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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 6,315 Documents
 384   385   386   387   388 
Mining and validating novel SSR markers based on coconut (Cocos nucifera L.) whole genome and their use for phylogenetic analysis ANDI NADIA NURUL LATHIFA HATTA; DEWI SUKMA; ISMAIL MASKROMO; SUDARSONO SUDARSONO
Biodiversitas Journal of Biological Diversity Vol. 23 No. 10 (2022)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d231019

Abstract

Abstract. Hatta ANNL, Sukma D, Maskromo I, Sudarsono. 2022. Mining and validating novel SSR markers based on coconut (Cocos nucifera L.) whole genome and their use for phylogenetic analysis. Biodiversitas 23: 5122-5131. The coconut (Cocos nucifera L.) genome sequences were available at the chromosome level in 2019, and they can be used to develop the whole genome SSR markers. This study aimed to conduct in silico analysis of the whole coconut genome to mine SSR sequences, design SSR markers distributed across coconut chromosomes, validate the designed primers to generate SSR markers, and use them for the phylogenetic analysis of coconuts. The SSR loci were mined from publicly available coconut genomes. Targeted primers for amplifying 20 dinucleotide SSR loci were selected and used for phylogenetic analysis of coconuts. The SSR mining identified 543,774 dinucleotide repeat motifs across the coconut genome, and most of the dinucleotide SSRs are AG (46.18%) and AT (40.03%) repeats. Primer pairs targeted to amplify 876 SSR loci and distributed in 16 coconut chromosomes were successfully designed and deposited in a public data repository for public access. The 237 SSR primer loci were novel and could generate new SSR markers. Among 20 selected and tested primers, 18 produced SSR markers, and 15 pairs yielded polymorphic markers when used to evaluate 25 coconut accessions. The analysis showed that the designed SSR primers were informative for evaluating coconut genetic diversity and phylogenetic analysis.
Identification and screening of enzymatic abilities of Ktedonobacteria from forest soil of Cisolok Geothermal Area, Indonesia MAZYTHA KINANTI RACHMANIA; FITRIA NINGSIH; DHIAN CHITRA AYU FITRIA SARI; YURIZA ESHANANDA; YASUTERU SAKAI; SHUHEI YABE; AKIRA YOKOTA; WELLYZAR SJAMSURIDZAL
Biodiversitas Journal of Biological Diversity Vol. 23 No. 9 (2022)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d230935

Abstract

Abstract. Rachmania MK, Ningsih F, Sari DCAF, Eshananda Y, Sakai Y, Yabe S, Yokota A, Sjamsuridzal W. 2022. Identification and screening of enzymatic abilities of Ktedonobacteria from forest soil of Cisolok Geothermal Area, Indonesia. Biodiversitas 23: 4686-4695. This study aimed to provide information on culturable Ktedonobacteria from forest soil in the Cisolok geothermal area and their potential as enzyme producers. Twelve ktedonobacterial isolates were obtained from this study and identified based on full-sequence of the 16S rRNA gene. Seventeen isolates (including five isolates from previous studies) were used for enzymatic screening and phylogenetic analyses. Screening of amylolytic (0.5% soluble starch) and cellulolytic (0.5% carboxymethylcellulose) (CMC) activities from ktedonobacterial isolates was performed on a ten-fold diluted R2A agar medium, and were incubated at 30 °C for 21 days. The EzBioCloud search revealed that all isolates showed low sequence similarities with Dictyobacter aurantiacus S-27T (97.82 to 98.18%) as their closest related species. The phylogenetic tree showed that all isolates belong to the genus Dictyobacter (family Dictyobacteraceae of the class Ktedonobacteria). All isolates formed a monophyletic group and were placed as the sister clade to D. aurantiacus, as supported by a very strong bootstrap value (99%). Screening of amylolytic and cellulolytic abilities showed that most isolates (88.23%) were able to degrade both 0.5% starch and 0.5% CMC as substrates. This study revealed the presence of Ktedonobacteria with amylolytic and cellulolytic abilities in the forest soil of Cisolok geothermal area.
Diversity and ecology of Pteridophytes in Cendil heath forest and Gurok Beraye tropical rainforest, Belitung Island, Indonesia ABYAN SETYA PRIAMBUDI; TATIK CHIKMAWATI; SULISTIJORINI SULISTIJORINI; YULIAN FAKHRURROZI
Biodiversitas Journal of Biological Diversity Vol. 23 No. 9 (2022)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d230945

