bluuebunny/crossref_metadata_2025 huggingface dataset:
Short Communication: Restoration of seagrass Enhalus acoroides using a combination of generative and vegetative techniques
Authors: Ambo-Rappe Rohani , La Nafie Yayu A. , Syafiuddin  , Limbong Steven R. , Asriani Nenni , Handayani Nur Tri , Lisdayanti Eka
Published: January 2020

Abstract. Ambo-Rappe R, La Nafie YA, Syafiuddin, Limbong SR, Asriani N, Handayani NT, Lisdayanti E. 2019. Short Communication: Restoration of seagrass Enhalus acoroides using a combination of generative and vegetative techniques. Biodiversitas 20: 3358-3363. Seagrass areas have been declining in extent worldwide, with associated loss in seagrass ecosystem functions and services. Seagrass restoration is important to mitigate, halt and reverse such declines and their consequences. Generative propagation has benefits in terms of genetic biodiversity, however, survival of seagrass seedlings has often been poor especially in high energy environments. Terrestrial restoration often uses shade trees to protect vulnerable seedlings. This study aimed to evaluate the feasibility of a similar approach in the marine environment, using adult plants to protect seedlings of the tropical seagrass Enhalus acoroides (L.f.) Royle. Enhalus seeds taken from a donor bed were germinated and grown into seedlings, then planted in a location with high hydrodynamic exposure at three different densities (high, medium, and low). Adult Enhalus transplants were co-planted to provide three levels of protection: fifty (high), ten (medium), and none (no protection). Results showed that high-density seedling co-planting with high protection from adult transplants had significantly (p< 0.05) higher six-month survival rate compared to the other treatments. Our results indicate that, even in high energy environments, co-planting seedlings with adult transplants may combine the advantages of generative and vegetative propagation methods, promoting greater short-term effectiveness in terms of seedlings survival and growth in the restored seagrass meadows.
Genetic diversity of Rhizophora mucronata in eastern region of Timor Island, Indonesia as revealed by RAPD
Authors: Ihwan Ihwan , Uslan Uslan , Widodo Nashi , Hakim Luchman
Published: January 2020

Abstract. Ihwan, Uslan, Widodo, Hakim L. 2019. Genetic diversity of Rhizophora mucronata in eastern region of Timor Island, Indonesia as revealed by RAPD. Biodiversitas 20: 3364-3371. Mangrove ecosystems have essential functions in producing organic materials, protecting against erosion, and supporting the area between land and sea. Rhizophora mucronata is a dominant mangrove species in all coastal areas of Timor Island, East Nusa Tenggara, Indonesia. Recent reports suggest that mangroves have been affected by anthropogenic pressure and natural disasters. The aim of this study was to determine the genetic diversity of R. mucronata in the east region of Timor Island. This study is important in supporting mangrove protected management planning in the region. The sampling was carried out in six mangrove vegetation sites, DNA was isolated from the leaves and used for PCR-RAPD using six primers. Dendrogram analysis of the species was determined based on UPGMA (unweighted pair group method) and the similarity coefficient from Nei and Li using the MVSP program. The results showed that the six primers used generated a DNA length of 270-1345 bp, with the number of bands being 22-27. The percentage of polymorphism ranged from 73.91% to 86.96% in all primers used, with a polymorphic information content (PIC) value of 0.94. Thus, it can be concluded that the value of genetic diversity (He) from the R. mucronata mangrove population in Timor Island has a value of 0.666. The R. mucronata population in Abudenok and Tanjung Bastian has the highest genetic diversity with a value of 0.667, while the population in Tanjung Tuamese has the lowest genetic diversity with a value of 0.664. Based on the results of the dendrogram analysis, the R. mucronata population in Timor Island correlated with its geographical location. The adjacent populations have a tendency to form one subgroup.
New sources of sorghum resistant genotypes to downy mildew disease in Uganda
Authors: Kumi Frank , Badji Arfang , Mwila Natasha , Odong Thomas , Ochwo-Ssemakula Mildred , Tusiime Geoffrey , Gibson Paul , Biruma Moses , K. Louis Prom , E. Cuevas Hugo , Agbahoungba Symphorien , Rubaihayo Patrick
Published: January 2020

Abstract. Kumi F, Badji A, Mwila N, Odong T, Ochwo-Ssemakula M, Tusiime G, Gibson P, Biruma M, Prom KL, Cuevas HE, Agbahoungba S, Rubaihayo P. 2019. New sources of sorghum resistant genotypes to downy mildew disease in Uganda. Biodiversitas 20: 3391-3397.  Sorghum downy mildew (SDM) disease is still prevalent in Uganda at varying levels of incidence and severity. In this study, a total of 100 sorghum genotypes, five (5) from (U.SA, India, and Sudan) and 95 genotypes from Uganda were evaluated for resistance to downy mildew and other agronomic traits during the second growing season of 2016 (August-December). The experiment was conducted in two locations at Makerere University Agricultural Research Institute at Kabanyolo (MUARIK) and Abi-Zonal Agricultural Research and Development Institute (Abi-ZARDI) research station at Arua. The experimental design used was 10 x 10 alpha lattice design with three replicates. Data were collected on plant disease incidence (PDI), plant disease severity (PDS), area under disease progress curve (AUDPC), days to 50% flowering, plant height, 1000 seed weight, and grain yield. Results for analysis of variance showed highly significant differences (P < 0.001) in genotypes, location, and AUDPC, yield and yield components. Disease incidence varied significantly (P < 0.001) between locations, and Arua recorded highest disease incidence and severity of 80.6 and 2.8, respectively. Results from correlation analysis showed a highly significant (P < 0.001) positive association of downy mildew disease incidence with AUDPC (0.835) which suggests that the severity of SDM disease increased with disease incidence, whiles significant (P < 0.001) negative correlation was recorded for days to 50 % flowering (-0.302), 1000 seed weight (-0.471), and grain yield (-0.585), suggesting that grain yield and yield component decreased significantly with increase in SDM incidence and severity. Two resistant (PI 656061 and PI 533831) and four moderately resistant (E 40, MAKSO 8, PI 655990 and Epuripur) genotypes were identified from this study. These genotypes were recommended for sorghum breeding program against downy mildew disease.
Arbuscular mycorrhizal fungi associated with adaptive plants in gold mine tailing
Authors: Tuheteru Faisal Danu , HUSNA  , ALBASRI  , ASRIANTI ARIF  , SUTRI AYU WULAN  , KARTINI KRAMADIBRATA
Published: January 2020

