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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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Isolation, lytic activity, and genomic characterization of hospital wastewater phages infecting Mycobacterium smegmatis, a surrogate for tuberculosis bacteria RINA HIDAYATI PRATIWI; RIRI NOVITA SUNARTI; ARIF NURKANTO; DASMO DASMO; HANUM ISFAENI
Biodiversitas Journal of Biological Diversity Vol. 27 No. 6 (2026)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d270613

Abstract

Abstract. Pratiwi RH, Sunarti RN, Nurkanto A, Dasmo, Isfaeni H. 2026. Isolation, lytic activity, and genomic characterization of hospital wastewater phages infecting Mycobacterium smegmatis, a surrogate for tuberculosis bacteria. Biodiversitas 27 (6): d270613. https://doi.org/10.13057/biodiv/d270613. In Indonesia, Tuberculosis (TB) remains a major public health problem, with increasing case numbers and high mortality rates. The increasing prevalence of drug-resistant tuberculosis has encouraged exploration of bacteriophages as alternative antibacterial agents. This study aimed to isolate and characterize lytic bacteriophages from hospital wastewater capable of infecting Mycobacterium smegmatis, a surrogate host commonly used in tuberculosis-related research. Wastewater samples were collected from several hospital sewage outlets in Palembang and subjected to enrichment and plaque assay screening using M. smegmatis as the host bacterium. Three lytic bacteriophage isolates, designated HS, BR, and CH, were successfully obtained and characterized based on plaque morphology, phage titers, and lytic activity. All exhibited clear, small plaques (≈1.0 mm) characteristic of lytic morphology, with titers ranging from 2.3×10⁵ to 2.9×10⁵ PFU/mL. The lytic activity assay revealed that all phages significantly reduced bacterial growth within 10 hours. The CH phage achieved the highest inhibitory effect, reducing bacterial optical density (OD600) by 21%, compared to 14% reductions by HS and BR phages. Notably, CH phage-initiated lysis as early as the first hour, indicating a short latency period and strong infectivity. These results demonstrate that hospital wastewater is a promising source of mycobacteriophages with potential therapeutic value against mycobacterial infections. Among the isolates obtained, CH showed the most promising lytic performance and genomic characteristics, suggesting its potential for further investigation in bacteriophage-based strategies against mycobacterial infections. The WGS analysis demonstrates that the isolated bacteriophage represents a TehO-like phage lineage with high genomic similarity to several Pseudomonas bacteriophages. Genome analysis of the isolated bacteriophage revealed a modular genome organization characteristic of dsDNA bacteriophages, containing structural genes, DNA replication genes, and a lysis module encoding an endolysin.
Chromosome karyotype analysis of Sapindus rarak (lerak) from Ungaran, Central Java, Indonesia ANANDA PUTRI DEWANTARI MASAILLA; ENDANG YUNIASTUTI; PARJANTO PARJANTO
Biodiversitas Journal of Biological Diversity Vol. 27 No. 6 (2026)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d270620

Abstract

Abstract. Masailla APD, Yuniastuti E, Parjanto. 2026. Chromosome karyotype analysis of Sapindus rarak (lerak) from Ungaran, Central Java, Indonesia. Biodiversitas 27 (6): d270620. https://doi.org/10.13057/biodiv/d270620. Sapindus rarak (lerak), a member of the family Sapindaceae and the soapberry group, has long been utilized as a natural cleaning agent due to its high saponin content. Despite its potential as an environmentally friendly and renewable resource, genetic information on this species remains limited. This study aimed to analyze the karyotype of S. rarak to provide fundamental cytogenetic data that can support plant breeding and conservation efforts. Two types of S. rarak, namely yellow and brown variants originating from Ungaran, Central Java, Indonesia, were used as research materials. Chromosome analysis was conducted using the squash preparation method, followed by microscopic observation and measurement of chromosome number, size, and centromere position. The data were analyzed descriptively to determine the karyotype characteristics. The results showed that both S. rarak types have the same chromosome number, 2n = 28, with chromosome sizes ranging from 0.856±0.145 to 2.487±0.222 µm. The karyotype formula was determined as 2n = 2x = 28 = 13m + 1sm, indicating a predominance of metacentric chromosomes. These findings provide essential baseline genetic information that can be used for species identification, support plant breeding programs, and contribute to the development of S. rarak as a sustainable, eco-friendly natural soap resource.
Antimicrobial activity and metabolite profiling of lactic acid bacteria isolated from solid and liquid tofu waste RYAN MOULANA; YULIA SARI ISMAIL; DEWI YUNITA; DALLYA IZLA; CUT YULVIZAR
Biodiversitas Journal of Biological Diversity Vol. 27 No. 6 (2026)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d270621

