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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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Fungal diversity in the temple with an Internal Transcribed Spacer (ITS) molecular and morphological approach CHANTIKA WIJAYANTI; NENGAH DWIANITA KUSWYTASARI; MAYA SHOVITRI; EDO DANILYAN; ENNY ZULAIKA
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/d250737

Abstract

Abstract. Wijayanti C, Kuswytasari ND, Shovitri M, Danilyan E, Zulaika E. 2024. Fungal diversity in the temple with an Internal Transcribed Spacer (ITS) molecular and morphological approach. Biodiversitas 25: 2896-2906. Red bricks and andesite stones comprise most of Indonesia's temple architecture. Red brick is a highly porous building material that weathers rapidly in temples. Physical and biological weathering are the main causes of temple weathering. Rain and other physical elements can raise the temple's humidity, encouraging the growth of lichen and fungus. Many studies have been conducted to investigate the fungal variety in temples made of andesite stones, but the diversity found in these studies has only been identified at the genus level. This research aimed to determine the variety of fungi in the temples by employing morphological and molecular approaches like ITS biomarkers. Macroscopic characterization involves visual inspection of the colony's color on its surface and back and its edges, texture, diameter, shape, and surface to perform morphological identification. Meanwhile, the slide culture method was used for microscopic characterization, utilizing character observations such as reproductive and hyphal structures. Several steps were involved in the molecular identification process: DNA extraction using the Genomic ex Promega Corp Wizard kit, ITS marker-based DNA amplification visualized with Gel Documenter, DNA sequencing, BLAST searches to determine the isolate species, and MEGA 11 phylogenetic tree reconstruction. Class Eurotiomycetes, which includes Talaromyces funiculosus (CB L1B isolate), Talaromyces purpureogenus (CB L3A isolate), Penicillium oxalicum (CB L4A isolate), Penicillium cataractarum (CT TL3 isolate), and Aspergillus aflatoxiformans (CT TL4 isolate), was the most prevalent among the identified species from the classes Sordariomycetes and Eurotiomycetes. Purpureocillium lilacinum (CBL1C isolate), Trichoderma anaharzianum (CB L3B isolate), and Fusarium equiseti (CT L41 isolate) were the discovered species from the Sordariomycetes class.
Taxonomic study on selected species of stingless bees (Hymenoptera: Apidae: Meliponini) in Sulawesi Island, Indonesia MANAP TRIANTO; TUTY ARISURYANTI; HARI PURWANTO; ROSICHON UBAIDILLAH
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/d250547

Abstract

Abstract. Trianto M, Arisuryanti T, Purwanto H, Ubaidillah R. 2024. Taxonomic study on selected species of stingless bees (Hymenoptera: Apidae: Meliponini) in Sulawesi Island, Indonesia. Biodiversitas 25: 2290-2306. Stingless bees are strong candidates as alternative crop pollinators. They are found throughout the tropics, with the exception of the Pacific islands. There are three tropical regions in the world, namely the tropical Americas (Neotropic), Sub-Saharan Africa (Afrotropic), and Indoaustralian (Austroasiatic) region. In this research, we explored the morphological and morphometric characteristics of stingless bees in Sulawesi Island, Indonesia. The genera and species identification of stingless bees were based on morphological characters and coloration, such as the structure and color of the antenna, head, thorax, wing, leg and abdomen. Morphological and morphometric identification of 10 species of stingless bees consisting of five genera, namely the genera Heterotrigona, Homotrigona, Lepidotrigona, Tetragonula, and Wallacetrigona. The genus Tetragonula consists of six small species (<4 mm), namely T. biroi, T. clypearis, T. fuscobalteata, T. laeviceps, T. pagdeni, and T. sapiens. The genera Heterotrigona, Homotrigona, Lepidotrigona, and Wallacetrigona are a group of large stingless bees (>4 mm), each consisting of one species, namely H. itama, H. canifrons, L. terminata, and W. incisa. H. itama and H. canifrons are new records on Sulawesi Island. These species are found in Lore Lindu National Park (TNLL). Until 2023, these species were only found in Java, Kalimantan and Sumatra. This research can be used as a guide in the identification and validation of stingless bee species on Sulawesi Island.
Diversity of epipelic microalgae in a shallow, tropical estuary of Northern Mindanao, Philippines ERWIN JONES A. TUCONG; EMILIE G. TUBIO; VENUS E. LEOPARDAS
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/d250946

