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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 40 Documents
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Search results for , issue "vol. 20 no. 4 (2019)" : 40 Documents clear
A novel Bacillus sp. isolated from rotten seaweed: Identification and characterization alginate lyase its produced DEWI SESWITA ZILDA; YULIYANTI YULIANTI; RIZKY FAUZIYAH SHOLIHAH; SUBARYONO SUBARYONO; YUSRO NURI FAWZYA; HARI EKO IRIANTO
Biodiversitas Journal of Biological Diversity Vol. 20 No. 4 (2019)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d200432

Abstract

Abstract. Zilda DS, Yulianti Y, Sholihah RF, Subaryono S, Fawzya YN, Irianto HE.2019. A novel Bacillus sp. isolated from rotten seaweed: identification and characterization alginate lyase its produced. Biodiversitas 20: 1166-1172. Alginate lyase has been known as potential biocatalyst not only for industrial but also medicinal application especially for the production of oligosaccharides which have distinct bioactivities. An alginate lyase, AlgT513, has been isolated from rotten seaweed bacterium strain T513 and characterized. The bacterium showed low similarity (95%) with Bacillus tequilensis strain 10b based on 16S rDNA sequence indicating that AlgT513may be a novel Bacillus species. The bacterium forms a clear zone on solid medium with 0.5% sodium alginate addition. The optimum temperature and pH were 50ºC and 8 respectively. AlgT513 maintained stability at board pHs of 4-9 and temperature of 45ºC. Metal ions Mg2+, Ca2+ and K+ increase the activity of the enzyme while Zn2+, Co2+ and Li+ strongly inhibit it. NaCl inhibits AlgT513 activity where most of the alginate lyases need it to reach maximum activity. AlgT513 is suggested as a serine metalloenzyme due to inhibition of ethylenediaminetetraacetic acid (EDTA) and phenylmethylsulfonyl fluoride (PMSF).
Isolation and molecular identification of antimicrobial-producing Lactic Acid Bacteria from chao, South Sulawesi (Indonesia) fermented fish product RISKY NURHIKMAYANI; BUDI SETIADI DARYONO; ENDAH RETNANINGRUM
Biodiversitas Journal of Biological Diversity Vol. 20 No. 4 (2019)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d200418

Abstract

Abstract. Nurhikmayani R, Daryono BS, Retnaningrum E. 2019. Isolation and molecular identification of antimicrobial-producing Lactic Acid Bacteria from chao, South Sulawesi (Indonesia) fermented fish product. Biodiversitas 20: 1063-1068. Chao is traditional fermented fish made of anchovy (Stolephorus sp.), rice, salt, and fermented naturally on controlled environment. The product comes from Pangkep Regency, South Sulawesi. Chao has the potential for the source of high-grade lactic acid bacteria isolates, especially for antimicrobial compound. Antimicrobial compound produced by lactic acid bacteria is a biopreservative compound with many advantages. The purposes of this investigation were to isolate antimicrobial-producing lactic acid bacteria from chao and to identify their isolates based on the molecular properties. Lactic acid bacteria were isolated from chao using Man Ragosa Sharpe Agar (MRSA) medium added with 0.1 % CaCO3, followed by the ability test to produce antimicrobial compound against Staphylococcus aureus FNCC 0047 as an indicator. The spectrum of crude antimicrobial as cell-free supernatant (CFS) was determined by antagonism against S. aureus FNCC 0047 and Escherichia coli FNCC 0049 on agar well diffusion test. Selected isolates of antimicrobial-producing lactic acid bacteria molecularly identified from 16S rRNA marker using primer 27F and 1492R. We obtained four isolates of lactic acid bacteria that showed the antimicrobial activity. This crude antimicrobial compound could inhibit both gram-positive Staphylococcus aureus FNCC0047 and gram-negative bacteria Escherichia coli FNCC0049. The highest crude antimicrobial activity of isolates was observed on IB1C strain. The results of molecular characterization suggested that the IB1C and IB3B strain were identified as Lactobacillus plantarum, whereas IB3E and IB3F were identified as Pediococcus pentosaceus.
Identification and hemolytic activity of jellyfish (Rhopilema sp., Scyphozoa: Rhizostomeae) venom from the Persian Gulf and Oman Sea HOSSEIN JAFARI; HOSSEIN HONARI; JAMIL ZARGAN; SAEID TAMADONI JAHROMI
Biodiversitas Journal of Biological Diversity Vol. 20 No. 4 (2019)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d200440

