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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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The dynamics of Chlorella spp. abundance and its relationship with water quality parameters in intensive shrimp ponds HAYATI SOEPRAPTO; HERI ARIADI; UBAD BADRUDIN
Biodiversitas Journal of Biological Diversity Vol. 24 No. 5 (2023)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d240547

Abstract

Abstract. Soeprapto H, Ariadi H, Badrudin U. 2023. The dynamics of Chlorella spp. abundance and its relationship with water quality parameters in intensive shrimp ponds. Biodiversitas 24: 2919-2926. Chlorella spp. is a plankton genus belonging to the phylum Chlorophyta and is commonly found in the shrimp farming ponds. This plankton might serve as natural feed especially for the post-larvae stage shrimps. This study aims to investigate the dynamics of Chlorella spp. abundance and its correlation with the N:P ratio in the intensively managed shrimp ponds. The study was conducted using a causal ex-post facto design with data collection through purposive sampling. The results showed that the plankton abundance in the observed ponds was moderate consisted of 4 class and 7 genera. The dominant genus was Chroococcus spp. and Chlorella spp. with abundance ranging from 2.50E+05 to 2.60E+05 cells/mL. Plankton abundance correlated with water quality conditions, including pH of 7.9, salinity of 19-20‰, temperature of 28.50-28.75°C, dissolved oxygen of 5.12-5.39 mg/L, nitrite of 0.035-0.072 mg/L, phosphate of 0.011-0.025 mg/L, organic matter of 95.77-102.32 mg/L, and alkalinity of 125-130 mg/L. There was also correlation between the increase in plankton biomass and nutrient solubility. The abundance of Chlorella spp. was negatively correlated with the N:P ratio of the water in the ponds. Based on dynamic model analysis, the most ideal N:P ratio is 1:20 from several simulations of 1:10, 1:20, 1:30, and 1:40. The dynamics of Chlorella spp. abundance followed an oscillatory pattern from the beginning of cultivation to harvest with the most ideal N:P ratio of 1:20. This understanding is important for making environmental engineering concepts in pond aquatic ecosystems.
Identification polymorphism of LHR and FSHR genes in Indonesian Holstein dairy cattle associated with productive and reproductive traits YULIATI WAHYU SETYORINI; EDY KURNIANTO; SUTOPO SUTOPO; SUTIYONO SUTIYONO
Biodiversitas Journal of Biological Diversity Vol. 24 No. 5 (2023)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d240544

Abstract

Abstract. Setyorini YW, Kurnianto E, Sutopo, Sutiyono. 2023. Identification polymorphism of LHR and FSHR genes in Indonesian Holstein dairy cattle associated with productive and reproductive traits. Biodiversitas 24: 2898-2905. Luteinizing and follicle-stimulating hormones and their receptors play an important role in the reproductive system’s hormonal activity and physiological function. This study aimed to identify the genotype variation of the Luteinizing Hormone Receptor (LHR) gene exon 11 and the Follicle-stimulating Hormone Receptor (FSHR) gene exon 10 and to elucidate the associating between polymorphism with the milk and reproductive traits in dairy cattle. A total of 100 samples of deoxyribonucleic acid (DNA) from Indonesian Holstein dairy cattle were used in this study. Polymerase Chain Reaction Restriction Fragment Length Polymorphism (PCR-RFLP) was performed for genotyping of the Single Nucleotide Polymorphism (SNP) of the LHR and FSHR genes with the HhaI and AluI restriction enzymes, respectively. The collected phenotype data were milk production, quality, and reproductive trait. In addition, the general linear model procedure in the SAS program was carried out to investigate the association of genotypes with productive and reproductive traits. The results showed that the LHR gene in the population of this study was monomorphic, while the FSHR gene was polymorphic with three genotypes, namely CC, CG, and GG. The sequences of the FSHR gene indicated the presence of a mutation at nucleotide number 2037 that substitutes cytosine for guanine. Cows with the CC genotype showed better parameter service per conception (P<0.05) than the other genotypes but did not correlate with other reproductive parameters and milk traits. Therefore, it was concluded that SNP g.2037C>G polymorphism at FSHR gene exon 10 was identified in the Indonesian Holstein Dairy cattle population and associated with service per conception parameters but not with milk trait.
Chemical composition, antioxidant, and antibacterial activity of Ruta graveolens (Rutaceae) YOUNIS SAADI SAEED; JASSIM FATEHI ALI; MOHAMMED ARAFAT MOHAMMED
Biodiversitas Journal of Biological Diversity Vol. 24 No. 6 (2023)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d240609