Abstract

Abstract. Tucong EJA, Tubio EG, Leopardas VE. 2024. Diversity of epipelic microalgae in a shallow, tropical estuary of Northern Mindanao, Philippines. Biodiversitas 25: 3237-3245. Microphytobenthos are important primary producers in many of the most critical ecosystems, including the estuary. However, environmental variables, including season, influenced their abundance and diversity. In this study, spatial and temporal patterns of epipelic microalgae in Talabaan Estuary Naawan, Misamis Oriental, were conducted last October 2016 and February 2017 to represent wet and dry seasons, respectively. The species composition and diversity of epipelic microalgae samples were assessed using an improvised corer (2 cm, inner diameter). Only the upper 10 mm. of the cored sample was analyzed. Forty-eight species belonging to 33 families and 35 genera were identified and documented in the estuary. Diatoms (Class Bacillariophyta) were found to be the most dominant group, with about 90% of the epipelic microalgae community composed mainly of chains of cells and formed in colonies. Navicula sp. and Nitzschia sp. were among the species found in all sampled stations. The common occurrence of this species across all stations in wet and dry seasons indicated that they are the typical euryhaline species of this tropical estuary. The abundance and diversity of the epipelic microalgae community were found to vary across stations and seasons (p<0.05), but the interaction between these variables did not differ significantly. When abiotic and biological factors were regressed, a significant relationship was found with temperature, while all other factors exhibited no considerable variation. This highlights the effect of seasons in shaping benthic microalgae communities and is an essential factor in structuring microphytobenthic communities in an estuary.
Antibacterial, antioxidant and anti-inflammatory activities of red, brown, and black sorghum (Sorghum bicolor) cultivated in a dry land area LINCE MUKKUN; ENOS TANGKE ARUNG Tangkearung; MAYA ISMAYATI; YASINTA LETEK KLEDEN; PRISCA DEVIANI PAKAN; ELIAS ST. O. NGURU; NETTY MARIA NAIBAHO
Biodiversitas Journal of Biological Diversity Vol. 25 No. 8 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d250828

Abstract

Abstract. Mukkun L, Arung ET, Ismayati M, Kleden YL, Pakan PD, Nguru ESO, Naibaho NM. 2024. Antibacterial, antioxidant and anti-inflammatory activities of red, brown, and black sorghum (Sorghum bicolor) cultivated in a dry land area. Biodiversitas 25: 2560-2569. In an effort to find natural sources for skin treatment, several varieties of sorghum (Sorghum bicolor L. Moench) were evaluated. Sorghum is one of the most important food crops, it is mainly grown in semi-arid areas, because of its ability to tolerate both drought and low soil fertility. This study aimed to evaluate the antibacterial, antioxidant, and anti-inflammation properties of seven types of colored sorghums. Two species of bacteria, Propionibacterium acnes and Staphylococcus epidermis, were used to evaluate the antibacterial properties of sorghum extracts. The results exhibited that sorghum has potent antibacterial activity against P. acnes, ranging from very strong to strong, while moderate to high against S. epidermis. The red Sumba exhibited very strong antibacterial properties against P. acnes and S. epidermis. The brown Sumba showed the highest level of antioxidant activity among other types of sorghum, measured at 82.21%. The brown Sabu had high anti-inflammation activity with an IC50 value of 70.92 ?g/mL. The phenolic compounds found in colored was 57.69 to 64.12% Gallic Acid Equivalent (GAE), dry weight. Six major bioactive compounds were detected using GC-MS, including methyl ester of hexadecanoic acid, n-hexadecanoic acid, methyl ester of 11,14-octadecadienoic acid, 9,12-octadecadienoic acid (Z, Z)-, methyl ester of 4-octadecenoic acid, cis-13,16-docasadienoic acid, aspidospermidin-17-ol, and 1-acetyl-19,21-epoxy-15,16-dimethoxy. Further studies are needed to investigate the effect of compounds extracted from colored sorghums as a commercial anti-acne in the future.
Primer design of the CO1 gene (Cytochrome Oxidase-1) for Sumatran elephant (Elephas maximus sumatranus) for rapid detection using real-time PCR method MAQQITA TUNJUNG SARI; ARI SUSILOWATI; SETIA BETARIA ARITONANG; OKID PARAMA ASTIRIN; NITA ETIKAWATI; VIRA SAAMIA
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/d251044

