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HAYATI Journal of Biosciences

hayati
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Published by Institut Pertanian Bogor

ISSN : 19783019 EISSN : 20864094 DOI : -

Core Subject : Science, Agriculture,

Agriculture, Biological Sciences & Forestry Earth & Planetary Sciences

HAYATI Journal of Biosciences (HAYATI J Biosci) publishes articles and short communication in tropical bioscience fields such as development, biotechnology, biodiversity and environmental issues. HAYATI J Biosci covers wide range of all life forms topics including virus, microbes, fungi, plants, animal and human. HAYATI J Biosci has been also indexed/registered in Crossref, DOAJ, CABI, EBSCO, Agricola and ProQuest.

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Articles 1,077 Documents

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The Distribution and Abundance of Black Band Disease and White Syndrome in Kepulauan Seribu, Indonesia Ofri Johan; Dietriech Geoffrey Bengen; Neviaty Putri Zamani; . Suharsono; Michael John Sweet
HAYATI Journal of Biosciences Vol. 22 No. 3 (2015): July 2015
Publisher : Bogor Agricultural University, Indonesia

Coral diseases that have emerged since the early 1970s have caused significant regional ecological impacts. However, there has been a paucity of research into coral disease in South-East Asia, including Indonesia. This study provides baseline coral disease data in the Kepulauan Seribu Marine National Park. In this study we show a positive correlation between overall coral cover and the dominant reef building coral Montipora spp. and found two main diseases, black band disease (BBD) and WS, were highly prevalent throughout all reefs. Based on spatial location, the highest abundance of BBD (0.08 col./m2) was found at sites nearer (zone 1) to the mainland, whilst for WS (0.05 col./m2) highest abundance was found at middle sites (zone 2). According to the temporal data, the highest abundance of BBD (0.77 col./m2) was found during the transition period (between wet and dry seasons), whereas for WS higher abundance occurred within the dry season (0.07 col./m2). There was a significant difference in disease abundance among seasons which was correlated with increasing temperature and light intensity along with variations in total organic matters, nitrite and phosphate levels. Moreover, the middle sites experienced additional stress from the waste material originating from the mainland.

Metagenomic of Actinomycetes Based on 16S rRNA and nifH Genes in Soil and Roots of Four Indonesian Rice Cultivars Using PCR-DGGE . Mahyarudin; Iman Rusmana; Yulin Lestari
HAYATI Journal of Biosciences Vol. 22 No. 3 (2015): July 2015
Publisher : Bogor Agricultural University, Indonesia

The research was conducted to study the metagenomic of actinomycetes based on 16S ribosomal RNA (rRNA) and bacterial nifH genes in soil and roots of four rice cultivars. The denaturing gradient gel electrophoresis profile based on 16S rRNA gene showed that the diversity of actinomycetes in roots was higher than soil samples. The profile also showed that the diversity of actinomycetes was similar in four varieties of rice plant and three types of agroecosystem. The profile was partially sequenced and compared to GenBank database indicating their identity with closely related microbes. The blast results showed that 17 bands were closely related ranging from 93% to 100% of maximum identity with five genera of actinomycetes, which is Geodermatophilus, Actinokineospora, Actinoplanes, Streptomyces and Kocuria. Our study found that Streptomyces species in soil and roots of rice plants were more varied than other genera, with a dominance of Streptomyces alboniger and Streptomyces acidiscabies in almost all the samples. Bacterial community analyses based on nifH gene denaturing gradient gel electrophoresis showed that diversity of bacteria in soils which have nifH gene was higher than that in rice plant roots. The profile also showed that the diversity of those bacteria was similar in four varieties of rice plant and three types of agroecosystem. Five bands were closely related with nifH gene from uncultured bacterium clone J50, uncultured bacterium clone clod-38, and uncultured bacterium clone BG2.37 with maximum identity 99%, 98%, and 92%, respectively. The diversity analysis based on 16S rRNA gene differed from nifH gene and may not correlate with each other. The findings indicated the diversity of actinomycetes and several bacterial genomes analyzed here have an ability to fix nitrogen in soil and roots of rice plant.

