bluuebunny/crossref_metadata_2025 huggingface dataset:
Bacterial diversity in cheese wastewater using Next-Generation Sequencing (NGS)
Authors: ESTIKOMAH SOLIKAH ANA , SURANTO SURANTO , SUSILOWATI ARI , MASYKURI MOHAMMAD
Published: May 2024

Abstract. Estikomah SA, Suranto, Susilowati A, Masykuri M. 2024. Bacterial diversity in cheese wastewater using Next-Generation Sequencing (NGS). Biodiversitas 25: 482-490. Cheese wastewater (whey) has a high content of organic substances, including lactose, protein, and fat. The lactose in whey wastewater can also be used as a bacterial growth medium. Bacterial community structure is an essential aspect of microbial water quality. The bacterial diversity data obtained can then be used to evaluate the existence of bacteria that might be useful for making microbiological products. This research employs Next Generation Sequencing (NGS) technology to determine the diversity and abundance of bacteria based on 16S rRNA gene amplicons for further processing of whey wastewater. The NGS-based technique overcomes the limitations of conventional bacterial culture techniques. The effectiveness and accuracy of microbial diversity analysis employing NGS technology are high. The research method includes the steps of sample preparation, DNA extraction using a ZymoBIOMICS DNA Microprep Kit (D4300), PCR amplification of the V3-V4 16S rRNA gene region, DNA sequencing, and a bioinformatics-statistical analysis. The results show that bacterial diversity in whey wastewater was found to have an average number of Operational Taxon Units (OTUs) of 259 tags. The metagenomics study of the microbial community in whey wastewater successfully detected the dominant genus of bacteria, which can benefit the management of whey wastewater. The presence of Lactobacillus and Acetobacter confirms that cheese whey wastewater exists in Yogyakarta Province. Acetobacter can oxidize ethanol to produce acetic acid, a pungent odor characteristic that causes environmental pollution. On the other hand, the presence of Lactobacillus and Acetobacter shows that whey wastewater can be reprocessed to produce fermented beverages, thereby improving their value and minimizing the impact of environmental pollution.
Osmoregulation pattern, condition factor, and gonadal maturity level of sea urchins in the various ecosystems of Panjang Island, Jepara, Indonesia
Authors: SURYANTI SURYANTI , ANGGORO SUTRISNO , A’IN CHURUN , WIDYORINI NINIEK
Published: May 2024

Abstract. Suryanti S, Anggoro S, A’in C, Widyorini N. 2024. Osmoregulation pattern, condition factor, and gonadal maturity level of sea urchins in the various ecosystems of Panjang Island, Jepara, Indonesia. Biodiversitas 25: 502-509. Panjang Island has a diversity of ecosystems. It is also famous for its abundance of echinoids, especially sea urchins. Currently, research on sea urchins in Panjang Island is mostly limited to studies on the abundance and maturity of gonads. This study investigates the osmoregulation patterns, condition factors, and maturity indices of sea urchin gonads in different ecosystems that are sea urchin habitats on Panjang Island, Jepara, Indonesia. Sampling is done randomly, while the research method is a case study. The results showed that there are 2 species of sea urchins found on Panjang Island, namely Diadema setosum Leske, 1778 and Echinothrix calamaris Pallas, 1774. Analysis of osmoregulation patterns showed that sea urchins at station 1 were hyperconformers, while sea urchins at stations 2 and 3 were hypo-conformers. Sea urchins at 3 stations had a positive allometric growth pattern (b>3) and a high condition factor (K>1). The average Gonadosomatic Index (GI) calculation result was 8.72%, while the type of ecosystem of the research stations influenced the color and texture of different gonads. Sea urchins are in immature, mature, and spawning stages, so the sea urchins on Panjang Island were partially spawned.
Length-weight relationship and condition factors of Lepturacanthus savala in Lampung Bay, Indonesia
Authors: JULIAN DAVID , REZA MUHAMMAD , PUTRA MUHAMAD GILANG ARINDRA
Published: May 2024

Abstract. Julian D, Reza M, Putra MGA. 2024. Length-weight relationship and condition factors of Lepturacanthus savala in Lampung Bay, Indonesia. Biodiversitas 25: 510-515. Scarce information exists regarding the growth aspects of ribbon fish (Lepturacanthus savala Cuvier, 1829) in Lampung Bay waters. Thus, this study aimed to analyze the growth characteristics as fundamental information for managing L. savala fishery resources in the waters of Lampung Bay. The method of this quantitative and descriptive study was to analyze the growth of L. savala. Length, weight, and sex ratio data were acquired through a purposive sampling method based on the catch results from gillnet landings at Lempasing Fishing Port, Bandar Lampung. A total of 347 specimens were collected during data collection from May to August 2023, with a length range between 21.6-59.8 cm of total length (TL) and the highest frequency observed in the length interval class of 33-36 cm, consisting of 105 specimens. The results showed that the growth pattern of L. savala is positively allometric, with a value of b equal to 3.0915. The sex ratio between males and females is 1:2.4. The condition factor values ranged from 0.0442 to 2.9281, with the highest average value observed in June for males and females, reaching 1.03.
Diversity of morphology, pathogenicity, and host range of Colletotrichum spp. associated with chili anthracnose in East Priangan, Indonesia
Authors: HODIYAH IDA , SURYAMAN MAMAN , HARTINI ELYA , JUHAENI ADE H. , LAKSANA BUDI Y. , AISYAH AISYAH , BENATAR GILANG V.
Published: May 2024

