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Biodiversitas Journal of Biological Diversity
Published by Universitas Sebelas Maret
ISSN : 1412033X     EISSN : 20854722     DOI : https://doi.org/10.13057/biodiv/d230231
Core Subject : Science, Agriculture,
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology
The Biodiversitas Journal was first published in 2000 by the Department of Biology, FMNS, Universitas Sebelas Maret, Surakarta, Indonesia, then in 2006 it was co-published by the Society for Indonesian Biodiversity and that department; since 2017 it was also hosted by Smujo. From 2003-2012 it was accredited by DGHE, Ministry of Education, R.I., since 2014 was indexed by Scopus, where DOAJ and Google Scholar was indexed first.
Arjuna Subject : Biokimia, Genetika dan Biologi Molekuler - Biokimia, Genetika dan Biologi Molekuler (Lain-Lain)
Articles 6,269 Documents
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Short Communication: New records of Mactra clams (Bivalvia: Mactridae) from Madura Island, Indonesia CATHERINE BERLIANA WIJAYA; RENI AMBARWATI; NUR ROHMATIN ISNANINGSIH
Biodiversitas Journal of Biological Diversity Vol. 24 No. 12 (2023)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d241230

Abstract

Abstract. Wijaya CB, Ambarwati R, Isnaningsih NR. 2023. Short Communication: New records of Mactra clams (Bivalvia: Mactridae) from Madura Island, Indonesia. Biodiversitas 24: 6684-6691. Mactridae is a family of bivalves found in shallow waters, such as living at high tide lines, in tidal areas, and below low tide lines. More mactrid bivalves could be discovered, and further studies are needed in Indonesian waters. Madura Island has a variety of bivalves, and Mactra clams could also be discovered on this island. Therefore, this study aimed to identify Mactra clams from Madura Island, Indonesia, and analyze their morphological characters. Samples were collected at Nepa and Badur Beaches during low tides, and then identified based on morphological characteristics. A stereo microscope observation and detailed descriptions were carried out to obtain the qualitative characteristics, while the quantitative ones, included shell length and height, palial line height, and diameter. The environmental parameters of this two-beach were also evaluated. Data were analyzed descriptively. The results showed two new records of Mactridae members at both beaches, namely Mactra luzonica Reeve, 1854, Mactra dissimilis Reeve, 1854. Mactra dissimilis revealed morphological variation, namely in the coloration on both the exterior and interior of the shell. There were three variations of M. dissimilis, namely bluish-white shell, brownish-white shell, and white shell. The findings of M. dissimilis and M. luzonica are regarded as new records for Madura Island, Indonesia.
Selection of rice aroma from crossing aromatic rice x T250.7 mutant genotype using DNA marker ISHAK ISHAK; FLOREAN FEDORA
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/d250537

Abstract

Abstract. Ishak I, Fedora F. 2024. Selection of rice aroma from crossing aromatic rice x T250.7 mutant genotype using DNA marker. Biodiversitas 25: 2191-2197. Breeding fragrant rice using conventional approach was considered ineffective due to time consuming, therefore molecular breeding using DNA markers was introduced. This research aimed to utilize marker-assisted selection (MAS) for detection of fragrance gene in rice related to molecular breeding. Crossing between aromatic rice (Sinar 1) and non-aromatic rice (T250.7 mutant genotype) showed the results at F1 plants and found the DNA fragment size of 257 bp for fragrance genes in rice was at TS1, TS2, TS3, TS4, TS5, and TS.7 genotypes, whereas, TS6 did not show a fragment DNA at 257 bp. It was predicted that the TS6 genotype did not cross between variety Sinar 1 with T250.7. The F2 seeds were selected and morphologically, they had slender seeds and continued planting for F2 plants. Based on DNA marker identification, it revealed that 75% of the rice plants carried aroma. Similarly, the selected F3 plants continued to be planted and molecular identification indicated that aroma segregation was the same as that in the previous generation. Plants with the number of accessions of 721, 761, and 7210 were predicted to have homogeneity in aroma after detection using molecular markers. The MAS in breeding programs can shorten the duration of rice selection.
Vegetation structure and carbon stock of restored mangrove on abandoned shrimp pond in the International Mangrove Botanical Garden Rama IX, Thailand JETSADA WONGPROM; SUTIDA MANEEANAKEKUL; ANUCHA TARA; WASAN CHANDAENG; DECHA DUANGNAMON; APISADA RUEANGKET; DUSIT WECHAKIT; POONSRI WANTHONGCHAI; CHATREE MAKNUAL
Biodiversitas Journal of Biological Diversity Vol. 24 No. 10 (2023)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d241064

