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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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Morphology and COI barcodes reveal local loaches (Nemacheilus spp.) from Pasuruan River, East Java, Indonesia CAHYA AJENG VALENTA TRESNA SULUNG; NISZAMUDDIN EL CHAIR; DWI ANGGOROWATI RAHAYU; ENDIK DENI NUGROHO; RUSDIANTO RUSDIANTO
Biodiversitas Journal of Biological Diversity Vol. 25 No. 7 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d250702

Abstract

Abstract. Sulung CAVT, Chair NE, Rahayu DA, Nugroho ED, Rusdianto. 2024. Morphology and COI barcodes reveal local loaches (Nemacheilus spp.) from Pasuruan River, East Java, Indonesia. Biodiversitas 25: 2806-2819. The family Nemacheilidae is one of the most diverse and widespread family of freshwater fishes. The nemacheilid loach in the Pasuruan river is relatively abundant; however, there is limited information available about this species. Therefore, further research is necessary to identify loaches from the Pasuruan area. This research aimed to identify the local loach species from Pasuruan District. The pectoral fins were stored in pure-grade ethanol and subjected to DNA extraction, polymerase chain reaction (PCR), and sequence analysis using bioinformatics tool, BOLD systems, and Automatic Barcode Gap Discovery (ABGD) web. The morphological identification revealed two local loaches, Nemacheilus chrysolaimos Valenciennes 1846 and Nemacheilus fasciatus Valenciennes 1846. The high haplotype diversity (Hd) of 0.9 and nucleotide diversity (?) of 0.1 indicate a wide range of genetic variations. The frequency of parsimony informative sites at 25.6% and 16 polymorphic sites and the overall ts/tv ratio of 2.3. The phylogenetic trees demonstrated a clear and unambiguous branching pattern for N. fasciatus and N. chrysolaimos forming their own monophyletic branches. Kimura's 2-parameter genetic distance of the COI gene sequences between these two species was 0.11. This finding was strengthened by morphological and molecular identification results, which indicated that there are two local loach species in Pasuruan District.
Diversity and functional annotation of bacteria community associated with the epithelial surface of Hippocampus kuda (yellow seahorse) and its surrounding environment NOEL JOHN IAN FEBEN S. MAGUATE; SHARON ROSE M. TABUGO
Biodiversitas Journal of Biological Diversity Vol. 25 No. 5 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d250541

Abstract

Abstract. Maguate NJIFS, Tabugo SRM. 2024. Diversity and functional annotation of bacteria community associated with the epithelial surface of Hippocampus kuda (yellow seahorse) and its surrounding environment. Biodiversitas 25: 2230-2240. Hippocampus kuda, commonly known as the yellow seahorse, hosts various microorganisms crucial for its well-being and interactions within its ecosystem. This research aimed to analyze and understand the bacterial community associated with H. kuda by employing V3-V4 16S rRNA gene amplicon sequencing on the Illumina MiSeq platform. Four distinct libraries were constructed, representing the epithelial surfaces of both male and female seahorses and samples from water and soil/sediment habitats. Following rigorous quality control and processing, 187,972 Amplicon Sequence Variants (ASVs) were identified. The predominant ASVs were attributed to genera such as Vibrio, Roseobacter, Photobacterium, Ruegeria, Candidatus, Pseudoalteromonas, Synechococcus, Flavobacterium, and Altererythrobacter, along with some unidentified genera belonging to the Proteobacteria phylum. As indicated by the Shannon index, alpha diversity analysis demonstrated the highest bacterial diversity on the epithelial surface of male seahorses (MS), with a value of 3.2363. Moreover, the functional annotation of bacterial community was conducted using the PICRUSt algorithm within the Parallel-Meta Suite (PMS) software. This analysis uncovered various functional categories, such as metabolism, genetic information processing, and cellular processing. Overall, the findings underscore the role of the microbiome on the skin and surrounding environment in influencing the growth and health of H. kuda seahorses. Notably, this study represents the first documentation of the bacterial community inhabiting the epithelial surface of H. kuda, shedding light on its significance in the ecology of these marine organisms.
Ecological conditions of growth and breeding analysis of Viburnum opulus L. populations in the Kazakhstan part of the Altai Mountains ALEVTINA N. DANILOVA; TATIANA A. VDOVINA; ELENA A. ISAKOVA; YURI A. KOTUKHOV; AIDAR A. SUMBEMBAYEV
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/d250904

