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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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Bacterial and yeast optimization in Arabica coffee fermentation to enhance winey flavor INTAN TAUFIK; FATHYA ISTIQOMARIL SYACHNOORMALIETA; KHAERUNISSA ANBAR ISTIADI; FAUZIE FITRIA RUSDIANA; DEA INDRIANI ASTUTI
Biodiversitas Journal of Biological Diversity Vol. 25 No. 11 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d251126

Abstract

Abstract. Taufik I, Syachnoormalieta FI, Istiadi KA, Rusdiana FF, Astuti DI. 2024. Bacterial and yeast optimization in Arabica coffee fermentation to enhance winey flavor. Biodiversitas 25: 4265-4274. The natural fermentation process of Arabica coffee often needs more consistency in producing high-quality coffee due to the process's challenging control involving diverse microbial communities, including those of bacteria and yeast. This study has isolated specific bacteria and yeast strains from natural fermentation and utilized them as inoculum to optimize the coffee fermentation process, accentuating the wine's aromatic flavors by adjusting the bacteria-to-yeast ratio and inoculum percentage. Eight bacteria and five yeast were initially isolated from natural fermentation processes and further assayed for their enzymatic activity. The highest enzymatic activity, including pectinolytic, cellulolytic, amylolytic, and proteolytic activities from each bacterial and yeast, were selected for identification using DNA sequencing and phylogenetic tree construction. The identification results showed that the bacteria Klebsiella sp. and the yeast were Pichia kudriavzevii. Next, the growth curves of the two isolates were analyzed to determine the optimal fermentation time. The results indicated that one day was sufficient for optimal bacterial and yeast growth. Using the isolates bacteria Klebsiella sp. and yeast Pichia kudriavzevii revealed that a bacteria-to-yeast ratio of 1:10 with a 15% (v/w) inoculum resulted in the highest cupping score with a prominent wine flavor note compared to the control. Employing bacterial and yeast inoculum in Arabica coffee fermentation has the potential to improve coffee quality and consistently improve overall product standards.
Species-specific and landscape carbon storage analysis of mangrove forest in Segara Anakan Lagoon, Cilacap, Central Java, Indonesia ENDANG HILMI; HENDRAYANA .HENDRAYANA; SESILIA RANI SAMUDRA; NABELA FIKRIYYA; TEUKU JUNAIDI; TRI NUR CAHYO; NAFSHA ATIKA PUTRI; AFIDA NADZIROTUL UMMAH
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/d250848

Abstract

Abstract. Hilmi E, Hendrayana, Samudra SR, Fikriyya N, Junaidi T, Cahyo TN, Putri NA, Ummah AN. 2024. Species-specific and landscape carbon storage analysis of mangrove forest in Segara Anakan Lagoon, Cilacap, Central Java, Indonesia. Biodiversitas 25: 2748-2755. Mangrove forests are one of the world's largest carbon pools. However, each mangrove species has a different capacity to sequester and store carbon in its biomass. Therefore, at the landscape scale, there are also differences in carbon storage and percent carbon between habitat sites influenced by dominant species and stand density due to differences in environmental conditions. This study aims to analyze each mangrove species' percent carbon and carbon storage and develop a mangrove landscape in Segara Anakan Lagoon, Cilacap District, Central Java Province, Indonesia. This study used destructive methods to collect mangrove samples. The percentage of carbon of each species was analyzed using a formulation of volatile and ash values, while carbon stock for each species was estimated using allometric equations. Landscape analysis of carbon stocks was based on mangrove stand density. The results showed that the carbon percentage of mangrove species averaged between 42.48-53.34% with Rhizophora spp. (R. apiculata, R. mucronata and R. stylosa) and Bruguiera gymnorrhiza having the highest carbon percentage of 47.1-55.6%, followed by Sonneratia spp. and Avicennia with 43.0-48.6%, Ceriops spp., Aegiceras spp., Heritiera littoralis and Xylocarpus spp. with 43.0-48.2%, and Nypa fruticans had the lowest carbon percentage with 39.1-41.0%. At the landscape scale, Segara Anakan had mangrove biomass between 34.83-786.61 tons/ha with carbon stock between 7.85-186.09 tons C/ha. Based on percent carbon, the mangrove landscape in Segara Anakan was dominated by B. gymnorrhiza, R. apiculata, R. stylosa, Ceriops tagal, and R. mucronata. Avicennia marina, Aegiceras corniculatum, N. fruticans, R. apiculata, and Sonneratia alba dominated mangrove landscapes based on carbon storage. The results of this study indicate that carbon storage in mangrove ecosystems is important to support carbon conservation because it has a high percentage of carbon and large carbon storage.
Exploration of cadmium-resistant bacteria in cadmium-contaminated rice fields in Karawang District, Indonesia NOVRIANTY RIZQI AZIS; YULIA NURAINI; CAHYO PRAYOGO; RIZKY MAULANA ISHAQ
Biodiversitas Journal of Biological Diversity Vol. 25 No. 10 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d251025