Abstract

Abstract. Wongprom J, Maneeanakekul S, Tara A, Chandaeng W, Duangnamon D, Rueangket A, Wechakit D, Wanthongchai P, Maknual C. 2023. Vegetation structure and carbon stock of restored mangrove on abandoned shrimp pond in the International Mangrove Botanical Garden Rama IX, Thailand. Biodiversitas 24: 5821-5830. The conversion of mangrove forest into shrimp aquaculture has severely impacted biodiversity and increased carbon emissions. Restoration program is thus urgently needed for such mangrove forests. In this study, we investigated the vegetation structure and composition, and biomass and carbon stock of restored mangrove on abandoned shrimp pond. Observation plots at restoration sites with age of 3-year-old (MF3) and 14-year-old (MF14) were established in the International Mangrove Botanical Garden Rama IX, Chanthaburi Province, Thailand and at abandoned shrimp pond (ASP) and protected mangrove forest (PMF) as reference sites. The diameters and heights of mangrove species were measured and identified in order to determine the vegetation structure, composition, biomass, and carbon stock. Soil samples from four soil depths, i.e. 0-15, 15-30, 30-50, and 50-100 cm, were collected to quantify the soil carbon stock. The results showed the good growth of Rhizophora stand planted at the restored sites with high vegetation biomass and carbon stock. This species also promoted species diversity, suggesting that Rhizophora spp. are suitable species for the restoration of abandoned shrimp pond. The vegetation biomass and carbon stock of MF14 (230.99 t ha-1 and 102.54 t C ha-1, respectively) was higher than that of PMF (133.84 t ha-1 and 64.94 t C ha-1, respectively). Higher vegetation and soil carbon stocks of the restored mangrove forest was positively influenced by the Rhizophora stand. However, the ecosystem carbon pool of PMF was higher (366.38 t C ha-1). This result indicates that the conservation of mangrove forest is significant to maintain the forest diversity, ecosystem function, and reducing carbon emissions, while mangrove forest restoration is essential to improve the vegetation structure and increase the soil and vegetation carbon stocks.
In vitro mutagenesis on patchouli (Pogostemon cablin Benth.) with gamma-ray irradiation on leaf explants RUT NORMASARI; ESTRI LARAS ARUMINGTYAS; RURINI RETNOWATI; WAHYU WIDORETNO
Biodiversitas Journal of Biological Diversity Vol. 24 No. 12 (2023)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d241201

Abstract

Abstract. Normasari R, Arumingtyas EL, Retnowati R, Widoretno W. 2023. In vitro mutagenesis on patchouli (Pogostemon cablin Benth.) with gamma-ray irradiation on leaf explants. Biodiversitas 24: 6407-6414. Patchouli oil production in Indonesia has yet to meet international market demand, one of which is the quality of the patchouli superior seeds. Patchouli is propagated vegetatively through cuttings, causing limited variability and decreasing plant quality. In vitro mutagenesis with gamma-ray irradiation can increase plant genetic variability and produce superior patchouli plants. This study aimed to produce patchouli variants through in vitro mutagenesis by gamma-ray irradiation on patchouli leaf explants. To accomplish the research objectives mentioned above, the research stages included in vitro mutagenesis through gamma-ray irradiation, shoot regeneration, plantlet growth, and molecular analysis using SSR (Simple Sequence Repeat). Gamma-ray irradiation inhibited the growth of explants and shoot formation but could increase plantlet growth ability at low doses of 15-30 Gy. The dose of gamma-ray irradiation that caused the death of explants in fifty percent of the tested population (LD50) was 69 Gy. Molecular analysis of SSR on 50 plants regenerated from gamma-irradiated explants revealed monomorphic and polymorphic fragments compared to non-irradiated and donor plants. Primers Pca1 and Pca2 showed the highest percentage of polymorphic, with 77.3 and 50%, respectively. Gamma irradiation during in vitro culture is an alternate method for increasing genetic variety in patchouli breeding.
Biotic and dragonfly diversity indices as ecological quality evaluation in Lahat District Rivers, South Sumatra, Indonesia ANANDA RACHMAWATI; INDRA YUSTIAN; YULIA PUJIASTUTI; SUPARMAN SHK; ARINAFRIL ARINAFRIL
Biodiversitas Journal of Biological Diversity Vol. 24 No. 11 (2023)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d241127