Abstract

Abstract. Danilova AN, Vdovina TA, Isakova EA, Kotukhov YA, Sumbembayev AA. 2024. Ecological conditions of growth and breeding analysis of Viburnum opulus L. populations in the Kazakhstan part of the Altai Mountains. Biodiversitas 25: 2845-2857. The purpose of this paper was to study the ecological growth conditions of Viburnum opulus populations and the variability of the main morphological parameters of the vegetative and generative spheres of the species at the interpopulation level in the Kazakhstan part of the Altai Mountains as a future promising donor for breeding work. As a result of field research, using route-reconnaissance, traditional geobotanical, and morphometric methods, 24 isolated locations of V. opulus were discovered in the Kazakhstan Altai in the geographical areas of Kalbinsky, Western, and Southern Altai. These areas' ecological conditions of the species growth were studied for the first time, based on which the characteristics of plant communities with the participation of V. opulus were compiled. It was found that the species grows mainly in three types of associations: tree-shrub, shrub-meadow in the forest zone, and steppe shrub-meadow in the mountain-steppe zone. Plant communities with the participation of V. opulus occupy areas on the northwestern and southeastern mountain slopes associated with river valleys. The vertical range of distribution of the species varies from 395 to 913 masl. The total area of the territory occupied by plant communities with the participation of V. opulus was 198.85 ha. Furthermore, when studying interpopulation variability in 9 populations isolated from each other and located in different ecological and geographical growing conditions, 3 main groups of characteristics were identified depending on the degree of variability. High variability was revealed in the height of the shrubs, fruits in the cluster and their weight, the color of ripe berries, taste indicators for fruit bitterness from 1 to 4 points, and yield. Promising populations regarding productivity were identified in Kalbinsky, Western, and Southern Altai, depending on the ecological and geographical growth in the Kazakhstan Altai.
Metabolite profiling, in vitro antioxidant and a-glucosidase inhibitory properties of Timonius ternifolius leaves MAINGELLINE B. VIVIT; RAMJEE G. BATUYONG; ALONDRA FAE T. DAMIAN; CECILE A. GAOAT; KRISTIAN GAY D. BELTRAN; ANABELLE B. ALEJO; MICHAEL A. CALARAMO; FRANKLIN V. IBANA; MAE ANN R. BATUYONG
Biodiversitas Journal of Biological Diversity Vol. 25 No. 7 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d250724

Abstract

Abstract. Vivit MB, Batuyong RG, Damian AFT, Gaoat CA, Beltran KGD, Alejo AB, Calaramo MA, Ibana FV, Batuyong MAR. 2024. Metabolite profiling, in vitro antioxidant and a-glucosidase inhibitory properties of Timonius ternifolius leaves. Biodiversitas 25: 3027-3034. The genus Timonius (Rubiaceae) possesses different pharmacological properties. One understudied endemic species under this genus from the Philippines is the Timonius ternifolius (Bartl. ex DC.) Fern.-Vill. Hence, this study investigates the physicochemical properties and phytochemical constituents of the leaf ethanolic extract (EE) and subjected to solvent partitioning to yield the following subfractions: hexane (HE), ethyl acetate (EA), and methanol (ME) extracts, which were utilized for the in vitro antioxidant, a-glucosidase and a-amylase assays. Quantitative tests of T. ternifolius leaves revealed the following physicochemical properties: herbal tea-like odor, fibrous and fluffy appearance, 50.07% moisture content, 3.10% total ash content, and a slightly acidic pH value of 5.13. The liquid chromatography-mass spectrometry (LC-MS) analysis has identified eight putative compounds namely glabrolide, aloinoside B, 2-benzyl octanal, geumonoid, (±) gomisin M1, 25-O-Acetyl-7,8-didehydrocimigenol-3-O-a-D-xylopyranoside, lucialdehyde B, and kadsuric acid. The extracts' concentrations of flavonoids, phenols, and terpenoids were 1.23±0.19 mg QE/g, 20.77±0.77 mg GAE/g, and 6.07±0.53 mg/g, respectively. Antioxidant profiling among the subfractions showed EE exhibiting the highest at 59.15±2.08 µg/mL (IC50 value). Moreover, significant a-glucosidase inhibition was noted in the EE extract at 99.74%, EA at 99.71%, and ME at 99.45%. The results showed that T. ternifolius leaves are a promising lead source of pharmacologically active compounds with antioxidant and antidiabetic activities, expanding information on plant-derived alternative treatments and developing medicinal products.
Diversity of airborne fungi in cultured and urban sites in Basra Province, Iraq MOHANAD KHALAF MOHAMMED AMEEN
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/d250906