Abstract

Abstract. Sari MT, Susilowati A, Aritonang SB, Astirin OP, Etikawati N, Saamia V. 2024. Primer design of the CO1 gene (Cytochrome Oxidase-1) for Sumatran elephant (Elephas maximus sumatranus) for rapid detection using real-time PCR method. Biodiversitas 25: 3840-3849. The population of Sumatran elephants is classified as endangered according to the IUCN due to conflicts between humans and elephants, resulting in many elephants being killed by humans to obtain ivory to be sold. The traded ivory is often processed into other ornaments. A rapid forensic examination with real-time PCR using the molecular approach of the CO1 gene (Cytochrome Oxidase-1) is necessary to determine the original species of the processed elephant ivory. This research aims to design and optimize a primer for identifying Sumatran elephants (Elephas maximus sumatranus). The CO1 gene primer for Sumatran elephants was designed using the Primer3Plus and IDT websites. The primers were used to amplify and identify the species of Sumatran elephants from blood, feces, and urine samples. Blood and feces samples were collected from Sumatran elephants at Taru Jurug Zoo Surakarta, while feces and urine samples were taken from Sumatran elephants at Ragunan Zoo Jakarta. DNA from blood and urine samples was extracted using the TIANamp Genomic DNA Kit, and DNA from feces samples was extracted using the TIANamp Stool DNA Kit. The purity and concentration of the obtained DNA extracts were measured. The designed primers were synthesized by Macrogen (Korea), and primer optimization was performed with a PCR gradient. The identification process of Sumatran elephant DNA extract samples was conducted by amplification using real-time PCR quantification with the standard curve method. The results of this research include the COI-270 primer with the sequences 3'-TTAGGTCAACCAGGCTCTCTTC-5' and 5'-AGGATATACGGTCCAACCAGTG-3', capable of amplifying the target 270 bp and having a single peak at the melt curve temperature of 79°C. The identification protocol with specific COI-270 primer can be used in forensic examinations to identify samples originating from Sumatran elephants.
A mid-Holocene pollen record of mangrove diversity on the coast of Ujung Genteng, the southern edge of Sunda Shelf, Indonesia SEPTRIONO HARI NUGROHO; YAN RIZAL; YAHDI ZAIM; EKO YULIANTO; PURNA SULASTYA PUTRA; AGUS MEN RIYANTO; AMAR AMAR
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/d251027

Abstract

Abstract. Nugroho SH, Rizal Y, Zaim Y, Yulianto E, Putra PS, Riyanto AM, Amar. 2024. A mid-Holocene pollen record of mangrove diversity on the coast of Ujung Genteng, the southern edge of Sunda Shelf, Indonesia. Biodiversitas 25: 3653-3664. The Sunda Shelf provides the most informative data for studying mangrove ecosystems. However, the southern edge of the Sunda Shelf adjacent to the Sunda megathrust zone has yet to be studied. This study aimed to provide a paleoecology record of the Ujung Genteng mangrove ecosystem during the mid-Holocene (over 6,300 cal year BP (Before Present). We looked at changes in a mangrove ecosystem using pollen and radiocarbon data from the UG 7B core. Rhizophora sp. initially dominated at c. 6,200-6,100 cal year BP. The ecosystem gradually declined, transitioning to a back mangrove environment. A decrease in the mangrove and back mangrove pollen since 4,200 cal year BP, indicating a shift away from the mangrove forest. In contrast, higher non-mangrove pollen frequency indicates a closer distance to the lowland. By 400 cal year BP, all mangrove pollen vanished, and the environment became almost completely terrestrial. The implications of this research contribute to improved insights into mangrove resilience and resistance to environmental and anthropogenic stressors, aiding effective coastal management and adaptation strategies. Our study also highlights the unique conditions of Sunda Shelf paleoecology, contributing to a more comprehensive regional knowledge and offering an important reference for further investigations on coastal ecosystem dynamics.
Biodegradability and formulation of triclosan-degrading and plant-growth-promoting Pseudomonas sp. MS45 MERRY KRISDAWATI SIPAHUTAR
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/d250719

