Biocontrol Activity, Mode of Action, and Colonization of Aureobasidium pullulans Dmg 30 DEP on Controlling Early Blight Disease on Tomato Plant

We investigated the biocontrol activity of A. pullulans Dmg 30 DEP against Alternaria solani causal agent of early blight. Biocontrol activity was tested by the in vivo and ad planta. Biocontrol activity were tested by investigating the antibiosis capabilities with dual culture method, paper dish assay, two-compartment petri dish assay, and trapping and identification of volatile organic compounds (VOCs) with GC-MS. Lysis activity was examined by observing the clear zone formed by growing yeast on chitin agar and skim milk agar. The ability of hyperparasitism was assessed by the agar block method, and observed by light microscopy and scanning electron microscopy (SEM). The results showed that A. pullulans Dmg 30 DEP plays a role in the suppression of early blight disease at 106 cells/ml and 107 cells/ml yeast cell density. The mechanism involved in biocontrol activity is the production of VOCs, the production of chitinase and protease enzymes, the production of siderophore and hyperparasitism. The result shows that A. pullulans Dmg 30 DEP was colonizing the tomato leaves following the areole.

Isolation and Identification of Actinomycetes Associated with Moss on the Surface of the Borobudur Temple Stone

Mosses growing on the surface of the Borobudur Temple will affect the aesthetic value of the temple. Interaction between moss and actinomycetes may trigger the growth of moss that can cause an increase in biodeterioration of stone. The purpose of this study was to isolate and identify the actinomycetes associated with moss on the surface of decayed stone of Borobudur Temple as well to assess their ability for phosphate solubilizing. Actinomycetes were isolated using serial dilution method and were identified based on 16S rRNA gene sequences. A total of 37 actinomycetes were isolated from three sampling sites. The isolates found belong to five genera (Gordonia, Microbacterium, Micromonospora, Nocardia, and Streptomyces) and distributed among four families (Microbacteriaceae, Micromonosporaceae, Nocardiaceae, and Streptomycetaceae). Isolates of actinomycetes composed of 19 Streptomyces Group and 18 Rare Actinomycetes Group. Nineteen isolates (51.35%) were identified as genus Streptomyces. Seventeen isolates (45.94%) showed abilities to release soluble phosphate and most of the isolates belong to the genus Streptomyces. The isolates have been collected will be deposited to Indonesian Culture Collection (InaCC) to enrich the collection of actinomycetes from ancient stone in Indonesia and will be used as a source of reference material research, taxonomic, or as source for further study.

Taxonomic Approach for Species Diversity of Yeasts and Yeasts-like Fungi through D1/D2 Region of Large Subunit Ribosomal DNA Sequences

The identification of yeasts or yeasts-like fungi and verify their diversity are principal aspect for bioindustry and ecosystem sustainability. Taxonomic approach provides identification tool to ensure the taxonomic position of yeasts and yeasts-like fungi which definitely set to utilization concerns. The aim of this study is to understanding the taxonomic position of yeasts and yeasts-like fungi from the distinctive of its sequences relationship. Yeasts and yeasts-like fungi strains were isolated through various culture dependent methods from natural resources samples of Karimun Besar Island, Province of Riau Islands, Indonesia. The identification process was performed through amplifying the accurate DNA-based in D1/D2 region of large subunit (26S) ribosomal DNA. As the result, a total of 85 isolates of yeasts and yeasts-like fungi were obtained with 16 closest related taxa through phylogenetic tree construction. Ascomycetous was the predominating group representing 91% of the total isolates sequences followed by Basidiomycetous (8%) and Zygomycetous (1%). The black yeasts (yeasts-like) known as Aureobasidium melanogenum was predominant species with represent to 54% of total isolates and present in particular habitat. Taxonomically, there are six isolates are represent to be novel taxa candidates which pretend to enhance genetic resources of yeasts and yeasts-like fungi especially from Indonesia. In addition, this information provides specific technique to reach specific yeasts or yeasts-like fungi species in nature by managing the sample collection and culture methods.

Three novel species of d-xylose-assimilating yeasts, Barnettozyma xylosiphila sp. nov., Barnettozyma xylosica sp. nov. and Wickerhamomyces xylosivorus f.a., sp. nov

This study describes three novel xylose-assimilating yeasts, which were isolated from decayed wood collected from Bung Hatta Botanical Garden in West Sumatra and Cibodas Botanic Garden in West Java, or from litter from Eka Karya Bali Botanic Garden in Bali, Indonesia. Phylogenetic analysis was performed based on the sequences of the D1/D2 domains of the large ribosomal subunit (LSU), the small ribosomal subunit (SSU), the internal transcribed spacer (ITS) and elongation factor-1α (EF-1α), and the three strains were found to represent three novel species belonging to genera Barnettozyma or Wickerhamomyces. The morphological, biochemical and physiological characteristics indicated that the strains were distinct from other closely related species. Strains 13Y206^T and 14Y196^T belonging to the Barnettozyma clade are described as the type strains of Barnettozyma xylosiphila sp. nov. (type strain 13Y206^T=NBRC 110202^T=InaCC Y726^T; MycoBank MB808598) and Barnettozyma xylosica sp. nov. (type strain 14Y196^T=NBRC 111558^T=InaCC Y1030^T; MycoBank MB819485). Strain 14Y125^T belonging to the Wickerhamomyces clade is described as the type strain of Wickerhamomyces xylosivorus f.a., sp. nov. (type strain 14Y125^T=NBRC 111553^T=InaCC Y1026^T; MycoBank MB819484).