Abstract

Abstract. Jafari H, Honari H, Zargan J, Jahromi ST. 2019. Identification and hemolytic activity of jellyfish (Rhopilema sp., Scyphozoa: Rhizostomeae) venom from the Persian Gulf and Oman Sea. Biodiversitas 20: 1228-1232. The present study investigated the hemolytic capacity of the crude venom extracted from isolated nematocysts of Rhopilema sp. Scyphozoa: Rhizostomeae. Nematocyst was used at various concentrations to evaluate the hemolytic activity by using the nematocysts of human, mice, and sheep. Mean concentration-dependent hemolysis could be observed from 200 µg/mL of protein equivalents or higher with variable potencies in different species. The crude venom was analyzed using sodium dodecyl sulfate-polyacrylamide gel electrophoresis SDS-PAGE. Molecular weight with 3 clear bands including 45, 65 and 95 kDa appeared to be the major protein components of the venom. The results of our experiments indicated that venom of Rhopilema sp. induces hemolysis in the studied species and determined that the increase in the amount of toxin has a positive correlation with the increase of cell lysis. This study showed that the venom of Rhopilema sp. may have many biologically active principles, which need further studies in the future.
Metagenomic analysis of microbial community in over-fermented tempeh ARTINI PANGASTUTI; RIZAL KHOIRUN ALFISAH; NUR IFFAH ISTIANA; SITI LUSI ARUM SARI; RATNA SETYANINGSIH; ARI SUSILOWATI; TJAHJADI PURWOKO
Biodiversitas Journal of Biological Diversity Vol. 20 No. 4 (2019)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d200423

Abstract

Abstract. Pangastuti A, Alfisah RK, Istiana NI, Sari SLA, Setyaningsih R, Susilowati A, Purwoko T. 2019. Metagenomic analysis of microbial community in over-fermented tempeh. Biodiversitas 20: 1106-1114. Tempeh is a traditional Indonesian food which is made from soybeans through a fermentation process using Rhizopus as a starter culture. Tempeh is now considered as a functional food with many beneficial effects to human health beyond its nutritional value. The microbial community during the further fermentation process of tempeh give typical characteristic taste and flavor. Therefore the over-fermented tempeh is used as a flavoring in some dishes. Metagenomic analysis needed to know the involvement of microbial communities since most of the microbes involved in further fermentation process are unculturable. This research aimed to study the diversity of the microbial community in the over-fermented tempeh (72 hours) using the metagenomic analysis. Seventeen OTUs of fungi in over-fermented tempeh were detected. Among them, 9 OTUs had significant abundance: six species were identified as Tryblidiopsis sichuanensis, Candida sp.2_1., Kluyveromyces marxianus, Trichosporon asahii, Trichosporon gracile, and Trichosporon ovoides, one species was identified in the order level Mucorales, and two fungi species could not be determined. Species of the order Mucorales was the dominant species in over-fermented tempeh (72 hours) with a relative abundance of 62.46%, followed by Kluyveromyces marxianus with a relative abundance of 3698%. Meanwhile, 132 OTUs of the bacterial community was detected, the predominant 10 genera were Chryseobacterium, Lactococcus, Lactobacillus, Streptococcus, Acetobacter, Novosphingobium, Comamonas, Escherichia, Klebsiella, and Stenotrophomonas, in which Lactobacillus agilis, Lactococcus sp., and Klebsiella sp., were most abundant with relative abundance of 27%, 26.3%, and 13% respectively.
The favorable alleles of AKIRIN2:c.*188G>A, EDG1:c.-312A>G and TTN:g.231054C>T as candidate markers for high-marbling are very low in Bali cattle SAIFUL ANWAR; ARI SULISTYO WULANDARI; WIDYA PINTAKA BAYU PUTRA; SYAHRUDDIN SAID
Biodiversitas Journal of Biological Diversity Vol. 20 No. 4 (2019)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d200405