The Pearl Sac Formation in Male and Female Pinctada maxima Host Oysters Implanted With Allograft Saibo La Eddy; Ridwan Affandi; Nastiti Kusumorini; Yulvian Sani; Wasmen Manalu
HAYATI Journal of Biosciences Vol. 22 No. 3 (2015): July 2015
Publisher : Bogor Agricultural University, Indonesia

An experiment was conducted to study the effect of male and female host oysters on the pearl sac formation in Pinctada maxima oyster. One hundred sixty oysters were used in a completely randomized design with 2 x 4 factorial arrangement and 20 replications. The 1st factor was that sex of host oyster consisted of two levels that is males and females. The 2nd factor was week after nucleus implantation with four levels that is 1, 2, 3, and 4 weeks. The parameters observed were the percentage of successful oysters to form the pearl sac, the speed of pearl sac formation, the percentage of nucleus coverage by the pearl sac, histology of the pearl sac growth and development, and haemolymph glucose, calcium and phosphorus concentrations. Our results showed that the percentages of host oysters that succeeded in forming a pearl sac were 80% and 75% in female and male host oysters, respectively. There was no statistical difference in nucleus rejection and mortality in male and female host oysters but the results indicated that male host oysters showed a numerically higher nucleus rejection. The speed of pearl sac growth and the percentage of nucleus coverage by the pearl sac in female host oysters were better than those in male host oysters. Haemolymph calcium, phosphorus and glucose concentrations, oxygen consumption, and histological development of the pearl sac were not different between male and female host oysters. Pearl sac formation in the female host oysters was better than that in male host oysters.

Sucrase Activity and Exopolysaccharide Partial Characterization From Three Weissella confusa Strains Amarila Malik; Sheilla Sheilla; Wangi Firdausi; Tri Handayani; Endang Saepudin
HAYATI Journal of Biosciences Vol. 22 No. 3 (2015): July 2015
Publisher : Bogor Agricultural University, Indonesia

Exopolysaccharides (EPSs) produced by lactic acid bacteria have been well known for their important economic value in food, pharmaceutical and health industries. Large extracellular enzyme sucrases are used by lactic acid bacteria to polymerize EPS, i.e. fructansucrase and glucansucrase. This study aimed to characterize sucrase activity of three Weissella confusa strains MBF8-1, MBF8-2 and MBFCNC-2(1), which were isolated previously from local beverages and their EPS products as well. All strains showed ability to form mucoid and slimy colonies by visual inspection on agar plate using raffinose as substrate suggesting that they possessed fructansucrase activity besides glucansucrase. Obtained EPS products were characterized by HPLC analysis after hydrolysis using 3% TCA at 100C for 1 hour, and by viscosity as well. All strains exhibited similar peak patterns, assuming that all of them possessed fructan EPS product. Supernatant and cell pellet were also analyzed by in situ activity assay performing periodic acid Schiff staining after polyacrylamide gel electrophoresis; only cell pellet showed sucrase activity. Viscosity observation showed that EPS products from all strains were able to increase the viscosity slightly.

Rhizopus Species from Fresh Tempeh Collected from Several Regions in Indonesia Anastasia Tatik Hartanti; Gayuh Rahayu; Iman Hidayat
HAYATI Journal of Biosciences Vol. 22 No. 3 (2015): July 2015
Publisher : Bogor Agricultural University, Indonesia

Recent changes in taxonomy of Rhizopus, which are now heavily relying on molecular approach, create significant problem in assigning species name to particular Rhizopus strains isolated from various sources, including tempeh. The present study aims to determine 36 strains of Rhizopus from tempeh originated from 26 locations in Indonesia, using combination of molecular phylogenetic analysis based on internal transcribed spacer ribosomal DNA sequence, physiology, and morphology to species level. The results showed that most of the strains belong to R. microsporusecomplex, and only one strain belongs to R. delemar. Morphological variations within R. microsporus were observed, but under current approach they were insufficient for infraspecific delimitation. The current report is an important contribution in validating the identity of Rhizopus from fresh tempeh in Indonesia.

