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INDONESIA
Journal of Tropical Biodiversity and Biotechnology
Published by Universitas Gadjah Mada
ISSN : 25409573     EISSN : 25409581     DOI : -
Core Subject : Science, Agriculture, Social,
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Environmental Science Immunology & microbiology
Journal of Tropical Biodiversity and Biotechnology (JTBB) is an authoritative source of information concerned with the advancement of tropical biology studies in the Southeast Asia Region. It publishes original scientific work related to a diverse range of fields in tropical biodiversity, functional biology, and biotechnology.
Arjuna Subject : -
Articles 20 Documents
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Search results for , issue "Vol 8, No 3 (2023): December" : 20 Documents clear
In Silico Approach for DNA Barcoding using Phylogenetic Analysis of Coelogyne spp. based on the matK, rpoC1, rbcL and nrDNA Markers Pratiwi, Apriliana; Kinasih, Anggiresti; Meidianing, Maura Indria; Kurniawan, Febri Yuda; Semiarti, Endang
Journal of Tropical Biodiversity and Biotechnology Vol 8, No 3 (2023): December
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.73130

Abstract

In silico biology is considered as an effective and applicable approach to initiate various research, such as biodiversity taxonomical conservation. Phylogenetic analysis using in silico taxonomy method for orchid species can provide data on genetic diversity and evolutionary relationships. One particular method that can be used to evaluate specific targets of gene loci in the taxonomic study is DNA barcoding. This research was conducted to determine the specific target locus gene using matK, rbcL, rpoC1, and nrDNA markers for DNA barcoding of the Coelogyne genus with in silico approach using phylogenetic analysis. All marker sequences were collected from the NCBI website and analysed using several softwares and methods, namely Clustal X for sample sequence alignment and MEGA 11 for phylogenetic tree construction and analysis. The results showed that the gene locus in Coelogyne recommended was the nrDNA gene locus. Phylogenetic analysis revealed that the use of the nrDNA gene locus was able to separate 17 Coelogyne species with two outgroup species, namely Cymbidium and Vanilla, then followed with ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) while the other gene loci, namely maturase K (matK) and polymerase beta' subunit (rpoC1) provided a visual phylogenetic tree in which the two outgroup species entered into the same clade as the Coelogyne species. Thus, the results of this study can be used as a reference to support the Coelogyne breeding and conservation program. 
The Status, Trends, and Limitations of Philippine Mollusk Production and Trade Based on Available Databases and Publications Ordinario, John Alberto H; Anticamara, Jonathan A.
Journal of Tropical Biodiversity and Biotechnology Vol 8, No 3 (2023): December
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.73325

Abstract

Mollusk trade is vital in many coastal areas and island communities throughout the Philippines because it provides livelihoods, food, and incomes to millions of Filipinos via fisheries (e.g., shellfish fishing and gleaning), shell craft, arts, shell trading and collections, and aquaculture. However, the assessments of the national trends and status of mollusc production and trade in the Philippines are largely non-existent in peer-reviewed literature. The main purpose of this paper is to present and evaluate the status and trends of traded Mollusks in the Philippines based on available online databases and a systematic review of published literature. To date, available databases on Philippine mollusk trade showed an initial increase in traded volume (the 1970s to 2006) but decreased afterward. In contrast, the traded mollusk value continued to generally increase over time (albeit the observed decrease between 2011 and 2016), indicating value increase as mollusk volume decreased. However, there is a great need to (1) resolve many of the obvious inconsistencies in data entries across all the available mollusk trade databases (BFAR, PSA, and CITES) and (2) provide field assessment of the Philippine mollusk trade and the conservation status of all traded mollusk taxa in the country. 
Advancement in Plant Tissue Culture-Based Research for Sustainable Exploitation of Well-Known Medicinal Herb Bacopa Monnieri Vinod, Abhijith; Sharma, Shivika; Sharma, Vikas
Journal of Tropical Biodiversity and Biotechnology Vol 8, No 3 (2023): December
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.74937

