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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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Non-synonymous Single Nucleotide Polymorphism on TLR1A gene as a candidate for immune function of Indonesian indigenous chicken HENI INDRIJANI; NENA HILMIA; ASEP ANANG; MUHAMAD SYAHID PANJI PANGESTU
Biodiversitas Journal of Biological Diversity Vol. 25 No. 6 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d250612

Abstract

Abstract. Indrijani H, Hilmia N, Anang A, Pangestu MSP. 2024. Non-synonymous Single Nucleotide Polymorphism on TLR1A gene as a candidate for immune function of Indonesian indigenous chicken. Biodiversitas 25: 2434-2441. TLR1A is a candidate gene related to the immune system in chickens, which contributes to disease resilience, which could impact their productivity. This study aimed to determine mutations in the TLR1A gene in three indigenous Indonesian chickens namely, Pelung, Black Kedu and Sentul. A total of 127 DNA samples were used and consisted of 38, 41 and 48 respectively for Pelung, Black Kedu and Sentul chickens. DNA was isolated from white blood cells and amplification of TLR1A gene was conducted in part of exon 4 using PCR with specific primer. The sequencing results for the TLR1A gene were analyzed to identify mutations using the BioEdit and MEGA X programs. The results showed genetic polymorphisms in the TLR1A gene in Indonesian indigenous chicken. One synonymous mutation, g.710C>T, in which amino acid coded leusine at 207th, and four non-synonymous mutation, i.e., g.822A>G, altered amino acids coding from threonine to alanine (T245A), g.835C>T, which altered amino acids coding 249th from threonine to methionine (T249M), g.1015G>A that altered amino acids coding 309th from serine to aspargine (S309N) and g.1165T>G that changed amino acid from arginine to proline R359P. All mutation frequencies for the alleles are lower than those for the non-mutation alleles. The non-synonymous mutation of the TLR1A gene might alter the metabolism of this hormone related to the immune system in chickens.
Potency of tubers and rhizomes of Java local foods as prebiotics and their effects toward bacterial diversity in mice cecum YUDHA WASKITA; ARTINI PANGASTUTI; SHANTI LISTYAWATI; SITI LUSI ARUM SARI
Biodiversitas Journal of Biological Diversity Vol. 25 No. 4 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d250423

Abstract

Abstract. Waskita Y, Pangastuti A, Listyawati S, Sari SLA. 2024. Potency of tubers and rhizomes of java local foods as prebiotics and their effects toward bacterial diversity in mice cecum. Biodiversitas 25: 1544-1553. Tubers and rhizomes (TR) as Java local foods were less attention by people. Local foods contain IP (indigestible polysaccharides) content as prebiotic. The study aimed to analysis the prebiotic potency of TR extracts based on IP content and their effects toward increasing probiotic bacterial number, the TR extracts toward short-chain fatty acid (SCFA) profiles in probiotic media, and the TR extracts toward SCFA profiles and bacterial diversity in mice cecum. Tubers used were purple yam (Dioscorea alata var. purpurea), air potato (D. bulbifera), porang (Amorphophallus muelleri), Asiatic yam (D. esculenta), Asiatic bitter yam (D. hispida), white spot giant arum (A. paeoniifolius), yam bean (Pachyrizus erosus), and Hausa potato (Coleus rotundifolius). Rhizomes used were taro (Colocasia esculenta), arrowroot (Maranta arundinacea), and canna lilly (Canna indica). Work steps were extraction of TR, DNS assay, total sugar assay after acidic and enzymatic digestion, stimulation on increasing probiotic bacterial number (Lactobacillus plantarum and Bifidobacterium bifidum), SCFA production of probiotics, mice treatment, SCFA extraction in cecum, and determination of cecum bacterial communities. The highest IP contents were arrowroot, purple yam, air potato, porang, Asiatic yam, and taro extracts. These extracts except taro have higher IP content than inulin. The highest increasing probiotic bacterial number and SCFA production were shown by arrowroot extract rather than purple yam, air potato, and inulin. Bacteria communities had a high diversity value that showed micro-ecosystem balance in the cecum. Arrowroot was the same with inulin in increasing probiotics SCFA producers (Lachnospiraceae NK4A136, [Ruminococcus], Lactobacillus, Bacteroides, and Bifidobacterium) and decreasing pathogenic bacteria (Lachnoclostridium, Helicobacter, and Lawsonia) in mice cecum compared with control feed. Mucispirillum as a pathobiont-commensal had the same abundance in three feed treatments. Bacteria fermentation in the cecum produced the highest SCFA concentration in the 5% arrowroot feed treatment. Arrowroot had better prebiotic potency for the future.
The role of VDR and TNF gene polymorphism in cytokine regulation in type I diabetes mellitus of the Uzbek population, Samarkand, Uzbekistan FARIZA RAYIMOVA; GAVHAR DUSHANOVA; BEGALI ALIKULOV; ZAYNITDIN KAMALOV; MALIKA RUZIBAKIEVA; FARANGIZ NABIYEVA; ASATILLO RAJABOV
Biodiversitas Journal of Biological Diversity Vol. 25 No. 3 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d250349