Abstract. Hodiyah I, Suryaman M, Hartini E, Juhaeni AH, Laksana BY, Aisyah, Benatar GV. 2024. Diversity of morphology, pathogenicity, and host range of Colletotrichum spp. associated with chili anthracnose in East Priangan, Indonesia. Biodiversitas 25: 533-541. Chilies, in Indonesia, encounter several obstacles that impact their production and quality. Chili production in Indonesia has seen oscillations, partly due to the detrimental effects of anthracnose disease produced by the Colletotrichum fungus species. The disease has a detrimental effect on the quality of fruit, foliage, and plants, resulting in unpredictable yields and significant losses, especially during the rainy season. Although chilies has important economic value in Indonesia, more comprehensive studies are needed on chili anthracnose in the East Priangan area, West Java Province, Indonesia. The purpose of this research was to specifically investigate the incidence of chili anthracnose and to isolate the pathogen responsible for the disease. Colletotrichum isolates were subjected to morphological characterization and pathogenicity tests to assess their virulence. In addition, the research evaluated the possible spectrum of hosts that these isolates might infect in order to determine their effect on other commodities. In East Priangan, chili anthracnose disease was found everywhere with severe disease incidence. Highest disease incidence was recorded in Garut District (100%), and the lowest was in Ciamis District (50.5%). The isolation results showed that a total of 18 diverse isolates were isolated from three chilli species at different altitudes. Macroscopic and microscopic characteristics showed variability, with growth rates ranged from 0.24 to 3.7 mm per day and diverse conidia shapes and sizes. The pathogenicity test confirmed the virulence of 17 isolates, causing symptoms with concave circular wound diameters ranged from 6.88 to 61.08 mm. Host range results demonstrated the pathogenicity of specific isolates to tomatoes, strawberries, and grapes, with strawberries exhibited higher severity levels (28.05 to 56.38 mm lesions). Gaining comprehensive knowledge about the variety and widespread occurrence of chili anthracnose in this particular area is essential for formulating effective measures to minimize its adverse effects on chili cultivation and guarantee the long-term viability of the chili sector in Indonesia. To our knowledge, this is the first study of chili anthracnose in the East Priangan region.
Diversity of fungi and dynamics of ethanol concentration during fermentation of porang (Amorphophallus oncophyllus)
Authors: HELMI HENNY , KUSMIADI RIWAN , MAHARDIKA ROBBY GUS , KARSININGSIH ENI
Published: May 2024

Abstract. Helmi H, Kusmiadi R, Mahardika RG, Karsiningsih E. 2024. Diversity of fungi and dynamics of ethanol concentration during fermentation of porang (Amorphophallus oncophyllus). Biodiversitas 25: 542-552. Fermentation can be an alternative to process porang (Amorphophallus oncophyllus). As one of the fermentation products, ethanol can degrade starch and consequently increase the purity of glucomannan in porang flour. However, ethanol can also inhibit the growth of microorganisms that play a role in fermentation. This study aimed to determine the ethanol concentration and investigate the fungal diversity during the fermentation of porang tubers. Ethanol analysis was analyzed by Headspace Gas Chromatography coupled with flame ionization detection, and Starch content was analyzed by colorimetric method. Fungal metagenome was amplified at the Internal transcribed spacer (ITS) region of nuclear DNA (rDNA) and followed by sequencing using Oxford Nanopore Technology (ONT). The result showed that the ethanol concentration increased during 48 hours of fermentation, followed by decreased starch content. The highest fungal diversity index occurred at 48 hours of fermentation. Ethanol and fungal enzymatic activity can degrade the starch. During fermentation, the Candida parapsilosis population increased until 24 hours after fermentation. Cyberlindnera subsufficiens population increased at 48 hours fermentation until 72 hours fermentation. Fungal diversity and ethanol concentration had decreased at 72 hours of fermentation, so porang fermentation should be stopped at 48 hours. Candida parapsilosis could be the candidate of starter for fermentation porang due to the capability of this species to produce ethanol to degrade starch.
The diversity, ethnobotany and nutrient contents of Dioscorea for post-disaster food security in Lombok, Indonesia
Authors: INDRIYATNO INDRIYATNO , WIJAYANTO NURHENI , BATUBARA IRMANIDA , SUPRIYANTO SUPRIYANTO
Published: May 2024

Abstract. Indriyatno, Wijayanto N, Batubara I, Supriyanto. 2024. The diversity, ethnobotany and nutrient contents of Dioscorea for post-disaster food security in Lombok, Indonesia. Biodiversitas 25: 553-564. Earthquakes caused damage to infrastructure, houses, and roads in Lombok in 2018. After the earthquake, there was a shortage of food. Adaptation to address food shortage can be overcome by using local food sources, including those from the Dioscorea genus. The study aims to analyze the diversity and distribution, ethnobotany and nutrient contents of the Dioscorea genus in Lombok Island. Botanical explorations were conducted to identify the intraspecific varieties in the form of local types/names complemented with ethnobotanical study through structured interviews. The nutrient contents were determined using a standardized method in proximate analysis. The study found 12 local types of Dioscorea belonging to four species which are used by the community for adaptation after earthquake disaster, namely: D. bulbifera (kentang), D. bulbifera (engal), D. alata (uwi sawa), D. alata (lami), D. alata (uwi kuning ampenan), D. alata (uwi putih ampenan), D. alata (uwi ungu dara kunci), D. alata (uwi putih batu layar), D. alata (uwi ungu batu layar), D. esculenta var. apiculata (surak), D. esculenta var. spinosa (gembili) and D. pentaphylla (buyut). The highest diversity of Dioscorea is found in climate type C3 (8 local types), followed by climate type E (5 local types), climate type D4 (4 local types), climate type B2 (3 local types), and climate type C2 and D3 (1 local type). The local community utilizes the Dioscorea genus in several cultural events including when celebrating the Prophet Muhammad's birthday. The nutritional value of Dioscorea genus is high due to its carbohydrate content (66,09-76,96%), protein content (3.79­-10.84%), fat content (1.70-9.58 %) and fiber content (0.32-6.81%). This study shows the potential of Dioscorea to be used as food sources that are cheap, easy to grow, and more adaptive to different environmental conditions to help post-earthquake communities.
Exploration of Oryza sativa drought-responsive element binding protein 2A (OsDREB2A) gene in several local Indonesian rice varieties
Authors: YULIZA YULIZA , SALAMAH ANDI , PUSPITANINGRUM HARDINI
Published: May 2024