Abstract

Abstract. Anwar S, Wulandari AS, Putra WPB, Said S. 2019. The favorable alleles of AKIRIN2:c.*188G>A, EDG1:c.-312A>G and TTN:g.231054C>T as candidate markers for high-marbling are very low in Bali cattle. Biodiversitas 20: 965-970. Marbling is one of primary factors influencing the palatability of beef. The AKIRIN2, EDG1 and TTN genes are considered as the three candidate genes responsible for high-marbling in beef cattle. This study aimed to investigate the genetic polymorphism of the SNPs of AKIRIN2:c.*188G>A, EDG1:c.-312A>G and TTN g.231054C>T in Bali cattle. A total of 125 DNA samples of Bali cattle were genotyped for AKIRIN2 and TTN gene and 82 DNA samples for EDG1 gene using PCR-RFLP method. In the present study, it was found that the A allele of AKIRIN2:c.*188G>A, the G allele of EDG1:c.-312A>G and the T allele of TTN g.231054C>T that considered as the favorable alleles were found to be very low in Bali cattle (0.004, 0.000, and 0.004, respectively). This results indicated that the polymorphism of AKIRIN2:c.*188G>A, EDG1:c.-312A>G and TTN g.231054C>T were very low and can be considered as monomorphic in Bali cattle. These findings suggested that Bali cattle may not genetically potential as a high-marbling cattle breed. However, the other specific genes for high-marbling still needs to be investigated in Bali cattle.
Economic valuation of Lansa Mangrove Forest, North Sulawesi, Indonesia CALVYN FA SONDAK; ERLY Y KALIGIS; ROBERT A BARA
Biodiversitas Journal of Biological Diversity Vol. 20 No. 4 (2019)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d200407

Abstract

Abstract. Sondak CFA, Kaligis EY, Bara RA. 2019. Economic valuation of Lansa Mangrove Forest, North Sulawesi, Indonesia. Biodiversitas 20: 978-986. Mangrove forest gives many benefits and services to human and environment. Even though it contributes many benefits and services, coastal ecosystems threatened as one of the most critical ecosystems in the world. The study aims to estimate the economic value of ecosystem services provided by Lansa mangrove forest, Wori Sub-district, North Minahasa District, North Sulawesi Province, Indonesia. Here, we describe the use value (direct and indirect value) and non-use value (option and existence value), and emphasize the components of ecosystem services fish resources, firewood, coastal protection, biodiversity, carbon (C) removal and mangrove sustainability because these directly influence human welfare. Their market price calculated fish and C removal value. Coastal barrier and firewood were approached using the replacement cost method. Biodiversity value was calculated using Indonesia mangrove forest biodiversity value. Contingent Valuation method was used to find out people willing to pay for the sustainability of mangrove forest. Lansa mangrove forest total economic value (TEV) was IDR 4,431,197,603 or equal to US$ 305,600 (US$ 1,959 ha-1). The success of this mangrove valuation has potentially large implications for future policy-making of its’ ecosystem service values.    
Some structural characteristics of mixed natural forest stand at a 10-year period in the Hyrcanian Region: Case study of Shourab Forest, Mazandaran Province, Iran MOJTABA AMIRI
Biodiversitas Journal of Biological Diversity Vol. 20 No. 4 (2019)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d200403