Abstract

Abstract. Azis NR, Nuraini Y, Prayogo C, Ishaq RM. 2024. Exploration of cadmium-resistant bacteria in cadmium-contaminated rice fields in Karawang District, Indonesia. Biodiversitas 25: 3637-3644. Cadmium is a heavy metal naturally present in the soil, but its presence can increase due to human activities (anthropogenic). Increased cadmium content in soil due to human activities can occur due to agricultural activities, such as the continuous use of chemical fertilizers and pesticides. These chemical products contain harmful heavy metals such as cadmium, which results in soil pollution due to the accumulation of these metals in the soil and the entry of these metals into agricultural products, thus affecting health. The problem can be solved by soil bioremediation that utilizes indigenous bacteria. This study aims to explore cadmium-resistant bacteria with high resistance levels that can be used for the bioremediation of cadmium-contaminated soil. Cadmium-resistant bacteria were explored from 4 locations in Karawang District, Indonesia, with soil cadmium content >0.5 ppm, namely 2 locations in Telukjambe Village, 1 in Purwajaya Village, and 1 in Lemahmukti. 14 cadmium-resistant bacterial isolates with different characteristics were obtained from these 4 locations. Microbiological tests conducted include Gram staining test, resistance test, pathogenicity test, and bacterial DNA test. Seven bacterial isolates were found to be non-pathogenic to humans and plants. The best three bacterial isolates from 7 non-pathogenic isolates with resistance ability 50-500 ppm can potentially be used as a bioremediation of cadmium-contaminated soil. The three isolates are isolates B1, B6, and B12. DNA test results stated that isolate B1 is Shewanella decolorationis strain NSSD01, B6 is Chryseobacterium cucumeris strain E1-3, and B12 is Aeromonas hydrophila strain GX5.
Bird community structure and host plant in Sukamade Resort, Meru Betiri National Park, East Java, Indonesia ABDU ROHMAN; DICKY WAHYUDI; WACHJU SUBCHAN; JUMADIAWAN JUMADIAWAN
Biodiversitas Journal of Biological Diversity Vol. 25 No. 9 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d250952

Abstract

Abstract. Rohman A, Wahyudi D, Subchan W, Jumadiawan. 2024. Bird community structure and host plant in Sukamade Resort, Meru Betiri National Park, East Java, Indonesia. Biodiversitas 25: 3295-3308. Meru Betiri National Park (MBNP), East Java, Indonesia, is classified as a conservation area. Management of Biological Natural Resources (MBNR) refers to bird communities in a habitat. Damage to biological natural resources causes a high threat of bird vulnerability and extinction. Birds play a crucial role as indicators of the environment. This research aimed to determine the community structure of birds and host plants at the Sukamade resort. We recorded 49 bird species and 21 host plants. We are actively identifying location points according to habitat variations. Resort offices have the highest diversity (H ' = 2.774). The jungle track has the highest bird evenness index (E = 0.754). Parang Kulon has the highest dominance index (D = 0.162). Pycnonotus goiavier (pg) had the highest abundance found at each location. Pavo muticus (pm) is a protected species according to Indonesian national law. A total of 21 plants were documented as the dominant vegetation. Our research revealed that Ficus benjamina (FB) had the highest frequency of visits by pollinators, and the prevailing avian behavior observed was perching. The presence of Haliaeetus leucogaster (hl) nesting on Artocarpus elasticus (AE) trees was documented. Meanwhile, the Principal Component Analysis (PCA) results showed that four bird species, namely Merops leschenaulti (ml), Rhyticeros undulatus (ru), P. goiavier (pg), Pycnonotus simplex (ps), Anthracoceros albirostris (aa)) were correlated with two host plant species (A. elasticus (AE) and Albizia chinensis (AC)). Our results demonstrate a significant link between the presence of birds and host plants, underscoring their integral role in the ecology.
In vitro evaluation of synbiotics combinations of different inulin concentrations and multi-strains probiotics based on microbial growth and digestive enzymes production AYMAN ALAMEEN MOHAMMED; SITI ASLAMYAH; ZAINUDDIN ZAINUDDIN; MUHAMMAD IQBAL DJAWAD
Biodiversitas Journal of Biological Diversity Vol. 25 No. 10 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d251031

