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"ABSTRACTShrimp cultivation in ponds, especially Penaeus monodon Fabricius in Indonesia is depressed by disease, particularly due to white spot syndrome virus (VVSSV). Antibiotics, which have been used in large quantities in aquaculture are often cause for concern in promoting transfer of antibiotic resistance to human pathogens. Many' scientists reported that the application of probiotic bacteria provides a promising solution to these problems. Probiotic is now developed and used for shrimp culture in several countries such as: Thailand, China, Philippines. India, and Taiwan to increase the production target.The aim of this study was to find indigenous probiotic bacteria which can be used as therapeutic agent for vannamei shrimp (Litopenaeus vannamei) (Boone) toward WSSV. To achieve the aim above, a number of experiments were conducted, ie. 1) isolation and selection of indigenous probiotic bacteria based on shrimp?s survival rate; 2) selection of probiotic bacteria based on their ability to cure vannamei shrimp infected by WSSV, 3) efficacy test of probiotic bacteria on the hatching rate of the cysts of Artemia salina, and 4) identification of selected isolates based on sequence of 16S ribosomal RNA gene.The hypotheses of this studies were as follows: (a) indigenous probiotic bacteria can be isolated from several locations of shrimp fanning (b) indigenous probiotic bacteria n be used as therapeutic agent for shrimp towards WSSV, (c) indigenous probiotic bacteria show no negative effect towards other tropic level in aquaculture i.e. A. salina, and (d) selected probiotic bacteria can be identified based on 16S ribosomal RNA gene sequence analysis."

"Penelitian bertujuan mengisolasi dan mengidentifikasi khamir phylloplane Broussonetia papyrifera asal Bandung (Dago Pojok), Garut (Tunggilis dan Sukadanu), dan Trowulan, menguji kemampuan khamir antagonis dari daun B. papyrifera asal Desa Sukadanu dan Desa Tunggilis, Garut, Jawa Barat yang berpotensi sebagai agens biokontrol terhadap kapang-kapang penyebab kebusukan pada buah tomat pascapanen serta mengetahui viabilitas khamir setelah dipreservasi pada suhu -80 oC. Sebanyak 2.543 isolat khamir diperoleh dari empat wilayah sampling menggunakan metode washing dan membrane filter method. Pemilihan 82 isolat khamir representatif berdasarkan kemiripan morfologi koloni. Identifikasi khamir dilakukan berdasarkan sequence pada daerah internal transcribed spacer regions ribosomal DNA. Hasil identifikasi menunjukkan bahwa isolat khamir tersebut terdiri atas 17 genera dan 32 spesies: sebanyak 11 genera termasuk ke dalam Ascomycota (Saccharomycetes dan Dothidiomycetes), dan sebanyak enam genera termasuk Basidiomycota (Tremellomycetes, Microbotryomycetes, dan Ustilaginomycetes). Tiga kapang representatif berdasarkan hasil isolasi dari buah tomat dan uji patogenitas dapat menyebabkan kebusukan pada buah tomat pascapanen, yaitu Alternaria alternata, Lasiodiplodia theobromae, dan Syncephalastrum racemosum. Enam spesies khamir antagonis dapat menghambat pertumbuhan dan sporulasi A. alternata, L. theobromae, dan Syn. racemosum yaitu Candida saopaulonensis UICC Y-492, Candida pseudojiufengensis UICC Y-475, Debaryomyces hansenii UICC Y-488, Geotrichum candidum UICC Y-495, Hyphopichia burtonii UICC Y-496, dan Rhodotorula mucilaginosa UICC Y-476. Khamir antagonis dari B. papyrifera memiliki kemampuan menghambat pertumbuhan kapang A. alternata dan L. theobromae penyebab kebusukan pada buah tomat pada suhu 26--28oC selama 15 hari inkubasi. Khamir C. pseudojiufengensis UICC Y-475 dapat menghambat pertumbuhan kapang dan gejala kebusukan pada buah tomat (100%) disebabkan kapang A. alternata. Khamir C. saopoulenensis UICC Y-492 dan Rh. mucilaginosa UICC Y-513 dapat menghambat pertumbuhan kapang dan gejala kebusukan pada buah tomat (67%) yang disebabkan L. theobromae. Hasil pengujian viabilitas khamir setelah dipreservasi pada suhu -80oC selama 180 hari menunjukkan metode tersebut baik untuk preservasi jangka panjang empat spesies khamir potensial agens biokontrol pada buah tomat, yaitu khamir C. pseudojiutengensis UICC Y-475, C. saopoulenensis UICC Y-492, Hyp. burtonii UICC Y-496, dan Rh. mucilaginosa UICC Y-513. Seluruh strain yang diuji menunjukkan viabilitas yang tinggi (rerata CFU . 1x 108/ml). Jumlah sel khamir antara lain: C. pseudojiutengensis UICC Y-475 (1,08 x 108 CFU/ml), C. saopoulenensis UICC Y-492 (0,65 x 108 CFU/ml), Hyp. burtonii UICC Y-496 (1,76 x 108 CFU/ml), dan Rh. mucilaginosa UICC Y-513 (2,13 x 108 CFU/ml).