Abstract

Abstract. Amiri M. 2019. Some structural characteristics of mixed natural forest stand at a 10-year period in the Hyrcanian Region: Case study of Shourab Forest, Mazandaran Province, Iran. . Biodiversitas 20: 950-955. This research was carried out in Shourab Forest in the Hyrcanian region, Northern Iran over a 10-year period (1996-2005) and data were analyzed based on systematic random sampling with permanent sample plots; 0.1 ha. The results revealed that n.ha-1 and v.ha-1 in study area increased from 126.3 and 245.2 in 1966 to 202.8 and 313.1 in 2006, respectively. The analysis of tree frequency in diameter classes at the first and the end of the period indicated un-even aged regular stands. The highest increase of number of trees was observed in 15, 20 and 25cm diameter classes, While the maximum change in volume per hectare, is related to the diameter classes 30, 65, 70 and 100cm. The regeneration values in most of the vegetation stages (except; 0-2.5cm) increased after a 10 years harvesting period. Development stages of this regeneration were seedling (53.4-53.3%), sapling (37.3-33.5%), thicket (6.8-10.4%) and small pole (2.5-2.8%), in 1996 and 2006, respectively. These conditions show that the selection method has been successful in our study area. The change in the utilization method of shelter-wood system to selection cutting method had been a positive impact on the quantitative forest condition after a 10-year period. In general, it can conclude that structural characteristics of mixed beech-hornbeam stands such as live trees dimension including tree height and diameter, number and volume of trees per hectare are different during the time. And eventually, the manipulation in the stands should be well timed and planned based on quantified structural properties of stands.
Short Communication: Seed germination of twelve Indonesian begonias for conservation MUHAMMAD EFENDI; AISYAH HANDAYANI; INTANI QUARTA LAILATY
Biodiversitas Journal of Biological Diversity Vol. 20 No. 4 (2019)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d200435

Abstract

Abstract. Efendi M, Handayani A, Lailaty IQ. 2019. Short Communication: Seed germination of twelve Indonesian begonias for conservation. Biodiversitas 20: 1192-1197. Knowledge of seed quality is essential when seeds are stored for the long term. A preliminary study on Begonia seed conservation was conducted, to characterize morphology and germination testing on native Begonia from Indonesia. As many as 12 species of Indonesian Begonia were observed for the characteristics of fruit and seeds. Later, we tested the level of seed viability at different levels of fruit maturity. The experimental design used a Completely Randomized Design (CRD) with two factors. Data analysis was performed using the Statistical Tool for Agricultural Research (STAR) program and further testing the Duncan Multiple Range Test (DMRT) at a 5% significance level. Generally, all seeds were barrel-like in shape, the smallest size in B. muricata (252.42 µm length), and the largest size in B. areolata (up to 451.42µm length, while the operculum 28.48 µm-104.9 µm length). Most Begonia seeds start germinating in the second and third weeks after sowing. B. scottii, and B. verecunda, as well as B. longifolia, showed germination in the second week, while other species tended not to be simultaneous. Dry seed germination was higher than seed wet for eight weeks. B. longifolia and B. scottii had the highest germination in wet seed treatment: while in the dry seed treatment, the highest germination was showed by B. areolata and B. muricata.
Short Communication: A comparative study of phenotypes and starch production in sago palm (Metroxylon sagu) growing naturally in temporarily inundated and non inundated areas of South Sorong, Indonesia TOMAS YATER; HERMAN WAFOM TUBUR; CIPTA MELIALA; BARAHIMA ABBAS
Biodiversitas Journal of Biological Diversity Vol. 20 No. 4 (2019)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d200425