Abstract

The current review focuses on the plant Bacopa monnieri, one of prominent medical herbs in Indian ayurvedic system. The plant is well known for its cognitive and memory enhancing capabilities. The plant contains many useful alkaloids and secondary metabolites. Studies have shown that it has various promising pharmacological properties which have the potential to treat many illnesses and disorders such as asthma, bronchitis, rheumatism also in for renal disease, water retention, blood cleaning etc. This leads to the over exploitation of the plant which puts a stress on the naturally available stock of the plant, therefore, it becomes a necessity to find optimum methods for mass production of the plant and its important secondary metabolites. This review attempts to compile and to discuss the advancements in methods and techniques including type of culture vessels, plant growth regulators (PGRs), effect of stress, plant growth promoting rhizobacteria (PGPRs) interactions; for in vitro propagation of Bacopa monnieri and the enhanced production of its important bioactive (bacoside) for its sustainable exploitation. 
Region of Nuclear Ribosomal DNA (ITS2) and Chloroplast DNA (rbcL and trnL-F) as A Suitable DNA Barcode for Identification of Zingiber loerzingii Valeton From North Sumatera, Indonesia Prasetya, Eko; Lazuardi, Lazuardi; Harahap, Fauziyah; Rachmawati, Yuanita; Yusuf, Yusnaeni; Al Idrus, Said Iskandar; Prastowo, Puji
Journal of Tropical Biodiversity and Biotechnology Vol 8, No 3 (2023): December
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.76956

Abstract

Zingiber loerzingii Valeton is one of the species in the Zingiberaceae family found throughout Aceh and North Sumatra, Indonesia, with slimy flowers, yellowish white color, and dark orange stamens. Z. loerzingii is endemic in North Sumatra with a very limited distribution. The International Union for Conservation of Nature and Natural Resources classifies this plant into the vulnerable ones category. This study aims to examine the potential of DNA barcoding from nuclear DNA (ITS2) and DNA chloroplasts (rbcL and trnL-F) to identify Z. loerzingii plants. The research sample was obtained from two main distribution areas of Z. loerzingii in North Sumatra, Indonesia, namely Sibolangit Nature Reserve and Tangkahan Conservation Forest. The results showed that all the DNA barcode markers used were able to classify Z. loerzingii into the same group in the phylogenetic analysis. ITS marker is the most effective marker for classifying Zingiberaceae species compared to rbcL and trnL-F markers. The ITS2 marker has the lowest level of intraspecific and intraspecific genetic distance overlap compared to the rbcL and trnL-F markers. This research is expected to provide information related to the DNA barcode of Z. loerzingii in an effort to conserve this rare plant. 
Herbaceous Diversity in the Gumuk Ecosystem in Ledokombo District-Jember Regency with Varied Land Use Type Maisyaroh, Wiwin; Hakim, Luchman; Sudarto, Sudarto; Batoro, Jati
Journal of Tropical Biodiversity and Biotechnology Vol 8, No 3 (2023): December
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.77888

Abstract

Gumuk is a unique landscape in Jember Regency resulting from the eruption of Mount Raung that can provide ecosystem services through its ecological functions. Increased mining activity in Gumuk and land-use changes can lead to a decline in biodiversity and affect ecosystem services. This study aims to determine the diversity of herbaceous in the Gumuk ecosystem. Conducted in January - March 2021 in Ledokombo District, Jember Regency. The spatial distribution of Gumuk was carried out using GIS. Herbaceous sampling was carried out using 2x2 plots on three types of Gumuk utilisation, namely mixed gardens, sand mining, and stone mining. The results showed that there were 136 Gumuk in Ledokombo District. One hundred twenty herbaceous species (49 families) were found in all types of Gumuk. Mixed gardens have the highest species diversity (109 species, 49 families) compared to other types. Digitaria sanguinalis (L.) Scop. has high dominance in all types. Species dominance showed a moderate category for all types of Gumuk (D = 0.07). Community complexity in all types was in the high class (D' = 0.90) and species diversity was in the high class (H’ = 3.25). Evenness index € was different in the three types of Gumuk; in mixed gardens, the evenness of species was lower (0.23) than the other two types. 
Comparison of Light Intensity under the Canopy between Sal (Shorea robusta) and Akashmoni (Acacia auriculiformis) in Agroforestry Stands: Effect of Tree Size and Distance from Individual Trees Islam, Md. Al Forhad; Pitol, Md. Najmus Sayadat; Khan, Md. Nabiul Islam
Journal of Tropical Biodiversity and Biotechnology Vol 8, No 3 (2023): December
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.78063

