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All Journal ILMU KELAUTAN: Indonesian Journal of Marine Sciences Biosaintifika: Journal of Biology & Biology Education
Mahmoud, Hanan Hassan Alsheikh
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Agriculture, Biological Sciences & Forestry Earth & Planetary Sciences

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First Record Sparus aurata Larvae in Teluk Penyu Beach Cilacap, Indonesia, revealed by DNA Barcoding Nuryanto, Agus; Bhagawati, Dian; Winarni, Elly Tuti; Mahmoud, Hanan Hassan Alsheikh
ILMU KELAUTAN: Indonesian Journal of Marine Sciences Vol 28, No 4 (2023): Ilmu Kelautan
Publisher : Marine Science Department Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/ik.ijms.28.4.301-312

Abstract

Morphological identification often fails to reveal the taxonomic status of fish larvae. DNA barcoding using particular DNA segment is frequently successful in solving the faulty and might reveal overlooked species, including species outside their recognized geographic ranges, such as Eastern Atlantic seabream Sparus aurata. This study aims to assess fish larvae diversity in Teluk Penyu Beach, Cilacap Central Java, Indonesia, through the cytochrome c oxidase 1 barcoding. Fish larvae were collected using a larva net with a diameter of 60 cm and height of 150 cm and horizontal towing during the field trips in March and April 2021. Larvae morphotypes were determined based on their general morphological performance observed under a magnification lens according the available references. Eighteen larvae morphotypes were successfully barcoded, and 5% genetic distance was used as a species border. Fourteen fish larvae species were revealed, with intraspecific genetic distances between 0.00% and 4.12%, while intrageneric genetic distances ranged from 5.50% to 19.29%. An interesting finding was that one larva morphotype was barcoded as S. aurata with high genetic identity (99.19% to 99.68%) and low genetic distance (0.32% to 0.81%). The discovery provides the first new data on S. aurata in Teluk Penyu Beach Cilacap, Central Java, outside its recognized geographic range. Overall, this study provides information about fish larvae in Teluk Penyu Beach, essential for estimating the number and species of fish recruited in the southern Cilacap, which is vital for fisheries management. Nevertheless, new research requires further clarification of S. aurata in Teluk Penyu Beach.
DNA Barcoding of Ornamental Crab Geosesarma in South-Slope Mount Slamet Central Java, Indonesia Winarni, Elly Tuti; Rofiqoh, Aswi Andriasari; Bhagawati, Dian; Pulungsari, Anastasia Endang; Mahmoud, Hanan Hassan Alsheikh; Nuryanto, Agus
Biosaintifika: Journal of Biology & Biology Education Vol. 16 No. 2 (2024): August 2024
Publisher : Universitas Negeri Semarang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15294/biosaintifika.v16i2.2376

Abstract

Geosesarma shows intraspecific carapace color variation, which might lead to species misidentification. The problem can be solved using DNA barcoding. There is one research about Geoserarma from the southern slopes of Mount Slamet, but samples were only collected from the Banjaran River for morphological identification. Here, we collected samples from wider areas covering south slope and applied molecular identification. This research aims to assess Geosesarma diversity in south-slope Mount Slamet Central Java, Indonesia based on the cytochrome c oxidase 1 gene barcoding. Surveys were carried out at six sites. Taxonomic identification was done using the barcoding technique. Four morphotypes were obtained during the research. Three morphotypes with the square carapace were identified as Geosesarma, while the remaining one morphotype was included in Parathelphusa. The three Geosesarma morphotypes were barcoded as Geosersarma dennerle because their genetic identity was more than 97% of the G. dennerle sequence in Boldsystems. In contrast, the Parathelphusa morphotype was barcoded as P. convexa with a genetic identity of 97.50%. It can be concluded that the Geosesarma crab on the south-slope Mount Slamet only consists of one species but has carapace and claw color variations. The data are essential for Geosesarma market development and conservation in the region.
Comparison of Two Isolation Methods for Naturally Preserved DNA in Ambergris Fathurahman, Fabian Rizky; Suman, Ali; Mahmoud, Hanan Hassan Alsheikh; Nuryanto, Agus
Biosaintifika: Journal of Biology & Biology Education Vol. 17 No. 1 (2025): April 2025
Publisher : Universitas Negeri Semarang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15294/biosaintifika.v17i1.14302

Abstract

DNA extraction is a fundamental initial step in numerous molecular research studies. Different extraction methods are required for different biological samples to obtain high-quality DNA. Therefore, this step is one of the limiting factors for the success of molecular analysis. There has been no research evaluating an appropriate method to extract DNA from ambergris jetsam samples. This study aims to determine an appropriate method for extracting DNA from whale ambergris samples. The ambergris sample was collected from the southern coast of Cilacap. DNA extraction was performed using a commercial DNA isolation kit and the Chelex® 100 method. The extracted DNA was visualized using agarose gel electrophoresis followed by quantification with a UV Nanodrop spectrophotometer. The data were analyzed descriptively to determine the most effective extraction method. The success of the extraction was also assessed by measuring the DNA concentration using the Nanodrop spectrophotometer. The results showed that the commercial isolation kit failed to produce genomic DNA from whale ambergris, as indicated by the absence of stained DNA bands on the agarose gel. In contrast, the Chelex® 100 method successfully produced genomic DNA from ambergris, as evidenced by the presence of stained DNA bands on the agarose gel and a high quantity of genomic DNA after a Nanodrop measurement. It can be concluded that the Chelex® 100 method is more suitable than commercial kits for extracting DNA from ambergris samples. This finding contributes to the development of various scientific fields based on molecular data by providing evidence that each biological sample requires an appropriate method to obtain high-quality DNA.
Growth and Exploitation Rate of Mystus nigriceps Rukayah, Siti; Lestari, Windiarini; Nuryanto, Agus; Mahmoud, Hanan Hassan Alsheikh
Biosaintifika: Journal of Biology & Biology Education Vol. 17 No. 3 (2025): Inpress December 2025
Publisher : Universitas Negeri Semarang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15294/biosaintifika.v17i3.32684

Abstract

Mystus nigriceps is among the bagrid fish species that live in freshwater ecosystems, including Cicingguling River, Kebumen Regency, Central Java, Indonesia. Despite the economic importance and exploitation for food, the fish is rarely studied. Meanwhile, studies on the growth pattern and exploitation rate of M. nigriceps in the Cicingguling River are important because the population is also affected by river fragmentation due to reservoir development. Therefore, this study aims to analyze the growth pattern and exploitation rate of M. nigriceps in the Cicingguling River. Sampling was carried out using the purposive random sampling method in the Cicingguling River. A total of 9 stations were divided into 3 zones for 1 year, with a frequency of 12 times and an interval of once a month. The results showed that a length-weight relationship had an average b-value of 3.11, indicating a positive allometric pattern (b>3). The condition factor of female M. nigriceps (2.404) was higher than that of male fish (2.06). Total mortality (Z) was estimated at 4.85 per year, consisting of natural mortality (M) at 3.59 per year and fishing mortality (F) at 1.26 per year. These values suggest that the mortality of M. nigriceps is primarily driven by natural causes rather than fishing pressure. The exploitation rate was 0.26 per year, which is relatively low as it remains below the optimum threshold (Eoptimum = 0.5). This information is essential for fisheries management as a basis for M. nigriceps conservation in the Cicingguling River.
Co-Authors Agus Nuryanto Ali Suman Elly Tuti Winarni Fathurahman, Fabian Rizky Pulungsari, Anastasia Endang R Siti Rukayah Rofiqoh, Aswi Andriasari Windiarini Lestari