Abstract

Abstract. Priambudi AS, Chikmawati T, Sulistijorini, Fakhrurrozi Y. 2022. Diversity and ecology of Pteridophytes in Cendil heath forest and Gurok Beraye tropical rainforest, Belitung, Indonesia. Biodiversitas 23: 4775-4782. The tropical heath forest is a unique ecosystem type characterized by sandy and acidic soils with poor nutrients and water availability, making this ecosystem very vulnerable to disturbances. Yet, knowledge regarding the diversity and ecology of the biological elements of heath forests is still very limited, moreover, information on lesser-known plant groups, such as pteridophytes. Pteridophytes can be used as indicators of the quality of a forest ecosystem since they are cosmopolitan and have an excellent adaptation to various habitats. Belitung Island, Indonesia, is a region with a large proportion of tropical heath forest and small areas of tropical rainforest. There are only a few studies on comparison of the flora of the two ecosystem types on Belitung Island. This research aimed to compare the diversity and the ecology of pteridophytes that grow in the Cendil heath forest and the Gurok Beraye tropical rainforest, Belitung Island. The study used the cruise and the purposive sampling methods to record all pteridophytes within the sampling plots measuring 5 x 5 m alternately located on the right and left of line transects with a length of 50 meters each transect. Ecological data were calculated using the Important Value Index (IVI), Shannon-Wiener diversity index, Margalef richness index, Evenness index, Sorensen similarity index, Morisita distribution index, and Canonical Correspondence Analysis. The results showed that as many as 31 species of pteridophytes belonged to 14 families in the Cendil heath forest and Gurok Beraye tropical rainforest. The pteridophytes found in the Gurok Beraye tropical rainforest were higher (30 species) than that in the Cendil heath forest (9 species). There was high dominance of a few species in the Cendil heath forest due to the presence of three species with high IVI, namely Dicranopteris linearis, Palhinhaea cernua and Dicranopteris splendida. In contrast, pteridophytes in the Gurok Beraye tropical rainforest were evenly distributed with no high dominance species. Environmental parameters that affected the diversity and abundance of pteridophytes included temperature, light intensity, humidity, and altitude.
The diversity of agromorphological characters of Portulaca grandiflora in the MV8 population deriving from recurrent irradiation SYARIFAH IIS AISYAH; REGINA AGRITENIA MAYRISCHA SARASWATI; YOSHUA SHANDY YUDHA; WARAS NURCHOLIS
Biodiversitas Journal of Biological Diversity Vol. 23 No. 9 (2022)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d230908

Abstract

Abstract. Aisyah SI, Saraswati RAM, Yudha YS, Nurcholis W. 2022. The diversity of agromorphological characters of Portulaca grandiflorain the MV8 population deriving from recurrent irradiation. Biodiversitas 23: 4432-4439. A multipurpose ornamental plant, Portulaca grandiflora has the value of attractiveness and uniqueness, which lies in various agromorphological characters, primarily in flowers. The potential of P. grandiflora in qualitative characters such as new and unique shapes and colors of the morphology must be enhanced further to increase its economic and aesthetic significance as a floriculture commodity. The induced mutation technique has been proven to improve plants' morphological diversity, and even numerous novel cultivars are produced from artificial mutations. The recurrent irradiation technique was applied in the P. grandiflora mutation breeding program and produced new morphological variations of P. grandiflora until the MV7 generation (seventh generation of the mutation breeding program). The current study aimed to evaluate the diversity of morphological characters of P. grandiflora mutants in the MV8 population resulted from reccurent irradiation technique. Fifty-three selected mutants of P. grandiflora generation MV7 were multiplied by stem cuttings to create an MV8 population. The total MV8 population of P. grandiflora, the result of vegetative propagation, was 1104 plants. The diversity of morphological characters of P. grandiflora in the MV8 population was identified quantitatively (measurement) and qualitatively (visual observation). The results of this study reveal that several P. grandiflora mutants in the MV8 population have a new phenotypic appearance, chiefly in the qualitative characters of flowers. Besides, most of the P. grandiflora MV8 mutant population has inherited identical morphological characters from the previous generation (MV7 population). Further morphological analysis in the next generation needs to be conducted to evaluate the morphological stability of P. grandiflora mutants to develop new cultivars and to investigate the possibility of new phenotypic variations caused by recurrent irradiation treatments.
Karyotyping of green, yellow and red matoa (Pometia pinnata J.R.Forst. & G.Forst.) from Central Java, Indonesia ENDANG YUNIASTUTI; ANANDA PUTRI DEWANTARI MASAILLA; NANDARIYAH NANDARIYAH; NAILU RAHMAH
Biodiversitas Journal of Biological Diversity Vol. 24 No. 1 (2023)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d240106