Abstract

Abstract. Rayimova F, Dushanova G, Alikulov B, Kamalov Z, Ruzibakieva M, Nabiyeva F, Rajabov A. 2024. The role of VDR and TNF gene polymorphism in cytokine regulation in type I diabetes mellitus of the Uzbek population, Samarkand, Uzbekistan. Biodiversitas 25: 1329-1336. After 2000, diabetes became one of the most common diseases in the world. Special attention is paid to the research to determine the variability of genetic processes in patients in the origin and development of this disease. The article is devoted to the study of the connection between the polymorphism of genotypes GG, GA, AA polymorphism BsmI of the VDR- (Vitamin D receptor) gene and GG, GA of the TNF-A-308G/A- (Tumor necrosis factor A) gene with the regulation of cytokines TNF? and IL6-Interleykin 6 in sick and healthy individuals of the Samarkand region of the Uzbek population. The analysis of the BsmI polymorphism of the VDR gene and TNF-A-308G/A indicates the involvement of certain genotypes in the Type 1 Diabetes Mellitus (T1DM) pathogenesis. The age of onset of the disease in the studied population is from 7 years, but the increase in the incidence of diseases begins from 10 years. Type 1 diabetes is more common in females. Studies of the relationship between the cytokines TNF? and IL6 show their high content depending on the genotypes GG, GA, and AA of the BsmIA polymorphism of the VDR gene and the genotypes GG and GA of the gene. TNF-A-308G/A. However, the highest rates were recorded in individuals with the AA genotype of the BsmI polymorphism of the VDR gene. The obtained results can serve as fundamental knowledge in revealing and explaining the mechanisms of cytokinin control in people with diabetes in different populations of the same nation.
Bacterial diversity in different growing mediums of oil palm seedlings associated with potassium use efficiency SRI WENING; RETNO DIAH SETIOWATI; DIAN RAHMA PRATIWI; IKHWAN FADLI PANGARIBUAN; EKO NOVIANDI GINTING
Biodiversitas Journal of Biological Diversity Vol. 25 No. 8 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d250809

Abstract

Abstract. Wening S, Setiowati RD, Pratiwi DR, Pangaribuan IF, Ginting EN. Bacterial diversity in different growing mediums of oil palm seedlings associated with potassium use efficiency. Biodiversitas 25: 3386-3393. Plant genotype, environmental conditions, and agronomical practices influence nutrient use efficiency. Understanding whether specific microbial communities support the nutrient use efficiency of specific genotypes is very important. This study aimed to understand the bacterial diversity in three different growing mediums of oil palm seedlings with potassium-use efficient characters. The three kinds of medium were medium 1 (sandy soil, recommended dose of fertilizer except for potassium (75% of a recommended dose of potassium)); medium 2 (sandy soil, recommended dose of fertilizer except for potassium (0% of potassium)); and medium 3 (topsoil, recommended dose of fertilizer at five months after planting). A metagenomic approach was conducted using a long-read sequencing platform, allowing the full-length 16S rRNA gene to be sequenced. The alpha diversity analysis showed that medium 3 had the most identified species, while medium 2 had the lowest. Based on the relative abundance, Lactobacillus helveticus was the most abundant species, and Lactobacillus was the most abundant genus in medium 1. Ralstonia pickettii was the most abundant species, and Dyella was the most abundant genus in medium 2. For medium 3, Chujaibacter soli was the most abundant species that dominated the bacteria community, and Lactobacillus was the most abundant genus. These findings were related to the bacteria's function in the respective medium for plant nutrient uptake or utilization. The number of shared species between medium 1 and medium 3 was the highest compared to other medium compositions. It suggested the specific relationship of the potassium-use efficient seedling with the characteristic of the growing medium and the most abundant species or genus of bacteria found. Further research is needed to understand the interactions and influences of bacteria and other microorganisms in the mediums, and the specific genus or species found in potassium-use efficient oil palm seedling mediums.
Novel exploration of the presence and morphological features Spirometra (Cestoda: Diphyllobothriidae) in Javan spitting cobra snakes (Naja sputatrix) in Sidoarjo, Indonesia RYANKA EDILA; MUSTOFA HELMI EFFENDI; LUCIA TRI SUWANTI; HYUCK-KEUN KWON; NNABUIFE BERNARD AGUMAH
Biodiversitas Journal of Biological Diversity Vol. 25 No. 8 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d250803

