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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 record of Stenotrophomonas sp. as endosymbiont bacteria in Rhizopus microsporus Dewi Peti Virgianti; Desi Natalia; I Nyoman Pugeg Aryantha
Biodiversitas Journal of Biological Diversity Vol. 21 No. 4 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210449

Abstract

Abstract. Virgianti DP, Natalia D, Aryantha INP. 2020. Short Communication: New record of Stenotrophomonas sp. as endosymbiont bacteria in Rhizopus microsporus. Biodiversitas 21: 1678-1685. Rhizopus sp. are closely related to humankind in many aspects of human life. Several species of Rhizopus are important in food, agriculture, and health industries. Rhizopus microsporus has endosymbiont bacteria that has been identified as Burkholderia sp. This study aimed to identify the endosymbiont bacteria in R. microsporus isolated from Moringa oleifera Lam leaves. Ring technique, simple method of agar heap technique and antibiotic technique, was conducted to purify the hyphae and to eliminate ectosymbiont and contaminant bacteria outside the hyphae. The presence of endosymbiont bacteria in R. microsporus was determined by using LIVE/DEAD® BacLight Bacterial Viability Kits L13152 and the Fluorescent in Situ Hybridization (FISH) method using EUB338 probes. It was suggested that the culturable endosymbiont bacteria was identified as Stenotrophomonas sp. based on the phylogenetic tree using the 16S rDNA
Optimization and characterization of enterocin Enterococcus faecalis K2B1 isolated from Toraja’s Belang Buffalo Milk, South Sulawesi, Indonesia Hasria Alang; JONI KUSNADI; TRI ARDYATI; SUHARJONO
Biodiversitas Journal of Biological Diversity Vol. 21 No. 3 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210351

Abstract

Abstract. Alang H, Kusnadi J, Ardyati T, Suharjono. 2020. Optimization and characterization of enterocin Enterococcus faecalis K2B1 isolated from Toraja’s Belang Buffalo Milk, South Sulawesi, Indonesia. Biodiversitas 21: 1236-1242. The growing bacterial resistance needs to be controlled with effective antimicrobials. Bacteriocins are proteinaceous toxins produced by bacteria to inhibit the growth of pathogens. Bacteriocin industry has substantially grown, replacing the role of chemical preservatives in enhancing shelf-life and food safety. Bacteriocin produced by genera Enterococcus can be used as an antimicrobial against pathogen. In this study, we used Enterococcus faecalis K2B1 which was first isolated from Toraja’s Belang Buffalo Milk Makassar, Indonesia. The study aimed to optimization and characterization of Enterocinroduced by Enterococcus faecalis K2B1, isolated from Toraja’s Belang buffalo milk. Research Method: including optimization and characterization of antimicrobial metabolite (BLIS) using MRS broth with different initial pH (pH 6, 7 and 8), and partial purification with ammonium sulfate on different concentration (40, 60 and 80 %). Result showed that BLIS production was most optimal on MRS broth at initial pH of 8 after13th hour fermentation, at late exponential phase. BLIS characterization visibly active at high temperatures and very wide range of pH, and disappeared after treating with proteinase-K. Crude had a broad spectrum, was sensitive to Proteinase-K and estimated to have molecular weight of 5 kDa.
Short Communication: Sarocladium oryzae associated with sheath rot disease of rice in Indonesia Syafiqa Pramunadipta; Ani Widiastuti; Arif Wibowo; Haruhisa Suga; Achmadi Priyatmojo -
Biodiversitas Journal of Biological Diversity Vol. 21 No. 3 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210352

Abstract

Abstract. Pramunadipta S, Widiastuti A, Wibowo A, Suga H, Priyatmojo A. 2020. Short Communication: Sarocladium oryzae associated with sheath rot disease of rice in Indonesia. Biodiversitas 21: 1243-1249. One of the obstacles in increasing rice production is the presence of sheath rot pathogen infection, which causes changes in color on the rice sheath to brown or reddish-brown, sometimes does not produce rice grain. The major fungal pathogens that cause sheath rot disease are Sarocladium oryzae and Fusarium spp. The loss of rice yields reaches 85%. The disease found in six provinces, some of which are the largest rice-producing centers in Indonesia. A total of twenty-four Sarocladium sp. were isolated from leaf sheath symptom on potato dextrose agar and water agar medium. Sheath rot pathogen identification based on molecular method was performed using internal transcribed spacer (ITS) rDNA gene sequencing. Necrosis occurs after artificial inoculation in Ciherang rice variety was observed and showed that all isolates were pathogenic. Morphological characterization of the isolates identified them as Sarocladium sp. Molecular identification showed that six representatives isolates belonging to S. oryzae. These findings are important information about the fungal pathogen that causes sheath rot disease in Indonesia, and in studies for formulating control measures of the pathogen in the future to prevent the disease epidemic on rice. This is the first report about the existence of sheath rot disease, morphological characterization and molecular identification of S. oryzae in various rice fields in Indonesia.
Abundance of ants (Hymenoptera: Formicidae) and the functional groups in two different habitats Ananto Triyogo; Budiadi; Siti Muslimah Widyastuti; Sena Adi Subrata; Suwito Susetyo Budi
Biodiversitas Journal of Biological Diversity Vol. 21 No. 5 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210535