Abstract

Abstract. Mohammed AA, Aslamyah S, Zainuddin, Djawad MI. 2024. In vitro evaluation of synbiotics combinations of different inulin concentrations and multi-strains probiotics based on microbial growth and digestive enzymes production. Biodiversitas 25: 3693-3702. This study aimed to isolate and characterize inulin from sweet potatoes, and to determine the best synbiotics combination between inulin and multi-strains probiotics (MSP) (Bacillus spp., Rhizopus sp., and Saccharomyces sp.) using an in vitro methods. In the first phase, inulin was extracted using two methods, namely rotary evaporator and freeze-dryer, and subsequently characterized through fourier transform infrared spectrometry (FT-IR). The results showed that freeze-dryer was more effective compared to evaporator method. In the second phase, an in vitro method was used to evaluate the effect of inulin concentrations (0, 1, 3, and 5 mL), type of medium (nutrient agar (NA), potato dextrose agar (PDA)), and incubation time (24 and 48 hours) on MSP growth by measuring microbial growth and digestive enzymes production. The results showed significant differences (P<0.05) in microbial growth based on inulin concentration and incubation time. Higher inulin concentrations led to increased growth of all probiotics strains compared to lower concentrations in both media. In addition, the 48-hour incubation time generally led to a higher microbial growth compared to 24 hours. The findings of this study also showed distinct patterns in the production of protease and amylase enzymes, with higher doses of inulin fostering protease production and lower doses being more conducive to amylase production.
Assessment of spatio-temporal dynamics of mangrove forest in Teluk Pangpang, Banyuwangi, East Java, Indonesia ZAINUL HIDAYAH; HERLAMBANG AULIA RACHMAN; DWI BUDI WIYANTO
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/d250736

Abstract

Abstract. Hidayah Z, Rachman HA, Wiyanto DB. 2024. Assessment of spatio-temporal dynamics of mangrove forest in Teluk Pangpang, Banyuwangi, East Java, Indonesia. Biodiversitas 25: 3138-3150. Mangrove forest in Teluk Pangpang, Banyuwangi District, East Java, Indonesia is located in a semi-enclosed bay area on the east coast of Java Island and bordering with Bali Strait. Since 2020, this location has been designated as an Essential Ecosystem Area (EEA) by the Indonesia Ministry of Environment and Forestry. Regardless of its designation as an EEA, information on vegetation stucture and spatio-temporal changes of Teluk Pangpang’s mangrove forest is limited. The availability of multi-temporal medium to high-resolution satellite imagery data enables researchers to monitor the condition of mangrove ecosystem using long-term data and reliable spatial continuity. The objective of this study is to investigate vegetation community structure of mangrove forest in Teluk Pangpang, as well as to determine the changes in extent and condition of mangrove forest measured as Mangrove Health Index (MHI) between 2015 and 2023 using remote sensing and GIS analysis. Spatio-temporal dynamics of MHI was determined using Sentinel-2 imagery data from 2015, 2018 and 2023. Meanwhile, a series of extensive survey in 15 transects with a total of 75 plots were conducted to obtain field data. The results showed that Rhizophora apiculata Blume and R. mucronata Lam. were the most important species with Important Value Index (IVI) of 140.91 and 148.24, respectively. Meanwhile, Sentinel-2 image processing results revealed a major increase in mangrove’s area, from 643.35 ha in 2015 to 737.51 ha in 2023. Furthermore, MHI analysis indicated improving conditions of mangrove ecosystem, as evidenced by the significant increased of mangroves area at the excellent MHI category (MHI>66.8) from 11.00 ha in 2015 to 175.86 ha in 2023. Based on Principal Component Analysis (PCA) several environmental parameters were strongly correlated to MHI including salinity, DO, TSS and mangrove’s diversity index. The findings of this study, primarily the application of MHI approach, may provide an alternative strategy for monitoring the dynamics of vegetation cover of mangrove forest in Teluk Pangpang and other mangrove areas in Indonesia.
Association of sago plants with weeds in agroecosystem in Ambon Island, Maluku, Indonesia MUHAMMAD RIADH ULUPUTTY; SAMIN BOTANRI; MARWANYANI KAMSURYA; JAHRA PELU; NURENY GOO; MAIMUNA LA HABI; AMINUDDIN UMASANGADJI
Biodiversitas Journal of Biological Diversity Vol. 26 No. 7 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d260702