Abstract

Abstract. Moulana R, Ismail YS, Yunita D, Izla D, Yulvizar C. 2026. Antimicrobial activity and metabolite profiling of lactic acid bacteria isolated from solid and liquid tofu waste. Biodiversitas 27 (6): d270621. https://doi.org/10.13057/biodiv/d270621. The production of tofu generates two types of waste by-products: solid (tofu pulp) and liquid (tofu whey). These by-products are rich in carbohydrates and proteins, which can support the growth of lactic acid bacteria (LAB). The objective of this study was to isolate and phenotypically characterize presumptive LAB isolates from tofu waste and to evaluate their antimicrobial activity against Escherichia coli, Staphylococcus aureus, and Candida albicans. Presumptive LAB were isolated using De Man, Rogosa, and Sharpe (MRS) agar supplemented with 1% CaCO₃ and phenotypically characterized based on Gram-positive reaction, catalase-negative activity, and cocci or rod-shaped cell morphology. Antimicrobial activity was evaluated using the disc diffusion method with cell-free supernatants (CFS) as a preliminary antimicrobial screening approach. The results showed that eight presumptive LAB isolates were obtained, consisting of three isolates from solid tofu waste (LPT1-LPT3) and five from liquid tofu waste (LCT1-LCT5). LPT1 demonstrated the largest inhibition zone against S. aureus (12.77 mm; strong category), while LCT1 exhibited the largest inhibition against E. coli (7.26 mm; moderate category). However, no antifungal activity was detected against C. albicans. GC-MS metabolite profiling of isolates LPT1 and LCT1 identified 18 chemical compounds, with acetic acid detected as the dominant metabolite in both isolates. These findings indicate that LAB isolated from tofu waste may represent a potential source of antimicrobial metabolites. However, further quantitative and molecular analyses are required to clarify the contribution of specific metabolites to the observed antibacterial activity.
Genetic diversity of Olive Ridley turtles (Lepidochelys olivacea) in West and North Lombok, Indonesia AHMAD IZZUL RIFQI ANSORI; AGUS SABDONO; SUBAGIYO SUBAGIYO; NI LUH ASTRIA YUSMALINDA; NI PUTU DIAN PERTIWI; LUH PUTU CANDRA APRILIANI; NI KOMANG ROSSA SRI SAVITRI; ANDRIANUS SEMBIRING
Biodiversitas Journal of Biological Diversity Vol. 27 No. 6 (2026)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d270618

Abstract

Abstract. Ansori AIR, Sabdono A, Subagiyo, Yusmalinda NLA, Pertiwi NPD, Apriliani LPC, Savitri NKRS, Sembiring A. 2026. Genetic diversity of Olive Ridley turtles (Lepidochelys olivacea) in West and North Lombok, Indonesia. Biodiversitas 27 (6): d270618. https://doi.org/10.13057/biodiv/d270618. The Olive Ridley turtle (Lepidochelys olivacea) is a globally distributed species playing a vital ecological role but remains classified as Vulnerable due to anthropogenic threats. This study investigates the genetic diversity and population structure of L. olivacea in West and North Lombok, Indonesia, using mitochondrial control region analysis. Previous genetic studies on this species in Indonesia have been limited to populations in Bali, making this the first report on Lombok populations. As the first genetic study of this species in Lombok, it aims to provide essential data to support evidence-based conservation and sustainable management strategies in the region. A total of 24 tissue samples were collected and analyzed with mitochondrial DNA in the control region (mtDNA CR) amplified using the PCR method, sequencing, and bioinformatic tools including Basic Local Alignment Search Tool (BLAST), Molecular Evolutionary Genetics Analysis version 11 (MEGA11), and DnaSP. All sequences showed high similarity (99.30%-100%) with L. olivacea reference sequences in GenBank. Phylogenetic analysis revealed that all samples clustered within the same global L. olivacea clade, consistent with conspecific classification. However, within this clade, the Lombok population exhibited notably low genetic diversity (Hd = 0.500) and moderate genetic structuring (FST = 0.27390), indicating limited gene flow and potential local isolation. These findings underscore the need for region-based conservation strategies that incorporate genetic data to maintain the adaptive potential and long-term viability of L. olivacea populations in Indonesia.
Microbial diversity of bacterial cellulose starter culture revealed by 16S rRNA gene amplicon sequencing ALEYDA NUR HALIZAH WAHYUDI; TRI ARDYATI; ARIE SRIHARDYASTUTIE
Biodiversitas Journal of Biological Diversity Vol. 27 No. 6 (2026)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d270614