Abstract. Tuheteru FD, Husna, Albasri, Arif A, Wulan SA, Kramadibrata K. 2019. Arbuscular mycorrhizal fungi associated with adaptive plants in gold mine tailing. Biodiversitas 20: 3398-3404. Arbuscular mycorrhizal fungi (AMF) are fungi from division Glomeremycota within the kingdom Fungi, which have a broad ecological range and symbiosis with a variety of vegetations, including vegetations in gold post-mining areas or gold tailings. The study of identifying types of AMF in gold tailings in Southeast Sulawesi is still limited. The purpose of this study was to identify the types of AMF in the rhizosphere of adaptive plants in gold tailings land in Bombana District, Southeast Sulawesi. Soil samples were collected from adaptive plants in Perseroan Terbatas (PT) Panca Logam Makmur, Bombana District, Southeast Sulawesi Province, Indonesia. AM Fungi spores were isolated and identified based on their morphological characteristics (shape, size, color, attached hyphae, and spore ornamentation). Five types of AMF were identified, namely Glomus aggregatum, Sclerocystis sinuosa, Acaulospora scrobiculata, A. tuberculata, Scutellospora pellucida, and two genera that had not been identified up to species, Glomus sp. and Scutellospora sp. In addition to spores, the symbiosis of AM Fungi with adaptive plants was also demonstrated by the structure of AM Fungi in plant roots with a rate of 74% colonization. S. pellucida and S. sinuosa were recorded as new species in Indonesia and Sulawesi, respectively. While A. tuberculata is a type of AMF that enriches AMF diversity in Southeast Sulawesi.
The DNA barcode of red fruit pandan (Pandanaceae) cultivar from Wamena, Papua Province, Indonesia based on matK gene
Authors: ZEBUA LISYE IRIANA , TRI GUNAEDI  , I MADE BUDI  , NELLY LUNGA
Published: January 2020

Abstract. Zebua LI, Gunaedi T, Budi IM, Lunga N. 2019. The DNA barcode of red fruit pandan (Pandanaceae) cultivar from Wamena, Papua Province, Indonesia based on matK gene. Biodiversitas 20: 3405-3412. The red fruit pandan has been used by the people of Wamena in central highlands of Papua as medicinal plants, food ingredients, and religious ceremonies. Based on morphological characters, there are 39 cultivars of red fruit pandan in New Guinea. A standard method for plant species identification through DNA barcodes has been recommended to use matK gene. The research aimed to determine similarities in DNA barcode sequences of six red fruit pandan cultivars with its close relative that listed in NCBI system and to recommend the reliable DNA barcode for identification of this cultivar. Polymerase Chain Reaction was employed DNA to amplify matK gene fragments using an available forward primer (5’CGA TCT ATT CAT TCA ATA TTT C 3’) and reverse primer (5’TCT AGC ACA CGA AAGTCG AAG T 3’). The software BLAST, Bioedit, and ClustalX were used to analyze the data. Barcode DNA of red fruit pandan showed 1474 bp nucleotides sequence based on matK gene. An indication of six red fruit pandan cultivars showed that high similarity 99% with Pandanus conoideus Lam. It can be concluded that matK gene can be used to determine the species level in Pandanus.
Hydrocarbon degradation by bacteria from rhizospheres of Imperata cylindrica at oil mining site in Wonocolo, Bojonegoro, Indonesia
Authors: Sari Mutiara Arum , ENDAH RETNANINGRUM
Published: January 2020

Abstract. Sari MA, Retnaningrum E. 2019. Hydrocarbon degradation by bacteria from rhizospheres of Imperata cylindrica at oil mining site in Wonocolo, Bojonegoro, Indonesia. Biodiversitas 20: 3422-3429. High oil mining activities cause environmental pollution at the oil mining site. Petroleum spills and waste to the river flow cause blackish discoloration along the riverbank and also some types of plants die. The utilization of rhizospheric bacteria (rhizobacteria) as a bioremediation agent is considered as appropriate for reducing petroleum contaminants. The purposes of this study were to analyze the ability of hydrocarbon degradation by selected rhizobacteria isolates, to identify molecularly and analyze the genetic relationship of hydrocarbon-degrading rhizobacteria based on 16S rRNA gene sequencing. The rhizobacteria of cogongrass (Imperata cylindrica L.) were isolated from oil mining site in Wonocolo, Kedewan, Bojonegoro, East Java, Indonesia. The 5 isolates of rhizobacteria were then cultured on Bushnell-Haas Mineral Salt (BHMS) medium with the addition of 0.015% crude oil for analyzing their growth based on their cell densities using the Total Plate Count method. The optimal rhizobacteria growth obtained (MTMW2 isolate) was selected and further analysed its ability for hydrocarbon degradation through measuring of Total Petroleum Hydrocarbon (TPH). Its rhizobacteria were then identified using 16S rRNA gene sequencing. The MTMW2 isolate revealed specific growth rate of 0.14 in BHMS medium with the addition of 0.015% crude oil. After 10 days of incubation, the isolates could degrade Total Petroleum Hydrocarbon in the medium as much as 96.1%. The results of molecular identification and phylogenetic tree construction showed that MTMW2 isolate was identified as Pseudomonas aeruginosa.
Specific features of the development of Rhopalosiphum padi in connection with migration and transfer of the viral infection to host and non-host plants using potato as an example
Authors: Gandrabur Elena S , ALLA B. VERESHCHAGINA
Published: January 2020

