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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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Morphological and molecular identificationof fungal pathogens causing gummosis disease of Citrus spp. in Indonesia JULINDA B.D. HENUK; MEITY S. SINAGA; SRI H. HIDAYAT
Biodiversitas Journal of Biological Diversity Vol. 18 No. 3 (2017)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d180330

Abstract

Henuk JBD, Sinaga MS, Hidayat SH. 2017. Morphological and molecular identificationof fungal pathogens causing gummosis disease of Citrus spp. in Indonesia. Biodiversitas 18: 1100-1108. Gummosis is one of the most important diseases of citrus. The disease is caused by several species of Phytophthora, i.e. P. nicotianae, P. palmivora, P. citrophthora; as well as Lasiodiplodia theobromae (synonyms: Botryodiplodia theobromae and Diplodia natalensis; teleomorph Botryosphaeria rhodina). The objective of this study was to identify the isolates of fungal pathogens, i.e. Phytophthora spp. and B. theobromae and/or D. natalensis from several different areas of citrus central production in Indonesia based on their morphological and molecular characteristics. This study included two activities, i.e. (i) collection, isolation, and identification of pathogenic fungi from infected tissues, basal stem roots, and soil surface and rhizosphere; and (ii) extraction of genomic DNA and amplification of DNA fragments using PCR technique for molecular characterization. Results of morphological characterization and DNA sequence analysis revealed that gummosis was caused by Botryodiplodia theobromae Pat. (Teleomorph Botryosphaeria rhodina (Cooke) Arx.)), and P. citrophthora.
Distribution of Cichlopsis leucogenys (Aves: Turdidae) in Brazil and its relation to protected areas HUILQUER FRANCISCO VOGEL; MANOELE MARCOLIN BERNARDON; CLAUDIO HENRIQUE ZAWADZKI
Biodiversitas Journal of Biological Diversity Vol. 18 No. 3 (2017)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d180332

Abstract

Vogel HF, Bernardon MM, Zawadzki CH. 2017. Distribution of Cichlopsis leucogenys (Aves: Turdidae) in Brazil and its relation to protected areas. Biodiversitas 18: 1116-1121. The Rufous-brown Solitaire (Cichlopsis leucogenys Cabanis, 1851) is endangered in Brazil, and the demarcation of priority areas is needed for its in situ conservation. Accordingly, we reviewed the distribution of C. leucogenys and assessed its association with protected areas (PAs) by analyzing 70 occurrence records from 1942 to 2014 that were collected from online datasets. Of these records, 38 (54.4%) were from Bahia State, 27 (38.5%) were from Espírito Santo State, and five (7.1%) were from Minas Gerais State, and the Biological Reserve Augusto Ruschi (Espírito Santo State), State Park Serra do Conduru (Bahia State), and Serra do Ouro Environmental Protected Area (Bahia) were identified as key PAs. One record described an observation of the species at 45 m above sea level, which is lower than expected. We verified the potential occurrence of the species in 31 PAs that were located in southern Bahia to the mountains in both Espírito Santo and Minas Gerais. The Ilhéus-Itabuna region should be given special attention during conservation efforts, owing to records of species presence outside PAs, which should also be considered by management plans.
Genetic variation of the mangrove species Avicennia marina in heavy metal polluted estuaries of Cilegon Industrial Area, Indonesia JEPRIANTO MANURUNG; ISKANDAR Z. SIREGAR; CECEP KUSMANA; FIFI GUS DWIYANTI
Biodiversitas Journal of Biological Diversity Vol. 18 No. 3 (2017)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d180331

Abstract

Manurung J, Siregar IZ, Kusmana C, Dwiyanti FG. 2017. Genetic variation of the mangrove species Avicennia marina in heavy metal polluted estuaries of Cilegon Industrial Area, Indonesia. Biodiversitas 18: 1109-1115. Mangrove forests are often facing various anthropogenic disturbances, particularly in the industrial area. However, information on the status of industrial heavy metal pollution and its impact on the genetic variation of mangrove species, such as Avicennia marina, particularly in Indonesian industrial area has not been assessed. In this study, the classification of heavy metals in two estuaries of Cilegon Industrial Area (Pelabuhan Warna Sari and Krakatau) and one estuary outside Cilegon Industrial Area (Pulau Sangiang) were determined by Sediment Quality Guidelines- States Environment Protection Agency (SQGs-USEPA). Furthermore, the genetic diversity of 72 individuals of A. marina in the three estuaries were examined using four microsatellite loci (M3, M64, M81 and M98). The results showed that Krakatau area was the heavily polluted estuary based on SQGs-USEPA and have a lower genetic variation (He= 0.54) than Pelabuhan Warna Sari (moderately polluted, He= 0.56) and Pulau Sangiang (non-polluted, He= 0.60) suggesting a notable of deficiencies of genetic variation of A. marina in heavy polluted estuary compared to moderately and non-polluted estuary. Considering the low level of genetic variation in heavily polluted area, transplantation among estuaries and introduction of propagules from non-polluted estuary or other regions are needed as one of the conservation efforts.
Short Communication: The nest characteristics of Wreathed Hornbill (Rhyticeros undulatus) in Mount Ungaran, Central Java, Indonesia MARGARETA RAHAYUNINGSIH; NUGROHO EDI KARTIJONO; AMIN RETNONINGSIH
Biodiversitas Journal of Biological Diversity Vol. 18 No. 3 (2017)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d180334