Abstract

Abstract. Saeed YS, Ali JF, Mohammed MA. 2023. Chemical composition, antioxidant, and antibacterial activity of Ruta graveolens (Rutaceae). Biodiversitas 24: 3162-3168. The present study was carried out to investigate the antioxidant and antibacterial activities of phenolic components isolated from the leaves of Ruta graveolens L. The phenolic compounds were extracted in different organic solvents (hexane, ethanol, and ethyl acetate) and analyzed by column chromatography, thin-layer chromatography, and high-performance liquid chromatography. Three discrete fractions were collected and subsequently examined: one from ethyl acetate extraction (I) and two from ethanolic extraction (II and III). No fractions from hexane were obtained. In particular, the ethanolic fractions were analyzed by HPLC analysis which contained the most bioactive compounds. The major phenolic compounds from the ethanol extracts were catechol and coumarin (1.104966 and 16.612227 mg/kg), followed by catechol and hydroquinone (0.144731 and 1.90781 mg/Kg), whereas, resorcinol and coumarin from the ethyl acetate extracts (14.78298 and 21.75253 mg/kg). The ethanol extract had the highest level of antioxidant activity, and other fractions had antioxidant effects at different levels; because the three fractions' phenolic chemicals have varied redox characteristics, their impacts vary in strength. The highest inhibition zones (mm) of Bacillus cereus and Staphylococcus aureus at 24 ?g/mL for fractions II and I were 23 and 22 mm, respectively. At 24 ?g/mL, Escherichia coli and Proteus vulgaris had inhibition zones of 21 and 20 mm, respectively. Fraction I and II did not show Escherichia coli and Proteus vulgaris inhibition zones (mm) at 1.5 µg/mL. Finally, the study's results suggest that using R. graveolens ethanol extracts may be a natural source of antioxidants and anti-infectious agents.
Anatomical, morphological and physiological leaf characters of black betel (Piper betle L. var. nigra) in varying natural and man-made habitats PARAMITA CAHYANINGRUM KUSWANDI; NUR AENI ARIYANTI; MUHAMAD FAHMI YUNUS; CHE NURUL AINI CHE AMRI
Biodiversitas Journal of Biological Diversity Vol. 24 No. 6 (2023)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d240618

Abstract

Abstract. Kuswandi PC, Ariyanti NA, Yunus MF, Amri CNAC. 2023. Anatomical, morphological and physiological leaf characters of black betel (Piper betleL. var. nigra) in varying natural and man-made habitats. Biodiversitas 24: 3236-3244. Piper betle L. var. nigra or black betel (known as Sirih hitam in Indonesia) contains valuable secondary metabolites, such as alkaloids, flavonoids, saponins, tannins, phenols, carotenoids, steroids and terpenoids. Black betel leaf extract has been shown to have antimicrobial activity thus there is a prospect to be developed as a promising herbal plant. Nevertheless, little information is available about its development as a medicinal plant. This research studies the influence of different habitats on several characters of black betel leaves with the aim to understand the suitable environmental conditions for the optimum growth of black betel plants. We used a survey method and random sampling of black betel leaves in four locations in Java Island, Indonesia, namely Banyuwangi which represents natural habitat, and Karanganyar, Ngaglik and Pakem which represent man-made habitats. Measurements of temperature, humidity, soil moisture and light intensity were carried out at each location. Analyses of leaf area, leaf water content, total leaf chlorophyll content and flavonoid content were undertaken and statistically analyzed using SPSS software. Leaf transverse sections were also observed. The results showed that the environmental parameters differed in the four locations. Leaves samples from the natural habitat in Banyuwangi were significantly different (P<0.05) from the three man-made habitats for chlorophyll and flavonoid content. For water content, significant difference was only for Banyuwangi samples with those from Karanganyar and Pakem. For leaf area, significant difference was only found between the Banyuwangi samples and Karanganyar. Observations on the transverse cross section of midrib of black betel leaves from the four locations showed structures that are generally found in Piper betle species, namely the presence of an epidermal layer, trichomes in the abaxial part of the leaf, several layers of the hypodermis, visible vascular tissue and the presence of secretion cells. There were several differences in the leaf anatomy such as greater number of trichomes on the leaves from Karanganyar, the secretory cells that were more visible in the leaves from Ngaglik and Banyuwangi and the sclerenchymal tissue that was more visible in the leaves from Banyuwangi. Such differences are likely influenced by variations in environmental parameters thus showing that the man-made habitat in the Karanganyar location can affect leaves characters similar to black betel plant grown in its natural habitat in Banyuwangi.
Biotransformation of dioxins by assembling RW1 upper pathway gene cassettes in Escherichia coli THAMER Y. MUTTER; GERBEN J. ZYLSTRA; XING HUANG
Biodiversitas Journal of Biological Diversity Vol. 24 No. 7 (2023)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d240701