Abstract. Gandarabur ES, Vereshchagina AB. 2019. Specific features of the development of the bird cherry-oat aphid Rhopalosiphum padi (L.) in connection with migration and transfer of the viral infection to host and non-host plants using potato as an example. Biodiversitas 20: 3439-3447. Using Rhopalosiphum padi (L.), which lives in the North-West of the Russian Federation, as an example, the long-term data on the timing of its spring migration from bird cherry to herbaceous plants are summarized and their analysis, related to the wing formation in aphid colonies and the accompanying weather conditions, is given. It was found out, those peculiarities of behavior of spring emigrants of Rh. padi during the host selection depend on the motivation for a long-distance flight, include repeated take-off and testing and may be accompanied by visits to the non-host plants during 4 days. Migration and settling behavior of aphids underlie their ability to transfer non-persistent viruses to host and non-host plants. The obtained data allow adjusting the methods of plant protection including the viral infection.
Bioactive compound profile of melon leaf extract (Cucumis melo L. ‘Hikapel’) infected by downy mildew
Authors: Pratama Ozie Akbar , TUNJUNG WORO ANINDITO SRI , SUTIKNO SUTIKNO , DARYONO BUDI SETIADI
Published: January 2020

Abstract. Pratama OA, Tunjung WAS, Sutikno, Daryono BS. 2019. Bioactive compound profile of melon leaf extract (Cucumis melo L. ‘Hikapel’) infected by downy mildew. Biodiversitas 20: 3448-3453. Plants express specific secondary metabolites (phytoalexin) in response to infection. Downy Mildew which infects melon plants (Cucumis melo L. ‘Hikapel’) caused by Pseudoperonospora cubensis Rostovtsev. Hikapel is one of superior melon cultivar produced from research in the Laboratory of Genetics, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia. Bioactive content of Hikapel melon leaf under normal condition and infected by Downy Mildew yet to be researched. This research aims to screen bioactive profile of Hikapel leaf extract that has potential as phytomedicine. Leaf extract is compared between healthy plants and infected by Downy Mildew. Dried melon leaf was powdered using mortar and pestle. Leaf powder was extracted using hexane solvent. Extract was analyzed using a Shimadzu GCMS-QP2010S. Analysis found useful compounds like phytol, methyl ricinoleate, methyl linoleate, methyl stearate, and 1-hexacosanol. with therapeutic activity such as antibacterial, antifungal, antioxidant, antiinflammatory, antidiuretic, antidiarrheal, lowering blood LDL-C level, insulin level booster, antiproliferative, and anticancer. Some bioactive compounds are only synthesized in Hikapel melon leaf under stress conditions.
The In vivo evaluation of anticryptosporidiosis activity of the methanolic extract of the plant Umbilicus rupestris
Authors: BENHOUDA AFAF , DJAHIDA BENHOUDA  , MASSINISSA YAHIA
Published: January 2020

Abstract. Benhouda A, Benhouda D, Yahia M. 2019. In vivo evaluation of anticryptosporidiosis activity of the methanolic extract of the plant Umbilicus rupestris. Biodiversitas 20: 3478-3483. Umbilicus rupestris (Crassulaceae) is a medicinal plant used in general traditional medicine to cure inflammation and irritation of the skin. The present research is aimed to evaluate the antiparasitic activity of the methanolic extract of the plant URMeOH of U. rupestris against the Cryptosporidium infection in immunocompetent and immunosuppressed rats experimentally infected. Twenty-one female rats were divided into two groups. Control group (group I) and experimental group (Group II). The group I was further divided into three equal groups (normal group infected and immunosuppressed infected group). The experimental group was divided into two immunosuppressed and four equal groups and two immunocompetent infected. Cryptosporidium oocysts were isolated from bovine species stools and used to infect rats. Experimental subgroups received URMeOH two as dose 100mg/kg b.w. and 200 mg/kg b.w. and continued until 15 days. Two weeks after the administration of URMeOH, feces of rats were examined for the detection of Cryptosporidium oocysts by Ziehl-Neelsen and immunofluorescence techniques, the animals were sacrificed; their small intestines were processed and examined for the detection of pathological lesions after histopathological study. In addition, the activity of myeloperoxidase (MPO) was measured in sections of the jejunum. Concerned the results, we observed a statistically significant (P<0.001) increase in the number of oocysts of Cryptosporidium in the stool for sub infected immunosuppressed groups and an increase of MPO activity compared to the corresponding subgroups immunocompetent subgroups. The URMeOH could remove Cryptosporidium oocysts from feces and intestinal sections subgroup infected immunocompetent rats receiving URMeOH. Moreover, the oocysts were significantly reduced in all other subgroups experimental infected compared to infected control subgroups. Intestinal sections in all subgroups received URMeOH revealed a more or less normal architecture. In addition, the reduction of MPO activity level was also detected in all experimental subgroups.
High genetic connectivity in a scleractinian coral (Lobophyllia corymbosa) around Sulawesi, Indonesia
Authors: Umar Widyastuti , A.R. TASSAKKA ASMI CITRA MALINA , JOMPA JAMALUDDIN
Published: January 2020