Abstract

Abstract. Yuniastuti E, Masailla APD, Nandariyah, Rahmah N. 2023. Karyotyping of green, yellow and red matoa (Pometia pinnata J.R.Forst. & G.Forst.) from Central Java, Indonesia. Biodiversitas 24: 40-46. Matoa (Pometia pinnata J.R.Forst. & G.Forst.) belongs to Sapindaceae family and is widely distributed naturally in Indonesia. However, research on matoa plants,especially for the genetic aspect is poorly reported. Genetic information, through chromosome analysis can be helpful in plant breeding programs. This study aimed to analyze karyotype of chromosomes green, yellow and red matoa collected from Central Java, Indonesia. Chromosome analysis in this study used the squash preparation method. This research was the first karyotyping of matoa using 3 types based on exocarp colors, namely green, yellow and red skin matoa. Each type of matoa was repeated 4 times. The results showed that three types of matoa skin colors have the same number of chromosomes, namely 2n=2x=22 with each chromosome size of green, yellow, and red matoa are 1.070±0.251 ?m, 1.025±0.281 ?m, 006±0.252 ?m, respectively and all of matoa have a metacentric chromosome’s form. The karyotype formula for each type of matoa is 2n=2x=22=11m.
Molecular identification of anaerobic fungi isolated from buffalo rumen with their growth rate, cellulase enzyme activity, and fermentation products characteristics SINTA AGUSTINA; KOMANG GEDE WIRYAWAN; SRI SUHARTI; ANJA MERYANDINI
Biodiversitas Journal of Biological Diversity Vol. 23 No. 12 (2022)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d231243

Abstract

Abstract. Agustina S, Wiryawan KG, Suharti S, Meryandini A. 2022. Molecular identification of anaerobic fungi isolated from buffalo rumen with their growth rate, cellulase enzyme activity, and fermentation products characteristics. Biodiversitas 23: 6448-6455. Anaerobic fungi are essential microbes in the degradation process of feed fiber in the rumen with the ability to produce fibrolytic enzymes and rhizoids that can penetrate feed particles. The activity of cellulase enzymes in fungi is influenced by several factors such as the type of feed and livestock used as a source of isolate. Therefore, this research aimed to analyze the types of anaerobic fungi isolated from buffalo based on their DNA nitrogenous bases composition and also to evaluate the growth rate, cellulase enzyme activity, and fermentation product concentration of anaerobic fungi. The growth rate of fungi was examined by measuring the biomass formed, while cellulase enzyme activity was carried out using CMC, Avicel, and Filter Paper as substrates. The fungal fermentation products were analyzed using the HPLC and GC methods. The results showed that the fungi isolated from buffalo rumen were closely related to anaerobic fungi type Piromyces sp., Caecomyces sp., and Neocallimastix frontalis, with different growth rate, cellulase enzyme activity, and the fermentation products concentration in each type of anaerobic fungi. Therefore, it can be concluded that anaerobic fungi isolated from buffalo rumen can degrade cellulose. It was also discovered that fungi Neocallimastix frontalis had a higher growth rate, cellulase enzyme activity (CMCase, avicelase, and FPase), and fermentation products than Piromyces sp. and Caecomyces sp.
Regeneration failure and seedling growth of Dipterocarpus gracilis, a vulnerable dipterocarp in a tropical monsoon forest in Central Java, Indonesia NESTY PRATIWI ROMADINI; SAPTO INDRIOKO; WIDIYATNO WIDIYATNO; ENY FARIDAH
Biodiversitas Journal of Biological Diversity Vol. 23 No. 9 (2022)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d230963