Abstract

Agroforestry is now inevitable for meeting the snowballing demand for food of the growing number of people worldwide. The light environment is the most important driving force for the growth and development of crops in agroforestry stand. The present study aims to quantify the light interception in two different agroforestry types, where one was composed of Shorea robusta (Sal) with Ananas comosus and another was Acacia auriculiformis (Akashmoni) with Ananas comosus. The relative Photosynthetically Active Radiation (PAR) was measured by a pair of quantum sensors in four directions from some individual trees. Spatial variation of PAR was also explored in both stand types. The results revealed that RPAR did not significantly (P>0.05) vary among four directions of individual trees in S. robusta but the A. auriculiformis showed a significant difference (P<0.001) along the four directions. Also, RPAR was significantly different (P<0.001) at different distances from individual trees under the canopy of both tree species. When the stand-level spatial variation of RPAR was considered, A. auriculiformis (0.177) and S. robusta (0.171) showed no significant difference (P>0.05) in the light environment. Our findings explored that both the tree species would be suitable species for agroforestry practices in the area. For the betterment of the natural S. robusta forest responsible authorities should encourage people to avoid A. auriculiformis plantations near the natural S. robusta forest which will enhance the conservation of S. robusta cover in its natural habitat. 
Birds Species on Vertical Stratification of Mangrove Vegetation Nusa Lembongan, Bali Indonesia Ginantra, I Ketut; Muksin, I Ketut; Joni, Martin
Journal of Tropical Biodiversity and Biotechnology Vol 8, No 3 (2023): December
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.78394

Abstract

This study aims to determine the use of vertical stratification of mangrove vegetation by bird species in the mangrove ecosystem of Nusa Lembongan. The study was conducted at seven mangrove ecosystem sites, in April-July 2021. Observation of the number of birds in each vegetation strata was carried out using the point count method. The association of the use of vegetation strata by bird species was carried out by Detrended correspondence analysis (DCA) statistical test. The results showed that total of 32 species are found in the mangrove ecosystem of Nusa Lembongan which belong to 26 families. There is a strong association between bird species and the vertical strata of vegetation. The species of birds associated with pure mangrove vegetation are; strata I, namely Amaurornis phoenicurus (Pennant,1769), Ardea purpurea Linnaeus, 1766, Sterna bergii M.H.K.Lichtenstein, 1823, Passer domesticus (Linnaeus, 1758), and Pycnonotus aurigaster (Vieillot, 1818); strata II are Todiramphus chloris (Boddaert, 1783), Todirhamphus sanctus (Vigors and Horsfield, 1827), Alcedo coerulescens Vieillot, 1818 and Butorides striata (Linnaeus, 1758); strata III are Hypothymis azurea (Boddaert, 1783), Lanius schach Linnaeus, 1758, Merops philippinus Linnaeus, 1767, Nectarinia jugularis Linnaeus, 1766 and Gerygone sulphurea Wallace, 1864; strata IV are Collocalia linchi Horsfield & F.Moore,1854, Oriolus chinensis Linnaeus, 1766, Hirundo tahitica Gmelin,1789 and Pycnonotus goiaver (Scopoli, 1786). The bird species associated with mixed mangrove and dryland vegetation are strata I, namely species Turnix suscitator (J.F.Gmelin, 1789), Acridotheres javanicus Cabanis, 1851, Anthreptes malacensis (Scopoli, 1786), Passer domesticus (Linnaeus,1758), Pycnonotus aurigaster (Vieillot, 1818), Spilopelia chinensis (Scopoli, 1786) and Geopelia striata (Linnaeus, 1766); strata II, namely Alcedo coerulescens Vieillot, 1818, Zosterops chloris Bonaparte, 1850, Todirhamphus sanctus (Vigors and Horsfield,1827) and Todiramphus chloris (Boddaert, 1783); strata III, namely Anthreptes malacensis (Scopoli,1786), Cacomantis merulinus (Scopoli,1786), Hypothymis azurea (Boddaert,1783), Copsychus saularis (Linnaeus,1758), Nectarinia jugularis Linnaeus, 1766, Gerygone sulphurea Wallace, 1864 and Merops philippinus Linnaeus,1767; strata IV, namely Collocalia linchi Horsfield & F.Moore,1854, Hirundo tahitica Gmelin,1789 and Corvus sp. Factors influencing strata preference by birds are resources, both food and space, as well as the bioecological characteristics of the birds themselves.  
Stomata characters of sugarcane (Saccharum officinarum L.) mutants of GMP3 variety at PT Gunung Madu Plantations, Lampung, Indonesia Mahfut, Mahfut; Kendari, Putri; Syarif, Admi; Wahyuningsih, Sri; Susiyanti, Endah
Journal of Tropical Biodiversity and Biotechnology Vol 8, No 3 (2023): December
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.79860