Abstract. Umar W, Tassakka ACMAR, Jompa J. 2019. High genetic connectivity in a scleractinian coral (Lobophyllia corymbosa) around Sulawesi, Indonesia. Biodiversitas 20: 3484-3492. The life cycle of scleractinian corals begins with a pelagic larval phase subject to the influence of currents, with the potential to disperse propagules over vast geographical distances. We investigated the mitochondrial COI genome to investigate genetic population structure and potential biophysical barriers (in particular water mass movements) that could affect connectivity between populations in the seas around Sulawesi, in the Indonesian Coral Triangle. Lobophyllia corymbosa was selected as representative of corals with a broadcast spawning reproductive strategy and relatively long Pelagic Larval Dispersal (PLD) period. Analysis of mtDNA sequences from 103 colonies collected at depths of 3 to 10 meters in 4 locations (Manado, Toli-Toli, Spermonde, and Wakatobi) resulted in FST = 0.00632, indicating no genetic isolation or significant differentiation. The tendency towards genetic homogeneity across the entire population indicates that gene flow has been maintained, most likely through widespread dispersal of propagules within the study area. The dominant surface flow directions recorded during the reproductive period of this species provide support for this gene flow model, as the currents could enable dispersal and recruitment patterns maintaining connectivity between L. corymbosa populations around Sulawesi.
Isolation and molecular identification of carbohydrase and protease producing Bacillus subtilis JCM 1465 isolated from Penen Hot Springs in North Sumatra, Indonesia
Authors: Edy Fachrial  , Sari Anggraini  , Harmileni  , Titania T Nugroho  , Saryono
Published: January 2020

Abstract. Fachrial E, Anggraini S, Harmileni, Nugroho TT, Saryono. 2019. Isolation and molecular identification of carbohydrase and protease producing Bacillus subtilis JCM 1465 isolated from Penen Hot Springs in North Sumatra, Indonesia. Biodiversitas 20: 3493-3498. The application of enzymes industrially is increasing every year and thermophilic microbes are a promising source of these enzymes for industrial use due to their temperature stability. The aim of this study, therefore, was to isolate, characterize and identify the enzyme producer-thermophilic bacteria from the Penen Hot Spring in Deli Serdang, North Sumatra, Indonesia. In the experimental setup, carbohydrase activities including inulinase and amylase were determined by the formation of clear zone around the colonies after soaking with Lugol on the TSA medium supplemented with 1% inulin powder and 1% starch. Similarly, the protease activities were determined by the formation of clear zone around the colonies on Skim Milk Agar Medium. Then, of the 11 isolates, only one known as UTMP 12 showed maximum enzyme activity. The isolate was then characterized based on morphology and biochemistry and found to be Bacillus subtilis strain JCM 1465 (accession number NR_113265, homolog 99.72%). Furthermore, this is the first study on carbohydrase and protease activities of Bacillus subtilis strain JCM 1465 and the result shows that the thermophilic bacteria are needed in the production of carbohydrase and protease.
Characteristics of sago pith and sago bark waste from Seram Island, Maluku, Indonesia
Authors: Siruru Herman , WASRIN SYAFII  , I NYOMAN J. WISTARA  , GUSTAN PARI
Published: January 2020

Abstract. Siruru H, Syafii W, Wistara I. N. J, Pari G. 2019. Characteristics of Metroxylon rumphii (pith and bark waste) from Seram Island, Maluku, Indonesia. Biodiversitas 20: 3517-3526. Sago (Metroxylon rumphii Martius) pith waste (SPW) and sago bark waste (SBW) are lignocellulosic materials that can be used for various needs directly or indirectly. It is necessary to understand SPW and SBW characteristics to maximize their utilization. In this study, we analyzed the proximate, ultimate, and crystallinity by XRD, the functional groups by FTIR, morphology by SEM, and the derivate analysis of hot water-soluble extractives by GCMS. The contents of SPW and SBW hot-water soluble extractive, lignin, and holocellulose were 57.7 and 4.9%, 6.1 and 29.4%, and 45.74 and 66.74%, respectively. The volatile matter, ash content, silica, fixed carbon, C, H, and O contents of the SPW and SBW were 81.48 and 84.56%, 1.30 and 3.04%, 1.25% and 2.03, 12.77 and 18.06%, 37.93 and 44.64%, 6.37 and 6.49%, and 47.75 and 51.10%, respectively. The degree of crystallinity of SPW was 15.04%, while that of SBW was 47.28%, where both have a monoclinic structure with the main peak by 2Ɵ 16° and 26°. SPW and SBW contained several minerals such as silica, boron, sulfur, and phosphorus. The surface morphology of the SPW was porous with a small diameter and thin cell wall, while that of SBW was covered by minerals. Nitrogen, alcohol, and sugar group compounds were found more in SPW, whereas phenol compound was more in SBW. SBW has high lignin content and SPW has a very large amount of hot water-soluble extractive.
Short communication: First record of Arapaima gigas (Schinz, 1822) (Teleostei: Osteoglossomorpha), in the Brantas River, Sidoarjo, East Java, Indonesia
Authors: Fadjar Mohamad , Islamy R Adharyan , Herawati Endang Yuli
Published: January 2020

Abstract. Fadjar M, Islamy RA, Herawati EY. 2019. Short communication: First record of Arapaima gigas (Schinz, 1822) (Teleostei: Osteoglossomorpha), in the Brantas River, Sidoarjo, East Java, Indonesia. Biodiversitas 20: 3527-3531. The arapaima (= Arapaima gigas) is the largest freshwater fish in the Neotropical region, obligate air-breathing fish that known to reach up to 3 m - 3.90 m in length and 200 kg in weight endemic to the Amazon basin. Arapaima gigas is giant osteoglossomorph and obligate air‐breathing fish and also a native species of the Amazon basin. We present the first record of Arapaima gigas (Schinz, 1822) in Brantas River, Sidoarjo, East Java, Indonesia with diagnostic meristic and morphometrics of the specimens analyzed following Stewart method. Herein, it recorded from the Brantas River basin. This record based on the finding of one live specimen on the tributary of Brantas River basin, and in situ observation of juveniles and adults in the river).
Production of cellulase from Aspergillus niger and Trichoderma reesei mixed culture in carboxymethylcellulose medium as sole carbon
Authors: Dia Septiani  , HERMAN SURYADI  , Abdul Mun'im  , WIBOWO MANGUNWARDOYO
Published: January 2020