Abstract

Abstract. Mutter TY, Zylstra GJ, Huang X. 2023. Biotransformation of dioxins by assembling RW1 upper pathway gene cassettes in Escherichia coli. Biodiversitas 24: 3648-3656. Rhizorhabdus wittichii RW1 (formerly known as Sphingomonas) is one of the few bacterial strains known to grow and metabolize dibenzofuran and dibenzo-p-dioxin as a carbon source. The rare ability of strain RW1 to transform both substrates suggests the involvement of unidentified genes. Its genome sequence showed that RW1 has an extreme redundancy of ring cleavage dioxygenases and hydrolases. RW1 genes were assembled on an expression vector to provide additional experimental evidence that both substrates are metabolized in RW1 by two different sets of hydrolases. Three different combinations of the ring cleavage dioxygenase gene (dbfB2) with three hydrolases (dxnB1, dxnB2, and dxnB3) were cloned on an expression vector (pET30a) in Escherichia coli BL21 (DE3), and the enzymes' roles were tested against DD and DF transformation. The results of the heterologous expression in E. coli showed that DbfB2 can transform both intermediates 2,2?,3-trihydroxybiphenyl (THD) and 2,2?,3-trihydroxybiphenyl ether (THDE) from DF and DD, respectively. The two hydrolases DxnB1 and DxnB2 are involved only in transforming the DF intermediate 2-hydroxy-6-oxo-6-(2-hydroxyphenyl)-hexa-2,4-dienoate (2OH-HOPDA) into salicylate. The newly identified hydrolase DxnB3 is involved only in transforming 2-hydroxy-6-oxo-6-(2-hydroxyphenoxy)-hexa-2,4-dienoate (2OH-O-HOPDA) into catechol in the DD pathway. The study clarifies and answers the question regarding the rare ability of other organisms that can degrade dibenzofuran but can’t degrade dibenzo-p-dioxin. The results showed that the hydrolases involved in DD degradation differ from those involved in DF degradation, as previously known that the same hydrolases are involved in the two pathways. All genes are assembled on one cassette for the first time, which has never been done previously.
Genetic characterization of superior durian (Durio zibethinus L.) accessions in Batang District, Central Java, Indonesia based on ISSR markers MUHAMMAD ISBAT AMRULLAH; ENNI SUWARSI RAHAYU; ELING PUWANTOYO; RIA IKA MAHARANI; SOLICHIN SOLICHIN; SRIYADI SRIYADI; TRI YANUAR HADIPRASETYA; AMIN RETNONINGSIH
Biodiversitas Journal of Biological Diversity Vol. 24 No. 9 (2023)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d240922

Abstract

Abstract. Amrullah MI, Rahayu ES, Puwantoyo E, Maharani RI, Solichin, Sriyadi, Hadiprasetya TY, Retnoningsih A. 2023. Genetic characterization of superior durian (Durio zibethinus L.) accessions in Batang District, Central Java, Indonesia based on ISSR markers. Biodiversitas 24: 4811-4819. Durian (Durio zibethinus L.) has the highest level of genetic diversity in the genus of Durio. The genetic diversity of D. zibethinus in Batang District, Central Java, Indonesia needs to be explored to obtain data on superior durian accessions that are adaptive in the area. This study aimed to analyze the genetic diversity of 40 superior durian accessions from 13 locations in Batang District using 10 Inter Simple Sequence Repeat (ISSR) primers. Genomic DNA was isolated from leaves using a modified CTAB method. PCR products were electrophoresed on 2% agarose and yielded 161 ISSR alleles with a percentage of 100% polymorphic alleles. The level of genetic diversity based on Nei's gene diversity and Shannon's Information index are 0.277 and 0.434, respectively. The durian accessions studied have a similarity coefficient of 0.22-0.86 and are divided into two main clusters. Siwatu 1 and Siwatu 2 accessions have the highest genetic similarity coefficient (0.86), while Butternuts and Watu Tembogo 1 accessions show the lowest genetic similarity coefficient (0.05). Specific alleles were found in 11 durian accessions. The molecular characterization results show the high genetic diversity of superior durian accessions in Batang District and add to the list of local superior durian accessions in Indonesia.
Morphological parameters, heritability, yield component correlation, and multivariate analysis to determine secondary characters in selecting hybrid maize NUR FADHLI; MUH FARID; MUHAMMAD AZRAI; AMIN NUR; ROY EFENDI; SLAMET BAMBANG PRIYANTO; ANDI DIRHAM NASRUDDIN; FIRA NOVIANTI
Biodiversitas Journal of Biological Diversity Vol. 24 No. 7 (2023)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d240712