Abstract

Abstract. Triyogo A, Budiadi, Widyastuti SM, Subrata SA, Budi SS. 2020. Abundance of ants (Hymenoptera: Formicidae) and the functional groups in two different habitats. Biodiversitas 21: 2079-2087. Land development often affects the quantity and diversity of ants (Hymenoptera: Formicidae). The aim of this study, therefore, was to determine and compare the ant species abundance and the functional groups between two different habitats, representing land development, including pioneer and agroforestry. This research involved a survey of the ants at the Forest Research Education (FRE) of Wanagama I Yogyakarta, and data were accumulated over a period of five months (April, May, June, July, and August). In addition, pit-fall trap and direct collection methods were used, involving the placement of 54 pit-fall traps at two habitats, and the ant specimens were retrieved after a two day period. The results show the total individual abundance of 2,310 and 2,067, on agroforestry and pioneer, respectively. Furthermore, the species richness and diversity index was higher in agroforestry (7; 2.01), compared with pioneer (6; 1.49), where the three dominant species include, Anoplolepis gracilipes, Solenopsis sp., Odontoponera denticulata; and Anoplolepis gracilipes, Odontoponera denticulata, Camponotus sp., respectively. Conversely, the highest amount of invasive ants (Solenopsis sp.) was observed in agroforestry, which negatively impacted on the presence of native species (Odontoponera denticulata). In addition, PCA analysis showed the development of three ant groups on each habitat, hence agroforestry made more real differences in the aspect of species abundance, and none in terms of richness. Therefore, notable differences were observed in the ant communities between both habitats, and agroforestry was indicated as a disturbed area, based on the increment in tramp and invasive ants, alongside low abundance of native and functional groups.
Short Communication: Plant species richness and diversity in Karangsambung-Karangbolong National Geopark, Indonesia angga yudaputra; Puguh Rahardjo
Biodiversitas Journal of Biological Diversity Vol. 21 No. 4 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210457

Abstract

Abstract. Yudaputra A, Rahardjo P. 2020. Short Communication: Plant species richness and diversity in Karangsambung-Karangbolong National Geopark, Indonesia. Biodiversitas 21: 1735-1742. The information on plant species richness and diversity in Karangsambung-Karangbolong National Geopark, Central Java is very limited. This study aimed: (1) to investigate plant species richness and abundance as well as floristic composition in Karangsambung-Karangbolong National Geopark; (2) to reveal the potential uses of plant species recorded in the area. Square sampling plots were applied for nine sampling locations. Square plot of 10 x 10 m was applied to record tree, while nested plots of 5 x 5 m and 2 x 2 m were applied to record sapling and understorey plants including shrubs and herbs, respectively. The highest plant species richness was found in the location with higher elevation and mountainous topography. The species abundance reaches its maximum values at low to moderate elevation. Shannon Diversity Index (H) showed that tree and sapling have moderate diversity, whereas understorey plant has high diversity. Melastoma malabathricum, Clidemia hirta, Zingiber zerumbet, and Ageratum conyzoides are the most abundant plants in this Geopark. Most of plants recorded have potential benefit as medicinal uses.
Morpho-molecular identification and pathogenicity test on fungal parasites of guava root-knot nematode eggs in Lampung, Indonesia I Gede Swibawa I Gede; YUYUN FITRIANA; SOLIKHIN; RADIX SUHARJO; F.X. SUSILO; EKA RANI; MEI SRI HARYANI; RACHMANSYAH A. WARDANA
Biodiversitas Journal of Biological Diversity Vol. 21 No. 3 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210334