Abstract. Septiani D, Suryadi H, Mun’im A, Mangunwardoyo W. 2019. Production of cellulase from Aspergillus niger and Trichoderma reesei mixed culture in carboxymethylcellulose medium as sole carbon. Biodiversitas 20: 3539-3544. Cellulase is one of hydrolytic enzymes that breakdown cellulose into glucose. Cellulases are promising to be applied in natural products which may improve the yield of bioactive in plant extract through cellulose depolymerization. Cellulases from mixed culture of Aspergillus niger and Trichoderma reesei can produce a high cellulase activity because of the synergism activity among endoglucanase, exoglucanase, and also β-glucoside. Cellulase production and partial purification of monoculture and mixed culture (1:1) of these fungi on carboxymethylcellulose media were investigated in this study. Total cellulase activity was measured by filter paper assay followed by protein estimation with Bradford method. The crude extract of Aspergillus niger monoculture has the highest cellulase activity (0.131 U/mL, P<005) followed by mixed culture (0.109 U/mL) and Trichoderma reesei (0.106 U/mL). The cellulase activity of partially purified cellulase from mixed culture significantly increased (0.335, 0.348, 0.374 U/mL, P<0.05) compared to crude extract along with stepwise addition of ammonium sulfate. Cellulase activity of mixed culture at 80% ammonium sulfate increase up to 2.238-fold and showed highest value (P<0.05) compared to monocultures. In conclusion, combination of Aspergillus niger and Trichoderma reesei fungi in carboxymethyl cellulose media followed by 80% ammonium sulfate precipitation can be a promising cellulase production with high cellulase activity.
Population parameter Population parameters and bio-exploitation status of Indian Mackerel (Rastrelliger kanagurta Cuvier, 1816) in Mayalibit Bay, Raja Ampat, Indonesia
Authors: Oktaviani Dian , Setiya Triharyuni  , Duto Nugroho
Published: January 2020

Abstract: Oktaviani D, Triharyuni S, Nugroho D. Population parameters and bio-exploitation status of Indian mackerel (Rastrelliger kanagurta Cuvier, 1816) in Mayalibit Bay, Raja Ampat, Indonesia. Biodiversitas 20: 3545-3552. A small-scale fishery in Mayalibit bay, Raja Ampat is one among rare fisheries systems existing in Indonesia. The area already designated as a conservation zone, and Indian mackerel is the main target species by fishers. This species plays a significant role in supplying domestic food. Fisher harvest with a small wooden boat, no engine, one-night fishing using Petro-lamp, and harvested with a scoop net. Monthly based biological observations on population parameters were carried out from March 2011 to April 2012. The result shows that the fish landed with size from 10.0 to 27.0 cm, and 70% of the sample is within 21-23 cm length. Monthly length-weight relationships indicate b value statistically equal to 3. The average unsexed Fulton condition factor index is 1.516 + 0.13 and illustrates the fishes were in suitable environmental conditions. The growth rate (K) is estimated at 0.97, while length infinity (L∞) is 28.4 cm. To evaluate the fishery, repeated observation of fishing in Mayalibit bay conducted in 2016. A productivity and susceptibility analysis was applied to predict its bio-exploitation status, and the results indicate that harvest levels are relatively at low-to-medium risk. Nevertheless, most of the fish caught in the bay by traditional knowledge consisted of mature cohorts while limited desk study to semi-industrial fishing targetted the same species in surrounding waters indicated that a significant proportion of undersize or immature individuals are in their landing. This phenomenon suggested that managing the existing local knowledge could significantly contribute to maintaining sustainable spawning stocks in the conservation zone.
The potential of Cosmos sulphureus flower extract as a bioherbicide for Cyperus rotundus
Authors: Respatie Dyah , Prapto Yudono , Purwantoro Aziz , Trisyono Y. Andi
Published: January 2020

Abstract. Respatie. D. W, Yudono P, Purwantoro A, Trisyono Y.A. 2019. The potential of Cosmos sulphureus flower extract as a bioherbicide for Cyperus rotundus. Biodiversitas 20: 3568-3574. Cosmos (Cosmos sulphureus Cav.) flower is recognized as natural source of bioherbicide compounds for several weeds. The purple nutsedge (Cyperus rotundus L.) is an important weed, and this research was aimed to determine the effects of cosmos flower extract on this weed. Dried cosmos flowers were threshed and extracted using maceration method with 70% alcohol. The experiment was conducted in the greenhouse using a completely randomized design (CRD) with three replications. Purple nutsedge tubers were planted in polybags and treated with cosmos flower extract applicated once to three times with 300 mL polybag-1 at the concentration of 40%. Different levels of inhibitions on purple nutsedge growth were observed at 30 and 60 days after sowing (DAS) due to the presence of gallic acid in the extract. Growth parameters for purple nutsedge were analyzed using Analysis of Variance (ANOVA) and followed by Least Significant Differences (LSD) at α=0.05. Significant reductions in the number of mother shoots, daughter shoots, and roots, length of mother leaves, length of rhizomes, root, and total leaf area of the purple nutsedge treated with the cosmos flower extract at 30 DAS compared to those in the control. A significant reduction was also observed in foliage dry weight, underground organs dry weight, and total dry weight of purple nutsedge. The three application times yielded maximum inhibition. In addition, these treatments reduced N, P, and  K content, chlorophyll content, and photosynthesis rates at 30 DAS. These results suggest that cosmos flower extract has the potential for controlling purple nutsedge.
Short Communication: rbcL and matK chloroplast DNA composition of green chireta (Andrographis paniculata) from Indonesia
Authors: Arif Muhammad Fauzi , Aristya Ganies Riza , Subositi Dyah , Sari Aniska Novita , Kasiamdari Rina Sri
Published: January 2020