Abstract

Abstract. Sipahutar MK. 2024. Biodegradability and formulation of triclosan-degrading and plant-growth-promoting Pseudomonas sp. MS45. Biodiversitas 25: 2980-2992. This study presents the isolation of Pseudomonas sp. MS45, a microorganism that can consume triclosan (TCS) as its only carbon and energy source, leading to its detoxification. The rarity of a toxicity study of TCS before and after biodegradation treatment is addressed in this study. Allium cepa's genotoxicity exposed TCS's cytotoxicity, generating multiple damaged chromosomes, in contrast to the insignificant consequences of its broken-down metabolites. The study also optimized the different kinetic parameters for TCS-specific biodegradation and Pseudomonas sp. MS45-specific growth. The biodegradation pattern followed the Michaelis-Menten model with a maximum specific biodegradation rate (Vmax) of 0.01 µmole h-1 mg cell protein-1 and a half saturation constant (Ks) of 21.98 µM. The growth pattern followed the Haldane model with a maximum specific growth rate (µmax) of 0.03 h-1, half saturation constant (Ks) of 4.56 µM, and TCS inhibition constant (Ki) of 32.81 µM. In addition to its TCS-degrading ability, Pseudomonas sp. MS45 also possesses various plant growth promotion traits, and it was incorporated into two solid carrier formulations: vermiculite and rice bran. The study found that vermiculite, especially with PEG, was the most consistent formulation for Pseudomonas sp. MS45, in terms of maintaining bacterial survival and TCS-degrading ability. This study marks the initial report on the biodegradation and formulation of TCS-destroying and Plant-Growth-Promoting (PGP) Pseudomonas sp. MS45, offering promising implications for environmental and agricultural applications.
Moringa oleifera as a potential bioactive agent against Gram-positive and negative bacteria: In-silico analysis of 1YN5 and 3RG1 receptor binding CUT NILA THASMI; HAFIZUDDIN HAFIZUDDIN; HUSNURRIZAL HUSNURRIZAL; DASRUL DASRUL; AMALIA SUTRIANA; BASRI A. GANI; MUHAMMAD NAZAR
Biodiversitas Journal of Biological Diversity Vol. 25 No. 8 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d250812

Abstract

Abstract. Thasmi CN, Hafizuddin H, Husnurrizal H, Dasrul, Sutriana A, Gani BA, Nazar M. 2024. Moringa oleifera as a potential bioactive agent against Gram-positive and negative bacteria: In-silico analysis of 1YN5 and 3RG1 receptor binding. Biodiversitas 25: 3411-3421. The natural antioxidant extract of Moringa oleifera Lam. simultaneously possesses anti-inflammatory, anti-infertility, antimicrobial, and antioxidant properties. This research aims to investigate the active chemical compounds isolated from the leaves of M. oleifera and examine the chemical interaction between the selected compounds and the 1YN5 and 3RG1 proteins based on the molecular docking model. M. oleifera leaves were collected from the Kajhu Village, District of Aceh Besar, Province of Aceh, Indonesia. The bioactive compounds were isolated through cold extraction by using the maceration technique. Chemical analysis and characterization of bioactive compounds were carried out by Fourier Transform Infrared Spectroscopy (FTIR) and Gas Chromatography-Mass Spectrometry (GC-MS). The antioxidant bioactivity/Free Radical Scavenging Potency (FRSP) was determined using a 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical assay. The molecular docking process refers to the modified MOE software docking protocol. The data obtained were analyzed descriptively. The ethanolic extract of M. oleifera leaf contains 38 bioactive compounds. Several bioactive compounds have high peak area percentages, including Oxirane, hexadecyl- (20.22%), TRICYCLO [20.8.0.0E7,16] TRIACONTA (14.35%), acetic acid (CAS), ethyl acetate (11.32%), n-Hexadecanoic acid (8.94%), and oleic acid (8.12%). Molecular docking showed that oleic acid, oxirane, hexadecyl, and 1-Heptacosanol have greater affinity to the 1YN5 gene, while octadecanoic acid and tetracontane have better binding affinity to the 3RG1 proteins. The bioactive compound 1-Heptacosanol bound both to the 1YN5 and 3RG1 proteins. The ethanolic extract of M. oleifera leaves possessed better IC50 (6.07 ppm), relatively twice lower when compared to the positive standard, Vitamin C (10.58 ppm). The M. oleifera ethanol extract exhibits antioxidant bioactivity in the very strong category. The bioactive compound 1-Heptacosanol shows binding affinity with both 1YN5 and 3RG1 proteins.
Molecular characterization of Sweet potato feathery mottle virus and sweet potato yield loss due to its infection GUSTI NGURAH ALIT SUSANTA WIRYA; DEWA GEDE WIRYANGGA SELANGGA; LISTIHANI LISTIHANI; I GEDE RAI MAYA TEMAJA; I PUTU SUDIARTA
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/d250604