Abstract

Abstract. Rachmawati A, Yustian I, Pujiastuti Y, Suparman Shk, Arinafril. 2023. Biotic and dragonfly diversity indices as ecological quality evaluation in Lahat District Rivers, South Sumatra, Indonesia. Biodiversitas 24: 6059-6068. The Lematang, Sandaran, and Kungkilan rivers have been reported to be polluted by coal mining activities. This study aimed to evaluate the ecological conditions using a dragonfly as a bio-indicator. Dragonfly surveys were conducted using direct observation procedures in 11 research sites determined by purposive sampling based on positions of the upstream, midstream and downstream of the river entering the coal mining area, including settling ponds managing waste from post-mining activities (stockpiles and disposal). Dragonflies were captured by visual observations, direct capture, and sticky traps. Data were analyzed by calculating the Dragonfly Biotic Index (DBI) and Diversity Index. The correlation between dragonflies and environmental factors was analyzed using Canonical Correspondence Analysis (CCA) according to Jaccard’s index. The results showed there were 23 species of dragonflies. Larvae and exuviae were found in Aeshnidae and Libellulidae families. Dragonfly species with the highest DBI values were seen in Rhyothemis triangularis, Tholymis tillarga, Zyxomma petiolatum, Atrocalopteryx atrata, Libellago lineata and Rhinocypha fenestrata. Sandaran River had the highest DBI value and diversity index because of the undisturbed condition of the area, which had natural vegetation and unpolluted water conditions. The Kungkilan River will become the focus of river rehabilitation, starting with the reclamation of the river riparian area.
High-throughput analysis using 16S rRNA sequencing of bacterial communities associated in selected mangrove species from Bayug Island, Iligan City, Philippines STEFENIE KATRIN V. SIBLOS; SHARON ROSE TABUGO
Biodiversitas Journal of Biological Diversity Vol. 25 No. 1 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d250107

Abstract

Abstract. Siblos SKV, Tabugo SR. 2023. High-throughput analysis using 16S rRNA sequencing of bacterial communities associated in selected mangrove species from Bayug Island, Iligan City, Philippines. Biodiversitas 25: 53-61. Mangrove ecosystems are recognized globally as highly productive ecosystems, that play a crucial role in carbon sequestration, erosion control, water purification, and as essential breeding grounds for diverse aquatic life. They also offer specialized ecological niches, accommodating a diverse range of organisms, including bacterial communities. This study aimed to investigate bacterial communities of Bayug Island in Iligan City, Philippines, inhabiting six mangrove species, namely Rhizophora stylosa Griffith, Rhizophora apiculata Blume, Rhizophora mucronata Lam., Sonneratia alba Sm., Ceriops tagal (Perr.) C.B.Rob., and Nypa fruticans Wurmb and their possible functions within the mangrove forests. Genomic DNA was extracted from the six pooled soil samples, and the V3-V4 region of the 16S rRNA gene was sequenced using the Illumina MiSeq platform. Six amplicon libraries, corresponding to the mangrove species were analyzed with Parallel Meta Suite software, yielding 173,270 amplicon sequence variants (ASVs) after quality control. The study identified the top five most abundant ASVs in the mangrove rhizosphere, linked to the genera Vibrio, Stenotrophomonas, Serratia, Pseudoalteromonas, and Achromobacter. Among the mangrove species, S. alba exhibited higher alpha diversity according to the Shannon index. PICRUSt analysis revealed that microorganisms are involved in biodegradation, xenobiotic metabolism, and other metabolic processes within the mangroves. These bacteria could find applications in environmental cleanup, bioremediation, waste treatment, and soil health improvement. This result contributes to the ongoing ecological restoration of mangrove forests at the research site.
Antibacterial activity of Paederia foetida leaves using two different extraction procedures against pathogenic bacteria MELDA YUNITA; MORGAN OHIWAL; MUHAMMAD ZEIN ELFITRASYA; HALIDAH RAHAWARIN
Biodiversitas Journal of Biological Diversity Vol. 24 No. 11 (2023)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d241110