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The study was aimed to isolate and identify phylloplane yeasts from Broussonetia papyrifera plants from Bandung (Dago Pojok), Garut (Tunggilis and Sukadanu), and Trowulan; to investigate the yeasts with antagonistic abilities against moulds which attack post-harvest tomato fruits; and to observe the yeast viability after preservation at a temperature of -80 oC. Two thousand five hundred and forty-three yeast isolates were obtained using the washing method and the membrane filter method. Eighty-two representative yeast isolates were selected based on similarity of colony morphology. Identification was based on sequence data of internal transcribed spacer regions of ribosomal DNA (ITS rDNA).

The identification result showed that the 82 representative isolates were consisted of 17 genera and 32 species. Eleven of these genera are belong to Saccharomycetes and one genus belongs Dothidiomycetes (Ascomycota). Six genera are belong to Tremellomycetes, Microbotryomycetes, and Ustilaginomycetes (Basidiomycota). Three representative moulds obtained from the pathogenicity test were able to cause serious damage on post-harvest tomato fruits. These moulds were identified as, i.e. Alternaria alternata, Lasiodiplodia theobromae, and Syncephalastrum racemosum. Six antagonistic yeasts were able to inhibit growth and sporulation of post-harvest tomato moulds, i.e. Candida saopaulonensis UICC Y-492, Candida pseudojiufengensis UICC Y-475, Debaryomyces hansenii UICC Y-488, Geotrichum candidum UICC Y-495, Hyphopichia burtonii UICC Y-496, and Rhodotorula mucilaginosa UICC Y-476. The antagonistic yeasts were tested for their abilities to inhibit growth of A. alternata and L. theobromae which cause fruit rot on post-harvest tomatoes at 26--28oC for 15 days. Candida pseudojiufengensis UICC Y-475 was able to inhibit growth of A. alternata and reduce fruit rot symptoms in tomato fruit (100%). Candida saopoulenensis UICC Y-492 and Rh. mucilaginosa UICC Y-513 were able to inhibit growth of L. theobromae and reduce fruit rot symptoms in tomato fruit (67%).

The yeast viability was observed after being preserved at -80oC on day-1 (H1), day-7 (H7), day-14 (H14), day-30 (H-30), and day-180 (H-180). The results showed that all strains do not lose their viability after freezing at -80oC for 180 days. The number of cells for each strain after revival from preservation after 180 days were counted: C. pseudojiufengensis UICC Y-475 (1,08 x 108 CFU/ml), C. saopoulenensis UICC Y-492 (0,65 x 108 CFU/ml), Hyp. burtonii UICC Y-496 (1,76x 108 CFU/ml), and Rh. mucilaginosa UICC Y-513 (2,13 x 108 CFU/ml)."

