites such as cyclo (Leu-Pro), cyclo (Pro-Val), p-cymene, o-cymene, and methoxy-phenyl oxime. Several compounds remained unidentified through molecular networking analysis, suggesting they might be novel. These findings indicated the diversity of secondary metabolites and biological activities of Streptomyces sp. RC4 is significantly influenced by medium and solvent compositions.
Proposal to list the Peruvian tuco-tuco (Ctenomys peruanus, Ctenomyidae, Rodentia) as a critically endangered species CÉSAR EDGARDO MEDINA; YASMY KARINA MEDINA; EDWIN FREDY BOCARDO
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/d251238

Abstract

Abstract. Medina CE, Medina YK, Bocardo EF. 2024. Proposal to list the Peruvian tuco-tuco (Ctenomys peruanus, Ctenomyidae, Rodentia) as a critically endangered species. Biodiversitas 25: 5005-5011. The Peruvian tuco-tuco, Ctenomys peruanus Sanborn and Pearson 1947, is a subterranean rodent endemic to High Andes of southern Peru. This rodent is historically known by four record localities dating back to the 1950s, and a fifth locality in 2011, all based on specimens housed in natural history museums, is now facing a critical situation. Recent surveys in 17 localities in Arequipa, Moquegua, Tacna, and Puno regions revealed the local extinction of C. peruanus at previously recorded sites while identifying two new localities; however, currently, the species only lives in one locality (Callacami, Puno). This remaining population of fewer than 50 mature individuals is under intense hunting pressure for human consumption and traditional medicinal practices, and it is experiencing a continuous loss of the extension and quality of its habitat due to overgrazing and agricultural expansion. Our research is the first effort to fill a 72-year gap with no field data for C. peruanus. Therefore, we propose to categorize C. peruanus as a Critically Endangered species (CR) according to the criteria established by the International Union for Conservation of Nature's Red List of Threatened Species. The authorities and academic community are urged to join efforts to curb the aforementioned anthropogenic threats and devise and implement management and conservation plans for C. peruanus in Peru.
Diversity of freshwater shrimp species of the genus Macrobrachium (Decapoda: Caridea) in the big river of East Kalimantan, Indonesia MAULIDA NUR ANNISA; KANTHI ARUM WIDAYATI; JUSMALDI JUSMALDI; ACHMAD FARAJALLAH
Biodiversitas Journal of Biological Diversity Vol. 26 No. 3 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d260348

Abstract

Abstract. Annisa MN, Widayati KA, Jusmaldi, Farajallah A. 2025. Diversity of freshwater shrimp species of the genus Macrobrachium (Decapoda: Caridea) in the big river of East Kalimantan, Indonesia. Biodiversitas 26: 1474-1484. Freshwater prawns are widely distributed in Indonesia, belonging to the subphylum Crustacea and order Decapoda. Freshwater shrimp commonly found in Indonesia belong to the families Atyidae and Palaemonidae. The Palaemonidae family is usually dominated by species of the genus Macrobrachium. Information on freshwater shrimp diversity in East Kalimantan, Indonesia, has never been reported, while water quality in East Kalimantan is declining due to increased exploitation of natural resources. This study was conducted to provide baseline information on freshwater shrimp species diversity for the future, before further changes occur in the East Kalimantan region and we provide Cytochrome Oxidase subunit I (COI) sequence data for molecular identification. Methods used for species identification based on morphological characters and species confirmation through molecular analysis using Cytochrome Oxidase subunit I (COI) gene fragments for molecular analysis. This study reports the diversity of freshwater shrimp in East Kalimantan, the results of morphological analysis showed confirmation of 7 species of freshwater shrimp. The family Palaemonidae consists of 7 species: Macrobrachium rosenbergii, M. lanchesteri, M. scabriculum, M. mammillodactylus, M. sintangense, M. equidens, and M. villosimanus. Molecular confirmation of species of the genus Macrobrachium using the COI gene showed genetic distance values ranging from 0 to 0.024. The species in this study have been confirmed based on genetic distance values and phylogenetic trees.
DNA barcoding of Mugilogobius mertoni and M. rambaiae from Siberut and Enggano Islands, the small outermost islands of Sumatra, Indonesia DEWI IMELDA ROESMA; DJONG HON TJONG; SYAIFULLAH SYAIFULLAH; DYTA RABBANI AIDIL
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/d260138