Abstract. Yuliza, Salamah A, Puspitaningrum H. 2024. Exploration of Oryza sativa drought-responsive element binding protein 2A (OsDREB2A) gene in several local Indonesian rice varieties. Biodiversitas 25: 574-582. Drought is one of the abiotic stress factors that reduces rice productivity in Indonesia. OsDREB2A is a member of the DREBP subfamily of AP2/ERF transcription factors and participates in drought stress by directly binding to DRE elements to regulate downstream gene expression. However, further research is still needed to observe each OsDREB2A gene in local Indonesian rice varieties. This research aims to explore the OsDREB2A gene in several local Indonesian rice varieties, namely from Java (Ciherang, Situbagendid, Way Apo, Inpara 32 and Inpari 42), Kalimantan (Black Rice),  Aceh (Sigupai) and West Sumba (Pare Lambem and Pare Bakato Kaka). DNA was isolated from the leaves of each variety, amplified using PCR, and then electrophoresed and sequenced. Sequencing data were analyzed using DNA Baser, BioEdit and then visualized using the SWISS-MODEL server, Rice Genome Annotation Project Database, and chromosome map tools. The results showed that nine samples had 100% query cover with the Pokkali OsDREB2A (KU159743.1) cultivar sequence, 99.86% similar percent identity compared to cultivar R180 and WAB540-1-B-P-6-1-1, 99.75% similar percent identity compared to cultivar FL-478 and 99.62% similar percent identity compared to cultivar Nona Bokra. The amino acid structure of each cultivar refers to chromosome 1 at the LOC_Os01g07120 locus.
Effect of Curvularia andropogonis infection on secretory tissues and phenylalanine ammonia lyase enzyme of Cymbopogon nardus
Authors: SOLEKHA ROFIATUN , PUSPANINGRUM NI N. T. , RAMADANI AISYAH H. , HAPSARI FEBIANTI D. , ERMAVITALINI DINI , PURNOBASUKI HERY
Published: May 2024

Abstract. Solekha R, Puspaningrum NNT, Ramadani AH, Hapsari FD, Ermavitalini D, Purnobasuki H. 2024. Effect of Curvularia andropogonis infection on secretory tissues and phenylalanine ammonia lyase enzyme of Cymbopogon nardus. Biodiversitas 25: 598-604. Cymbopogon nardus L. oil production decreased due to red spot disease caused by Curvularia andropogonis fungal infection. The objective of this study was to investigate the infection effect of C. andropogonis on secretory tissue formation in citronella leaf epidermis and the enzymatic defense expression response in C. nardus. Anatomical responses were observed from leaf secretory structure slide while PAL reactions were measured from enzyme activity in leaf samples of three treatment groups with healthy, wounded, and infected conditions. The morphological results of infected leaves changed from green to brownish triggered by pathogenic infection conditions that activated the PAL enzyme pathway and phenylpropanoid production as a defense. The results showed that the density of cells storing secondary metabolites flavonoids, tannins, and saponins in infected leaves increased compared to wounded and healthy ones. Secondary metabolites flavonoids, tannins, and saponins in wounded leaves increased compared to healthy leaves. It was observed that enzymatic response escalated when infection occurred. PAL enzyme activity test of C. nardus leaves showed that infected leaves had the highest value (0.0051 U/mL), followed by wounded leaves (0.0033 U/mL) and healthy leaves (0.0027 U/mL). Likewise, the specific activity of PAL enzyme in infected leaves was highest (0.121 U/mg), followed by injured leaves (0.040 U/mg) and healthy leaves (0.022 U/mg). The overall results exhibited that C. andropogonis infection affects the quality of secretory tissue and increases PAL enzyme activity as a form of defense. By detecting secretory tissue and defense enzymes after infection, further research can be carried out regarding controlling Curvularia andropogonis infections by engineering enzymes and secondary metabolites.
High-quality genomic DNA extraction methods of Yellow Spathoglottis Blume complex for next-generation sequencing
Authors: JASIM JASIM HAIDER MAHMOD , OTHMAN AHMAD SOFIMAN , NORDIN FARAH ALIA , TALKAH NURUL SHAKINA MOHD
Published: May 2024

