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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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Enhancement of manganese extraction in a biochar-enriched bioleaching column with a mixed culture of indigenous bacteria Endah Retnaningrum; WAHYU WILOPO; I WAYAN WARMADA
Biodiversitas Journal of Biological Diversity Vol. 22 No. 5 (2021)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d220560

Abstract

Abstract. Retnanimgrum E, Wilopo W, Warmada IW. 2021. Enhancement of manganese extraction in a biochar-enriched bioleaching column with a mixed culture of indigenous bacteria. Biodiversitas 22: 2949-2955. Biochar can improve manganese ore extraction during bioleaching by inducing redox reactions and providing a porous matrix for bacterial attachment. In this research, the effect of variations in biochar concentration on the performance of a bioleaching column with a mixed culture of Acidithiobacillus sp. KL3 and Bacillus niacini KB3B1 were studied comprehensively for 30 days. Addition of 0.4% biochar resulted in 89% manganese extraction. Bioleaching with biochar promoted the oxidation of sulfur and yielded high sulfate concentrations, much better pH, and excellent oxidation–reduction potential conditions. The bacteria in the mixed culture survived and adapted to the extreme column environment by releasing extracellular polymeric substance, as evidenced by the sharp increase in the content of the material in the column to 135.7 mg/g over 30 days of incubation. The synergistic effect of the bacteria in the mixed culture greatly contributed to the mechanism of manganese extraction in the column, as indicated by changes in relative bacterial abundance, which is related to bacterial community succession during bioleaching. The relative abundance of B. niacini KB3B1 gradually increased and peaked at 30% over 9 days of measurements. By comparison, the abundance of Acidithiobacillus sp. KL3 first decreased over 9 days of bioleaching and then increased to a maximum of 80% in the final stages of the process. This finding reveals that biochar addition could enhance the mechanisms of bioleaching and improve the yield of manganese extraction.
Genetic diversity and morphological responses of Capsicum annuum varieties under aluminum stress ANDRIYANI ANDRIYANI; Nurul Jadid
Biodiversitas Journal of Biological Diversity Vol. 22 No. 5 (2021)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d220516

Abstract

Abstract. Andriyani, Jadid N. 2021. Genetic diversity and morphological responses of Capsicum annuum varieties under aluminum stress. Biodiversitas 22: 2576-2582. Capsicum annuum is one of the most cultivated vegetable crops in the world. Its fruit contains various beneficial metabolites which possess antioxidant activities. Fertilizers play important role to increase plant productivity. However, excessive use of fertilizers could harm the environment. Heavy metals, including aluminum (Al), contamination have been reported to negatively affect plant production and inhibit root growth. C. annuum var Ciko, Lingga, Lembang1, and Tanjung2 are commonly cultivated in Indonesia. However, the genetic diversity of those plants and their responses to Al stress condition are still unknown. Therefore, our study aimed to analyze the genetic diversity of four C. annuum cultivars and to observe their morphological responses under Al stress conditions. The genetic diversity was analyzed using five universal inter-simple sequence repeat (ISSR) primers. Our results showed that the PIC values ranged from 0 (primer 825) to 0.6375 (Primer 9). The UPGMA phylogenetic construction also demonstrated that the cv. Lembang1 is closely related to the cv Lingga. Meanwhile, cv Tanjung 2 is closely related to the cv. Ciko. Each cultivar also performed different morphological responses under Al stress conditions. Our data showed that Al affected significantly root growth but not affected their plant height. Aluminum at 100 ppm significantly decreased root length of cv. Lingga
Land change-based forest management scenario in the typology of island clusters in Maluku Province, Indonesia Patrich papilaya; I NENGAH SURATI JAYA; TEDDY RUSOLONO; NINING PUSPANINGSIH
Biodiversitas Journal of Biological Diversity Vol. 22 No. 9 (2021)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d220920