Abstract

Abstract. Wirya GNAS, Selangga DGW, Listihani L, Temaja IGRM, Sudiarta IP. 2024. Molecular characterization of Sweet potato feathery mottle virus and sweet potato yield loss due to its infection. Biodiversitas 25: 2355-2362. Sweet potatoes are one of the main sources of carbohydrates for Balinese. "Nasi selo," one of Bali's specialties, uses sweet potato as one of its main ingredients. For the past few years, cultivated sweet potatoes in Bali, Indonesia, manifested symptoms of diseases, particularly purple ring spots, occurring on its young and old leaves. The causative agent of the purple ring symptom is still unknown. Therefore, this study aims to analyze the molecular characteristics of SPFMV Bali isolate and the yield loss estimation it causes. Research methods that were used in this study are survey, sampling, virus identification with RT-PCR using universal Potyvirus as its primer, and field observation to assess the yield loss estimation. Field observation was conducted in five districts in Bali province: Badung, Gianyar, Bangli, Karangasem, and Klungkung. The result indicates that SPFMV infection has been found in these 5 districts, with the highest incidence and severity occurring in Bangli at 86% and 53%. The nucleotide homology of the SPFMV Bali isolates gene has the closest genetic relationship with isolates found in South Korea (MH388494, MH388494) and East Timor (MF572056), at >99%. Based on the latest phylogroup classification, SPFMV is categorized into phylogroups A and B. Phylogroup A consists of SPFMV with O-I strain, O-II strain, and EA strain; phylogroup B only consists of SPFMV with RC strain. Isolate SPFMV found in Bali, has an O strain that belongs to the same group as the O-I strain, also seen in South Korea, East Timor, and China. Actual yield loss that was found by comparing sweet potatoes suffering from purple rings symptom with the one without purple rings symptom reveals a yield loss of 50.9%. Harvested sweet potatoes with purple ring symptoms showed quality deterioration in malformation, discoloration, hollowing, and changes in color and shape. Yield loss of up to 29.53% in fields with a disease severity of 53% has caused a loss of IDR 2,105,166.
Nutritional composition of gedi (Abelmoschus manihot) leaves powder in comparison to common natural galactagogue plants in Indonesia GRACE MARLINA WINATA; HARDINSYAH HARDINSYAH; SRI ANNA MARLIYATI; RIMBAWAN RIMBAWAN; DIMAS ANDRIANTO
Biodiversitas Journal of Biological Diversity Vol. 25 No. 8 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d250830

Abstract

Abstract. Winata GM, Hardinsyah H, Marliyati SA, Rimbawan R, Andrianto D. 2024. Nutritional composition of gedi (Abelmoschus manihot) leaves powder in comparison to common natural galactagogue plants in Indonesia. Biodiversitas 25: 2583-2589. Galactagogue is a substance believed to help initiate, maintain, and increase breast milk production. Low or no breast milk production and perceived insufficient milk are the most common reasons that cause a mother to stop breastfeeding earlier. To help this problem, natural galactagogue consumption is highly recommended. Gedi (Abelmoschus manihot (L.) Medik) plant is locally used in Indonesia as food ingredient and medicinal plant. The leaves have been believed for generations to increase breast milk production. This study aimed to evaluate the macro- and micronutrient content of gedi leaves powder, compared to torbangun (Coleus amboinicus) and katuk (Sauropus androgynous) leaves powder as common natural galactagogue plants in Indonesia. Clean fresh leaves were oven-dried and ground. Carbohydrates, crude fiber, protein, fat, ash, energy, water, vitamins A, B1, B2, B6, B9, C, E, and K, mineral calcium, iron, magnesium, sodium, zinc, phosphorus, and potassium were analyzed using standard methods. The analysis result showed that gedi leaves powder contained highest carbohydrate (51%), crude fiber (10.3%), vitamin K (1,110 µg/100 g), mineral magnesium (700 mg/100 g), sodium (89.6 mg/100 g), and calcium (2,671 mg/100 g) content, which were significantly different compared to torbangun and katuk leaves powder (P<0.05). Total energy (344 kcal/100 g), protein (25%), ash (13.6%), zinc (4.8 mg/100 g), potassium (2,314 mg/100 g), and iron (8.9 mg/100 g) content of gedi leaves powder were between torbangun and katuk leaves powder. This study showed that gedi leaves powder had a high carbohydrate, crude fiber, vitamin K, and mineral, especially calcium and magnesium, and sufficient protein and energy content, compared to torbangun and katuk leaves powder as common natural galactagogue plants in Indonesia. Further research in the extraction, bioactive compound, and in vivo study has to be carried out to scientifically prove the galactagogue effects of gedi leaf powder.

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