Abstract

Abstract. Edila R, Effendi MH, Suwanti LT, Kwon H-K, Agumah NB. 2024. Novel exploration of the presence and morphological features Spirometra (Cestoda: Diphyllobothriidae) in Javan spitting cobra snakes (Naja sputatrix) in Sidoarjo, Indonesia. Biodiversitas 25: 3318-3324. The study aimed to investigate the presence of spargana infection and provide a detailed description of the morphology, morphometry and histology in Javan spitting cobra snakes (Naja sputatrix Boie 1827) from Sidoarjo, Indonesia. Ethical approval was obtained and 51 living wild-caught N. sputatrix were collected from local sellers. All samples were euthanized and observed for the presence of plerocercoid. Identification of the plerocercoid as the larval infective stage was made using a carmine staining method drawn by using a camera lucida and routine histological study using hematoxylin-eosin staining. The positive rate of snakes in this study was 54.9%. A total of 165 spargana were collected which divided 82(49.6%) infecting muscles, 31 (16.7%) in viscera and 52 (31.5%) located in subcutaneous tissues. The plerocercoid length and width were 50-95 mm and 1.42-1.81 mm. Morphological analysis confirmed Spirometra characteristics and histological sections provided insights into spargana's structural complexity. This study represents the first detailed exploration of the morphological features, morphometry, and histology of Spirometra plerocercoids in Indonesia. The high prevalence of spargana in N. sputatrix underscores the importance of improving epidemiological databases, stringent wildlife trade regulations, and awareness programs to prevent sparganosis in Indonesia.
Health status of coral reef at Moramo Bay Marine Conservation Area, Southeast Sulawesi, Indonesia DEDY OETAMA; LUCHMAN HAKIM; TRI D. LELONO; MUHAMMAD MUSA
Biodiversitas Journal of Biological Diversity Vol. 25 No. 4 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d250413

Abstract

Abstract. Oetama D, Hakim L, Lelono TD, Musa M. 2024. Health status of coral reef at Moramo Bay Marine Conservation Area, Southeast Sulawesi, Indonesia. Biodiversitas 25: 1454-1464. Moramo Bay is one of the regional Marine Conservation Areas (MCA) in Indonesia which is categorized as a Marine Tourism Park based on the Decree of the Minister of Maritime Affairs and Fisheries of the Republic of Indonesia Number 22 of 2021. This bay is located in Southeast Sulawesi Province and has an area of 21,902.34 ha, consisting of a core zone, limited-use zone, and other zones. The ecosystems found in Moramo Bay include coral reefs, mangroves, and seagrass. The coral reef ecosystem in this area covers 2,528.19 ha with good visual conditions of the reef. The present study aims to provide detailed information concerning the condition of live hard corals and reef fishes, including abundance, diversity, evenness, dominance, and water quality by using point intercept transect (PIT) and underwater visual census (UVC) methods. The study was carried out at 7-10 meters of seawater depth in May-October 2023, focusing on both the core and limited-use zones and consisting of three study stages: field observation, data collection, and data analysis. Data collection covered identifying coral growth through literature study before performing descriptive analysis. The study revealed the percentage of live hard coral cover of 53%, referred to as a good category, and other variable percentages including dead coral (4%), dead coral with algae (9%), soft coral (4%), fleshy seaweed (1%), rubble (17%), sand (8%), silt (1% ) and sponge (2%). Furthermore, 25 families of reef fishes were found, belonging to 48 genera, 102 species, and 2,364 individuals, with an ecological index of abundance of 1.05 ind.m-2, diversity (2.86), evenness (0.83), and dominance (0.10). The coral reef health data issued by the present study implies that Moramo Bay MCA may be preserved as an alternative area for coral reef studies associated with global issues, for instance, climate changes. Protecting and increasing the sustainability of coral reefs is an absolute entity that must be considered by a local government.
Local community perceptions on the conservation of hornbill (Family Bucerotidae) in West Kalimantan, Indonesia FIRMAN H. KURNIAWAN; RIKI RAHMANSYAH; ARYF RAHMAN; HARDIYANTI HARDIYANTI; JIMMI KURNIAWAN; INDEKA D. PUTRA; YOKYOK HADIPRAKARSA
Biodiversitas Journal of Biological Diversity Vol. 25 No. 4 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d250440