Abstract

Abstract. Papilaya PPE, Jaya INS, Rusolono T, Puspaningsih N. 2021. Land change-based forest management scenario in the typology of island clusters in Maluku Province, Indonesia. Biodiversitas 22: 3756-3763. This study aims to describe the development of forest area utilization scenarios with biophysical, social and spatial trend approaches. In this study, spatial trends were identified using forest and land cover maps from 2000 to 2018, and the methods used include change detection, spatial trend and overlay. The study was designed using forest cover scenarios along with spatial trends and social and biophysical approaches. The results of the 5 typologies of island clusters analysis showed that forest degradation has occurred in an area of ± 77102 ha between 2000 and 2018 with an average of 4283.4 ha/year. Furthermore, Total Land Cover Loss at the location of the five island cluster typology for 18 years was found to be ± 422805 Ha with an average of ± 23489.06 ha/year. The land capability was categorized into 3 classes. Therefore, the five spatial trends were known to form in the typology of five island clusters with different directions and magnitudes.
Fieldwork during pandemic: Backyard bird survey and making student’s biological field practice works Nurul Laksmi Winarni; Bhisma G. Anugra; Shania Anisafitri; Nabilla N. Kaunain; Dimas H. Pradana
Biodiversitas Journal of Biological Diversity Vol. 22 No. 4 (2021)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d220435

Abstract

Abstract. Winarni NL, Anugra BG, Anisafitri S, Kaunain NN, Pradana DH. 2021. Fieldwork during pandemic: Backyard bird survey and making student’s biological field practice works. Biodiversitas 22: 1887-1894. The COVID-19 pandemic situations had forced universities to shutdown face-to-face lectures and change it to online teaching. This change had brought significant challenges to biological courses which need field practice in their syllabus and therefore field practice should be adjusted and innovative. During November-December 2020, we compared students' field practice from the Ornithology class to urban bird survey to evaluate whether the data collected by students can contribute to citizen science as well as to enhance field practice during online courses. We used point count methods to survey bird communities in urban environment in Jakarta and its satellite cities. We found that the students tended to observe the most abundant birds such as the cave swiftlet and Eurasian tree sparrow and missed unfamiliar species which were smaller-sized birds that use aerial and upper canopy. It was suggested that the data from field practice can also support citizen science when prioritized to common, abundance species. In addition, best practices for field practice were provided, emphasizing the independent field practice incorporating technology in which the results were communicated to the students. Hence, strengthening field practice for biological courses is important to support biodiversity conservation research and activities.
Reef fish community structure in the islands of Paraja Bay, Pandeglang District, Banten, Indonesia MUJIYANTO MUJIYANTO; YAYUK SUGIANTI; YUSUF ARIEF AFANDY; RISNAWATI RAHAYU; R. ARIEF BUDIKUSUMA; ADRIANI SRI NASTITI; AMRAN RONNY SYAM; SRI ENDAH PURNANINGTYAS
Biodiversitas Journal of Biological Diversity Vol. 22 No. 10 (2021)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d221033

Abstract

Abstract. Mujiyanto, Sugianti Y, Afandy YA, Rahayu R, Bidikusuma RA, Nasriri AS, Syam AR, Purnaningtyas SE. 2021. Reef fish community structure in the islands of Paraja Bay, Pandeglang District, Banten, Indonesia. Biodiversitas 22: 4402-4413. Paraja Bay waters have five small islands that coexist with Ujung Kulon National Marine Park and act as a buffer zone for the diversity of fishery resources. This study aimed to assess the reef fishes community structure at small islands in Paraja Bay. Observations were made in 20 locations during August and September 2019 in the five small islands. Reef fishes community structure showed 106 species as included major group (54 species), indicator group (24 species) and target group (28 species), among five small islands, i.e. Badul, Mangir, Oar, Sumur and Umang Islands. The highest reef fishes abundance was founded in Umang Island waters. Several target fish species recorded during the study were mature fish (such as those targeted by fishermen). Only a small proportion were juveniles. Reef fish community structure was categorized as stress community to stable community with its indication was low diversity value, high evenness index, and low dominance. The low diversity index value illustrates that the level of uniformity of reef fish species in Paraja Bay waters is high. This condition is evidenced by each coral fish group's evenness index included in the main species group around 0.93 to 0.98. The target species is 0.88 to 0.99.
Identification of conserved peptide upstream open reading frames (CPuORFs) in oil palm (Elaeis guineensis) genome ANDREA PUTRI SUBROTO; REDI ADITAMA; ZULFIKAR ACHMAD TANJUNG; CONDRO UTOMO; TONY LIWANG
Biodiversitas Journal of Biological Diversity Vol. 22 No. 4 (2021)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d220428