Abstract

Abstract. Roesma DI, Tjong DH, Syaifullah, Aidil DR. 2025. DNA barcoding of Mugilogobius mertoni and M. rambaiae from Siberut and Enggano Islands, the small outermost islands of Sumatra, Indonesia. Biodiversitas 26: 386-395. Siberut and Enggano Islands are the small and outermost islands of Sumatra, Indonesia. These two islands' unique geological history allows evolutionary processes to produce high levels of endemicity. One of the interesting fish genera from the Siberut and Enggano Islands is Mugilogobius. Based on morphological identification, it was estimated there are two Mugilogobius species in the Siberut and Enggano Islands. Molecular identification of Mugilogobius using the Cytochrome Oxidase I gene (known as DNA barcoding) needs to be done to prove it. The liver tissue was used for molecular analysis. The BLAST analysis showed that Mugilogobius from Siberut and Enggano Islands have a similarity range of 97.49%-96.06% with Mugilogobius GenBank. Based on the 558 bp sequence analyzed, Mugilogobius mertoni and Mugilogobius rambaiae from Siberut and Enggano Islands have a low sequence of divergences at 0.0%-0.4%, respectively. M. rambaiae from Siberut and Enggano Islands share the same haplotype. The ability of the species to maintain their genetics and the similarity of conditions between the two islands share their high genetic similarities. M. mertoni and M. rambaiae from Siberut and Enggano Islands have a high sequence of divergences at 3.0-4.6% with M. mertoni and M. rambaiae GenBank, respectively. The long-distance location, the presence of the ocean as a barrier, and differences in habitat conditions contribute to the high variations between Mugilogobius from two islands and other populations. Mugilogobius from Siberut and Enggano Islands has a sequence of divergence at 12.4%-17.3% compared to other Mugilogobius species, supporting their differences at the species level in the same genera. This study contributed to presenting the first molecular data of Mugiologius that can be used as a sequence reference for identification and the sequences became the genetic richness data of fish in the small and outermost islands of Sumatra, Indonesia (Siberut and Enggano Islands).
Metagenomic insights into bacterial communities in eco-enzymes and their microbial diversity and abundance TITTA NOVIANTI; HENNY SARASWATI; H. HAFSAH; SEPRIANTO SEPRIANTO
Biodiversitas Journal of Biological Diversity Vol. 26 No. 5 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d260514

Abstract

Abstract. Novianti T, Saraswati H, Hafsah H, Seprianto. 2025. Metagenomic insights into bacterial communities in eco-enzymes and their microbial diversity and abundance. Biodiversitas 26: 2157-2166. The aim of microbial diversity analysis of eco-enzymes is to optimize their benefits in various fields, such as for use in disinfectants, household cleaning agents, liquid fertilizers, and more. Metagenomic profiling is an effective method of analyzing microbial diversity that involves determining the nucleotide sequences of microbial DNA and allows the identification and taxonomic classification of certain bacteria. In this study, metagenomic analysis was carried out on eco-enzymes derived from mangosteen peel, orange peel, and a mixture of 16S rRNA gene primers. We visualized the amplification results using electrophoresis to confirm the length of the DNA base band obtained. We then sequenced the Polymerase Chain Reaction (PCR) products using MinKNOW software (version 23.04.5; Oxford Nanopore Technologies, Oxford-UK). The bioinformatics metagenomic analysis included chronological visualization, Sankey phylogenetic analysis, heat map graphing, and Venn diagram visualization. The study's results showed that in the mangosteen peel eco-enzyme there were bacteria from 7 different phyla. The results of the alpha-diversity index analysis showed the highest value of 2,050 compared to other samples. However, the abundance of each species was lower than that in the other samples. In contrast, the orange peel eco-enzyme had only one bacterial phylum, and the mixed vegetable eco-enzyme had two bacterial phyla. This finding indicates that mangosteen peel eco-enzyme has the most abundant bacterial diversity from different phyla than orange peel eco-enzyme and mix-vegetables, which may cause diversity in the enzyme content produced.
Evaluation of the effects of Glycyrrhiza glabra and Syzygium aromaticum extracts on gene expression of Streptococcus mutans in patients with dental caries MAREH L. AL-AMILI; KAMIL M. AL-JOBORI
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/d260141

Abstract

Abstract. Al-Amili ML, Al-Jobori KM. 2025. Evaluation of the effects of Glycyrrhiza glabra and Syzygium aromaticum extracts on gene expression of Streptococcus mutans in patients with dental caries. Biodiversitas 26: 418-423. Dental caries, primarily associated with Streptococcus mutans, is among the most widespread diseases, particularly in developing regions such as Iraq. Licorice (Glycyrrhiza glabra) and clove (Syzygium aromaticum) are plants with significant economic value and antibacterial properties that potentially serve as alternatives to chemically synthesized antibiofilm agents. This study aimed to evaluate the antibacterial activity of G. glabra and S. aromaticum extracts against S. mutans and to compare their effects with those of antibiotics, mouthwashes, and toothpaste through gene expression analysis of gtfB and gtfD using RT-qPCR. In total, it did not include the methodology or provide details about the Sub-MIC because it was published separately as a second research study in another journal.100 specimens were collected from patients clinically diagnosed by dental physicians at the Hay Al-Hussein Specialized Center in Maysan City, Iraq. RNA was extracted from dentinal lesion specimens and reverse transcribed into complementary DNA (cDNA). Quantitative polymerase chain reaction (qPCR) was performed to analyze the expression of the gtfB and gtfD genes using the housekeeping gene 16S rRNA as an internal control. The analysis assessed the effects of licorice extract, clove extract, combined extracts, chlorhexidine mouthwash at sub-minimum inhibitory concentration (sub-MIC), and lacalut toothpaste on S. mutans. RT-qPCR results revealed that clove extract significantly reduced the expression of gtfB compared to other treatments, with fold changes of 0.178, 0.454, and 0.191. Licorice extract notably suppressed gtfD expression, with fold changes of 0.215, 0.390, and 0.003 for isolates 74, 80, and 46, respectively. These findings suggest that the plant extracts inhibited specific biofilm-related genes without necessarily reducing the overall bacterial growth. Therefore, these natural extracts can be developed as innovative natural anti-plaque agents.
Morphology and molecular studies to reveal the taxonomic status of endemic fish Barbonymus belinka of Lake Singkarak, West Sumatra, Indonesia VIOLA MUTIARA SALIS; Djong Hon Tjong; Syaifullah Syaifullah; Dahelmi Dahelmi; Aadrean Aadrean; Dewi Imelda Roesma
Biodiversitas Journal of Biological Diversity Vol. 26 No. 2 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d260203

