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Bamboo is one of the plants which propagated by tissue culture technique however, the emergence of microbial contaminant caused decrease of bamboo production. A type of microbe that caused the contamination on Semiarundinaria fastuosa tissue culture is bacteria. This study aimed to isolate bacterial contaminant and understanding its biodiversity. Bacterial isolation and phenotypic characterization were done by observing morphology, physiological test, biochemical test, identification and numeric phenetic analysis. Twelve bacterial contaminants was isolated and based on profile matching with Bergey’s Manual of Determinative Bacteriology, six isolate was a member of genus Bacillus, one isolate Enterococcus, two isolate Xenorhabdus, one isolate Morococcus, one isolate Corynebacterium, and one isolate belongs to genus Sarcina. A dendrogram created using Simple Matching coefficient (SSM) parameter and average linkage algorithm shown that on the 71% similarity index, all 12 OTU was grouped in one cluster. However, a dendrogram produced by Jaccard’s coefficient (SJ) parameter and average linkage algorithm on 70% similarity index divided 12 OTU on to 12 clusters.

Efforts to control mercury pollution have been made for the last twenty years using various biological, physical, and chemical approaches. Streptomyces is able to degrade mercury because it possesses the mercuric reductase enzyme encoded by merA. The merA from Streptomyces isolate AS2 (Accession numbers LC026157) has been cloned into the expression vector pEt-28c(+). Therefore, it is critical to study recombinant mercuric reductase protein's expression and to analyse the protein structure. Expression of merA from an AS2 isolate was successfully performed in the host Escherichia coli BL21. Detection of mercuric reductase using SDS-PAGE showed a dominant band at 55–70 kDa. E. coli BL21 induction by IPTG was optimal at concentrations of 1 and 1.2 mM, and the optimal incubation times were 18 hours. The highest specific activity of mercuric reductase was 294.07 U/mg. Mercuric reductase protein in Streptomyces AS2 shares high homology with Lysinibacillus sphaericus (Swiss-Model), and similar folding to that of c5c1Yc refers to mercuric reductase from L. sphaericus using Phyre2. Based on amino acid sequences, the result revealed that Streptomyces AS2 strains were a group of Streptomyces lividans. These results give new insight to study further into a potential of MerA for bioremediation in the environment.

The final goal of this study is to make a modern systematic-based inventory of amylolytic bacterial isolates producing of bioplastic Poly-β-hydroxybutyrate (PHB) from sago starch substrate. The identity of three local bacterial isolates was examined in this study, using a polyphasic approach. A data set based on phenotypic characteristics, namely morphological, physiological, biochemical and chemical character, namely whole cells protein profiles using SDS-PAGE method, together with phylogenetic studies based on 16S rRNA sequences was used to identified by polyphasic approach. Phenotypic characteristics of 3 local bacterial isolates and 4 reference strains to members of genus Bacillus was analyzed by numerical analysis using MVSP 3,1 program to determine the value of similarity. Based on the preliminary characterization of the profile matching method showed that the three isolates of bacteria producing PHB namely PSA10, PPK5 and PPK6 are members of the genus Bacillus. The results of numerical analysis based on phenotypic characteristic and chemical character of the three bacterial isolates producing PHB with reference strains showed that the PSA10 isolate bacterial identical with Bacillus megaterium, PPK5 isolate identical with Bacillus subtilis and PPK6 isolate identical with Bacillus cereus, and these results also support by the molecular phylogenetic analysis. Therefore, the polyphasic taxonomy is an effective approach to uncover the identity of the novel bacterial isolates.

Isolation of catechin-degrading fungus from pine litter samples was done using minimal medium that containing catechin as sole carbon and energy source. A total of 53 isolates were chosen to represent different colonial types of catechin degrading-fungus. The isolates were screened for their ability to degrade catechin in three stages. The first stage of screening was based on their ability to grow on solid medium containing 2 mM, and as a result, 28 isolates were selected. The second stage of screening on the same medium but containing 4 mM of catechin resulting in 14 selected isolates. The third stage screening was based on their mean growth rate constant (k), instantaneous growth rate constant (m) and generation time (g) on minimal medium containing 4 mM catechin. The result showed that four isolates (D9, K2, K11, and S11) were the best catechin degradator. Further growth kinetic study (k, m ,and g) of selected isolates indicated that D9, K2, and S11 grew well on the medium containing 40 mM, but K11 was inhibited by concentration of higher than 10 mM. Catechin biodegradation process was determined by following the decrease of catechin concentration on liquid medium. It was found that isolate K2 had higher ability to degrade catechin than the isolate K11. Finally, the four selected isolates from the third stage were characterized in terms of macroscopic, microscopic and phenotypic characters and identified. The result of the study showed that the isolates D9, K2 and S11 were identified as member of Aspergillus niger group. The isolate D9 was very similar to isolate S11, while the isolate K2 was found to be the most similar with Aspergillus niger van Tiegh. IFO 6341. The isolate K11 was assigned to be member of the genus Trichoderma.