Abstract

Abstract. Subroto AP, Aditama R, Tanjung ZA, Utomo C, Liwang T. 2021. Identification of conserved peptide upstream open reading frames (CPuORFs) in oil palm (Elaeis guineensis) genome. Biodiversitas 22: 1829-1838. Upstream open reading frame (uORF) translation serves as one of several modulating mechanisms in gene expression. Conserved peptide uORF is a rare subset of uORF containing a peptide sequence that is conserved among eudicot families and negatively regulates the translation of its adjacent main ORF (mORF). This research aimed to identify oil palm CPuORFs by conducting a homology search between Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) CPuORF databases against the existing oil palm (Elaeis guineensis) genome. Using alignment by Hidden Markov Model (HMM) approach, 48 oil palm CPuORFs were discovered which were later divided into 24 homology groups (HG) based on its gene ontology. The high degree of sequence homology indicates a high conservation CPuORFs among oil palm, Arabidopsis and rice. The CPuORFs peptide sequence conservation between oil palm progenies was later validated by sequencing of CPuORF22 and CPuORF29 as a reference, from several DxP Tenera crosses, individual Duras from different origins and American oil palm (Elaeis oleifera). This is the first study of oil palm CPuORF discovery which might provide a better understanding of gene expression regulation in oil palm.
Diversity of sea cucumber from intertidal area of Pacitan and Bangkalan, East Java, Indonesia ELSA DIANITA AULIA; FARID KAMAL MUZAKI; DIAN SAPTARINI; EDWIN SETIAWAN; DAVIN SETIAMARGA; ISWATUL DIAH LUTVIANTI; SANIAH KUSNATUR ROSYIDAH; NUR ALI MUHAMMAD
Biodiversitas Journal of Biological Diversity Vol. 22 No. 4 (2021)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d220463

Abstract

Abstract. Aulia ED, Muzaki FK, Saptarini D, Setiawan E, Setiamarga D, Lutvianti ID, Rosyidah SK, Muhammad NA. 2021. Diversity of sea cucumber from intertidal area of Pacitan and Bangkalan, East Java, Indonesia. Biodiversitas 22: 2136-2141. Sea cucumbers have an important role in the regeneration and mineralization processes of marine sediments. They are echinoderm, and their existence influences the sustainability of other organisms in different types of marine ecosystems. The objective of the present study was to determine the diversity of sea cucumber at Tawang and Pidakan coasts in Pacitan, and Labuhan coast in Bangkalan with slight differences in habitat characteristics. Sampling was conducted from 1000 m2 marked plots using hand collecting during low tide. Species richness, composition, abundance, and diversity indexes such as Shannon-Wiener’s diversity index (H’), Simpson’s dominance index (D) and Pielou’s evenness index (J) were observed. The results showed that there were 19 species found in this study, which belonged to family Stichopodidae, Holothuruidea, and Synaptidae. The highest species richness, abundance, H’ and J value was from Tawang coast. Value of H’ was 2.620 in Tawang, followed by 2.001 in Pidakan, and 1.621 in Labuhan. The highest D index was at Labuhan coast (0.223) compared with Tawang (0.085) and Pidakan (0.158) coast.
Morphological evaluation and determination keys of 21 citrus genotypes at seedling stage Rahmat Budiarto; Roedhy Poerwanto; Edi Santosa; Darda Efendi
Biodiversitas Journal of Biological Diversity Vol. 22 No. 3 (2021)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d220364