Abstract

Abstract. Salis VM, Tjong DH, Syaifullah, Dahelmi, Aadrean, Roesma DI. 2025. Morphology and molecular studies to reveal the taxonomic status of endemic fish Barbonymus belinka of Lake Singkarak, West Sumatra, Indonesia. Biodiversitas 26: 536-550. Species identification is very important in taxonomy and conservation. There are some cases where the distinctive morphological characters of a species show minor differences; for example, the Balingka fish (Barbonymus belinka), endemic to Lake Singkarak, West Sumatra, Indonesia and the Kapiek fish (Barbonymus schwanefeldii). The local community around Lake Singkarak gives two names to the Balingka fish based on size (the larger ones are called Balingka, and the smaller ones are called Kapiek), it can affect the taxonomy and validity of biodiversity data. The lack of comprehensive information on B. belinka has led to the species being classified as Data Deficient (DD) on the IUCN Red List. Additionally, the presence of a DNA barcode for Balingka fish in the BOLD system, listed under a different species name than in GenBank (NCBI), raises concerns about potential species misidentification and data inconsistencies. A thorough taxonomy review of Balingka fish (B. belinka) is necessary, utilizing both morphological and molecular approaches. This study aims to clarify the taxonomy and investigate the phylogenetic relationships of the two fish species through morphological and molecular analyses, utilizing Cytochrome Oxidase-I and Cytochrome b gene sequences. Individual samples were used for morphological identification, while liver tissue was used for molecular analysis. The results showed morphometric variations, but meristic traits confirmed that both fishes belong to the same species, B. schwanefeldii. Molecular analysis shows a genetic distance of 0-1.4% for Cytochrome Oxidase-I gene and 0-2.3% for Cytochrome b gene, indicating the same species. Two specific bases at 585 bp of the Cytochrome Oxidase-I gene and four specific bases at 599 bp of the Cytochrome b gene are also found unique to B. schwanefeldii from Lake Singkarak, suggesting that these two fishes may represent the same species.
Enhancing sustainable livestock support through Kaliwo agroforestry in Southwest Sumba District, Indonesia WILHELMUS YAPE KII; AKHMAD SODIQ; JUNI SUMARMONO; NOVIE ANDRI SETIANTO; ZAINAL A. JELAN
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/d260108

Abstract

Abstract. Kii WY, Sodiq A, Sumarmono J, Setianto NA, Jelan ZA. 2025. Enhancing sustainable livestock support through Kaliwo agroforestry in Southwest Sumba District, Indonesia. Biodiversitas 26: 73-84. The agroforestry system is one of the most popular land management systems related to livestock production. The objectives of this study were to establish the roles of Kaliwo agroforestry and its interconnections with the livestock production system as a source of animal feed, a free-range habitat for poultry such as chickens and ducks, and sources of local materials for the construction of livestock enclosures within the Southwest Sumba District, Indonesia. The research used a qualitative descriptive method involving 420 farmers. We collected data using questionnaires, Focus Group Discussions (FGDs), and direct observation in three agro-ecosystem zones: lowland (Loura and Kodi) and highland (Wewewa). The triangulation method validated the data obtained from interviews, observations, and FGDs. We performed the descriptive analysis using both statistical and non-statistical methods. The findings indicated that farmers procured 18 species of forage from Kaliwo as feed for both ruminants (goats, buffaloes, and cattle) and non-ruminants (pigs and horses), particularly during the dry season when forage in pastures was scarce. Furthermore, Kaliwo serves as a free-range environment for poultry and livestock, including pigs and goats in Loura, and it constitutes the main source of materials for the construction of livestock pens. Farmers repurpose residual fodder and manure as organic fertilizer for a variety of crops cultivated in Kaliwo and small farms. Kaliwo is considered one of the key resources in livestock production systems for its long establishment and favourable adaptation to the natural environment. The integration of agroforestry practices with livestock husbandry can serve as a paradigm for sustainable livestock farming by leveraging local ecological wisdom.

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