Abstract

The induction of colchicine mutations is one method of breeding. PT Gunung Madu Plantations, for example, has induced mutations of commercial sugarcane (Saccharum officinarum L.) varieties, however, investigations on the impact of colchicine on stomatal characters have received less attention. Therefore, this study aimed to analyse the stomata character of 21 sugarcane mutants of the GMP3 variety at PT Gunung Madu Plantations, Lampung, Indonesia with a focused look at stomata aperture width, stomata length and width, number of stomata, stomatal density, and stomata index. The collected data were analysed using cluster and Principal Component Analysis (PCA) through MVSP software. This study showed that all GMP3 mutants had Graminae-type stomata. In terms of stomata length and width, the average size of the GMP3 variety mutant was greater than that of the control. The diversity of stomata characters is fairly high due to differences in stomata size between GMP3 and control mutants. With a similarity index of 0.20, the phenetic analysis of 21 mutants of the GMP3 variety revealed that the relationship between mutants and controls was getting further. A six-character principal component analysis revealed that axis I's total variation accounted for 40.54 percent of the variation and had an eigenvalue of 2.43, whereas axis II's contribution to the variation was 19.02 percent and had an eigenvalue of 1.14. The findings indicate that stomata are excellent taxonomic evidence for identifying and analysing sugarcane varieties induced by colchicine-induced breeding. 
Cobalamin and Thiamine Effect on Microalgae Biomass Production in the Glagah Consortium Setyaningrum, Tri Wahyu; Budiman, Arief; Suyono, Eko Agus
Journal of Tropical Biodiversity and Biotechnology Vol 8, No 3 (2023): December
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.81949

Abstract

The Glagah consortium is a mixed culture of various microalgae and bacteria isolated from Glagah Beach, Yogyakarta. Cobalamin and thiamine, which are given by symbiotic bacteria, are assumed will increase biomass. This study aimed to determine the effect of cobalamin and thiamine on microalgae biomass production in the Glagah consortium. The microalgae of Glagah consortium were cultivated for 10 days with vancomycin and gentamicin antibiotic as treatment and without antibiotics as a control. The parameters measured included the number of bacterial colonies, cobalamin and thiamine levels measured by LC-MS, chlorophyll a and b levels, cell density of microalgae and dry biomass. The highest level of cobalamin and thiamine was in the Glagah consortium without antibiotics. Cobalamin and thiamine increased in the exponential phase along with the increasing Staphylococcus sp. colonies. The Quantity of Staphylococcus sp. colonies in the exponential phase was 62.105 (cfu/mL). The level of cobalamin in the exponential phase was 2.33 µg/L and the level of thiamine in the exponential phase was 49.71 µg/L. The highest productivity dried weight biomass was 0.0134 g/L/day in the day-6th on the Glagah consortium without antibiotics. This result showed that microalgae and bacterial interaction was mutualism symbiosis involving cobalamin and thiamine that increased in the exponential phase along with the increasing Staphylococcus sp. colonies. This interaction was able to increase biomass microalgae.
Induction of Synthetic Polyploids of Porang (Amorphophallus muelerri Blume) and Assessment of Its Genetic Variability Using Morphological Data and RAPD Molecular Marker Suyono, Suyono; Indivia, Imey Tamara; Resmisari, Ruri Siti; Fitriyah, Fitriyah; Wahyudi, Didik
Journal of Tropical Biodiversity and Biotechnology Vol 8, No 3 (2023): December
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.82238

Abstract

This study uses morphological characteristics and RAPD markers to evaluate the polyploidization of synthetic porang. Seeds of triploid porang (2n=2x=26) were soaked in the different colchicine concentrations for 24 hours. After colchicine treatment, the porang seeds were planted to an MS medium that contained 2.2 µM of 6-benzylaminopurine (BAP), then, 40 days after planting in the MS media, the morphology and molecular of synthetic polyploid porang were characterized. For DNA extraction, a total of 100 mg of young leaves of porang plantlet was collected. One way Anova followed by the Duncan test (95%) was performed for phenotypic characterization. The number of different alleles, number of effective alleles, Shannon's information index, diversity, and unbiased diversity were assessed for genetic diversity. Synthetic polyploid porang has a higher total shoot, root, and wider leaves than normal porang. Polyploidy induction also successfully increased the genetic diversity of porang, and the genetic diversity will increase porang adaptability and sustainability of porang cultivation. 

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