Abstract

Abstract. Yunita M, Ohiwal M, Elfitrasya MZ, Rahawarin H. 2023. Antibacterial activity of Paederia foetida leaves using two different extraction procedures against pathogenic bacteria. Biodiversitas 24: 5920-5927. The objective of this study was to compare the effectiveness of the extraction methods between maceration and infundation of Paederia foetida (Linn.) leaves in suppressing the growth of Staphylococcus aureus and Escherichia coli with concentrations of 10, 25, 50, 75, and 100% using the disc-diffusion method. While phytochemical testing was performed by decoction method. The results of this study revealed that the macerated extract was able to inhibit both S. aureus and E. coli at all concentrations with the inhibition zones varied ranging from 5.8 ± 0.85 - 20.43 ± 0.06 mm and 4.9 ± 0.57 - 18.18 ± 0.67 mm, respectively. While the leaf infusion obtained from infundation method was found to be less able to inhibit both pathogenic bacteria (<1 mm). Results of phytochemical testing confirmed the result of inhibitory testing where macerated extract contained alkaloids, saponins, steroids, terpenoids, and tannins, while the leaf infusion only contained alkaloids and terpenoids. It can be concluded that macerated extracts of P. foetida leaves were far more effective in inhibiting the growth of S. aureus and E. coli. The study implies that the leaf extract of P. foetida can be considered and developed into a strong antibacterial in the future through good and appropriate bioprospecting.
Phytochemical profiling and antidiabetic evaluation of Peperomia pellucida as a potential alpha glucosidase inhibitor SHOLIHATIL HIDAYATI; AYU TRI AGUSTIN; ENI KARTIKA SARI; SHINTA MAYA SARI; RIAN ANGGIA DESTIAWAN; WARDA ATIKA SILVANA
Biodiversitas Journal of Biological Diversity Vol. 24 No. 11 (2023)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d241116

Abstract

Abstract. Hidayati S, Agustin AT, Sari EK, Sari SM, Destiawan RA, Silvana WA. 2023. Phytochemical profiling and antidiabetic evaluation of Peperomia pellucida as a potential alpha glucosidase inhibitor. Biodiversitas 24: 5972-5978. One strategy in post-prandial hyperglycemic control can be done by inhibiting the digestion of dietary carbohydrates through the inhibition of alpha glucosidase enzymes. This study was conducted to determine the antidiabetic activity of Peperomia pellucida in inhibiting the alpha glucosidase. An inhibitory activity analysis test was carried out on alpha glucosidase in vitro and in silico using alpha glucosidase. Molecular docking between receptors and ligands was performed using Hex 8.0 software. The setting column is set in Shape+Electro+DARS mode. The results showed ethanol extract and ethyl acetate fraction in vitro showed the ability to inhibit the activity of alpha glucosidase enzyme with C50 values of 13.43 mg/mL and 9.73 mg/mL respectively with IC50 positive control acarbose values of 8.11 mg/mL. The results of in silico analysis showed that the Patuloside A component was able to bind to the binding site of alpha glucosidase and gave the smallest binding energy value with a value of -321.4 kcal/mol compared to isovitexin, isoswertisin, pellucidatin, and caryatin-7-O-?-rhamnoside compounds. P. pellucida has the potential to be developed as an antidiabetic agent that has activity in inhibiting the work of the enzyme alpha glucosidase so that it can reduce blood glucose levels.
Variation of weekly home range characteristics of Sumatran elephants (Elephas maximus sumatranus) in Bentang Seblat, Bengkulu Province, Indonesia IRMA KUSUMA NINGRUM; YANTO SANTOSA; YUDI SETIAWAN
Biodiversitas Journal of Biological Diversity Vol. 24 No. 11 (2023)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d241103