"Penelitian mengenai eksplorasi senyawa aktif kapang endofit dari tumbuhan mangrove dan aplikasinya sebagai bioinsektisida telah dilakukan. Sebanyak 110 kapang endofit telah diperoleh dari akar, ranting, daun, dan serasah Rhizophora mucronata, Avicennia marina, dan Soneratia alba menggunakan enam jenis media dan lima jenis metode isolasi. Lima dari 110 isolat kapang endofit menunjukkan toksisitas tertinggi (menyebabkan mortalitas lebih dari 90% pada konsentrasi 80 ppm) terhadap larva Artemia salina. Kelima isolat kapang tersebut diidentifikasi berdasarkan data sequence daerah ITS rDNA dan pengamatan morfologi sebagai Emericella nidulans (BPPTCC 6035 dan BPPTCC 6038), Aspergillus flavus (BPPTCC 6036), A. tamarii (BPPTCC 6037), dan A.versicolor (BPPTCC 6039). Hasil pengujian aktivitas insektisida ekstrak etil asetat dari kultur filtrat biakan kelima strain kapang tersebut pada medium cair malt extract terhadap larva neonate dan instar III Spodoptera litura menunjukkan aktivitas sebagai racun lambung, racun kontak, attractant, racun saraf, dan menghambat perkembangan larva. Karakterisasi senyawa aktif dengan metode thin layer chromatography (TLC) yang dikombinasikan dengan beberapa reagen menunjukkan bahwa kelima ekstrak mengandung senyawa triterpenoid yang mengandung saponin; ekstrak yang dihasilkan oleh E. nidulans BPPTCC 6038 mengandung senyawa fenol; dan keempat ekstrak lain mengandung senyawa alkaloid. Formulasi dilakukan dengan menambahkan senyawa adjuvant berupa aseton sebagai pelarut, Tween 80 sebagai surfaktan, dan PEG 6000 sebagai sticker agent. Hasil pengujian aktivitas kelima formulasi terhadap larva neonate dan instar III S. litura menunjukkan bahwa seluruh formulasi memiliki aktivitas insektisida terhadap larva instar III S. litura lebih baik dibandingkan dengan kontrol positif, DeltametrinR (25 g/L).

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A study on the exploration of active compounds from mangrove endophytic fungi and their application as bioinsecticides was conducted. The isolation of mangrove endophytic fungi from roots, twigs, leaves, and leaf litter from Rhizophora mucronata, Avicennia marina, and Soneratia alba was conducted using a combination of six media with five isolation methods. Five of the 110 mangrove endophytic fungal isolates showed the highest toxicity (causing more than 90% larval mortality at 80 ppm) on Artemia salina larvae. Based on the DNA sequence data of the internal transcribed spacers (ITS) region of ribosomal DNA and morphological characteristics, these isolates were identified as Emericella nidulans (BPPTCC 6035 and BPPTCC 6038), Aspergillus flavus (BPPTCC 6036), A. tamarii (BPPTCC 6037), and A. versicolor (BPPTCC 6039). A bioassay on Spodoptera litura neonate and third instars larvae showed that five ethyl acetate of the five fungal filtrate extracts from malt extract broth medium exhibited attractant and insecticidal activities through stomach poisons, contact poisons, neurotoxins, and the inhibition of larval and pupal development. The chemical characterization of the five extracts using thin layer chromatography (TLC) combined with several reagents showed that the five extracts contained triterpenoid with saponin compounds, the extract from E. nidulans (BPPTCC 6038) contained phenolic compounds, and the four other extracts contained alkaloid compounds. Formulations were conducted by the addition of adjuvant: acetone as the solvent, Tween 80 as the surfactant, and PEG 6000 as the sticker agent. The insecticidal activity from five formulations on S. litura third instars larvae showed that the five formulations exhibited better insecticidal activity than DeltamethrinR (25 g/L) as the positive control."