Abstract

Abstract. Yater T, Tubur HW, Meliala C, Abbas B. 2019. Short Communication:  A comparative study of phenotypes and starch production in sago palm (Metroxylon sagu) growing naturally in temporarily inundated and non-inundated areas of South Sorong, Indonesia. Biodiversitas 20:  1121-1126. Sago palm forests and sago palm semi cultivation are generally spread in swampy areas, seasonally inundated areas and non-inundated areas. The objectives of this study are to determine and compare the phenotypes of and starch production by sago palms growing naturally in the temporarily inundated areas (TIA type) and non-inundated areas (WIA type) in South Sorong District, West Papua Province, Indonesia. Sago palms of both habitats were found to be the same variety based on analysis of vernacular names and general characteristics. Comparison of morphological characters related to starch production of TIA and WIA types showed that there were no significant differences between the two studied types. The distribution of starch along the sago trunk was observed to be uneven, higher starch accumulation was found in the middle part of the trunk which was significantly different from the lower and upper parts of the trunk.
Genetic diversity analysis of Tenera × Tenera and Tenera × Pisifera Crosses and D self of oil palm (Elaeis guineensis) parental populations originating from Cameroon LALU FIRMAN BUDIMAN; ARDHA APRIYANTO; ADI PANCORO; SUDARSONO SUDARSONO
Biodiversitas Journal of Biological Diversity Vol. 20 No. 4 (2019)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d200402

Abstract

Abstract. Budiman LF, Apriyanto A, Pancoro A, Sudarsono S. 2019. Genetic diversity analysis of Tenera × Tenera and Tenera × Pisifera Crosses and D self of oil palm (Elaeis guineensis) parental populations originating from Cameroon. Biodiversitas 20: 937-949. There are three types of oil palm (Elaeis guineensis Jacq.) based on the shell thickness, such as the Dura (D type, with a thick shell), the Pisifera (P type, with no or very thin shell) and the Tenera (T type, with medium shell thickness), respectively. The T type is a commercially grown oil palm, originated from hybridization between D × P types. The success of oil palm breeding depends on the availability of diverse parental populations, especially in the D and the P types. Unfortunately, the improved P type of oil palm may only be produced by crossing between Tenera (T × T) or between Tenera and Pisifera (T × P) while improved D type may easily be produced from selfing of a single Dura type palm (D self). Therefore, evaluation of the potential genetic diversity of Dura parental lines derived from D self and Pisifera lines derived from T × T or T × P is essential. The objectives of this research were to analyze the genetic diversity of T × T, T × P and D self oil palm progenies originated from Cameroon which would be used as parental population for breeding the commercial T types of oil palm in Indonesia, determine whether the progenies were from legitimate hybrids of the desired parents and evaluate their potential values for creating Tenera hybrid in the oil palm breeding programs. A total of 148 individuals from one combination of T × T and two T × P crosses and three D self-pollinations were evaluated. Genotyping was conducted using 16 SSR marker loci. The genotype data were analyzed using software for population genetic and genetic diversity analysis. Results of the analysis indicated the evaluated 16 SSR marker loci were either highly or moderately polymorphic based on their Polymorphic Information Content (PIC) values. Hence, they could be used for genetic diversity analysis of the evaluated oil palm progenies. Both the T × T and T × P progenies were more diverse than the D self-ones. Clustering and Principle Component Analysis (PCA) showed that all populations were grouped into three groups consisting of (1) B02 – T × P progenies, (2) B57 – T × T progenies, and (3) the rest of the populations (a mixture of the B01 – T × P progenies, and the three D self progenies). Moreover, the third group was further divided into five sub-groups, consisting of sub-group 3.1: the B01 progenies, and sub-group 3.2 to 3.5 comprising of a mix of individuals from members of at least two different D self progenies. All the studied T × T and T × P progenies could potentially be used as improved male parents for producing future Tenera oil palm hybrid varieties. The T x T and T × P progenies had a wider genetic distance than that of the D self progenies. Moreover, for practical breeding purposes, the members of D self oil palm progenies should not be grouped based only on the family but should be based on the results of the clustering analysis. The reported data should be beneficial for aiding future oil palm breeding in Indonesia.  

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