Abstract

Abstract. Wahyudi ANH, Ardyati T, Srihardyastutie A. 2026. Microbial diversity of bacterial cellulose starter culture revealed by 16S rRNA gene amplicon sequencing. Biodiversitas 27 (6): d270614. https://doi.org/10.13057/biodiv/d270614. Bacterial Cellulose (BC) is a biopolymer produced through microbial fermentation and widely applied in food, biomedical, and industrial fields. The performance of BC production is strongly influenced by the microbial composition of the starter culture. However, detailed information on the bacterial community structure of BC starter remains limited due to the constraints of culture-dependent methods. The aim of this research is to characterize the bacterial diversity and community composition of a BC starter culture using 16S rRNA gene amplicon sequencing and to complement the molecular data with culture-based enumeration. The starter culture was rejuvenated in coconut water medium and incubated at 30°C for 14 days. Cultivable bacteria capable of growing on Hestrin-Schramm medium were quantified using total plate count, yielding a population of (1.91±0.16) × 10⁹ CFU/mL. Amplicon sequencing analysis revealed a bacterial community with high richness but low evenness, characterized by strong taxonomic dominance. A total of 349 observed taxa were detected, with Firmicutes representing the dominant phylum (94.6%). At the genus level, Lentilactobacillus accounted for 86.9% of the relative abundance, while Lentilactobacillus parafarraginis was identified as the most abundant species (87%). These findings indicate that the BC starter culture analyzed in this research was dominated by lactic acid bacteria, particularly Lentilactobacillus. This pattern may suggest a possible role of Lentilactobacillus spp. in shaping the fermentation environment. The results provide a descriptive baseline for understanding the microbial ecology of BC starter culture to clarify the ecological significance of the dominant taxa.
Quantitative and qualitative morphological diversity among nine cherry tomato (Solanum lycopersicum) genotypes grown under lowland conditions ZULFIKAR DAMARALAM SAHID; ABDUL QADIR; MUHAMAD SYUKUR; KHARISMA FIRMAN ARIYANTO; ALDI KAMAL WIJAYA; PUNJUNG MEDARAJI SUWARNO; HENNY RUSMIYATI; ANDI NADIA NURUL LATHIFA HATTA
Biodiversitas Journal of Biological Diversity Vol. 27 No. 6 (2026)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d270622