Abstract

Rahayuningsih M, Kartijono NE, Retnoningsih A. 2017. Short Communication: The nest characteristics of Wreathed Hornbill (Rhyticeros undulatus) in Mount Ungaran, Central Java, Indonesia. Biodiversitas 18: 1130-1134. Java has three species of hornbills, one of them is the Wreathed Hornbill (Rhyticeros undulates Shaw, 1811) that can be found mainly throughout on Mount Ungaran, Central Java, Indonesia. The main threats to Wreathed Hornbill population are habitat fragmentation and forest clearing. The large trees used for nesting by the Wreathed Hornbill are usually located in areas of illegal logging. Therefore, it is necessary to study the characteristics of Wreathed Hornbill nests, especially in Mount Ungaran. Eight nests were discovered, six of which were active. The nests were found at 900-1200 m above sea level. Trees that were used as nest sites were between 24-35 m high, and had a diameter of 0.83-1.75 m. Nests were located at heights of 1-27 m, and had a hole diameter of 33-38 cm, hole length of 170-211 cm, entrance width of 4-11 cm, entrance length of 14-39 cm, nest thickness 6-18 cm, and a temperature of 20-21°C. The nest shapes were oval, ellipse, and irregular oval. Commonly, the Wreathed Hornbills used Syzygium glabratum, Syzygium antisepticum, and Cratoxylum formosum for nesting.
Variability of upland rice genotypes response to low light intensity ARIS HAIRMANSIS; YULLIANIDA YULLIANIDA; SUPARTOPO SUPARTOPO; ALI JAMIL; SUWARNO SUWARNO
Biodiversitas Journal of Biological Diversity Vol. 18 No. 3 (2017)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d180333

Abstract

Hairmansis A, Yullianida, Supartopo, Jamil A, Suwarno. 2017. Variability of upland rice genotypes response to low light intensity. Biodiversitas 18: 1122-1129. Plantation areas have a great potential to be utilized for upland rice production through intercropping. One of major constraints in the cultivation of upland rice as intercropping is low light intensity caused by shading. Improvement of rice varieties for shading tolerance is therefore important to increase rice production in upland areas. The objective of this study was to investigate the variability of upland rice genotypes responses to shading and identify the best genotypes for intercropping rice cultivation. Thirty-eight upland rice breeding lines, the shading tolerant rice variety Jatiluhur, and the shading susceptible rice variety IR64 were evaluated for their response to low light intensity in the greenhouse and the field. Greenhouse screening was conducted to determine their shading tolerance in vegetative stage while evaluation in the field was performed to evaluate their agronomic performance under 55% shading and normal conditions. Variation in upland rice genotypes on low light stress was revealed both in greenhouse and field trials. In the greenhouse trial, 12 genotypes showed higher survival rate compared to tolerant rice variety Jatiluhur. Field evaluation demonstrated that 55% shading increased plant height, reduced productive tiller number, delayed flowering time, increased spikelet sterility and reduced grain yield. Upland rice breeding line B11908F-TB-3-WN-1 showed high yield relative in shading condition compared to normal condition and had high-stress tolerance index (STI) which indicated the genotype was tolerant to shading.
Farmers and tumpang sari: Case study in Palintang Hamlet, Cipanjalu Village, Bandung, Indonesia BUDIAWATI S. ISKANDAR; JOHAN ISKANDAR; HIKMAT A. WIBAWA; RUHYAT PARTASASMITA
Biodiversitas Journal of Biological Diversity Vol. 18 No. 3 (2017)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d180335