Abstract

Abstract. Romadini NP, Indrioko S, Widiyatno, Faridah E. 2022. Regeneration failure and seedling growth of Dipterocarpus gracilis, a vulnerable dipterocarp in a tropical monsoon forest in Central Java, Indonesia. Biodiversitas 23: 4928-4939. Dipterocarpus gracilis Blume is a vulnerable native dipterocarp species on Java Island, Indonesia. Yet, limited understanding regarding its regeneration capacity in its natural habitat is available to support a sustainable population. The research aimed to investigate the survival and growth of D. gracilis seedlings across canopy openness (CO) in Kecubung Ulolanang Nature Reserve, Central Java, Indonesia. After 10 months of observation, the highest survival rate was found in CO >20%-25% (44%), and the lowest survival rate was observed in CO <15%-20% (20%). The highest relative growth rate of height (RGR H) and the relative growth rate of diameter (RGR D) were found in CO >20%-25% (1.03 ± 0.03 cm and 1.87 ± 0.03 mm). CO <15% showed the lowest RGR H and RGR D (0.6 ± 0.02 cm and 1.39 ± 0.02 mm). The RGR H and D showed a significant CO >20%-25% increase compared with other canopy classes. Pearson’s correlation between RGR D and CO was 0.466 (p >0.05). Our observation indicated that dry months were a critical period for seedling survival. This study showed poor regeneration capacity of D. gracilis, implying that failure in a seedling establishment over time would alter the tree demographics of D. gracilis.
The brown planthopper (Nilaparvata lugens) attack and its genetic diversity on rice in Bali, Indonesia Listihani Listihani; Putu Eka Pasmidi Ariati; ‪I Gusti Ayu Diah Yuniti; ‪Dewa Gede Wiryangga Selangga
Biodiversitas Journal of Biological Diversity Vol. 23 No. 9 (2022)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d230936

Abstract

Abstract. Listihani L, Ariati PEP, Yuniti IGAD, Selangga DGW. 2022. The brown planthopper (Nilaparvata lugens) attack and its genetic diversity on rice in Bali, Indonesia. Biodiversitas 23: 4696-4704. The brown planthopper (Nilaparvata lugens) is an important pest on rice crops in Indonesia. The genetic diversity of BPH isolates in western Indonesia has been extensively reported, whereas eastern Indonesia isolates have not been reported. This research aims to analyze genetic diversity and evaluate the BPH attack's intensity on Bali rice plants. The research method used was an observation of attack percentage, population dynamics, attack intensity, and genetic diversity of BPH in 9 districts in Bali (Badung, Gianyar, Klungkung, Bangli, Karangasem, Tabanan, Denpasar City, Buleleng, and Jembrana). Molecular identification was carried out on N. lugens DNA in the mtCOI fragment. BPH attacks of >50% were found in the districts of Gianyar, Bangli, Jembrana, and Badung. The BPH population was primarily found in Ciherang and IR-64 varieties of rice in the Badung Regency, with 43.67 BPH per rice hill. In general, rice varieties grown in all observation locations were susceptible to BPH, such as Ciherang, IR-64, Inpari 32, and Situbagendit. In the Ciherang and IR-64 varieties, the highest attack intensity average value reached 30%. The sequence of N. lugens isolate from Bali Jembrana showed the highest nucleotide and amino acid homology with N. lugens isolate FSD-034 from Pakistan (MK301229) biotype Y of 99.5 -99.74% and 100%, respectively. This study found N. lugens biotype Y in rice plants for the first time in Indonesia. This study reported that Rice varieties Situbagendit and Inpari 32, previously resistant to BPH, are reported as susceptible to BPH.
Interspecific associations of mangrove species and their preferences for edaphic factors and water quality BOY A. MARPAUNG; BUDIADI BUDIADI; AMBAR PERTIWININGRUM; LINA D. LESTARI; HANDOJO H. NURJANTO; WIDIYATNO WIDIYATNO
Biodiversitas Journal of Biological Diversity Vol. 23 No. 9 (2022)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d230929