Abstract

Abstract. Ameen MKM. 2024. Diversity of airborne fungi in cultured and urban sites in Basra Province, Iraq. Biodiversitas 25: 2870-2877. Atmospheric aerosols consist of particles with diverse sizes, shapes, fungal particles are relatively prevalent. They are related to air pollution and several plant, animal, and human health effects. This study was conducted to compare the airborne fungal biodiversity between cultivated and urban areas in Basra Province, Southern Iraq. Results showed that a total of 1654 fungal colonies consisted of 26 genera and two sterile mycelium belonging to 32 species. These fungal isolates belonged to three groups, namely Ascomycota, Zygomycota and Basidiomycota. Among them, Ascomycota had the highest percentage frequency (90.6%), followed by Zygomycota (6.25%) and Basidiomycota (3.12%). The highest i.e., 0.91and 0.9 fungal diversity was found in Abu Al-Khaseeb 2 and Ad-Dayr, respectively, while the lowest was in urban areas and desert nature as Um Qasr, Al-Zubair 0.78 for each. The highest frequency 18.2 10.9 8.8, and 8.5% of fungal isolates were Cladosporium herbarum, Aspergillus fumigatus, Aspergillus niger, and Penicillium sp., respectively. The highest similarity was 0.77 observed between the airborne fungal communities at the Alseeba and Altannumah sites. From the results of this study, it was concluded that airborne fungi can be influenced by the type of terrain they inhabit. There was greater diversity in cultivated areas compared to urban and non-cultivated areas.
Density and distribution of nipah (Nypa fruticans) on the western coast of Aceh, Indonesia DEWI FITHRIA; HAIRUL BASRI; INDRA INDRA; ZAINAL A. MUCHLISIN
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/d250917

Abstract

Abstract. Fithria D, Basri H, Indra I, Muchlisin ZA. 2024. Density and distribution of nipah (Nypa fruticans) on the western coast of Aceh, Indonesia. Biodiversitas 25: 2967-2973. Nypa fruticans Wurmb population on the west coast of Aceh, Indonesia, is under threat due to the frequent land conversion to plantations, aquaculture ponds, ports, and settlements, so reduced density and covered areas. Therefore, this study aims to analyze the density and distribution of nipah on the west coast of Aceh. The transect method was used with a size of 10x10m to count the number of trees, 5 x 5m to calculate the saplings, and 1 x 1m to count the seedlings. At each location, three sub-stations were determined purposively, namely (I) downstream near the mouth of the river, which is connected to sea waters, (II) towards upstream where nipah is still growing, as well as (III) between the upstream and downstream parts (mid area). The results showed that the density of nipah in Kuala Bubon for tree categories ranged from 12,700 to 14,800 ind. Ha-1, saplings 2,400 to 4,400 ind. Ha-1, and seedlings 110,000 to 140,000 ind. Ha-1. Meanwhile, in Kuala Tadu, the density of tree categories ranged from 1,900 to 3,800 ind. Ha-1, saplings 1,600 to 6,000 ind. Ha-1, and seedlings 60,000 to 80,000 ind. Ha-1. Moreover, the distribution index of Morishita in Kuala Bubon ranged from 0.02-0.72 and 0.05-0.58 in Kuala Tadu. The organic matter analysis in Kuala Bubon showed that C-organic ranged from 0.68-1.46%, N-total 0.09-0.12%, and P-total 1.55-4.1 mg/kg, while in Kuala Tadu, the values ranged from 0.66-3.63%, 0.05-0.15%, and 2.95-7.25 mg/kg respectively. Therefore, it was concluded that the density of nipah palm in both locations is very high and in good condition with uniformly distributed. However, the organic matter content at both locations was generally very low to low, except for C-organic at Kuala Tadu Station III and P element at Station II.
Association of soil bacterial diversity and composition with Fusarium wilt disease of bananas in Yogyakarta Province, Indonesia IRIANTI KURNIASARI; ARIF WIBOWO; SITI SUBANDIYAH; ANTHONY B. PATTISON
Biodiversitas Journal of Biological Diversity Vol. 25 No. 5 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d250545