"Penelitian bertujuan untuk memperoleh isolat-isolat khamir, memperoleh informasi spesies-spesies khamir yang berasal dari lebah madu Apis cerana dan substrat terkait, dan mengetahui pengaruh pemberian pollen substitute (PS) terhadap produktivitas koloni A. cerana. Khamir diisolasi dari telur, larva, pupa, lebah pekerja, lebah ratu, lebah jantan serta bee pollen, bee bread dan madu A. cerana, serta nektar dan serbuk sari dari bunga-bunga yang dikunjungi A. cerana. Khamir diisolasi menggunakan medium YMA dan YMA+sukrosa 50%. Identifikasi khamir dilakukan berdasarkan data sequence daerah internal trancribed spacer ribosomal DNA (ITS rDNA), analisis filogenetik dilakukan dengan metode Neighbor Joining, serta karakter morfologi dan fisiologi-biokimia. Sebanyak enam variasi PS dibuat untuk menguji preferensi A. cerana terhadap jenis PS. PS dalam bentuk pasta diberikan setiap hari selama 20 hari. Pengujian pengaruh pemberian variasi PS lokal dan PS impor terhadap produktivitas koloni A. cerana dilakukan selama 13 minggu. Sebanyak 1.409 isolat khamir diperoleh dari A. cerana dan substrat terkait. Lima puluh isolat representatif diseleksi untuk diidentifikasi. Hasil identifikasi menunjukkan bahwa 50 isolat khamir tersebut terdiri dari 12 genera dan 21 spesies. Sebanyak enam genera termasuk ke dalam phylum Ascomycota (class Hemiascomycetes, order Saccharomycetales),dan enam genera lainnya termasuk ke dalam phylum Basidiomycota (classes: Hymenomycetes, Urediniomycetes, dan Ustilaginomycetes). Hasil penelitian mengindikasikan adanya asosiasi dan interaksi antara spesies khamir dengan lebah madu. Hasil uji preferensi terhadap enam variasi PS lokal menunjukkan PS yang mengandung Candida hawaiiana CR015 asal bunga Brugmansia suaveolens (PS1) dan PS yang mengandung baker?s yeast (PS4) lebih disukai oleh A. cerana dibandingkan PS lain. Hasil uji produktivitas menunjukkan pollen substitute yang mengandung Candida hawaiiana CR015 asal bunga Brugmansia suaveolens (PS1) terbukti potensial dalam meningkatkan produktivitas koloni A. cerana setara dengan pollen substitute impor.

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The aims of this study were to obtain yeast isolates, to get species information from honeybee Apis cerana and related substrates, and to determine the effects of a pollen substitute (PS) on the productivity of A. cerana colonies.Yeasts were isolated from A. cerana eggs, larvae, pupae, workers, queens, drones, bee pollen, bee bread, honey, and nectars and pollens from flowers visited by A. cerana. The media used to isolate the yeasts were Yeast-Extract Malt-Extract Agar (YMA) and YMA+50% sucrose.

The yeasts were identified based on sequence data of internal transcribed spacer regions of ribosomal DNA (ITS rDNA). Phylogenetic analysis of yeasts based on ITS rDNA sequence data was performed by the neighbor-joining method. Morphological, physiological and biochemical characteristics of yeasts were observed. To determine the preference of A. cerana for pollen substitutes, honeybee colonies were fed daily with six varieties of pollen substitutes in patty form for 20 days. To examine the effects of pollen substitutes on the productivity of A. cerana, honeybee colonies were fed on local pollen substitutes (PSs) and imported PS for 13 weeks. A total of 1,409 yeast isolates were obtained from various substrates. Fifty representative isolates were selected for identification. The identification results showed that those 50 yeast isolates consisted of 12 genera and 21 species. Six of these genera belong to phylum Ascomycota, and class Hemiascomycetes, while the other six genera belong to phylum Basidiomycota and classes Hymenomycetes, Urediniomycetes and Ustilaginomycetes.

This study indicated that there is an association and an interaction between yeast species and honeybee. The preference test result showed that a PS containing Candida hawaiiana CR015 isolated from the flower of Brugmansia suaveolens (PS1) and a PS containing baker?s yeast (PS4) were favoured by A. cerana colonies.

The productivity test result showed that a PS containing Candida hawaiiana CR015. The preference test result showed that a PS containing Candida hawaiiana CR015 isolated from the flower of Brugmansia suaveolens (PS1) and a PS containing baker?s yeast (PS4) were favoured by A. cerana colonies. The productivity test result showed that a PS containing Candida hawaiiana CR015 isolated from the flower of Brugmansia suaveolens (PS1) was proved to potentially increase the productivity of A. cerana colonies and could be considered as good as imported pollen substitute."