Abstract

Abstract. Uluputty MR, Botanri S, Kamsurya M, Pelu J, Goo N, La Habi M, Umasangadji A. 2025. Association of sago plants with weeds in agroecosystem in Ambon Island, Maluku, Indonesia. Biodiversitas 26: 3105-3112. Sago plays an important role in maintaining food security in some areas in Indonesia, including in Maluku. Nonetheless, there is limited knowledge regarding weed species in the context of sago agroecology. The research aims to investigate interspecific association between sago plants and various weed species in sago cultivation ecosystem in Ambon Island, Maluku. Data collection was conducted by establishing 100 observation plots in three sampled areas where sago field occurred. Interspecific association was determined through two stages of analysis, namely determining the presence of association between species simultaneously, and continued by measuring the level of association between paired species. The results of pairwise chi-square analysis show that there is negative association within the same sago species and between three sago species of Metroxylon rumphii, M. longispinum, and M. sylvestre, indicating competition among them. Meanwhile, negative association between sago species and non-sago species occur with two species, namely Nephrolepis exaltata, and Homalomena rubra, suggesting that these two species act as weed in sago agroecology in Ambon Island. The findings of this study emphasize the attention to reducing the competition among sago plants as well as controlling the disturbance from the two weed species to increase sago yield quality and productivity.
Heavy metals concentration in sediment and their bioaccumulation in several organisms in Benoa Bay and Lembongan Island, Bali, Indonesia PUTU YUDI ADITYA PUTRI; RASTINA RASTINA; TRI PRARTONO; MEUTIA SAMIRA ISMET
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/d250744

Abstract

Abstract. Putri PYA, Rastina, Prartono T, Ismet MS. 2024. Heavy metals concentration in sediment and their bioaccumulation in several organisms in Benoa Bay and Lembongan Island, Bali, Indonesia. Biodiversitas 25: 3230-3238. Human activities could be responsible for introducing heavy metals into coastal areas, and it can contaminate coastal waters such as the tourism area of Benoa Bay and coastal ecosystems of Lembongan Island, Bali, Indonesia. This study aimed to assess the extent of heavy metals on the sediment of those area and their accumulation rate in several marine organisms, including macro-algae (Ulva sp.), seagrass (Thalassia hemprichii), and sea urchin (Diadema sp.). Samples of surface sediments and marine organisms were collected at six stations for both areas and the presence of five heavy metals (Fe, Pb, Cd, Cu, and Cr) was determined using the AAS method. The concentration those metals varied significantly across the six stations. The geo-accumulation index showed that the sediment has been contaminated by Pb and Cd. The ecological risk of heavy metals contamination in Benoa Bay was apparently higher compared to that in Lembongan Island. Marine organisms in Benoa Bay also significantly accumulated heavy metals than those observed in Lembongan Island. Bioconcentration factor (BCF) shows that Cd, Cr, and Pb were the most accumulated heavy metals in marine organisms (BCF>1). It, therefore, suggest that future studies of the bioavailability of heavy metals and exploration the varying capacities of marine organisms are required. Such important information can be used to predict the accumulation of heavy metals in human bodies, and the possibly daily consumption of marine organisms caught from Benoa Bay and Lembongan Island waters.
Abundance of fungi on rice straw compost and husk biochars by in-vitro heavy metals mycosorbent NURUL PUSPITA PALUPI; RORO KESUMANINGWATI; ARYA BAYA SRIPATI; ESTI HANDAYANI HARDI; FAHRUNSYAH FAHRUNSYAH; DWI ERMAWATI RAHAYU; RUDY AGUNG NUGROHO; SURYA DARMA; SURIA DARMA IDRIS
Biodiversitas Journal of Biological Diversity Vol. 26 No. 4 (2025)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d260447