Abstract. Arif MF, Aristya GR, Subositi D, Sai AN, Kasiamdari RS. 2019. Short Communication: rbcL and matK chloroplast DNA composition of green chireta (Andrographis paniculata) from Indonesia. Biodiversitas 20: 3575-3583. Green chireta (Andrographis paniculata (Burm.f.) Wall. ex Nees.) is often used by the traditional community as a medicinal herb in Indonesia. However, nucleotide study of green chireta from Indonesia has never been done. The objectives of this study were to analyze the rbcL and matK chloroplast gene composition of green chireta from Indonesia and to analyze the relationship with other Andrographis species. The result proved that all the DNA composition of green chireta used in this study was similar to the A. paniculata from GenBank. The rbcL composition was similar to A. paniculata KF521878, A. paniculata JQ922118, and A. paniculata JQ230990 from GenBank while the matK composition was similar to A. paniculata LC461762. Total 501 bp of rbcL and 639 bp of matK can be aligned produced 167 and 213 amino acid from translation. The amino acid translation result showed no different expression from rbcL genes but there was one sample expressed different translations from the matK gene. The phylogenetic tree was reconstructed using the Neighbor-Joining method with 1000 bootstrap values and the Kimura 2-Parameter (K2P) model in the MEGA7 software. Both rbcL and matK genes grouped the samples into the same clade as A. paniculata from GenBank. No variation was detected from the rbcL gene but two haplotypes were detected from the matK gene. This composition and sequence data serve as a database for Andrographis species from Indonesia which can be used for various studies.
Characteristics of catechin extracted from cocoa husks using microwave assisted extraction (MAE)
Authors: Djalal rosyidi  , DJALAL ROSYIDI  , PURWADI  , IMAM THOHARI
Published: January 2020

Abstract. Rahayu PP, Rosyidi D, Purwadi, Thohari I. 2019. Characteristics of catechin extracted from cocoa husks using microwave-assisted extraction (MAE). Biodiversitas 20: 3626-3631. Cocoa husks, a by-product of cocoa processing, were investigated as a source of catechin. The objective of this research was to investigate the best extraction time for catechin of cocoa husk using microwave-assisted extraction (MAE). Four different treatments (4, 6, 8, and 10 min) were tested. Catechin was analyzed using Fourier transform infrared (FTIR) spectroscopy, and total phenol content (TPC) and total catechin content (TCC) were determined by liquid chromatography-mass spectrometry (LC-MS). The longest extraction time (10 min) produced the highest phenolic content, although it was similar to that obtained at 8 min. The IR spectra of the cocoa husk extract were stable for the 4, 6, and 8 min extractions. However, the spectra after the 10 min extraction showed more peaks, especially for phenolic compounds and catechins. The mass spectra of catechin showed a peak at RT 3.11 and a protonated ion peak [M+H]+ at m/z 307. The results for TPC, TCC, FTIR, and LC-MS indicated that a 10 min extraction using MAE was the optimum treatment.
Short Communication: Species diversity of mangrove in Kutai National Park, East Kalimantan, Indonesia
Authors: Poedjirahajoe Erny , Sulistyorini Iin Sumbada , Komara Liris Lis
Published: January 2020

Abstract. Poedjirahajoe E, Sulityorini IS, Komara LL. 2019. Short Communication: Species diversity of mangrove in Kutai National Park, East Kalimantan, Indonesia. Biodiversitas 20: 3641-3646. Kutai National Park (KNP) in East Kalimantan, Indonesia is blessed with natural mangrove forests. However, there is only very little information relating to the species composition and mangrove diversity. Therefore, this study was conducted to assess the mangrove tree species diversity and richness in Kutai National Park, East Kalimantan, Indonesia. The study results showed that the mangrove trees density was 1,214 trees/ha in the line transect vegetation survey with 1.7 ha plot. The number of mangrove species in KNP was 17 from 6 families. The dominant species with large numbers of individuals were Rhizophora mucronata, Rhizophora apiculata, and Bruguiera sexangula. The diversity index was low in mangroves in Pandan Bay Estuary, and Kaba Bay compared to that in Lombok bay’s mangroves.
Macronutrient and mineral contents of five local black rice (Oryza sativa) cultivars in Indonesia
Authors: Nashrurrokhman Muh , Sayekti Puspa Restu , Safitri Ayu , Purwestri Yekti Asih , Pratiwi Rarastoeti
Published: January 2020