Abstract

Abstract. Swibawa IG, Fitriana Y, Solikhin, Suharjo R, Susilo FX, Rani E, Haryani MS, Wardana RA. 2020. Morpho-molecular identification and pathogenicity test on fungal parasites of guava root-knot nematode eggs in Lampung, Indonesia. Biodiversitas 21: 1108-1115. This study aimed to obtain and discover the identity of the species of fungal egg parasites of root-knot nematodes (RKN), which have a high pathogenic ability causing major losses in vegetable crops. The exploration of the fungi was carried out in 2016 and 2018 from Crystal guava plantations in East Lampung, Central Lampung, Tanggamus, and NirAma, a commercial product that has been used for controlling Meloidogyne sp. in Indonesia. Identification was carried out based on morphological characteristics and molecular-based gene sequential analysis of Intergenic Transcribed Spacer (ITS) 1 and ITS 4. A pathogenicity test was carried out in vitro and in a greenhouse using tomato plants as indicator plants. In the in vitro test, observations were made on the percentage of infected RKN eggs. The observations in the greenhouse test were carried out on RKN populations in the soil and roots of tomato plants, root damage (root knots), and damage intensity due to RKN infection. The exploration resulted in five isolates of fungal egg parasites of RKN from the guava plantations in East Lampung (2), Central Lampung (1), Tanggamus (1), and from the isolation results of commercial products (1). The isolates were given codes as B4120X (PT GGP PG1), B3010 (PT GGP PG4), B412G (PT GGP PG 4), B01TG (Tanggamus), and BioP (Commercial products). Based on their morphological characteristics, the isolates were classified into the genus of Paecilomyces. The results of molecular identification showed that the discovered fungi were Purpureocillium lilacinum (Thom.) Luangsa Ard. (Syn. Paecilomyces lilacinus (Thom.) Samson.). Based on the in vitro tests, the five fungal isolates were able to parasitize RKN eggs at 86.4-100%. In the greenhouse test, all isolates significantly suppressed nematode populations in the soil and tomato roots, inhibited the formation of root knots, and produced lower damage intensity compared to controls. Among all the isolates tested, B01TG had the best ability to infect nematode eggs (99.5%), suppressing the formation of root knots, nematode population in the soil and the roots of tomato plants, and the damage intensity compared to other isolates.
Methylene blue decolorizing bacteria isolated from water sewage in Yogyakarta, Indonesia Michelle; Rachel Arvy Nabasa Siregar; Astia Sanjaya; Jap Lucy; Reinhard Pinontoan
Biodiversitas Journal of Biological Diversity Vol. 21 No. 3 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210338

Abstract

Abstract. Michelle, Siregar RAN, Sanjaya A, Jap L, Pinontoan R. 2020. Methylene blue decolorizing bacteria isolated from water sewage in Yogyakarta, Indonesia. Biodiversitas 21: 1136-1141. The textile industry contributes to water pollution issues all over the world. One of the most commonly applied cationic dye in the textile industry is methylene blue. This study aimed to isolate bacteria with the potential to decolorize methylene blue from dye contaminated sewage water located in Kulon Progo District, Yogyakarta, where several textile industries within the proximity, are located. Characterizations of bacterial candidates were done morphologically and biochemically. Molecular identification was conducted by 16S rRNA sequencing. The ability of isolates to decolorize methylene blue was observed by the reduction of methylene blue’s maximum absorption at the wavelength of 665 nm. The results showed that isolates were identified as Comamonas aquatica and Ralstonia mannitolilytica. C. aquatica PMB-1 and R. mannitolilytica PMB-2 isolates were able to decolorize methylene blue with decolorization percentage of 67.9% and 60.3%, respectively when incubated for 96 hours at 37°C. These findings present information on the capability of the genus Ralstonia and Comamonas to decolorize methylene blue cationic dye.
Expression of Mx exon-13 SNPs in Kampong-Laying Type (Kamper) chicken crossbreeds of female Lohmann brown-classic and male Pelung Desiana Afifah; Indra Lesmana; Soenarwan Hery Poerwanto; Tri Joko; swarautama mahardhika; Budi Setiadi Daryono
Biodiversitas Journal of Biological Diversity Vol. 21 No. 4 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210428

Abstract

Abstract. Afifah D, Lesmana I, Poerwanto SH, Joko T, Mahardhika IWS, Daryono BS. 2020. Expression of Mx exon-13 SNPs in Kampong-Laying Type (Kamper) chicken crossbreeds of female Lohmann brown-classic and male Pelung. Biodiversitas 21: 1483-1487. The Gama Ayam Research Team has implemented marker-assisted selection (MAS) in selective breeding to provide a faster, more accurate, and more reliable selection of chicken. Mx gene expression has a vital role in chicken disease resistance. This research aimed to investigate the expression of Mx exon-13 single nucleotide polymorphisms (SNPs) in the population of female Layer Lohmann Brown-Classic, male Pelung, and its progenies Kampong-Laying Type (Kamper) chicken. The G1892A mutation in Mx exon-13 resulted in a change in the amino acid 631 of Mx. The substitution of serine to asparagine favored the ability of chickens to acquire immunity against viral diseases, including avian influenza. Asparagine (A allele) at position 631 is specific to Mx+ (resistant), whereas serine (G allele) is specific to Mx- (susceptible). DNA was amplified using the forward primer 5'-GCACTGTCACCTCTTAATAGA-3' and the reverse primer 5'-GTATTGGTAGGCTTTGTTGA-3' and then sequenced using the Sanger sequencing method. Four SNPs were obtained through Mx sequence alignment. They consisted of four substitutions (A20734T, C20737T, A20766G, and A20893G) with one haplotype. Mx exon-13 SNPs were detected in Pelung and Kamper. Therefore, Kamper chicken inherited the disease resistance gene of Pelung and could be a strong candidate for parental generation in the further selective breeding program.
Short Communication: Molecular characteristics and phylogenetic relationships of silurid catfishes (Kryptopterus, Ompok and Phalacronotus) from the Kampar River, Indonesia, based on the cytochrome b gene Roza Elvyra; DEDY DURYADI SOLIHIN; RIDWAN AFFANDI; MUHAMMAD ZAIRIN JUNIOR; MEYLA SUHENDRA
Biodiversitas Journal of Biological Diversity Vol. 21 No. 8 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210816