Abstract

Abstract. Fadhli N, Farid M, Azrai M, Nur A, Effendi R, Priyanto SB, Nasruddin AD, Novianti F. 2023. Morphological parameters, heritability, yield component correlation, and multivariate analysis to determine secondary characters in selecting hybrid maize. Biodiversitas 24: 3750-3757. Direct selection for grain yield traits in maize (Zea mays L.) is often inefficient under specific conditions, necessitating the accurate determination of secondary traits to facilitate implementation and enhance selection precision. This study aimed to examine the morphological parameters, heritability, yield component correlations, and multivariate analysis of hybrid maize for determining potential secondary traits through indirect selection. The experimental design employed a randomized complete block design (RCBD) comprising 17 genotypes, including 15 hybrid maize lines and 2 hybrid maize varieties (RK 457 and RK 57). The results revealed that weight of harvested cob character and yield traits demonstrated significant correlations with production. Correlation values were further analyzed using biplot analysis and path analysis to identify potential secondary traits. The principal component biplot analysis results indicated four characters as effective secondary traits for selection, namely weight of harvested cob, yield, weight of 1000 seeds, and moisture content. MSM53/BCY as a parent of JHD 05 displayed superior performance compared to the two commercial hybrid varieties. Based on path analysis results, the weight of harvested cob character exhibited the highest direct effect on production with a value of 0.93, indicating that weight of harvested cob is the best secondary trait for selection.
Satellite based analysis of mangrove cover and density change in mangroves of Tulang Bawang District, Lampung Province, Indonesia HARI KASKOYO; FERLI HARTATI; SAMSUL BAKRI; INDRA GUMAY FEBRYANO; BAINAH SARI DEWI; NUNING NURCAHYANI
Biodiversitas Journal of Biological Diversity Vol. 24 No. 5 (2023)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d240557

Abstract

Abstract. Kaskoyo H, Hartati F, Bakri S, Febryano IG, Dewi BS, Nurcahyani N. 2023. Satellite based analysis of mangrove cover and density change in mangroves of Tulang Bawang District, Lampung Province, Indonesia. Biodiversitas 24: 3019-3028. Being a threatened ecosystem of the world, mangroves require regular monitoring to identify areas that need improvement in conservation measures. Considering this, the present study aimed to assess the mangrove cover and density change in mangrove forest of Tulang Bawang District, Lampung Province, Indonesia. Data was collected by remote sensing techniques using satellite imagery viz., Landsat 5 in 2000 and 2010 and Landsat 8 in 2020. It was then analyzed using remote sensing method, namely Object-Based Image Analysis techniques using the unguided classification method to obtain mangrove cover data; while mangrove density information was obtained using the Normalized Difference Vegetation Index algorithm. The results revealed the decrease in mangrove cover and density between 2000 and 2020. The mangrove cover decreased from 7529 ha in 2000 to 5551 ha in 2020. Furthermore, density of mangrove forest has also witnessed change from dense density class in 2000 to medium density class in 2020. From this result, it is evident that mangroves of East Rawajitu Sub-district are degrading and require focused efforts to prevent the degradation. Communities, entrepreneurs, and governments have different motives for utilizing mangrove forests that result in damage, so reasonable efforts are needed to manage mangrove forests sustainably.
Floristic composition and structure of Eurycoma longifolia habitat in Muka Kuning Nature Tourism Park, Riau Islands, Indonesia ARIDA SUSILOWATI; HENTI HENDALASTUTI RACHMAT; KUSUMADEWI SRI YULITA; KESUMA WIJAYA
Biodiversitas Journal of Biological Diversity Vol. 24 No. 5 (2023)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d240537