"ABSTRAKPenelitian ini bertujuan untuk memberikan data tentang cyanobacteria yang dapat dibiakkan yang berasal dari sumber air panas di Indonesia dan usaha melestarikan kultur cyanobacteria dengan metode konservasi jangka panjang. Pengumpulan sampel dilakukan di enam lokasi sumber air panas di Jawa Barat, Indonesia., yaitu Ciseeng, Gunung Pancar, Rawa Danau Banten, dan 3 sumber air panas di Gunung Tangkuban Parahu (Domas kawah, Ciater, Maribaya), dalam periode 26 Februari 2012 dan 3 Juli 2012. Dari 1100 sampel (220 sampel segar dan 880 sampel pengayaan ), 140 isolat cyanobacteria dapat diisolasi, 44 isolat cyanobacteria yang dapat dikultur (culturable) dan pertumbuhannya stabil, serta 34 strain cyanobacteria dapat diidentifikasi. Sebagian besar strain cyanobacteria yang dapat dikultur yang diisolasi dari sumber air panas memiliki template DNA yang sulit. Tiga puluh empat strain diamplifikasi dengan polymerase chain reaction (PCR). Setelah dikonfirmasi dengan identifikasi berdasarkan 16S rRNA terhadap strain-strain yang telah diidentifikasi dengan karakter morfologi dan strain yang tidak dapat diidentifikasi dengan karakter morfologi, maka diperoleh 8 genera cyanobacteria, yaitu Synechococcus, Merismopedia, Leptolyngbya, Mastigocladus, Nostoc, Stanieria, Thermosynechococcus, dan Westiellopsis. Hampir semua cyanobacteria berbentuk coccoid dan berbentuk filamen dapat tumbuh optimal pada 35 °C. Kemungkinan, strain-strain cyanobacteria tersebut merupakan mikoorganisme termotoleran. Strain HS-16 (cyanobacteria berbentuk filamen) adalah satu-satunya strain yang bisa dikultur pada suhu 50 oC. Stanieria adalah genus yang unik dari cyanobacteria yang belum pernah dilaporkan dari Indonesia. Berdasarkan pohon filogenetik gen 16S rRNA, enam strain Stanieria yang diisolasi dari sumber air panas dikelompokkan menjadi dua kelompok yang terpisah dari cluster yang didalamnya termasuk S. cyanosphaeria (references strain). Hal tersebut mengindikasikan kemungkinan enam strain Stanieria merupakan dua spesies baru yang berbeda. Studi taksonomi cyanobacteria tampaknya harus didasarkan pada taksonomi polifasik, yaitu karakter morfologi, karakter molekuler (misalnya sekuen gen 16S rRNA), dan karakter kemotaksonomi (misalnya protein seluruh sel analisis oleh MALDI-TOF MS). Pada tingkat genus, identifikasi taksonomi dan rekonstruksi filogenetik berdasarkan sekuens gen 16S rRNA analisis sesuai dengan pengelompokan dari profil spektrum massa oleh MALDI-TOF MS. Database massa spektra protein perlu dikembangkan dan agar dapat digunakan untuk identifikasi cyanobacteria secara cepat oleh MALDI-TOF MS untuk pertama kalinya. Hasil dari penelitian telah membuka kemungkinan penggunaan MALDI-TOF MS untuk identifikasi cyanobacteria di tingkat spesies untuk masa datang.