Abstract. Jasim JHM, Othman AS, Nordin FA, Talkah NSM. 2024. High-quality genomic DNA extraction methods of Yellow Spathoglottis Blume complex for next-generation sequencing. Biodiversitas 25: 654-663. Advancements in genomic research have spurred a growing interest in extracting high-quality genomic DNA, particularly from intricate plant species like the Yellow Spathoglottis Blume Complex. The preparation of genomic DNA high-quality from a plant sample is a crucial step for genomic and genetic analysis studies. A variety of genomic DNA extraction methods such as the traditional Hexadecyltrimethylammonium Bromide (CTAB) method and commercially available kits have been reported. Even so, they are either low purity and yield or costly. We develop a good-quality genomic DNA extraction method from fresh and dried leaves of the Yellow Spathoglottis Blume complex in Peninsular Malaysia, specifically tailored for Next-Generation Sequencing (NGS) applications. Three DNA extraction methods were compared traditional CTAB, modified CTAB, and the DNeasy Qiagen plant mini kit methods. The yield and quality of extracted DNA were assessed by PCR amplification using nuclear ETS and ITS genes performed to evaluate the success of DNA extraction. Additionally, the suitability of the modified CTAB method for NGS library preparation and sequencing was tested. It demonstrated better PCR amplification results, yielding high-concentration bands for both ETS and ITS primers. Furthermore, the modified CTAB method proved suitable for high molecular weight DNA extraction, without contamination. The extracted DNA from Spathoglottis aurea exhibited high molecular weight and passed the quality control assessment for NGS library preparation. Sequencing results demonstrated an average quality score of 36.0, with an accurate base call rate of approximately 99.9%. The developed method enables reliable genomic analysis and sequencing of the Yellow Spathoglottis Blume complex, contributing to further research and understanding of this species group.
First report of Pyricularia oryzae the cause of blast disease in upland rice, in Lombok, West Nusa Tenggara
Authors: SANURIZA IRNA IL , SUPRAPTA DEWA NGURAH , KAWURI RETNO , SURIANI NI LUH , SUDANTHA I MADE , JAYADI IRFAN , IHWAN KHAERUL
Published: May 2024

Rice (Oryza sativa L.) is a maincrop cultivated by farmers in Indonesia. The demand for rice has increased, but rice production has decreased due to attacks by plant pests, including pathogen blast disease. This research aims to (i) determine the symptoms of blast disease in upland rice in Lombok, (ii) determine the incidence of blast disease in upland rice in Lombok, (iii) and identify the pathogen that causes blast disease in upland rice in Lombok. The research was conducted in Lombok, West Nusa Tenggara. A sampling of rice crop tissue infected by blast disease was taken from 50  dryland locations in Lombok West Nusa Tenggara. From each point, three samples of rice crops with blast symptoms were taken to obtain 150 samples. Samples are then isolated and identified at the macroscopic, microscopic, and molecular levels. The study results showed that the macroscopic characteristics of rice leaves were rhombus-shaped and brown, and the pathogen produced white mycelium with a fine structure. In contrast, microscopic characteristics showed that the shape of the hyphae was septate, the structure of conidiophore with autophagic cell death, long pyriform microconidia, and long pyriform macroconidia. Based on 18S rRNA gene analysis, the Blast Lombok isolate had a DNA fragment of ±550bp. Based on these results, it can be concluded that the cause of blast disease in upland rice in Lombok, West Nusa Tenggara, is P. oryzae.
Conserving dipterocarps biodiversity in remnant forests of small islands in Batam Island, Indonesia
Authors: SUSILOWATI ARIDA , WIJAYA KESUMA , MAWAZIN MAWAZIN , RACHMAT HENTI HENDALASTUTI , LISMAYATI YUNITA , KURNIAWAN HERI , GINTING IDA MALLIA
Published: May 2024

Abstract. Susilowati A, Wijaya K, Mawazin, Rachmat HH, Lismayati Y, Kurniawan H, Ginting IM. 2024. Conserving dipterocarps biodiversity in remnant forests of small islands in Batam Island, Indonesia. Biodiversitas 25: 726-733. The protected forest of Sei Harapan is a remnant forest in Batam Island, the Riau Islands Province, Indonesia and one of the keruing (Dipterocarpus spp.) habitats on Sumatra Island. Illegal logging for its wood and land degradation have significantly reduced the keruing population. The objective of this research was to assess the diversity of keruing species and floristic composition in the Sei Harapan Protected Forest. This study employed a vegetation analysis method using purposive sampling with plotted lines and the transect placement based on the keruing position. The research revealed more than 70 species, three of which were Dipterocarpaceae species, including Vatica pauciflora, Shorea curtisii, and Dipterocarpus rigidus. D. rigidus had the highest IVI at the sapling (52.80%) and pole (67.22%). However, D. rigidus ranked 13th in the seedling stage, with an IVI of 5.79%. The diversity index was high at the seedling stage (3.73), moderate at sapling (2.25), pole (2.76), and tree stage (2.89). The evenness index was high at all growth stages, with values of 0.94 (seedling), 0.98 (sapling), 0.91 (pole), and 0.81 (tree). The richness index at the seedling, pole, and tree stage were categorized as high, with values of 10.40, 5.39, and 7.09, respectively, whereas the richness index at the sapling stage was moderate at 3.51. The study finding pointed out that the existence of Sei Harapan remnant forest requires to be preserved considering its essential function for preserving high economic value tree species, especially Dipterocarp. The comprehensive conservation effort for dipterocarps species, is crucial considering the research findings revealed a problem of continuity of species regeneration and the emergence of new pioneer species as the consequence of anthropogenic disturbance.
Short Communication: Analysis of simple sequence repeats variations for the assessment of genotypic diversity in Centella asiatica (L.) Urb.
Authors: MARUZY ANSHARY , SUSANDARINI RATNA
Published: May 2024