Abstract

Abstract. Elvyra R, Solihin DD, Affandi R, Junior MZ, Suhendra M. 2020. Short Communication: Molecular characteristics and phylogenetic relationships of silurid catfishes (Kryptopterus, Ompok, and Phalacronotus) from the Kampar River, Indonesia, based on the cytochrome b gene. Biodiversitas 21: 3539-3546. The study of molecular characteristics and phylogenetic relationships among silurid catfishes (Kryptopterus, Ompok, and Phalacronotus) is very scarce. Existing data are mostly based on morphological characters. Genetic markers among Kryptopterus, Ompok, and Phalacronotus can be analyzed by exploring the nucleotide and amino acid sequences of the mitochondrial cytochrome b gene region (906 base pairs). This study aims to identify molecular characteristics and phylogenetic relationships of silurid catfishes from the Kampar River based on the cytochrome b gene. This research examined 14 silurids of four species from three genera in the Kampar River of Indonesia. Molecular phylogenetic trees were constructed using the neighbor-joining method. This study revealed that three amino acid sites can be used as specific genetic markers for characterizing Kryptopterus limpok. They are E (glutamic acid) at site 123, V (valine) at site 155, and M (methionine) at site 156. Two amino acid sites can be used as specific genetic markers of Ompok spp., A (alanine) at site 201 for O. hypophthalmus, and S (serine) at site 282 for O. eugeneiatus. Two amino acid sites, I (isoleucine) at site 197 and L (leucine) at site 284, can be used to identify Phalacronotus apogon from the Kampar River, Indonesia. The phylogram results based on genetic distance (p-distance) from nucleotide cytochrome b sequences generally showed that intraspecies of K. limpok, O. eugeneiatus, O. hypophthalmus and P. apogon from the Kampar River formed relationship groups within each species supported by high bootstrap values. Additionally, based on genetic distance, K. limpok data from the Kampar River samples and GenBank formed one relationship group within species of K. limpok with a high bootstrap value. This study proves that cytochrome b gene can be used to identify molecular characteristics and phylogenetic relationships of K. limpok, O. eugeneiatus, O. hypophthalmus, and P. apogon from the Kampar River, Indonesia.
Genetic diversity and structure of Ganoderma boninense isolates from oil palm and other plantation crops AGUSTIAMAN PURBA; RAHMAH HAYATI; LOLLIE A.P. PUTRI; DIANA CHALIL; INDRA SYAHPUTRA; Mohammad Basyuni
Biodiversitas Journal of Biological Diversity Vol. 21 No. 2 (2020)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d210204

Abstract

Abstract. Purba A, Hayati R, Putri LAP, Chalil D, Afandi D, Syahputra I, Basyuni M. 2020. Genetic diversity and structure of Ganoderma boninense isolates from oil palm and other plantation crops. Biodiversitas 21: 451-456. Oil palm is an economically important plant, which one of the most important sources of vegetable oil in the world. However, oil palm plantation and other crops face the treat basal stem rot (BSR) disease by Ganoderma boninense. A study on genetic diversity and structure of G. boninense is therefore needed in order to formulate improved control strategies for this disease. This work aimed to analyze the genetic diversity and structure of the G. boninense isolates derived from different hosts, 131 oil palm (Elaeis guineensis), six rubber (Hevea brasiliensis), three coconuts (Cocos nucifera), and three lontar palm (Borassus flabellifer). Genetic diversity and population structure of G. boninense isolates were investigated using six SSR markers with GenAlex 6.502 software. Results showed that several microsatellite loci indicated specific primary success rates, such as KT124402, KT124399, and KT124394, depicting high polymorphism content (>75%). This result suggested that these markers were equally effective in determining the polymorphisms of G. boninense isolates. A hierarchical analysis of molecular variance (AMOVA) revealed that genetic diversity mostly found among individuals within a population (88%), then among populations (8%), and within individuals (4%).. Phylogeny analysis showed two clusters of Ganoderma isolates. which was considered variation as dissimilar across with origin. The present study indicated that G. boninense from oil palm was predominantly comprised of a genetically distinct individual.

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