Isolation and Phylogenetic Analysis of Thermophile Community Within Tanjung Sakti Hot Spring, South Sumatera, Indonesia Heni Yohandini; . Julinar; . Muharni
HAYATI Journal of Biosciences Vol. 22 No. 3 (2015): July 2015
Publisher : Bogor Agricultural University, Indonesia

A community of thermophiles within Tanjung Sakti Hot Spring (South Sumatera) have been cultivated and identified based on 16S ribosomal RNA gene sequence. The hot spring has temperature 80C-91C and pH 7-8. We used a simple method for culturing the microbes, by enriching the spring water with nutrient broth media. Phylogenetic analysis showed that the method could recover microbes, which clustered within four distinct taxonomic groups: Anoxybacillus, Geobacillus, Brevibacillus, and Bacillus. These microbes closely related to Anoxybacillus rupiensis, Anoxybacillus flavithermus, Geobacillus pallidus, Brevibacillus thermoruber, Bacillus licheniformis, and Bacillus thermoamylovorans. The 16S ribosomal RNA gene sequence of one isolate only had 96% similarity with Brevibacillus sequence in GenBank.

Identification of Diagnostic Mitochondrial DNA Single Nucleotide Polymorphisms Specific to Sumatran Orangutan (Pongo abelii) Populations Puji Rianti; Dyah Perwitasari-Farajallah; Dondin Sajuthi; Joko Pamungkas; Alexander Nater; Michael Krützen
HAYATI Journal of Biosciences Vol. 22 No. 4 (2015): October 2015
Publisher : Bogor Agricultural University, Indonesia

The hypervariable region I of mitochondrial DNA has frequently been used to distinguish among populations, in particular in species with strong female philopatry. In such cases, populations are expected to diverge rapidly for hypervariable region I markers because of the smaller effective population size and thus increased genetic drift. This rapid divergence leads to the accumulation of mutations exclusively found in one population, which may serve as diagnostic single nucleotide polymorphisms (SNPs). To date, diagnostic SNPs distinctive to Sumatran orangutan populations have not yet been described. However, given the continuously declining numbers of Sumatran orangutans, this information can be vital for effective conservation measures, especially regarding reintroductions of orangutans in rehabilitation centers. Phylogenetic analyses of 54 samples of Sumatran orangutans from nine sampling sites with good provenance, we found five major clades and a total of 20 haplotypes. We propose a total of 52 diagnostic SNPs that are specific to Sumatran orangutan populations. Data can be used to develop restriction fragment length polymorphism assays to carry out genetic assignments using basic laboratory equipment to assign Sumatran orangutan to their population of origin.

Impact of Domestication on the Endophytic Fungal Diversity Associated With Wild Zingiberaceae at Mount Halimun Salak National Park Ivan Permana Putra; Gayuh Rahayu; Iman Hidayat
HAYATI Journal of Biosciences Vol. 22 No. 4 (2015): October 2015
Publisher : Bogor Agricultural University, Indonesia