Abstract. Nashrurrokhman M, Sayekti PR, Safitri A, Purwestri YA, Pratiwi R. 2019. Macronutrient and mineral contents of five local black rice (Oryza sativa) cultivars in Indonesia. Biodiversitas 20: 3647-3653. Nutrient composition is important information that can be used to support the development of black rice as functional food. In this study, the macronutrient and mineral compositions of five black rice cultivars were determined by measuring the contents of total carbohydrates, proteins, and lipids, and levels of the minerals Ca, Fe, and Zn of whole rice, refined rice, and rice bran. Rice samples were obtained from farmers who planted the black rice cultivars of Woja Laka, Toraja, Cempo Ireng “Seyegan”, Melik “Bantul” and Wedomartani. Proximate analysis and spectrophotometric methods were performed to measure the contents of macronutrients and minerals. Statistical analysis of all quantitative data was conducted by using One-way analysis of variance (ANOVA) (p<0.05) using the SPSS-25 program. Results showed that the contents of carbohydrates, proteins, and lipids in the five rice cultivars varied in the range of 61.80%-65.58%, 7.13%-9.10%, and 1.98%-3.23%, respectively. Carbohydrates found in refined rice were in the range of 62.71%-67.89%, while rice bran had protein and lipid contents varying in the range of 10.95%-11.48% and 5.70%-6.86%, respectively. Rice bran also had the highest mineral content and the highest mineral content was 30 μg/g Ca compared to Fe and Zn. Therefore, the macronutrient and mineral composition varied among the five black rice cultivars and rice components. The highest carbohydrate content was found in refined rice, while the highest proteins, lipids, and minerals (Ca, Fe, and Zn) contents were found in rice bran.
Characterization and potential of plant growth-promoting rhizobacteria on rice seedling growth and the effect on Xanthomonas oryzae pv. oryzae
Authors: Rahma Haliatur , NURBAILIS  , NILA KRISTINA
Published: January 2020

Abstract. Rahma H, Nurbailis, Kristina N. 2019. Characterization and potential of plant growth-promoting rhizobacteria on rice seedling growth and the effect on Xanthomonas oryzae pv. oryzae. Biodiversitas 20: 3654-3661. Xanthomonas oryzae pv. oryzae (Xoo), a major limiting factor in rice production, and the use of resistant Xoo varieties have failed to control the bacterial pathogens as well as increased yield. It is due to the diversity in pathotypes, caused by environmental factors, the nature of resistant variety used, and gene mutation. The aims of this study were to select rhizobacterial strains with the potential of suppressing Xoo growth and promoting the growth of rice seedlings. This experiment was conducted in a completely randomized design (CRD) using seven rhizobacterial isolates selected through a dual culture test, with four replications. There were four isolates that potential in inhibiting the growth of Xoo, namely KJKB5.4, LMTSA5.4, Bacillus cereus AJ34, and Alcaligenes faecalis AJ14, with inhibition diameters greater than 11.50 mm. Rhizobacterial supernatant of 4 potential isolates has a zone of inhibition ranging from 12.25 to 24.00 mm. Four potential isolates were also able to solubilize phosphate, produce indole acetic acid (IAA) growth hormone, and siderophore, as well as enhance the growth of rice seedlings. Based on the nucleic acid sequencing of LMTSA5.4, KJKB5.4, and RK12 isolates were identified as Stenotrophomonas malthopilia strain LMG 958 (99.13%) accession NR 119220.1, Stenotrophomonas pavanii strain LMG 25348 (95.84%) accession NR 118008.1 and Ochrobactrum ciceri strain ca-34 (92.91%) accession NR115819.1.
Short Communication: Diversity of Chlorpyrifos-degrading bacteria isolated from shallow aquifer of East Java Coastal Settlements, Indonesia
Authors: ROCHADDI BASKORO , Zainuri Muhammad , SABDONO AGUS
Published: January 2020

Abstract. Rochaddi B, Zainuri M, Sabdono A. 2019. Short Communication: Diversity of Chlorpyrifos-degrading bacteria isolated from shallow aquifer of East Java Coastal Settlements, Indonesia. Biodiversitas 20: 3662-3666. Wastes from inhabited regions, factories and maricultural practices through movement and penetration enter to groundwaters. A study was undertaken to determine the diversity of Chlorpyrifos-degrading bacteria isolated from a shallow aquifer of East Java coastal settlements. Fifteen of 116 bacterial strains isolated from shallow aquifer samples of 12 household wells were selected due to their capability of degrading Chlorpyrifos herbicide. These isolates were different in the ability of Chlorpyrifos degradation. They utilize Chlorpyrifos as the source of carbon and energy for their growth. Their initial degradation at 50 mg L−1 concentration within the first 4 days ranged between 26.81 and 70.12 %. The 16S rRNA gene sequence analyses indicated that the majority of the isolates belonged to members of Bacillus genera. These bacterial strains were Bacillus cereus (seven strains) and Bacillus paramycoides (four strains). Besides, three strains were identified as Bacillus subtilis and one strain as Bacillus thuringiensis. Bacillus cereus strain LCA1.1 was selected for further study on kinetic growth and Chlorpyrifos utilization. These bacterial strains have a great potential utility for the bioremediation of shallow aquifer of coastal settlement contaminated with Chlorpyrifos pesticides.
Developmental, morphological and molecular variation of commercial Ganoderma spp. accessions from southern Vietnam
Authors: Ho Viet The , Vo Thi Ngoc Ha , Le Ngoc Giau
Published: January 2020

Abstract. Ho VT, Vo TNH, Le NG. 2019. Developmental, morphological and molecular variation of commercial Ganoderma spp. accessions from southern Vietnam. Biodiversitas 20: 3684-3689. In Vietnam, the market value of Ganoderma spp. increases markedly recently due to the high demand as an effective medicine. However, the breeding programs for this mushroom are still less effective due to the poor knowledge of genetic composition. This study was conducted to investigate the diversity of some commercial Ganoderma spp. accessions from southern Vietnam using both traditional techniques using developmental and morphological characterization, and molecular method using ISSR markers. A total of nine Ganoderma spp. samples were collected from production areas and research institutes in southern provinces of Vietnam and targeted for developmental and molecular characterization. Developmental and morphological variations among accessions were evaluation. In addition, 20 ISSR markers were also utilized for further understanding genetic composition of these mushrooms. The obtained measurement data show a large variation among the studied Ganoderma spp. accessions in term of mycelia growth, diameter, shape, and dried weight of fruiting bodies. Molecular data from 20 ISSR markers also supported genetic variation of the examined samples. Based on the results of this study, the samples of Ganoderma spp. accessions from southern Vietnam can be divided into two main groups which are not correlated to geographical locations of sample collection sites. The results are potential for classification and provide new insights for molecular assisted selection of Ganoderma spp.
Molecular characterization of Mosaic Virus from the cocoa trees showing mosaic symptoms in Yogyakarta, Indonesia
Authors: Probowati Wiwit , SUSAMTO SOMOWIYARJO  , SEDYO HARTONO
Published: January 2020