Abstract

Abstract. Kurniasari I, Wibowo A, Subandiyah S, Pattison AB. 2024. Association of soil bacterial diversity and composition with Fusarium wilt disease of bananas in Yogyakarta Province, Indonesia. Biodiversitas 25: 2264-2275. Infection of banana plants with Fusarium oxysporum f. sp. cubense Tropical Race 4 (Foc-TR4) leads to a cascade of changes in the rhizosphere, resulting in changes to the soil physicochemical properties and bacterial community composition. This study aimed to determine the core taxa associated with different soil physicochemical properties and disease statuses and to identify the factors exerting the greatest influence on the soil bacterial community composition of bananas in Special Region of Yogyakarta Province, Indonesia. Rhizospheric soil from healthy and infected plants was collected from four banana locations, including Kulon Progo, Gunungkidul, Bantul, and Sleman districts, at 10-30 cm depth between May and September 2021. Laboratory analysis was conducted for soil physicochemical properties, and the abundance of Foc-TR4 was undertaken. Additionally, 16S rRNA gene-based metagenomics analysis was used to quantify bacterial diversity in all samples. Soil type significantly influenced the abundance and composition of the bacterial community more than disease status did. Contrarily, disease status groups influenced the complexity of bacterial network interaction more than soil type. Actinobacteriota, Proteobacteria, Chloroflexi, Acidobacteriota, and Bacteriodota are the major phyla associated with all soils. This study identified 60 bacterial genera as core members of the banana rhizosphere. These core bacterial genera include various plant growth-promoting bacteria involved in nitrogen fixation, phytohormone production, siderophore production, and biocontrol mechanisms for producing antifungal compounds. Our work provides a basis for future research on the soil bacterial composition associated with banana plants to enhance plant health against Fusarium wilt disease.
Effect of refugia plant (Zinnia sp.) population on the presence of stem borer (Scirpophaga innotata Walker) and natural enemies in rice OLSIVIANA OLSIVIANA; AMIR YASSI; MELINA MELINA
Biodiversitas Journal of Biological Diversity Vol. 25 No. 6 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d250635

Abstract

Abstract. Olsiviana, Yassi A, Melina. 2024. Effect of refugia plant (Zinnia sp.) population on the presence of stem borer (Scirpophaga innotata Walker) and natural enemies in rice. Biodiversitas 25: 2652-2660. This study supports biological control by preserving natural enemies in rice cultivation through habitat modification. The research aimed to analyze the effects of different population levels of refugia (Zinnia sp.) on pest attack rates, the presence and diversity of natural enemies of rice stem borer (Scirpophaga innotata Walker 1863), and rice (Oryza sativa L.) production. The study was designed using a Randomized Group Design (RGD) with four population treatment levels: control (no Zinnia sp.), sparse population (32 polybags of Zinnia sp.), medium population (96 polybags of Zinnia sp.), and dense population (160 polybags of Zinnia sp.). The results showed that the dense population (160 polybags of Zinnia sp.) produced the lowest stem borer infestation rate in the eighth week of observation (1.67%). Pests in all treatments belonged to four orders: Lepidoptera, Hemiptera, Coleoptera, and Diptera, with Hemiptera being the most prevalent. Natural enemies of rice pests belonged to three orders: Coleoptera, Hymenoptera, and Orthoptera. The dense population treatment (160 polybags of Zinnia sp.) yielded the highest values for diversity index (H') at 2.1785, species richness index (R) at 2.1837, and evenness index (E) at 0.9915. This treatment also achieved the highest average rice production at 8.64 tons/ha. Meanwhile, the highest dominance value (C) of 0.2489 was found in the control treatment. Thus, this study supports the idea that increasing the population of Zinnia sp. as a refugia plant can increase the diversity of natural enemies, reduce rice stem borer infestation, and increase rice plant production.
Species composition and size distribution of fishes in mangrove ecosystems in Kendari and Staring Bays, Southeast Sulawesi, Indonesia LATIFA FEKRI; KANGKUSO ANALUDDIN; YUSNAINI YUSNAINI; HASAN ELDIN ADIMU; ANDI CHADIJAH
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/d251030