Abstract

Abstract. Ningrum IK, Santosa Y, Setiawan Y. 2023. Variation of weekly home range characteristics of Sumatran elephants (Elephas maximus sumatranus) in Bentang Seblat, Bengkulu Province, Indonesia. Biodiversitas 24: 5854-5862. Bentang Seblat is one of the areas of conflict between Sumatran elephants and humans arising from space use problems because Sumatran elephants have specific preferences for habitat characteristics. This study aims to identify the characteristics of the weekly home range and analyze the relationship of weekly home range with habitat characteristics of Sumatran elephants in Bentang Seblat. GPS collar data from November 2020 until August 2022 were obtained from the Natural Resources Conservation Agency of Bengkulu-Lampung Province and habitat characteristics were obtained from Landsat 8 imagery. The data obtained were analyzed using chi-square test and Multiple Regression Analysis (MRA) with five variables: land cover, slope, distance from water sources, roads, and settlements. The results showed that the weekly home range was between 2.67 ha-239.98 ha, averaging 46.1 ha. The highest percentage of each habitat characteristic includes secondary forest (55.38%), flat slopes (59.01%), distances of 0-450 m from water sources (35.11%), distances of 0-400 m from roads (70.81%), and distances of 6-8 km from settlements (50.37%). The weekly home range is closely related to all habitat characteristics, with the highest level of relationship significance being the distance from water sources and the distance from the settlement.
Exploration of bacteriophages from waters in Palembang, Indonesia as biocontrol of antibiotic-resistant Escherichia coli RIRI NOVITA SUNARTI; POEDJI LOEKITOWATI HARIANI; SRI BUDIARTI
Biodiversitas Journal of Biological Diversity Vol. 24 No. 11 (2023)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d241128

Abstract

Abstract. Sunarti RN, Hariani PL, Budiarti S. 2023. Exploration of bacteriophages from waters in Palembang, Indonesia as biocontrol of antibiotic-resistant Escherichia coli. Biodiversitas 24: 6069-6081. The emergence and dissemination of antibiotic-resistant bacteria in the aquatic environment demand for utilization of bacteriophage (phage) therapy as an ecologically conscious alternative to mitigate the consequences of drug resistance. The presence of antibiotic-resistant Escherichia coli (E. coli) in the river of Palembang City is a matter of concern for public health. It is imperative to explore the potential of phages as biocontrol agents against antibiotic-resistant E. coli sourced from the rivers of Palembang City. The effectiveness of the phage was then evaluated in managing antibiotic-resistant E. coli in contaminated water. The exploration resulted in the acquisition of 12 phage isolates from various water sources. Specifically, three phage isolates were obtained from Kedukan River (FgSK11.2, FgSK22.2, FgSK31.3); three phage isolates were obtained from Buah River (FgSB13.2, FgSB13.3, FgSB33.1); and six phage isolates were obtained from PU River (FgPU11.2, FgPU11.3, FgPU31.3, FgPU33.1, FgPU33.2, FgPU33.3). The isolates have demonstrated the ability to lyse antibiotic-resistant E. coli bacteria. The findings indicate that bacteriophages can mitigate pollution in collected water samples. The phage cocktail utilized effectively inhibited the growth of antibiotic-resistant E. coli, reducing their population. Furthermore, the treatment resulted in satisfactory water quality improvements by reducing the Fe and Pb levels. The results of this study show a significant advancement in the use of phages as a first step in addressing the problem of E. coli pathogen-caused water pollution in Palembang City.

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