Mount Halimun Salak National Park is one of the tropical forest remnants in Java island. The national park has been recognized with high diversity of wild Zingiberaceae. Of that Zingiberaceae, two species namely Alpinia malaccensis (AM) and Horstendia conica (HC), were domesticated as garden plants in the surrounding area of the forest for medicinal use. The impact of domestication on the fungal endophytes associated with these two species of Zingiberaceae is reported here. Fungal endophyte diversity in the wild and domesticated AM and HC was analyzed based on the culturable fungi. Identification of species level used morphological and molecular approaches of ITS rDNA sequence. This study determined 19 species of fungal endophytes, namely Arthrinium malaysianum, Aspergillus flavipes, As. sydowii, Chaetomium globosum, Cladosporium oxysporum, Cladosporium sp., Colletotrichum boninense-complex, Co. cliviae-complex, Co. gloeosporioides-complex, Diaporthe sp., D. anacardii, D. gardenia, Exophiala sp., E. lecanii-corni, Guignardia mangiferae, Ochroconis gallopava, Penicillium citrinum, Pyricularia costina, and unsporulated Sydowiellaceae. Among them, A. malaysianum, C. globosum, Co. cliviae-complex, D. gardenia, and unsporulated Sydowiellaceae were only found in domesticated plants, while some others were absent. Colletotrichum boninense-complex was commonly found in both wild and domesticated plants. Domestication activity affected the diversity of endophytic fungi of AM and HC.

Encapsulated Synbiotic Dietary Supplementation at Different Dosages to Prevent Vibriosis in White Shrimp, Litopenaeus vannamei Anis Zubaidah; Munti Yuhana; . Widanarni
HAYATI Journal of Biosciences Vol. 22 No. 4 (2015): October 2015
Publisher : Bogor Agricultural University, Indonesia

The aim of this study was to evaluate the effect of encapsulated synbiotic (Bacillus sp. NP5 and oligosaccharide) dietary at different dosages on growth performance, survival rate, feed conversion ratio, and immune responses of Litopenaeus vannamei against Vibrio infection. The shrimps of the main treatments were fed by the diet that contained three different dosages of encapsulated synbiotic [0.5% (A), 1% (B), and 2% (C) (w/w)] with feeding rate of 5% of shrimp biomass (4 times a day). The shrimps of two control treatments (negative control and positive control) were fed only by commercial feed without supplementation of encapsulated synbiotic. The growth, feed conversion ratio, and survival rate were observed after 30 days of encapsulated synbiotic dietary. The shrimps were then challenged by injection of Vibrio harveyi (6 log colony forming units/mL) 0.1 mL/shrimp, excluded the negative control treatment. Afterward, the survival and immune responses were observed for 9 days after experimental infection. The shrimps treated with 2% encapsulated synbiotic (treatment C) in the diet showed the highest growth performance (2.98 ± 0.42%), feed conversion ratio (1.26 ± 0.19), and better immune responses i.e. total hemocyte counts, differential hemocyte count, phenoloxidase, and intestine bacteria observation compared to those of positive control treatment.

Growth and Survival Rate of Tilapia (Oreochromis niloticus) Larvae Fed by Daphnia magna Cultured With Organic Fertilizer Resulted From Probiotic Bacteria Fermentation Vivi Endar Herawati; Johannes Hutabarat; . Pinandoyo; Ocky Karna Radjasa
HAYATI Journal of Biosciences Vol. 22 No. 4 (2015): October 2015
Publisher : Bogor Agricultural University, Indonesia

Daphnia magna is a potential feed for fish. The aim of this research was to find the best treatment and effect of D. magna culture addition from fermented organic fertilizer, to growth and survival rate of Oreochromis niloticus larvae. There were five treatments, each with three repetitions used in the study. All treatments used chicken dung, and different combinations of rice bran, coconut oilcake waste and tilapia larvae. Feeding on tilapia was given by ad libitum method for five times a day until 14 days. Water quality during the research was maintained at temperature 28–29°C, DO 0.3 ppm and pH 8.1–8.2. Observed variables include relative growth rate, survival rate, food consumption rate and water quality. Our results showed that D. magna cultured by fermented organic fertilizer for tilapia larvae (O. niloticus) had high significant effect (p < 0.01) on the relative growth rate and survival rate. Treatment of D. magna cultured by 1.2 g/L chicken manure, 0.9 g/L rice bran and 0.3 g/L coconut oilcake showed the highest value on the relative growth rate (10.86%); survival rate (98.46%) and food consumption at first week (106.43%) and second week (152.76%).

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