Abstract

Abstract. Sahid ZD, Qadir A, Syukur M, Ariyanto KF, Wijaya AK, Suwarno PM, Rusmiyati H, Hatta ANNL. 2026. Quantitative and qualitative morphological diversity among nine cherry tomato (Solanum lycopersicum) genotypes grown under lowland conditions. Biodiversitas 27 (6): d270622. https://doi.org/10.13057/biodiv/d270622. Cherry tomatoes are a type of tomato that has seen increasing market demand post-global pandemic as a healthy fruit. Cherry tomato cultivation is generally carried out in highlands and faces competition from other vegetable cultivation. Therefore, developing cherry tomato varieties adapted to lowland conditions is necessary. Developing new superior varieties requires basic information for selecting the diversity of the parents used. Therefore, this study aims to evaluate the morphological diversity of Institut Pertanian Bogor (IPB) cherry tomato lines as cross-breeding parents in further studies. The study was conducted at the lowland greenhouse teaching factory of the vocational school, Institut Pertanian Bogor, Bogor, using automated irrigation and fertigation systems and a single-factor randomized complete block design. The results of this study indicate that there is diversity among nine Institut Pertanian Bogor cherry tomato lines (hybrid and non-hybrid lines) that have the potential to be used as parents in the development of new superior varieties. The seed germination percentage measured in this study varied (80-95%), with early flowering and harvest times (26 and 62 days after transplanting). The average fruit length, diameter, and weight (3.28 cm, 19.24 mm, and 7.23 g) measured in this study showed a vast morphological divergence, making them potential parent lines in cherry tomato breeding. Cluster analysis of nine genotypes based on their morphological characteristics resulted in three main groups, from which parents for breeding were selected. IPBTC 147 forms a distinct group due to its unique morphological characteristics, both quantitative and qualitative, which significantly differ from other genotypes, particularly in its fruit shape and color. This genotype has an average fruit weight of 5 g with the longest fruit stalk length (2.27 cm). The yellow color of this fruit has the potential to produce high diversity in the F2 when crossed with red fruit color. The morphological performance information of this research is expected to serve as a consideration for selecting parents for the development of cherry tomatoes adapted to lowlands.
Isolation and cellulolytic activity of bacteria from beef cattle feces using rice straw as enrichment substrate EULIS TANTI MARLINA; YULI ASTUTI HIDAYATI; ELLIN HARLIA; YASIN PRADANA MAULANA; GINA CHYNTHIA KAMARUDIN PUTERI
Biodiversitas Journal of Biological Diversity Vol. 27 No. 6 (2026)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d270617

Abstract

Abstract. Marlina ET, Hidayati YA, Harlia E, Maulana YP, Puteri GCK. 2026. Isolation and cellulolytic activity of bacteria from beef cattle feces using rice straw as enrichment substrate. Biodiversitas 27 (6): d270617. https://doi.org/10.13057/biodiv/d270617. Beef cattle (Bos indicus/taurus) feces contain diverse microbial communities with potential roles in lignocellulosic biomass transformation. This study aimed to evaluate the initial decomposition of rice straw and beef cattle feces, using this information as a basis for isolating and preliminarily identifying cellulolytic bacteria from beef cattle waste. Rice straw was mixed with beef cattle feces to initiate decomposition for 7 days. Changes in chemical composition and structure were assessed using fiber fraction analysis and Scanning Electron Microscopy (SEM). The addition of cattle feces reduced Acid Detergent Fiber (ADF) from 51.36% to 42.31%, Neutral Detergent Fiber (NDF) from 72.08% to 60.82%, lignin from 12.89% to 7.40%, cellulose from 38.47% to 34.91%, and hemicellulose from 20.72% to 18.51%. SEM showed increased surface roughness and fiber degradation (loosening and fragmentation), with structural changes that can be attributed to microbial activity. Based on this finding, microbial enrichment was carried out with cattle feces and rice straw, with the addition of molasses as a nutrient source for microbial growth. Seven bacterial isolates were obtained, among which three (LS-6, LS-11 and LS-14) exhibited the highest cellulolytic activity on Carboxy-Methyl Cellulose (CMC) agar and  dinitrosalicylic acid (DNS). Molecular level identification of these isolates through 16S rRNA gene sequence revealed that these isolates were closely affiliated with Bacillus safensis and Bacillus pumilus group. The results suggest that the isolates exhibit cellulolytic activity under the test conditions and may contribute to lignocellulose degradation. This study provides a first step for further research on cellulolytic bacteria from beef cattle feces for the effective use of lignocellulosic biomass.
Isolation and in vitro antagonistic activity of indigenous rhizosphere Trichoderma against Colletotrichum cf. musae causing banana anthracnose NGUYEN TRUNG TRUC; KHOA DANG DANG; QUACH VAN CAO THI; NGUYEN LE YEN NHI; NGUYEN MINH TRONG; LE VAN UT
Biodiversitas Journal of Biological Diversity Vol. 27 No. 5 (2026)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d270534