Abstract

Abstract. Susilowati A, Rachmat HH, Yulita KS, Wijaya K. 2023. Floristic composition and structure of Eurycoma longifolia habitat in Muka Kuning Nature Tourism Park, Riau Islands, Indonesia. Biodiversitas 24: 2836-2842. Eurycoma longifolia Jack, locally called as pasak bumi,is a popular medicinal plant which is known to have properties in curing various diseases. The root of E. longifolia is the organ that has the highest aphrodisiac content so hunting for the roots of E. longifolia destructively causes a significant population decline. Information regarding vegetation community around the habitat of this species is crucial in determining appropriate conservation actions. Muka Kuning Nature Tourism Park (TWA) located in Batam Island, Riau Islands Province is one of the natural habitats of E. longifolia, yet information regarding the state of vegetation in this area has not been obtained. This study aims to determine the floristic composition and structure of vegetation in the habitat of E. longifolia in Muka Kuning Nature Tourism Park focusing on the parameters of Important Value Index (IVI) and biodiversity indices. Vegetation analysis was applied using purposive sampling method based on the presence of E. longifolia individuals. The results showed that the IVI of E. longifolia at the growth stage of seedlings, saplings, poles and trees were 18.1%, 21.9%, 12.14% and 0%, respectively. No individual E. longifolia was found at the tree level which might be attributable to the habitus of this species which is small-sized tree or woody shrub with maximum height of 15 m. The vegetation community at the studied area had Shanon-Wienner diversity index (H') from 2.27 to 3.12 and the Evenness index from 0.88 to 0.98, which is categorized as high. The results of this study imply that the natural habitat of pasak bumi in the TWA Muka Kuning is classified as good and tighter area protection is highly recommended to protect valuable biodiversity in it including E. longifolia.
The carrying capacity of Nusa Penida Island, Bali, Indonesia for Bali myna (Leucopsar rothschildi Stresemann, 1912) JUNITA HARDINI; I GUSTI BAYU WIRAYUDHA; ALHALIMATA ROSYIDI; NI MADE AYU RITA; ILAROSA MAWANTI; LALU ACHMAD TAN TILAR WANGSAJATI SUKMARING KALIH; MARTIN JONI; FRANSISCUS XAVERIUS SUDARYANTO
Biodiversitas Journal of Biological Diversity Vol. 24 No. 6 (2023)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d240643

Abstract

Abstract. Hardini J, Wirayudha IGB, Rosyidi A, Rita NMA, Mawanti I, Kalih LATTWS, Joni M, Sudaryanto FX. 2023. The carrying capacity of Nusa Penida Island, Bali, Indonesia for Bali myna (Leucopsar rothschildi Stresemann, 1912). Biodiversitas 24: 3462-3470. This study is to analyze the carrying capacity of Nusa Penida Island on the existence of Bali myna (Leucopsar rothschildi Stresemann, 1912), because the population is increasing. Bali myna counting method: (i) Counting Bali myna on the tree where she sleeps. (ii) Counting Bali myna at the time of doing daily activities. Bali myna population in 2021, Ped Village 58 birds, and Toyapakeh Village 4 birds. In 2022, Bali myna in Ped Village had 102 birds, and in Toyapakeh Village 6 birds. On Nusa Penida Island, food sources of fruits and insects are abundant. There is enough nest box or tree hole to make a nest. Bali myna nest nuisance animals are bee honey (Trigona itama, Cockerel 1918 and ant (Ochetellus glaber (Mayr, 1862)), while predators are tokay gecko (Gekko gecko (Linnaeus 1758)), and water monitor (Varanus salvator Laurenti 1768). It is suspected that some Bali myna moved from Ped Village to Toyapakeh Village due to a large number of nesting disturbing animals in Ped Village. Until now, the people of Nusa Penida Island still carry out awig-awig (customary law) to protect Bali myna. From this research, it is known that the carrying capacity of Nusa Penida Island for Bali myna. The move of Bali myna from Ped Village to Toyapakeh Village is not due to a lack of carrying capacity but because of the presence of Bali myna nuisance animals.

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