Abstract. Maruzy A, Susandarini R. 2024. Short Communication: Analysis of simple sequence repeats variations for the assessment of genotypic diversity in Centella asiatica (L.) Urb. Biodiversitas 25: 734-740. Centella asiatica (L.) Urb. is a perennial plant widely known as herbal ingredient in traditional and modern medicine, as well as in the cosmetics industry. This herbaceous species grows in various types of habitat, and is known for its morphological variations among populations, indicating the existence of genotypic variation. In this study, the assessment of genotypic diversity using simple sequence repeats (SSR) was carried out on C. asiatica accessions from 32 populations collected from eight mountains in Central Java. Representative individuals from four populations grow at different altitudes were sampled in each mountain. Amplification of genomic DNA using the SSR primer mCaCIR002 produced a single amplicon of 180 bp. The results of SSR analysis showed that there is high genotypic diversity in C. asiatica which is characterized by variations in the number of microsatellite repeats of (CT)10 to (CT)19. Variations in the number of repeats are mainly caused by insertions and deletions in DNA sequences at the positions 102-145. Haplotype analysis also showed high genetic diversity within and between populations of C. asiatica, indicated by the haplotype diversity of 1.00 in all populations. The haplotype network analysis indicated that there was no gene flow between the four populations at each mountain where C. asiatica populations grow. The results of this study provide evidence for the role of SSR as a suitable molecular marker for studying genotypic diversity at the intraspecific level, and confirming the morphological variability in this species.
Vegetation diversity and habitat suitability modeling of the invasive plant Bellucia pentamera in conservation forests of West Sumatra, Indonesia
Authors: SOLFIYENI SOLFIYENI , FADHLAN ADLI , AZIZ AL , SYAHPUTRA GITO , AZZAHRA ANISA , MILDAWATI MILDAWATI
Published: May 2024

Abstract. Solfiyeni S, Fadhlan A, Aziz A, Syahputra G, Azzahra A, Mildawati M. 2024. Vegetation diversity and habitat suitability modeling of the invasive plant Bellucia pentamera in Conservation Forests of West Sumatra, Indonesia. Biodiversitas 25: 781-791. The invasive plant Bellucia pentamera has spread to several regions in Indonesia, including the province of West Sumatra. Mapping the distribution of this invasive plant needs to be done to facilitate its management. offers a comprehensive approach to delineate the potential ecological range of a species and assess habitat suitability. This study aimed to evaluate the impact of B. pentamera invasion on vegetation diversity, conduct potential distribution mapping, and assess B. pentamera habitat suitability in West Sumatra conservation forests. The study utilized observational methods to determine coordinate points for B. pentamera presence and conducted vegetation analysis. The results from the vegetation analysis revealed disparities in composition and structure across three study areas, with diversity indices ranging from 2.60 to 3.84. The similarity index between study areas was relatively low, below 50%. The MaxEnt analysis delineated suitable locations for B. pentamera using the ROC curve (AUC) model, yielding values of 0.947 for training data and 0.923 for testing data. MaxEnt modeling identified suitable habitat for B. pentamera concentrated at Lima Puluh Kota, Tanah Datar, Padang, Solok and South Solok districts. This study's findings indicate a broad distribution of this species, with over 5% of the habitat deemed suitable for B. pentamera.
Physicochemical and structural composition of black rice (Oryza sativa) flour from Java, Indonesia
Authors: NURHIDAJAH NURHIDAJAH , YONATA DIODE , BINTANAH SUFIATI , PRANATA BOBY
Published: May 2024

Abstract. Nurhidajah, Yonata D, Bintanah S, Pranata B. 2024. Physicochemical and structural composition of black rice (Oryza sativa) flour from Java, Indonesia. Biodiversitas 25: 811-818. Information regarding the characteristics of Indonesian black rice (Oryza sativa) flour from several varieties can provide a scientific base for developing its utilization. This study aimed to compare the physicochemical and structural composition of black rice varieties, namely Cempo Ireng, Melik, Sirampog, and Jeliteng from Java, Indonesia. Black rice was initially crushed to 100 mesh size. The flour's physicochemical and structural composition was then compared descriptively and the quantitative data was analyzed using the SPSS 22.0 software. As a result, significant differences were observed in starch content (68.45-71.08%), amylose content (13.99-18.49%), solubility (13.92-19.55%), swelling power (9.46-11.36%), water binding capacity (74.79-87.87%), and oil binding capacity (59.59-67.33%) of the four varieties of black rice flour. In addition, significant differences were also observed in the paste and thermal properties of various varieties. Morphological analysis shows that the flour structure has a similar shape, which is plate-shaped and contains many flakes. The relative crystallinity of Indonesian black rice flour ranges from 22.95% to 24.25%. This result reflects that all black rice flour particles have an A-type crystalline structure. All varieties of black rice flour have different physicochemical and structural compositions, except crystal structure that shows similarities (type A).
Combining eDNA metabarcoding and conventional method in rapid screening of fish diversity in Maros-Pangkep Global Geopark, South Sulawesi, Indonesia
Authors: AMBENG AMBENG , IQRAM MUHAMMAD , LITAAY MAGDALENA , HASYIM ZOHRAH , MOKA WILMA J. C. , TINUNGKI GEORGINA MARIA
Published: May 2024