Abstract

Abstract. Fekri L, Analuddin K, Yusnaini, Adimu HE, Chadijah A. 2024. Species composition and size distribution of fishes in mangrove ecosystems in Kendari and Staring Bays, Southeast Sulawesi, Indonesia. Biodiversitas 25: 3683-3692. Mangrove ecosystem plays very important role in supporting marine organisms including fishes, shells, etc. This study aimed to determine the species composition and size distribution of fishes living around the mangrove ecosystems in Kendari and Staring Bays, Southeast Sulawesi, Indonesia. Fish samplings were conducted using 6 gill nets fishing gear with mesh sizes of 1, 1.5 and 2 inches. Mangrove species composition was sampled using circular plots with diameter of 14 m. The fish conservation status and abundance were determined, while size distribution was analyzed in terms of frequency distribution of body weight, and correlation of body weight and body length. A total of 33 fish species were recorded across the two sampling sites with 30 species were found in Kendari Bay and 19 species were found in Staring Bay. The fish species are mostly classified as least concern based on the IUCN Red List. We found that species richness, presence and abundance of fishes varied according to the moon lightness periods during the fish catchments. The highest species richness was found in the dark moon both in Kendari and Staring Bays, while the lower fish richness was found in the transition from the dark to the full moon in Kendari Bay and the transition from the full moon to the dark moon in Staring Bay. Five fish species associated with mangroves of Kendari and Staring Bays were found more abundant and showed different size distribution pattern, i.e., normal shape of size distribution for Zenarchopterus dispar (Valenciennes, 1847), Ambassis dussumieri Cuvier, 1828 and Upeneus moluccensis Bleeker, 1855, while Mugil cephalus Linnaeus, 1758 and Acentrogobius viridipunctatus Valenciennes, 1837 showed L-shaped size distribution. These five dominant fishes showed well allometric relationships of body length and weight. Our findings suggested that mangrove ecosystems in Kendari and Staring Bays play an important role in maintaining fish diversity.
Predicting the current and future distributions of Pinus merkusii in Southeast Asia under climate change MUHAMMAD NUR SULTON; DEVI MAYANG AURINA; FARHAN MUHAMMAD; FARIZ PRADHANA ADIL FADZILAH; ZAHRA HANUN; MUHAMMAD INDRAWAN; SUGENG BUDIHARTA; JATNA SUPRIATNA; ILYAS NURSAMSI; AHMAD DWI SETYAWAN
Biodiversitas Journal of Biological Diversity Vol. 25 No. 3 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d250328

Abstract

Abstract. Sulton MN, Aurina DM, Muhammad F, Fadzilah FPA, Hanun Z, Indrawan M, Budiharta S, Supriatna J, Nursamsi I, Setyawan AD. 2024. Predicting the current and future distributions of Pinus merkusii in Southeast Asia under climate change. Biodiversitas 25: 1135-1143. Pinus merkusii Jungh. Et de Vriese is a native pine species of Southeast Asia with primary distribution in Indonesia, especially in the mountainous areas of northern Sumatra. The P. merkusii has an important role in the forest ecosystem including maintaining ecosystem stability, reducing soil erosion, and providing habitat for various types of flora and fauna. Climate change is expected to affect the growth, development and distribution of plants, so this study aims to predicting the current dan future distribution of P. merkusii in Southeast Asia under climate change. We used Maxent and Geographic Information System (GIS), which incorporated bioclimatic, edaphic, and UVB radiation variables, to predict the suitable areas of P. merkusii under current and future climate scenarios (RCP 2.6, RCP 4.5, RCP 6.0, and RCP 8.5) and three time periods (2030, 2050, and 2080). Our findings indicate that compared to current, there will be an increase of suitable areas for P. merkusii in 2030 across all climate scenarios with RCPs 2.6, 4.5, 6.0, and 8.5 represent 9.53%, 9.66%, 9.73%, and 9.91% of Southeast Asia terrestrial area, respectively. In 2050, such increase will continue under all climate scenarios with RCP 4.5 has the largest proportion of suitable area (10.39%). However, in 2080, the suitable areas are likely to reduce compared with 2050 with RCPs 2.6, 4.5, 6.0, and 8.5 have a percentage of 9.21%, 9.69%, 10.29%, and 9.81%, respectively. Our predictions showed that there will be a geographical shift of suitable area of P. merkusii into higher elevation and low latitude, migrating southeastward. Our findings about the potential future distribution of P. merkusii might be used as a reference for cultivation according to predicted suitable areas in the future.

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