Abstract

Abstract. Truc NT, Dang KD, Thi QVC, Nhi NLY, Trong NM, Ut LV. 2026. Isolation and in vitro antagonistic activity of indigenous rhizosphere Trichoderma against Colletotrichum cf. musae causing banana anthracnose. Biodiversitas 27 (5): d270534. https://doi.org/10.13057/biodiv/d270534. Banana is a high-yielding and economically important export crop. However, anthracnose caused by Colletotrichum spp. is a causative agent that reduces fruit quality and shelf life. Trichoderma is known for its antagonistic activity against a wide range of plant pathogens, including Colletotrichum species. The aim of the present study was to isolate Trichoderma isolates from rhizosphere soil samples and to evaluate their antagonistic activity against Colletotrichum sp. In the present study, ten Colletotrichum isolates were obtained and identified from banana fruits showing anthracnose symptoms. Among them, isolate C12.1 was the most frequently isolated and identified as Colletotrichum cf. musae. Trichoderma species were isolated from 15 rhizosphere soil samples of banana plants. The results showed that a total of 16 Trichoderma isolates were isolated from 15 soil samples from banana plants collected from different areas in Vinh Long Province. All Trichoderma isolates exhibited strong antagonistic activity against Colletotrichum sp. Notably, isolates TC1, TC2, TC5, TC9, TC10, and TC11 demonstrated the highest in vitro inhibition of mycelial growth, ranging from 80.61% to 87.88%. Among these, isolate TC5, which exhibited both strong inhibitory activity (87.88%) and significant extracellular enzyme production, was selected for PCR amplification and sequencing of the internal transcribed spacer (ITS) region. Isolate TC5 was likely the closest relative to Trichoderma hamatum and was identified as T. hamatum. In addition, six selected Trichoderma isolates were qualitatively assessed for extracellular enzyme production. All tested isolates were positive for cellulase, amylase, β-1,3-glucanase, and chitinase. The production of these enzymes highlights their role in mycoparasitism and supports the potential of Trichoderma isolates as effective biocontrol agents. Although the findings demonstrate promising antagonistic potential, the results are currently limited to in vitro assays and qualitative enzyme detection. Therefore, further studies under in vivo conditions are required to validate their efficacy before practical field application.
Growth-response variation among selected coliform isolates under antibiotic stress in the Brantas River, East Java, Indonesia RIDWAN MUHAMAD RIFAI; CAMAR AMERIL; BAKHRUL MUKHID FADILAH RAMADANI; LUTHFIYA ANNAILAH; ANIE YULISTYORINI
Biodiversitas Journal of Biological Diversity Vol. 27 No. 6 (2026)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d270615

Abstract

Abstract. Rifai RM, Ameril C, Ramadani BMF, Annailah L, Yulistyorini A. 2026. Growth-response variation among selected coliform isolates under antibiotic stress in the Brantas River, East Java, Indonesia. Biodiversitas 27 (6): d270615. https://doi.org/10.13057/biodiv/d270615. Domestic wastewater inputs can influence microbial diversity and Anti-Microbial Resistance (AMR) in river systems. However, growth-response diversity among AMR-related coliform isolates remains poorly characterized. This is particularly relevant in the upper Brantas, where millions of people live in its watershed. Most previous assessments have focused on endpoint susceptibility profiles, while temporal growth responses under increasing antibiotic exposure remain less explored. In this study, coliform bacteria were isolated from a single densely populated riverbank site in the upper Brantas River. Selected isolates were tentatively identified as Escherichia coli, Klebsiella aerogenes, Klebsiella variicola, and Klebsiella pneumoniae. All Klebsiella isolates were resistant to amoxicillin, and K. aerogenes also showed resistance to tetracycline. We performed growth assays using antibiotic levels based on the Clinical and Laboratory Standards Institute (CLSI) breakpoints. Klebsiella aerogenes maintained growth up to 4× CLSI breakpoint. At the same time, K. variicola and K. pneumoniae grew more slowly and showed biphasic patterns, whereas E. coli was entirely suppressed. These findings remind us that even isolates from the same river site and with similar susceptibility classifications can respond differently when exposed to antibiotics. Growth-response profiling adds valuable insights beyond standard susceptibility tests and can help us better understand the phenotypic diversity within environmental AMR reservoirs. To deepen our understanding, future research should include larger collections of isolates, samples from multiple locations, and molecular studies to uncover the mechanisms behind these varied responses.

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