Abstract. Ambeng, Iqram M, Litaay M, Hasyim Z, Moka WJC, Tinungki GM. 2024. Combining eDNA metabarcoding and conventional method in rapid screening of fish diversity in Maros-Pangkep Global Geopark, South Sulawesi, Indonesia. Biodiversitas 25: 819-828. A newly designated geopark by UNESCO, Maros-Pangkep Global Geopark, South Sulawesi, Indonesia owns great geodiversity, exceptional cultural heritage, and high biodiversity. However, the global biodiversity crisis that has hit the earth might also occur in Maros-Pangkep river systems, potentially threatening endemic freshwater fish and all other biota. It has been reported that there is high pressure on the environment along the watershed in the Maros-Pangkep rivers, including a high sedimentation rate downstream, which is linked to extreme erosion upstream and could eventually affect fish populations such as endemic ones. This should prompt a call for the authorities to build a strategy for monitoring and documenting aquatic biota such as fish to preserve biodiversity. Environmental DNA (eDNA) could be considered a method for monitoring fish species based on the DNA traces they shed in the water. Hence, this study aims to use eDNA to survey fish biodiversity in several rivers in the Maros-Pangkep Global Geopark and compare the result against the traditional gillnet method. The results showed that using two methods, 29 fish species in 19 families and 15 orders were obtained from the three rivers. Despite the majority of detected species, 25 species, as the result of using eDNA, 4 species were only detected using a traditional method which eDNA failed to identify. Among those species, several endemic and non-native species were successfully identified by either one or both methods. This could eventually be a suggestion for responsible authorities in biodiversity conservation to combine both approaches to monitor and conserve local biodiversity.
Freshwater fish diversity from Siberut Island, a small island in the western part of Sumatra, Indonesia
Authors: ROESMA DEWI IMELDA , TJONG DJONG HON , AIDIL DYTA RABBANI , PRAWIRA FURQAN DWIKI LINTANG , SAPUTRA ANDRI
Published: May 2024

Abstract. Roesma DI, Tjong DH, Aidil DR, Prawira FDL, Saputra A. 2024. Freshwater fish diversity from Siberut Island, a small island in the western part of Sumatra, Indonesia. Biodiversitas 25: 836-845. Indonesia is an archipelagic country with thousands of islands, including small islands with a variety of biodiversity, such as freshwater fish. Data and information on the fish biodiversity of small islands in the western part of Sumatra are limited, including Siberut Island. A study on freshwater fish diversity in Siberut Island was carried out using morphological and molecular methods. The study was conducted on seven rivers in the North and South Siberut Districts, Siberut Island. The study obtained 676 individuals, including 34 species, 26 genera, 16 families, and 10 orders. Oxudecidae is the family with the largest species (8), and Rasbora jacobsoni has the highest number of individuals (341). Species richness ranged from 2 to 18 species per site and was highest in the Srilanggai River. Siberut Island has low-moderate freshwater fish diversity. As many as 90 DNA barcodes of individuals from 34 species have been submitted to the Barcode of Life Data System. Freshwater fish groups do not receive enough attention from local communities and the government because of the richness of marine fish on Siberut Island. Apart from functioning as evidence of species richness, the results of this study are also useful for local communities' education.
The mangrove ecosystems on the north coast of Bangkalan, Indonesia, and its potential for mangrove ecotourism
Authors: NUGRAHA WAHYU ANDY , AMBARIYANTO AMBARIYANTO , INSAFITRI INSAFITRI
Published: May 2024

Abstract. Nugraha WA, Ambariyanto A, Insafitri. 2024. The mangrove ecosystems on the north coast of Bangkalan, Indonesia, and its potential for mangrove ecotourism. Biodiversitas 25: 859-868. Mangrove ecosystems have the potential to be used as objects of marine ecotourism, in addition to many ecological functions and one of the main producers in marine fisheries. Bangkalan has a mangrove area of 1500 hectares which has the potential to be used as ecotourism. However, there is no research that analyzes and identifies the suitability index of mangrove tourism along the north coast of Bangkalan, Madura. The purpose of this study was to determine mangrove species, mangrove density, and mangrove tourism suitability index on the north coast of Bangkalan in order to identify the potential of mangrove for eco-tourism. The research was done at 14 stations on the north coast of Bangkalan. Data calculation and analysis were carried out by calculating the thickness of mangroves forest, mangrove species, mangrove density, biota that can be found, tides, accessibility, and infrastucture that were used to calculate mangrove tourism suitability index. The results showed that mangrove thickness in the north coast of Bangkalan were 138 m-864 m. 17 mangrove species were found, with the highest number of species was found in site 13 (Labuhan Education Park) with 14 species. Mangrove density was between 400-3500 trees/ha, with 10 sites in dense category, 2 in average category, and 2 in low category. The results showed that all research sites were included in the sufficient criteria for mangrove tourism. Mangroves in Bangkalan have great potential to develop mangrove tourism since all research sites were included in the sufficient criteria for mangrove tourism.
Dynamic of coral recruits in the Karimunjawa National Park, Central Java, Indonesia
Authors: TARIGAN SUKMARAHARJA AULIA RACHMAN , MUNASIK MUNASIK , WIJAYANTI DIAH PERMATA , MUHIDIN MUHIDIN , ROHMAN ENDANG ABDUL , PARDEDE SHINTA
Published: May 2024