Abstract

Iskandar BS, Iskandar J, Wibawa HA, Partasasmita R. 2017. Farmers and tumpang sari: Case study in Palintang Hamlet, Cipanjalu Village, Bandung, Indonesia. Biodiversitas 18: 1135-1149. People of Palintang hamlet are recognized as one of the local communities reside in the high land of surrounding forest of Manglayang Mountain of West Java, Indonesia. Based on ecological or environmental history, they initially practiced the swidden farming in the natural forest of Manglayang, West Java. Moreover, some of them involved as labor in various activities of the culture systems during the Dutch colonial. After Indonesian independent, they have participated as laborer in the tumpang sari program of the Forest Service (Dinas Kehutanan) and the State Forestry Corporation (Perhutani). Nowadays,farmers of Palintang have intensively cultivated the pine forest for planting cash crops, including cabbage and potatoes. As a result, the farming practice in the forest has caused dilemma between providing cash income for local people and endangering the stability of environment for the near future. This paper presents the findings of research on the development of agroecosystems of a the Palintang people, in relation to social-ecological-changes, particularly the forest ecosystem changes. The method used in the study was combination of qualitative and quantitative. The result of study shows that the farmers of Palintang have continuously cultivated the forest for tumpang sari since the Dutch colonial period until now. Today, they have farmed the agroecosystems of the homegarden and mixed garden in their village land, and have intensively farmed vegetable garden in the forest of the Perhutani. Based on the inventory of crops in the mixed-garden (kebun or kebun campuran) and home garden, it was recoded 47 species and 42 species, respectively. The vegetables and fruits were predominantly found in both the mixed-garden and homegarden. The practice of the commercial vegetable crops as tumpang sari in the forests of the Perhutani has provided some benefits, including fulfilling cash income for farmer households, but some negative impacts on environment, such as pollution of pesticides have also occurred.
Development of protocols for genomic library construction of Agarwood (Aquilaria malaccensis) ULFAH J. SIREGAR; MUHAMMAD IQBAL MAULANA; UTUT W. SUHARSONO
Biodiversitas Journal of Biological Diversity Vol. 18 No. 3 (2017)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d180336

Abstract

Siregar UJ, Maulana MI, Suharsono UW. 2017. Development of protocols for genomic library construction of Agarwood (Aquilaria malaccensis). Biodiversitas 18: 1150-1158. Agarwood is one of non timber forest products (NTFP) which has high economic value. Diminishing agarwood trees in natural forest due to intensive harvesting has shifted the production paradigm to forest plantation. In order to support agarwood tree improvement, investigation on the agarwood tree genomes and genes involved in agarwood production is highly needed through genomic library construction. This research aimed at establishing cloning protocols for genomic library construction of agarwood tree (Aquilaria malaccensis) until sequencing process. Genomic DNA was isolated using DNeasy Plant Mini Kit from Qiagen, then was digested with EcoR1, and was ligated to pGem®-T Easy vector system before it was finally transformed and was cloned to E.coli strain DH5α. Confirmation of DNA inserts was done using PCR colony with universal primer of SP6 and T7, plasmid isolation and also PCR plasmid and plasmid DNA digestion used Quick Plasmid Miniprep Kit from Thermofisher. Cloned A. malaccensis DNA fragments were sequenced and BLAST at NCBI site. The cloning successfully obtained five white colonies which contain inserted A. malaccensis DNA fragments with the size of 136-225 bp. PCR colony, plasmid isolation, PCR plasmid, and plasmid DNA digestion had confirmed the existence of inserted A. malaccensis DNA genome inside the bacteria cells. Sequencing and BLAST showed that DNA inserts from colony number 6, 8, and 9 were not similar with A. malccensis sequence that was recorded in NCBI, indicating that the genomic region in this library construction is different from the genomic DNA sequences of A. malaccensis in NCBI.
The diversity of diurnal bird species on western slope of Mount Lawu, Java, Indonesia A.A. KRISANTI; A. CHOIRUNNAFI; N.O. SEPTIANA; F.W. PRATAMA; F. AMELIA; A. MANJASWARI; P.A. SEPTININGTYAS; A.S. WATI; J.Y. SATRIA; I.L. ANI; T. WIBOWO; SUGIYARTO SUGIYARTO
Biodiversitas Journal of Biological Diversity Vol. 18 No. 3 (2017)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d180327

Abstract

Krisanti AA, Choirunnafi’ A, Septiana NO, Pratama FW, Amelia F, Manjaswari A, Septiningtyas PA, Wati AS, Satria JY, Ani IL, Wibowo T, Sugiyarto. 2017. The diversity of diurnal bird species on western slope of Mount Lawu, Java, Indonesia. Biodiversitas 18: 1077-1083. Mount Lawu is one of the highest inactive volcanoes in Java Island, Indonesia. Mount Lawu attracts people to cultivate its area for agriculture, but without proper management, the biodiversity in Mount Lawu is in threat. This research aimed to get information about diurnal bird diversity on the western slope of Mount Lawu which includes a forest area (FA), an agroforestry area (AA), and a residential area (RA). Data collection was performed through point count method in 5 to 6 point per sites within certain time intervals after dawn and before sunset. There were 61 bird species from 26 families with a total number of 1416 birds being observed. The diversity index of the western slope was 2.480, and the highest Hmax among observed areas was the forest area (3.714). Collocalia linchi (Di 37.92) and Pycnonotus aurigaster (Di 19.42) were very common almost in all observation areas. The most similar ecosystem was FA and AA (J 0.176), followed by AA and RA (J 0.24), and FA and RA (J 0.393). A better management of Mount Lawu is necessary to improve human and biodiversity wellness. The result of this study could be used as additional data to consider a stronger protection for the biodiversity in Mount Lawu.
Characterization and performance of agronomic characters of soybean genotypes resistant to pod shattering AYDA KRISNAWATI; M. MUCHLISH ADIE
Biodiversitas Journal of Biological Diversity Vol. 18 No. 3 (2017)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d180338