Abstact. Probowati W, Somowiyarjo S, Hartono S. 2019. Molecular characterization of Mosaic Virus From the cocoa trees showing mosaic symptoms in Yogyakarta, Indonesia. Biodiversitas 20: 3698-3704. Indonesia is the world's second-biggest producer of cacao after Ivory Coast with its cacao plantations spreads over 1,652 million hectares and mostly managed by smallholders. Cacao as a beneficial commodity can provide job opportunities for over 1.64 million people, with its contribution of more than US-$ 1.6 billion/year to national income. However, pest and disease infections are inevitably common constraints for the cacao cultivators. One current disease is caused by Cacao Swollen Shoot Virus (CSSV). Despite its noticeable symptoms on the cacao trees suffering from the disease, the knowledge on both the virus existence and the prevention steps in dealing with it is lacking. The information on the diversity of mosaic virus will help us to comprehend its epidemiologic development and the needed countermeasures, as well as its evolution. This research is intended to study the mosaic disease virus molecularly, the virus was obtained from DR1 clones from Kalibawang cacao plantation in Kulon Progo, Yogyakarta. The virus morphology was observed using a transmission electron microscope applying quick dipping method. The PCR analysis with conserved region ORF1 primers was conducted to detect the viral existence in the infected trees. The identification of CSSV molecular characters was undertaken using PCR sequencing analysis which was then examined using BioEdit and Mega5 programs to initiate a relationship dendrogram. The result showed that the DR1 cacao tree clones from Kalibawang were infected by mosaic virus with mild visual severity of leaf typical symptom. From the electronic microscope observation, a ±100 nm rod-shaped viral particle with a diameter of 15.3 mm was found. On the molecular level, the cause of mosaic symptom has CSSV amplified at conserved regions with size 375 bp. The results are the first report confirming that the molecular cause of cacao mosaic disease in Indonesia is CSSV. The molecular characters of CSSV in Yogyakarta are very different from those found abroad.
Genetic x environment interaction on agronomic characters and yield components of sweet sorghum (Sorghum bicolor) mutant strain
Authors: Endang Endang , ISWARI SARASWATI DEWI  , AMIN NUR  , ROSSA YUNITA  , MASTUR
Published: January 2020

Abstract. Lestari EG, Dewi IS, Nur A, Yunita R, Mastur. 2019. Genetic x environment interaction on agronomic characters and yield components of sweet sorghum (Sorghum bicolor) mutant strain. Biodiversitas 20: 3705-3714. Sweet sorghum (Sorghum bicolor (L.) Moench) belongs to cereal plants that have prospects for commercial development in Indonesia, since it can adapt widely in sub-optimal land, and has many functions. However, there is still limited sweet sorghum variety that has been released in Indonesia. The study aimed to evaluate the influence of genetic x environment interaction on agronomic characters and yield components of sweet sorghum mutant strain. Adaptation test was held in 8 locations in Indonesia, namely Pekalongan, Bantul, Gunung Kidul, Lampung, Malang, East Lombok, Bontobili and Maros, from May to November 2017. The material tested was 10 M7 mutant strains and two check varieties (Numbu and Super 1). The experiment was arranged in a randomized complete block design (RCBD). There were three replications in form of blocks and each block consisted of 40 sorghum plants. The result showed that genetic x environment interaction affected the agronomic characters and yield components of sweet sorghum. Several characters such as plant height, panicle diameter, seed production, sugar brix and stem juice volume of sweet sorghum mutants were greater than check varieties. The highest seed yield was found in MB-1 strain of sweet sorghum mutant that cultivated in Pekalongan site.
Antioxidant activity of ethanolic extract of three Selaginella species from Java Island, Indonesia
Authors: Miftahudin M , Hasibuan Rini , Chikmawati Tatik
Published: January 2020

Abstract. Miftahudin, Hasibuan RS, Chikmawati T. 2019. Antioxidant activity of ethanolic extract of three Selaginella species from Java Island, Indonesia. Biodiversitas 20: 3715-3722. Three Selaginella species, S. ornata, S. plana, and S. willdenowii, from Java Island, Indonesia, have been known to have antioxidant properties; however, in vivo antioxidant activities of these species have not been reported. This research aimed to evaluate the in vivo antioxidant activity of ethanolic extract of three Selaginella species. The 70% ethanol extract of three Selaginella species at four different doses was administered to mice one day before being treated with oxidative stress. The liver tissue of mice treated with or without oxidative stress was analyzed their lipid peroxidation by measuring MDA concentration and Superoxide Dismutase (SOD) activities. The results showed that there were variations in antioxidant activity among the three Selaginella species. In general, the dose of 0.3 g extract kg-1 BW has been able to reduce lipid peroxidation and increase SOD activity. The administration of S. ornata extract to the mice at 1.2 g extract kg-1 BW reduced the MDA concentration to the lowest level, but the same dose of two other Selaginella extracts caused toxic effects in mice. The antioxidant activities of S. ornata and S. plana were better than that of S. willdenowii extract, and among those species, S. ornata has the best antioxidant activity.