Abstract

Abstract. Kurniawan FH, Rahmansyah R, Rahman A, Hardiyanti, Kurniawan J, Putra ID, Hadiprakarsa Y. 2024. Local community perceptions on the conservation of hornbill (Family Bucerotidae) in West Kalimantan, Indonesia. Biodiversitas 25: 1702-1710. Effective wildlife conservation strategies must consider local community perceptions to develop effective actions. This study explored community attitudes toward hornbill conservation in West Kalimantan, Indonesia. Between November 2018 and August 2019, we interviewed 513 respondents in ten villages in Kapuas Hulu District, West Kalimantan Province, Indonesia. We collected data on respondent’s demographics, socioeconomic status, human-forest interactions, animal hunting trends, knowledge of hornbill, hornbill hunting, and hornbill-cultural knowledge. Most respondents were Dayak, relying on the forest for farming and harvesting for subsistence and commercial purposes. Seven out of eight Kalimantan hornbill species are targeted for hunting, with Helmeted hornbills being the most targeted species (80%) in the past five years. In addition, 12% of respondents reported hunting hornbills for food. Our result suggests that hunting is related to socioeconomic conditions, given that a significant proportion of respondents had no steady income (56%) and limited economic resources as farmers (38%), and a significant portion was unemployed (46%). A decline in the cultural value of hornbills was also recorded, with 61% of respondents did not know about it. The respondents who know, generally only understand the hornbill utilization in the traditional ornament matter and lost the sacred value. Additionally, in this study, cultural narratives were successfully recorded by some older respondents who were aware of the cultural value of hornbills from age >55 years old (27%). Hornbill ecotourism is suggested to enhance and fortify the socioeconomic well-being of sustainable conservation practices and mitigate the unsustainable use of hornbill. To enhance public awareness, we suggest conducting conservation education activities and awareness campaigns targeted at individuals within the age <35 years old, where a majority of respondents at these ages (45%) are unaware of the cultural value of hornbills. A community-based hornbill monitoring program is also recommended to raise public awareness, although funding for this aspect is currently very limited.
Production and diversity analysis of cellulases from Anoxybacillus genus RAHMAT EKO SANJAYA; NI NYOMAN TRI PUSPANINGSIH; ALI ROHMAN; HAKIKI RAHMASARI; ROSLI MD. ILLIAS; NAWEE JANTARIT; KAZUHITO FUJIYAMA; ANDRE PRATAMA; FATIHA KHAIRUNNISA
Biodiversitas Journal of Biological Diversity Vol. 25 No. 6 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d250641

Abstract

Abstract. Sanjaya RE, Puspaningsih NNT, Rohman A, Rahmasari H, Illias RM, Jantarit N, Fujiyama K, Pratama A, Khairunnisa F. 2024. Production and diversity analysis of cellulases from Anoxybacillus genus. Biodiversitas 25: 2705-2718. Bioconversion of cellulose into sustainable renewable resources of oligosaccharides and glucose requires cellulase action. Genomic sequences of Anoxybacillus cellulases are available in GenBank databases, but no information about their biochemical properties. Anoxybacillus flavithermus TP-01 is a thermophilic, facultatively anaerobic, cellulase-producing bacterium isolated from the mountain of Gunung Pancar hot springs, Bogor, Indonesia. This study aimed to characterize the cellulase produced by Anoxybacillus flavithermus TP-01, a local Indonesian isolate. This cellulase was characterized and the diversity analysis on biochemical properties and structural characteristics was done by in silico approaches. SOPMA, SWISS-MODEL, I-TASSER, ProSA, and SAVES were used for computational analysis on physicochemical characterization, phylogenetic construction, functional analysis, multiple sequence alignment, and secondary-tertiary structure prediction. Physicochemical analysis showed pI<7, indicating acidic property for these proteins. Furthermore, the proteins were thermostable and hydrophilic, as proved by their relatively high aliphatic index and negative GRAVY values. The five sequence motifs harbored a conserved domain of the M42 peptidase/endoglucanase family. Alpha helix was the predominant secondary structure, and the tertiary structure fulfilled the structural quality criteria of QMEAN4, ERRAT, Ramachandran plot, and Z-score. Structural comparison between the template structure and the models revealed significant differences in the loop sections. This study identified a potentially thermostable cellulase of Anoxybacillus flavithermus TP-01, and provided new insights of the physicochemical, functional, and explores the structure-function relationship of cellulase from Anoxybacillus genus based on in silico data.
Sexual dimorphism phenomenon of first record Macrobrachium lar (Fabricius, 1978) from the southern Sukabumi, West Java, Indonesia RISKA RISMAWATI; MAJARIANA KRISANTI; ACHMAD FARAJALLAH
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/d250509