Abstract

Krisnawati A, Adie MM. 2017. Characterization and performance of agronomic characters of soybean genotypes resistant to pod shattering. Biodiversitas 18: 1158-1164. Pod shattering is one of the major obstacles of soybean cultivation in Indonesia’s tropical climate. A total of 24 soybean genotypes, including Anjasmoro (check variety for pod-shatter resistant), Argomulyo and Grobogan (susceptible to pod shattering). The field experiment was conducted in Banyuwangi (East Java, Indonesia) during the dry season II 2016. The experimental design was randomized block, consisted of 24 soybean genotypes as sample trait with four replications. Pods from six random plants at physiological maturity (R8) were detached for pod shattering evaluation. The pod shattering evaluation was conducted in Laboratory of Plant Breeding, Indonesian Legumes and Tuber Crops Research Institutes (Malang, Indonesia) by using oven method and ambient temperature method. The classification of shattering resistance was according to Bailey et al. (1997) and Mohammed (2010), i.e. resistant (0-10% shattered pods), intermediate (11-70 % shattered pods) and susceptible (71-100% shattered pods). The average shattered pods of 24 genotypes by oven method reached 42.67%, higher than those of ambient method (21.81%). Six soybean genotypes showed consistently resistant to pod shattering based on oven as well as ambient method. Pods position at lower part was more susceptible to pod shattering than those at middle and upper part. The limit of pod shattering was ranging from two to 38 days. Genotype of G511H/Anjs/Anjs-1-2 which characterized by pod shatter resistant, produced high yield, and large seed size, was potentially developed at the tropical area, such as Indonesia.
Sixteen years changes in tree density and aboveground biomass of a logged and burned dipterocarp forest in East Kalimantan, Indonesia TAKESHI TOMA; WARSUDI WARSUDI; YOKO OSONE; SUTEDJO SUTEDJO; TAMOTSU SATO; SUKARTININGSIH SUKARTININGSIH
Biodiversitas Journal of Biological Diversity Vol. 18 No. 3 (2017)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d180337

Abstract

Toma T, Warsudi, Osone Y, Sutedjo, Sato T, Sukartiningsih. 2017. Sixteen years changes in tree density and aboveground biomass of a logged and burned dipterocarp forest in East Kalimantan, Indonesia. Biodiversitas 18: 1159-1167. Changes in tree density and aboveground biomass (AGB) of a logged and burned lowland dipterocarp forest were monitored in Bukit Soeharto Research and Education Forest (BSREF) of Mulawarman University, East Kalimantan, Indonesia. A 9-ha plot was established in 1997 to investigate the effect of second felling and the subsequent recovery. Experimental felling was conducted in October 1997, and the plot was burned by uncontrolled fires between February and April 1998. Stem diameter of living trees (diameter at breast height ≥ 10 cm) in the plot was recorded annually. Allometric functions and the annual tree inventory were used to estimate changes in AGB. Tree density in the 9-ha plot was 429 trees ha−1 before the experimental felling.This decreased to 76 trees ha−1 in 2000 because of the felling and fires. Tree density increased to 515 trees ha−1 until 2008 and then decreased to 408 trees ha−1 in 2014. AGB of the 9-ha plot was 279 Mg ha−1 in 1997,which decreased to 96 Mg ha−1 in 2000 and then increased to 139 Mg ha−1 in 2014. After 16 years of the 1998 fires, in 2014, BSREF consists of a mosaic of forest stands that are dominated by either large late successional tree species or small pioneer trees. The former stands consisted of numerous late successional tree species that survived the felling and fires. The latter stands were dominated by a few pioneer species. In 2016, 16 years after the fire, these pioneer dominating stands are now undergoing a transitional stage from pioneer to late successional trees that grow longer and larger than the pioneer trees. Logged and burned forest stands may recover their AGB comparable to that of the original forest (≥400 Mg ha−1), if these stands are saved from further logging and fires in the longterm.

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