Abstract

Abstract. Marpaung BA, Budiadi, Pertiwiningrum A, Lestari LD, Nurjanto HH, Widiyatno. 2022. Interspecific associations of mangrove species and their preferences for edaphic factors and water quality. Biodiversitas 23: 4626-4635. Scientists from different regions have reported failures of mangrove restorations that were predicted due to the unsuitability of the species for the habitats. Habitat preferences should become an important consideration for mangrove restoration and management. This study aimed to find interspecific associations between species and examine the edaphic factors and water quality suitable for mangroves. Eight research stations (and 24 sample plots) were established purposively based on the vegetation structure and salinity levels in successful mangrove restorations in East Lampung in 2020. In each plot, vegetal data and sediment and water samples were taken. The species domination was analyzed using the important value index (IVI), and interspecific associations were determined using a 2x2 contingency table. The edaphic factors and water quality were analyzed using principal component analysis (PCA) to find factors that had significant correlations among others. The effects of the edaphic factors and water quality on species regeneration were analyzed using multiple linear regression by backward elimination to develop a model of habitat preferences for mangroves. Based on the results, Avicennia marina and Rhizophora sp. were the dominant species in all the zones. Still, the lack of interspecific association ( ) showed that both species had different preferences for the habitat. We found four principal components (PCs) of edaphic factors—i.e., the environmental (soil and surface) temperature, dusty clay and Ca, inorganic nitrogen (NH4-N and NO3-N), and Mg—and two PCs of water quality, i.e., nontoxic pollutants (total suspended solids and turbidity) and anthropogenic factors (NO2-N and PO4-P), as predictors for multiple linear regression. The seedlings of A. marina had no specific preferences for edaphic factors but significantly preferred nontoxic pollutants (R2 = 0.619), while the seedlings of Rhizophora spp. significantly preferred a specific environmental temperature, dusty clay and Ca, and inorganic nitrogen (R2 = 0.768), and nontoxic pollutants (R2 = 0.755). Combining A. marina and Rhizophora spp. in mangrove restorations should be avoided. Therefore, spatial planting patterns or sequential planting based on the succession stages of the habitat could be established.
The dynamics of soil carbon in revegetated post-coal mining sites: A case study in Berau, East Kalimantan, Indonesia WAHJUNI HARTATI; TRIYONO SUDARMADJI
Biodiversitas Journal of Biological Diversity Vol. 23 No. 10 (2022)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d231004

Abstract

Abstract. Hartati W, Sudarmadji T. 2022. The dynamics of soil carbon in revegetated post-coal mining sites: A case study in Berau, East Kalimantan, Indonesia. Biodiversitas 23: xxxx. Open pit mining practices cause the loss of vegetation cover as well as soil degradation. Post-mining land reclamation and revegetation are therefore enforced to recover the vegetation and soil quality. While several studies have revealed vegetation succession following post-mining revegetation, limited studies have focused on the carbon dynamics of the soil. This study aimed to investigate the dynamics of soil carbon stock due to mining operations and how it changed following revegetation. The research was carried out in the concession area of a coal mining company in Berau, East Kalimantan, which was divided into three sites: Sambarata Mining Operation (SMO) Site, Binungan Mining Operation (BMO) Site, and Lati Mining Operation (LMO) Site. At each site, eight research measurement plots (RMP) were established representing land with varying vegetational conditions, namely original land and post-mined lands with varying revegetation stages from open land to 12-year-old vegetation. The percentage of C content was calculated from 288 disturbed soil samples, while bulk density was analyzed from 144 whole soil samples using the Walkey & Black and gravimetric methods. We found that the C stock at the initial state after the mining operation was very low. Coal mining activities caused a loss of C in soil with an average value of 21.29%, or equal to 5.65 tons/ha. The biggest loss occurred at the SMO site (44.97%, or 13.04 tons/ha), while the smallest loss was found at the LMO site (2.24%, or 0.40 tons/ha). The carbon stock improved after revegetation, particularly in the SMO and LMO sites, and the rate of carbon stock enhancement in the soil differed across sites. The results also showed that soil carbon in the post-mining area of 10-30 cm was greater than that of the 0-10 cm layer. Along with the increasing age of plants, the vertical distribution of C stock shifted from the lower layer to the upper layer.

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