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ABSTRACT

This research aims to provide data on indigenous culturable cyanobacteria derived from hot springs in Indonesia and to preserve cyanobacterial cultures by a long-term preservation method. Sample collection was carried out at six hot spring locations in West Java, Indonesia., i.e., Ciseeng, Pancar Mountain, Rawa Danau Banten, and 3 hot springs at the Tangkuban Parahu Mountain (Domas crater, Ciater, Maribaya), between February 26, 2012 and July 3, 2012. From the 1100 samples (220 fresh samples and 880 enrichment), 140 isolates could be isolated, 44 isolates of cyanobacteria could be cultured and stable, and 34 strains could be identified. Most of the culturable cyanobacteria strains isolated from hot springs had a difficult DNA template. Thirty-four isolates were obtained for amplification by polymerase chain reaction (PCR). After confirmation by identification based on 16S rRNA of the isolates, 8 genera of cyanobacteria were obtained, i.e., Synechococcus, Merismopedia, Leptolyngbya, Mastigocladus, Nostoc, Stanieria, Thermosynechoccus, and Westiellopsis. Almost all coccoid and filamentous cyanobacteria grew optimally at 35 °C. The strains of cyanobacteria that could be cultured were most likely thermotolerant microorganisms. Strain HS-16 (filamentous cyanobacteria) was the only strain that could be cultured at a temperature of 50 oC. Stanieria was a unique genus of cyanobacteria that has never been reported from Indonesia. Based on the phylogenetic tree of 16S rRNA gene, six strains of Stanieria were grouped into two clusters that separated from the cluster that includes the reference strain of S. cyanosphaeria, this indicated the possibility of six strains belong to two different new species. Taxonomic study of cyanobacteria seems has to be based on polyphasic taxonomy, i.e., morphological characters, the molecular characters (e.g.16S rRNA gene sequence), and chemotaxonomical character (e.g. whole-cell protein analyses by MALDI-TOF MS). At the genus level, taxonomic identification and phylogenetic reconstruction based on 16S rRNA gene sequence analyses were congruent with the clusterization from mass spectra profile by MALDI-TOF MS. In house mass spectral database was developed and used to allow the rapid identification of cyanobacteria by MALDI-TOF MS for the first time. The results from this study has open the possibility to use MALDI-TOF MS for identification of cyanobacteria at the species level in the near future."

"Penelitian ini berfokus pada keanekaragaman taksonomi Class Ktedonobacteria, kemampuannya sebagai penghasil enzim, deskripsi takson baru, dan analisis whole genome. Tujuh belas isolat diperoleh dari sampel tanah di hutan dekat geyser, kawasan geotermal Cisolok, Jawa Barat. Sequence gen 16S rRNA dari semua isolat dibandingkan dengan spesies terdekat pada database EzBioCloud. Seluruh isolat memiliki nilai homologi yang rendah terhadap Dictyobacter aurantiacus S-27T (97,82-98,18%). Penapisan kemampuan enzimatik menunjukkan bahwa sebagian besar isolat (88,23%) menghasilkan amilase dan selulase. Komposisi bakteri dari enam sampel dianalisis dengan metode metabarcoding gen 16S rRNA pada daerah V1-V3 menggunakan Illumina Mi-Seq Next Generation Sequencing. Ktedonobacteria merupakan kelas yang paling mendominasi dalam Phylum Chloroflexota (17,74-89,49%) pada lima sampel; Namun, kelas tersebut tidak terdeteksi pada satu sampel (tanah di bawah batu besar). Empat puluh tujuh amplikon gen 16S rRNA dari taksa terdekat Ktedonobacteria berhasil diperoleh dari enam sampel yang mewakili garis keturunan baru pada tingkat takson yang tinggi. Strain S3.2.2.5 diisolasi dari tanah di dalam serasah batang bambu. Karakter fenotipik, genotipik, dan filogenetik menunjukkan bahwa strain tersebut mewakili spesies berbeda dari Genus Dictyobacter; sehingga diusulkan spesies baru Dictyobacter halimunensis sp. nov.

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This study focuses on the taxonomic diversity of the class Ktedonobacteria, their ability as enzyme producers, description of novel taxon, and whole genome analysis. Seventeen isolates were obtained from soil samples in the forest near geyser, Cisolok geothermal area, West Java. The 16S rRNA gene sequence of all isolates was compared with all related species in the EzBioCloud database. All isolates had low similarity values to Dictyobacter aurantiacus S-27T (97.82-98.18%). Primary screening of enzymatic abilities showed that most isolates (88.23%) were amylase- and cellulase-producing Ktedonobacteria. Bacterial composition analyses from six samples were performed based on the V1-V3 of 16S rRNA gene metabarcoding using Illumina Mi-Seq Next Generation Sequencing. Ktedonobacteria was the most dominating class within the phylum Chloroflexota (17.74-89.49%) in five samples; however, it was not detected in one sample (the soil under a big rock). Forty-seven 16S rRNA gene amplicons of Ktedonobacteria-related taxa were generated from six samples and represented the putative new lineages in high taxonomic rank. A strain S3.2.2.5 was isolated from soil inside a decayed bamboo stem. The phenotypic, genotypic, and phylogenetic data suggest this strain represents a distinct species of the Dictyobacter genera; hence, a new species, Dictyobacter halimunensis sp. nov. is proposed."