Abstract. Tarigan SAR, Munasik, Wijayanti DP, Muhidin, Rohman EA, Pardede S. 2024. Dynamic of coral recruits in the Karimunjawa National Park, Central Java, Indonesia. Biodiversitas 25: 869-880. After a disturbance event, coral reefs can recover naturally by recruiting new corals. These can be affected by environmental factors like the substrate's physical and biological structure, predation, and accidental mortality of recruits by grazers, as well as the number and size of parent corals supplying larvae. This study examined the connection between newly recruited corals and biological factors such as sea urchin density, herbivorous fish abundance, and hard coral coverage. The study was monitored changes in coral cover, juvenile coral density, herbivore abundance, and hard coral coverage at 43 locations and two depths (shallow; 2-3 m) and deep (8-10 m) from 2013 to 2022. The locations were distributed across six different zone systems: the core zone, protection zone, tourism zone, traditional fisheries zone, aquaculture zone, and rehabilitation zone. Multiple Linae Regression, ANOVA test, and Principal Component Analysis were employed to assess the relationship between coral recruitment and other variables. Results indicated that the coral recruitment density was not significantly different when comparing different zoning systems (two-way ANOVA test, P-value>0.05). Based on the PCA analysis, we found that in 2013 and 2019, excavator, sea urchin, browser, and hard coral have a positive relationship with coral recruitment, which implies that coral recruitment would increase as sea urchin, browser, and hard coral increase. Meanwhile, in 2019 and 2022, coral recruitment has a negative relationship with scraper, and also with hard coral growth (although only in 2022), implying that coral recruitment would decrease if scraper and hard coral increase. The study recommends restoring the role of herbivorous species in Karimunjawa National Park (KNP) by prioritizing them in conservation efforts and managing their populations.
Ammonium enrichment reduces the diversity and changes the composition of ammonia-oxidizing microbial communities in agricultural soil media
Authors: SAUKOLY SHERLY ASNATH , MEITINIARTI VINCENTIA IRENE , NUGROHO RULLY ADI , KRAVE AGNA SULIS
Published: May 2024

Abstract. Saukoly SA, Meitiniarti VI, Nugroho RA, Krave AS. 2024. Ammonium enrichment reduces the diversity and changes the composition of ammonia-oxidizing microbial communities in agricultural soil media. Biodiversitas 25: 916-923. Nitrification is the process of ammonium oxidation to form nitrites and nitrates. Ammonium availability in the soil is one of the factors influencing the activity, abundance, and diversity of ammonia-oxidizing microorganisms (AOM). This study aimed to determine the effect of enriching a soil media with different ammonium concentrations on the abundance and diversity of AOM as well as the potential for nitrification. Soil as the media was prepared from an agricultural land receiving cow dung sewage. The media was then placed in the microcosms, and was added to a nitrification medium containing ammonium at three levels; 0 (control soil), 200 (low ammonium-enriched soil), and 500 mg L-1 (high ammonium-enriched soil). The microcosms were further incubated for 42 days at room temperature. The nitrification potential determination was based on the formation of nitrite from ammonium oxidation. The abundance of AOM and the potential nitrification were measured every 14-day interval, including day 0 as the initial condition. The AOM composition was analyzed based on the similarity level of the amoA gene sequence to the NCBI BLAST GenBank database. However, this analysis was only conducted for the control and high ammonium-enriched soil. This study indicated that ammonium enrichment increased the nitrification activity and the abundance of AOM, but it decreased the diversity of AOM communities. There were positive correlations between nitrification and nitrate potential, as well as between ammonium content and AOM abundance. Negative correlations appeared between pH and nitrification potential, nitrate concentrations, ammonium concentrations, and MPN. The diversity of ammonium-oxidizing archaea (AOA) in the control soil was higher than in the high ammonium-enriched soil. The enrichment with ammonium also changed the AOA composition. The Candidatus Nitrosocosmicus oleophilus strain of the MY3 chromosome was the most dominant archaea in the control and high ammonium-enriched soil. This implies that the high diversity of AOA in this soil may be beneficial for further use of the soil as a source for inocula in the development of nitrifiers-based biofertilizers.
The impact of different management on pine-based agroforestry system and litter accumulation on the population and activity of cellulolytic bacteria
Authors: ARFARITA NOVI , NURAINI YULIA , RINADY MAYDELLA VISTA PUTRI , NOERHAYATI EKO , PRAYOGO CAHYO
Published: May 2024

Abstract. Arfarita N, Nuraini Y, Rinady MVP, Noerhayati E, Prayogo C. 2024. The impact of different management on pine-based agroforestry system and litter accumulation on the population and activity of cellulolytic bacteria. Biodiversitas 25: 924-936. Agroforestry leads to the accumulation of organic matter, and the environmental conditions, litter quality, and decomposing organisms influence the rate at which litter decomposes. Litter decomposition in agroforestry systems is slow due to the high lignin and phenolic substances content, low light intensity, and high humidity under the canopy's shading condition. Therefore, a study was carried out to address this issue to isolate cellulolytic bacteria capable of breaking down plant litter using a qualitative cellulase activity testing method. The complete randomized block design and Tukey's test were used to determine the treatment's significance. Six agroforestry systems were examined: pine-coffee, pine-banana, pine-cardamom, pine-cardamom, mixed garden, and citrus. The PK (Pine-Coffee) plot had the highest canopy cover, litter density, and cellulolytic bacteria. The study identified three cellulolytic bacteria isolates (PK1, PK13, and PK10) from the 50 isolated bacteria of PK plot, producing the largest clear zones on CMC media. These identified isolates belonging to the Bacillus genus were Gram-positive bacteria with rod-shaped cells. The different types of litter in agroforestry systems affect the content of lignin, polyphenols, cellulose, and C/N ratios, which can influence the abundance of cellulolytic bacteria and their potential cellulase activity.
Antimicrobial resistance in Campylobacter species isolated from commercially sold steak (beef) and raw cow milk in Abakaliki, Nigeria
Authors: AGUMAH NNABUIFE BERNARD , EFFENDI MUSTOFA HELMI , WITANINGRUM ADIANA MUTAMSARI , TYASNINGSIH WIWIEK , UGBO EMMANUEL NNABUIKE , NWAGWU CHINEKWU SHERRIDAN , UGBO IFUNANYA AGATHA
Published: May 2024