Abstract

Abstract. Rismawati R, Krisanti M, Farajallah A. 2024. Sexual dimorphism phenomenon of first record Macrobrachium lar (Fabricius, 1978) from the southern Sukabumi, West Java, Indonesia. Biodiversitas 25: 1929-1937. Macrobrachium lar (Fabricius, 1798), commonly known as monkey river prawn, is a widely distributed amphidromous species found in various freshwater habitat, displaying adaptability to different salinities. This habitat diversity often leads to the emergence of cryptic species, particularly in freshwater shrimp. Notably, M. lar exhibits sexual dimorphism. The degree of sexual dimorphism can differ among decapod crustaceans. This study reports the first discovery of M. lar in Sukabumi, West Java, collected in January 2023 from a river tributary in the Cibitung Sub-district with insights into the sexual dimorphism phenomenon. We conducted species confirmation through molecular analyses. We use the Cytochrome Oxidase subunit 1 (COI) gene fragment for molecular analysis. Phylogenetic tree values revealed that the samples we found proved to be M. lar, forming a group with M. lar from the Indian-West Pacific region and M. lar from Pangandaran. However, they were distinct from the outgroups M. idae and M. Lepidactyloides. In this study, we only use the adult sample, which is already well-developed. Morphological analysis indicated that all morphological characters in males were larger than in females, with significant sexual dimorphism observed in the second pereiopod and its parts (ischium, merus, carpus, and palm). Although the body sizes of males and females are significantly different in a positive direction, the most distinguishing feature facilitating the identification of both as the same species is the pattern on the second pereiopod, which has irregular blotches of brownish coloration.
Leaf beetle Phyllotreta striolata (Coleoptera: Chrysomelidae): Biology and infestation on Chinese flowering cabbage Brassica rapa var. parachinensis in Bogor, West Java, Indonesia DIAN AGUNG SANORA LAIA; NINA MARYANA; I WAYAN WINASA
Biodiversitas Journal of Biological Diversity Vol. 25 No. 7 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d250731

Abstract

Abstract. Laia DAS, Maryana N, Winasa IW. 2024. Leaf beetle Phyllotreta striolata (Coleoptera: Chrysomelidae): Biology and infestation on Chinese flowering cabbage Brassica rapa var. parachinensis in Bogor, West Java, Indonesia. Biodiversitas 25: 3099-3105. Chinese flowering cabbage (Brassica rapa var. parachinensis L.) holds significant economic value and provides essential nutrition. Bogor District, a primary region for vegetable production in Indonesia, faces a severe issue due to the leaf beetle Phyllotreta striolata Fabricius 1803 infestation on Chinese flowering cabbage plants. However, research on this pest in Indonesia is still limited. Observations on the biological aspects of P. striolata involved collecting and identifying adult P. striolata from Chinese flowering cabbage fields, along with biological observations focusing on the beetle's morphology and developmental stages. Population calculations of adult beetles and evaluation of P. striolata infestation intensity on Chinese flowering cabbage plants were conducted in four sub-districts in Bogor District. The average life cycle of this beetle was 27.15 days. The study revealed that the adult stage lasted an average of 119.10 days, with an average preoviposition period of 3.08 days. Adult populations tended to decrease with the age of Chinese flowering cabbage plants due to environmental factors and food source availability. Infestation intensity varied across locations, with Leuwimalang showing the lowest intensity (23.56%) and Laladon the highest (48.76%). These differences suggest that the environment in Leuwimalang may support the resistance of Chinese flowering cabbage plants to leaf pest attacks.

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