Discovery of synthesis and secretion of polyol esters of fatty acids by four basidiomycetous yeast species in the order Sporidiobolales

Polyol esters of fatty acids (PEFA) are amphiphilic glycolipids produced by yeast that could play a role as natural, environmentally friendly biosurfactants. We recently reported discovery of a new PEFA-secreting yeast species, Rhodotorula babjevae, a basidiomycetous yeast to display this behavior, in addition to a few other Rhodotorula yeasts reported on the 1960s. Additional yeast species within the taxonomic order Sporidiobolales were screened for secreted glycolipid production. PEFA production equal or above 1 g L^-1 were detected in 19 out of 65 strains of yeast screened, belonging to 6 out of 30 yeast species tested. Four of these species were not previously known to secrete glycolipids. These results significantly increase the number of yeast species known to secrete PEFA, holding promise for expanding knowledge of PEFA synthesis and secretion mechanisms, as well as setting the groundwork towards commercialization.

Pichia chibodasensis sp. nov., isolated in Indonesia

Three strains (14Y260T, 14Y268 and 14Y276) of xylose-assimilating yeasts were isolated from decayed wood and soil collected in West Java in Indonesia. A phylogenetic analysis was performed based on the sequences of the D1/D2 domains of LSU, SSU and EF-1α, and the three strains were found to belong to the genus Pichia. The morphological, biochemical, physiological and chemotaxonomic characteristics indicated that these strains were distinct from other closely related species. Strains 14Y260T, 14Y268 and 14Y276 belonged to the Pichia clade and represent a novel species, named Pichia chibodasensis sp. nov. ; The type strain is 14Y260T (=NBRC 111569T=InaCC Y1042T).

New species of the genus Metschnikowia isolated from flowers in Indonesia, Metschnikowia cibodasensis sp. nov

A novel species, Metschnikowia cibodasensis, is proposed to accommodate eight strains (ID03- 0093(T), ID03-0094, ID03-0095, ID03-0096, ID03-0097, ID03-0098, ID03-0099, and ID03-0109) isolated from flowers of Saurauia pendula, Berberis nepalensis, and Brunfelsia americana in Cibodas Botanical Garden, West Java, Indonesia. The type strain of M. cibodasensis is ID03- 0093(T) (= NBRC 101693(T) =UICC Y-335(T) = BTCC-Y25(T)). The common features of M. cibodasensis are a spherical to ellipsoidopedunculate shaped ascus, which contains one or two needleshaped ascospores, and lyse at maturity. Asci generally develop directly from vegetative cells but sometimes from chlamydospores. The neighbor-joining tree based on the D1/D2 domain of nuclear large subunit (nLSU) ribosomal DNA sequences strongly supports that M. cibodasensis (eight strains) and its closest teleomorphic species, M. reukaufii, are different species by a 100% bootstrap value. The type strain of M. cibodasensis, ID03-0093(T), differed from M. reukaufii NBRC 1679(T) by six nt (five substitutions and one deletion) in their D1/D2 region of nLSU rDNA, and by 18 nt (five deletions, four insertions, and nine substitutions) in their internal transcribed spacer regions of rDNA, respectively. Four strains representative of M. cibodasensis (ID03-0093(T), ID03-0095, ID03-0096, and ID03-0099) showed a mol% G+C content of 44.05 ± 0.25%, whereas that of M. reukaufii NBRC 1679(T) was 41.3%. The low value of DNADNA homology (5-16%) in four strains of M. cibodasensis and M. reukaufii NBRC 1679(T) strongly supported that these strains represent a distinct species.

An improved high-throughput Nile red fluorescence assay for estimating intracellular lipids in a variety of yeast species

A rapid and inexpensive method for estimating lipid content of yeasts is needed for screening large numbers of yeasts samples. Nile red is a fluorescent lipophilic dye used for detection and quantification of intracellular lipid droplets in various biological system including algae, yeasts and filamentous fungi. However, a published assay for yeast is affected by variable diffusion across the cell membrane, and variation in the time required to reach maximal fluorescence emission. In this study, parameters that may influence the emission were varied to determine optimal assay conditions. An improved assay with a high-throughput capability was developed that includes the addition of dimethyl sulfoxide (DMSO) solvent to improve cell permeability, elimination of the washing step, the reduction of Nile red concentration, kinetic readings rather than single time-point reading, and utilization of a black 96-well microplate. The improved method was validated by comparison to gravimetric determination of lipid content of a broad variety of ascomycete and basidiomycete yeast species.

Natural product libraries to accelerate the high-throughput discovery of therapeutic leads

A high-throughput (HT) paradigm generating LC-MS-UV-ELSD-based natural product libraries to discover compounds with new bioactivities and or molecular structures is presented. To validate this methodology, an extract of the Indo-Pacific marine sponge Cacospongia mycofijiensis was evaluated using assays involving cytoskeletal profiling, tumor cell lines, and parasites. Twelve known compounds were identified including latrunculins (1-4, 10), fijianolides (5, 8, 9), mycothiazole (11), aignopsanes (6, 7), and sacrotride A (13). Compounds 1-5 and 8-11 exhibited bioactivity not previously reported against the parasite T. brucei, while 11 showed selectivity for lymphoma (U937) tumor cell lines. Four new compounds were also discovered including aignopsanoic acid B (13), apo-latrunculin T (14), 20-methoxy-fijianolide A (15), and aignopsane ketal (16). Compounds 13 and 16 represent important derivatives of the aignopsane class, 14 exhibited inhibition of T. brucei without disrupting microfilament assembly, and 15 demonstrated modest microtubule-stabilizing effects. The use of removable well plate libraries to avoid false positives from extracts enriched with only one or two major metabolites is also discussed. Overall, these results highlight the advantages of applying modern methods in natural products-based research to accelerate the HT discovery of therapeutic leads and/or new molecular structures using LC-MS-UV-ELSD-based libraries.