Abstract

Abstract. Palupi NP, Kesumaningwati R, Sripati AB, Hardi EH, Fahrunsyah, Rahayu DE, Nugroho RA, Darma S, Idris SD. 2025. Abundance of fungi on rice straw compost and husk biochars by in-vitro heavy metals mycosorbent. Biodiversitas 26: 1983-1990. In Samarinda, all paddy fields are contaminated by heavy metals with concentrations exceeding the critical threshold and has disrupted human health and worsened the quality of the agroecosystem of rice fields. This study aims to evaluate the effectiveness of compost and biochar application in absorbing heavy metals in paddy field soil in Samarinda. The research method involves the application of compost, biochar, and their combination on paddy field soil contaminated with heavy metals using incubation experiment with 5 treatments and 4 replications, completely randomized design, and measured parameters (pH, Fe, Zn Cd, and Aspergillus niger). The results indicate that the use of compost significantly increases the population of A. niger and reduces the concentration of heavy metals such as Fe, Zn, and Cd in the soil. On the other hand, biochar has also proven effective in reducing the content of heavy metals, supported by its high adsorption capacity. The combination of compost and biochar shows better results compared to individual applications, indicating synergy between organic nutrients and adsorption capabilities. The correlation between the population of A. niger and heavy metals demonstrates a significant relationship, confirming the role of microbes in soil bioremediation. The practical implication of this research underscores the importance of organic fertilizer use in reducing heavy metal contamination, supporting sustainable agriculture, and reducing dependence on synthetic chemicals. Future research is recommended to further understand the mechanisms of bioremediation and soil microbe interactions in this context. In conclusion, the application of compost and biochar offers a holistic approach to effectively address heavy metal contamination issues, enhance soil quality, and support environmentally friendly agriculture.
Diversity of quantitative, qualitative, and vitamin C content characteristics in F5 generation of Capsicum baccatum HILDA ADINA RAHMI; MUHAMAD SYUKUR; DEWI SUKMA; SYARIFAH IIS AISYAH
Biodiversitas Journal of Biological Diversity Vol. 25 No. 9 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d250907

Abstract

Abstract. Rahmi HA, Syukur M, Sukma D, Aisyah SI. 2024. Diversity of quantitative, qualitative, and vitamin C content characteristics in F5 generation of chili pepper Capsicum baccatum species. Biodiversitas 25: 2878-2886. Chili is a popular vegetable worldwide, and Indonesia is one of the largest chili producers. However, the cultivation of Capsicum baccatum species is still uncommon in Indonesia. This study aimed to assess the diversity and heritability of yield and yield quality of F5 populations of C. baccatum. This study was conducted at the Experimental Field of Perumahan Alam Sinar Sari, Bogor. The experiment followed a randomized complete block design (RCBD) using 12 genotypes with three replications and four sample plants per replication. The F5 populations of the following genotypes were used: 4k-6p, 4k-7p, 7m-4q, 2m-2m, 7m-3q, 7m-3m, 7m-2q, 2m-2q, 7m-8m, 7m-1m, Bishop Crown, and Lemon Drop. The observations included quantitative, qualitative character,vitamin C contents, and soluble solids. The results showed that the fruit weight per plant ranged from 37.73 to 94.24 grams, while the number of fruits per plant ranged from 11.46 to 30.95. Fruit length ranged from 2.65 to 6.08 cm, and fruit diameter ranged from 15.70 to 41.43 mm. The weight per fruit ranged from 3.43 to 14.89 grams. Brightness or L* values ranged from 19.06 to 41.93, a* values ranged from 5.62 to 31.49, and b* values ranged from 22.90 to 57.45. The chroma value ranged from 30.87 to 64.20, and the hue value ranged from 46.54 to 80.23. The analysis of vitamin C content showed a range of 12.20 to 17.74 mg/20 g, and the test results of soluble solids ranged from 8.77% to 13.49%. All quantitative characters showed high heritability, indicating a strong genetic influence on these characters. The qualitative observations were analyzed, and the results showed that the 12 C. baccatum chilies had similarity coefficients ranging from 0.0 to 0.5. The similarity analysis resulted in grouping the 12 genotypes of C. baccatum into four main groups.

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