Abstract. Agumah NB, Effendi MH, Witaningrum AM, Tyasningsih W, Ugbo EN, Nwagwu CS, Ugbo IA. 2024. Antimicrobial resistance in Campylobacter species isolated from commercially sold steak (beef) and raw cow milk in Abakaliki, Nigeria. Biodiversitas 25: 950-956. This study aimed to ascertain antimicrobial resistance in Campylobacter species isolated from commercially sold steak (Beef) and raw cow milk in Abakaliki. Pools of milk samples and steak were bought at various outlets and analyzed using standard microbiological methods. Results showed that two species of Campylobacter, namely Campylobacter coli, were isolated from the samples. In raw cow milk, Campylobacter coli had a frequency of 65% higher than Campylobacter jejuni (20%). While in steak, C. coli was 34.53% higher than C. jejuni (19.10%). The antibiotic susceptibility profile for C. coli isolated from raw cow milk ranged from 61.54% to 100%, especially for trimethoprim and cephalexin. Resistance ranged from 0.00 to 38.46%. The highest resistance was recorded for tetracycline. The antibiotic susceptibility profile for C. coli isolated from steak recorded susceptibility values ranging from 60.53% to 86.84%. Cephalexin had the highest effect on C. coli isolates from steak. Resistance values ranging from 13.16% to 42.11% were recorded with Nalidixic acid as the least effective antibiotic. C. jejuni isolated from cow raw milk, susceptibility ranging from 0.00% to 100% was recorded, especially for Cefotaxime, Imipenem, Cephalexin, and Nalidixic acid. Resistance ranged from 0.00% to 100%, especially for Chloramphenicol and Kanamycin. For C. jejuni, susceptibility values ranged from 26.57% to 85.71%, with imipenem presenting the highest effect. Resistance values ranged from 23.81% to 71.43%. Gentamycin had the least effect. Adequate sanitation, personal hygiene, and appropriate use of antibiotics are highly recommended for food handlers and farmers to safeguard human health by reducing AMR challenges, even in milk and meat/meat products.
Interaction between Eichornia crassipes with Microbacterium sp. SpR3 and Micrococcus luteus RT-9 in Cr6+ reduction in liquid media
Authors: WULANDARI ANDRIYANI DEA , MEITINIARTI V. IRENE , KASMIYATI SRI
Published: May 2024

Abstract. Wulandari AD, Meitiniarti VI, Kasmiyati S. 2024. Interaction between Eichornia crassipes with Microbacterium sp. SpR3 and Micrococcus luteus RT-9 in Cr6+ reduction in liquid media. Biodiversitas 25: 957-963. Water Pollution caused by Cr6+ contamination is difficult to remove from the environment. One of the efforts to reduce Cr6+ contamination in water is by bioremediation. Bioremediation using the interaction of rhizosphere bacteria with aquatic plants can be employed to decrease the content of Cr6+ in water environment. This study aimed to determine the effect of adding Microbacterium sp. SpR3, Micrococcus luteus RT-9, and a mixture of both bacteria on the ability of Eichornia crassipes to reduce the concentration of Cr6+ in the growth media and the plant's growth potential. This study was conducted in the Microbiology Laboratory of the Faculty of Biology at Satya Wacana Christian University. Eichornia crassipes plans of similar size were grown in 450 mL of Hoaglands solution with Cr6+ 5 mg.L-1 in a container. The treatment in this study involves the addition of 50 mL (10% of the working volume) of Microbacterium sp SpR3 culture, Micrococcus luteus RT- 9, and a combination of both Cr6+-reducing bacteria. The reduction rate of Cr6+ concentration in the mixture of both types of bacteria reached 88.06%, which was higher compared to the control without the addition of the inoculum (87.08%). The inoculation of both Cr6+ reducing bacteria did not hibit the growth rate of the plants. The ability of Microbacterium sp. SpR3 and Micrococcus luteus RT-9 to reduce Cr6+ in liquid media can be employed in the bioremediation of Cr6+ contaminated wastewater.
Isolation and identification of bacterial pathogens causing ice-ice disease in Eucheuma cottonii seaweed at Seira Island Waters, Tanimbar Islands District, Maluku, Indonesia
Authors: TUHUMURY NOVIANTY C. , SAHETAPY JACQUELINE M. F. , MATAKUPAN JOLEN
Published: May 2024

Abstract. Tuhumury NC, Sahetapy JMF, Matakupan J. 2024. Isolation and identification of bacterial pathogens causing ice-ice disease in Eucheuma cottonii seaweed at Seira Island Waters, Tanimbar Islands District, Maluku, Indonesia. Biodiversitas 25: 964-970. Seaweed cultivation has proven to be beneficial and enhances the well-being of communities. Production of seaweed in the waters of Maluku has increased despite facing the problem of ice-ice disease. Therefore, this research aimed to isolate and identify bacteria on the Eucheuma cottonii seaweed species affected by ice-ice disease in the waters of Seira Island, Tanimbar Islands District, Maluku. It was conducted in August 2023 at three observation stations, and water quality samples were collected in situ at all three stations, including temperature, salinity, pH, dissolved oxygen (DO), and turbidity. Furthermore, bacterial isolation and identification were carried out at the Laboratory of Marine Aquaculture, Ambon. Bacteria isolation and purification were performed on TCBS media using the streak plate technique, while identification used the API 20E test. The results showed that water quality parameters supported seaweed growth. Four bacteria that caused ice-ice disease in the waters of Seira were identified as Vibrio alginolyticus, Vibrio fluvalis, Vibrio cholerae, and Aeromonas caviae. Moreover, all four bacteria found were gram-negative and pathogenic. Bacteria belonging to the genera Vibrio and Aeromonas have been proven to cause infections in marine organisms, including seaweed. In conclusion, four types of bacteria were identified in seaweed affected by ice-ice disease.