Abstract

Abstract. Budiarto R, Poerwanto R, Santosa E, Efendi D. 2021. Morphological evaluation and determination keys of 21 citrus genotypes at seedling stage. Biodiversitas 22: 1570-1579. The identification of citrus varieties is generally based on flower, fruit, and mature tree characters. The detailed and comprehensive identification of seedling stage is very limited, therefore present study aimed to identify and distinguish 21 citrus genotypes based on 50 morphological characters of vegetative shoot at seedling stage. Cluster analysis using complete linkage agglomerative method showed broader dissimilarities between C. x limon and C. x microcarpa. Unfortunately, this method was limited to differentiate six genotypes within Citrus reticulata Blanco due to extremely low dissimilarities found. All citrus seedlings have similarities in the forms of habitus, gland spots, arrangement and venation of leaf. The result of PCA determined petiole wing, spine, color, hair and fragrance of leaves as five morphological markers at seedling stage. In addition, there was a positive correlation between spine and leaf pleasant. Moreover, the details of morphological dissimilarities between genotypes were described in arranged determination keys.
Microsatellites to reveal genetic diversity and to distinguish four mangoes of Tegal District, Central Java, Indonesia ANNUR HIDAYAT; ENNI SUWARSI RAHAYU; MUHAMMAD ABDULLAH; Amin Retnoningsih
Biodiversitas Journal of Biological Diversity Vol. 22 No. 8 (2021)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d220845

Abstract

Abstract. Hidayat A, Rahayu ES, Abdullah M, Retnoningsih A. 2021. Microsatellites to reveal genetic diversity and to distinguish four mangoes of Tegal District, Central Java, Indonesia. Biodiversitas 22: 3467-3473. The Wirasangka mango is Tegal District’s flora of identity, which requires recognition, and its existence deserves to be preserved. However, based on the morphology of the fruit, most of the people of Tegal still have difficulty distinguishing the wirasangka mango from other mangoes. Molecular markers are needed to ascertain the differences between these mango varieties. Microsatellite DNA is a repeating DNA of stable DNA markers with high repeatability and polymorphism. This study analyzes the level of genetic diversity and microsatellite alleles that can differentiate four mangoes from Tegal District, Central Java, Indonesia, i.e. wirasangka, tengkueh, golek, and okyong. Eleven accessions of six locations in Tegal District were analyzed using ten microsatellite loci. The microsatellite amplification result was separated using electrophoresis in 6% polyacrylamide gel and then visualized with silver dye. A total of 35 microsatellite alleles were found measuring 100-1000 bp, ranging from 1-7 alleles for each locus. The average polymorphism information content (PIC) of 0.54 indicates that genetic diversity is relatively high and informative. Therefore, the microsatellite alleles can be used to differentiate mango varieties. The specific allele characteristic of wirasangka mango accession is locus AJ63516, with an allele size of 600-700bp.
Diversity, conservation, potential uses, and alien species of lowland plants of Batang Toru, Sumatra, Indonesia Hirmas F. Putra; Wendy A. Mustaqim
Biodiversitas Journal of Biological Diversity Vol. 22 No. 3 (2021)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d220365

Abstract

Abstract. Putra HF, Mustaqim WA. 2021. Diversity, conservation, potential uses, and alien species of lowland plants of Batang Toru, Sumatra, Indonesia. Biodiversitas 22: 1580-1591. A recent field inventory of lowland Sumatran plant diversity was carried out in two close sites of forest patches in the Batang Toru area. These are Muara Upu Swamp Forest and Simulak Anjing Hill Forest. This study aimed to investigate the species composition of two isolated lowland Sumatran forest patches on the west coast of the northern part of the island. The total number of species recorded was 181 species with 131 species known from Simulak Anjing Hill Forest, 54 from Muara Upu Swamp Forest, and only three species recorded from both sites. There are three species endemic to Sumatra, seven species listed as threatened according to the IUCN Red List, one species protected by the Indonesian government, and two are important records for Sumatra. Compared to the published literature, 88 species have been reported to have one or more uses, with 63 species have been used as the source of medicines, 19 as sources of fibers, 18 as the source of vegetables, and several other uses. Sixteen alien species were recorded including four species categorized as 100 world’s worst invasive species. It can be concluded that both areas are a home for important lowland plants of Sumatra as indicated by the presence of threatened, endemic, or poorly documented species. Besides that, there is also a need for concern about the presence of potential invasive alien species.

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