The phylogenetic relationships of the maleo (Macrocephalon maleo) were analyzed based on thefirst intron of rhodopsin nuclear gene sequence data obtained from 15 individuals, along withthose of 22 individuals taken from GenBank. The phylogenetic trees were reconstructed byNeighbor-Joining (NJ) method. Results indicated that 956 bp of RDP1 sequence, 414 (43.4%)sites were variable and 317 (33.2%) sites were phylogenetically-informative. The basecomposition for all species analyzed in this research were as follows: T 25.3%, C 26.3%, A18.5%, and G 29.9%. Analysis of RDP1 sequence produced trees that were remarkably wellresolved and had topologies at the marga level. The phylogenetic analysis showed that maleowas monophyly of Macrocephalon and closely related to Aepypodius, Talegalla, Leipoa andAlectura.

Linear Alkylbenzene Sulphonate (LAS) was the dominant pollutant in the river ecosystem. Indigenous strains of Pseudomonas in river ecosystem had highly potency to LAS degradation. This research was carried out to study relationship of indigenous strains of LAS degrading to Pseudomonas strains. Indigenous strains of bacteria of LAS degrading were characterized based on ARDRA (Amplified Ribosomal 16S rDNA Restriction Analysis) and 16S rDNA sequence. Result of the research shows that Pseudomonas strain J and R which LAS degrading from detergent polluted river ecosystem based on 16S rDNA sequence, isolate J has 98.37% similarity and it has relationship to P. pseudoalcaligenes LMG 1225T whereas isolate R has 84.86% similarity and related to P. stutzeri phen8.

Pathogenicity of 34 indigenous B. thuringiensis isolates against C. binotalis were determined. The pathogenicity test was conducted by using leaf dipped method with various spore concentrations. Third instar larvae of C. binotalis were used as insect test. Mortality data of test larvae were used to determine the pathogenicity of the isolates in terms of 72 hours LC50 by using probit analysis. The results of experiments showed YPPA 1. was the most pathogenic isolate, producing 72 hours LC50 = 9.5 x 103 spore.ml-1 with LT50 (1.5 x 107 spore.ml-1) of 24.6 hours while the ACH 2.3 was found to be the least pathogenic isolate with 72 hours LC50 = 2.3 x 106 spore.ml-1 and LT50 (1.5 x 107 spoore.ml-1) of 40.7 hours. The shortest LT50 (1.5 x 107 spore.ml-1 was found to be 18.2 hours produced by TUS.1 with 72 hours LC50 = 3.9 x 105 spore.ml-1 whereas the longest LT50 (1.5 x 107 spore.ml-1) was found tobe 83.2 hours produced by the SLK 4.1 with 72 hours LC50 = 3.1 x 104 spore.ml-1. Therefore, it can be concluded that both YPPA.1 and TUS.1 isolates are potential candidate to be developed for biological control agent.

The objective of this research was to investigate the capabilities of bacteria isolated from industrial tanning waste to degrade TCMTB. The bacteria was initialy screened, based on their tolerance to various concentration of TCMTB using paper disk method. Then, those strains were further analyzed in terms of their ability to produce ammonia (NH4+) and sulphate (SO42-). Degradation activity was measured based on remaining residue of TCMTB analyzed using HPLC. The superior strain that showed the highest activity in degradation of TCMTB then were characterized and identified based on phenotypic and 16S rDNA sequence analysis. The result of the experiments showed that four selected strains among seven were choosen based on their high tolerance to various concentration of TCMTB, namely PK1, PK2, PK4 and PK6. All four strains showed the ability to produce ammonia and sulphate but three of which, namely PK2, PK4 and PK6 showed the high capability to degrade TCMTB. One particular strain (PK2) was observed to degrade TCMTB 40.8% within 7 days, but the others were less than 30%. Based on the phenotypic characteristics and 16S rDNA sequence analysis, the best strains (PK2) was identified to be member of genus Pseudomonas.

A new strain characterized as Bacillus sp. PSA10 was found to produce poly-β-hydroxybutyrate (PHB) at concentration of 52.28% (g PHB/g dry cell weight) in shaken flask culture, using sago starch as a carbon source. This research is aimed to determine the optimum culture condition of PHB production Bacillus sp. PSA10 at laboratory scale. Optimization of PHB production was conducted in this research, in terms of inoculum concentration, concentration of the major components in minimal medium, environmental condition and incubation time. The result showed that optimum conditions for the production of PHB by Bacillus sp. PSA10 were achieved at minimal medium (Ramsay medium) with 5% (v/v) inoculum concentration, 2% (w/v) sago starch, 1.0 g/l (NH4)2SO4, 6.7 g/l Na2HPO4.7H2O, and 0 g/l KCl. The optimum environmental conditions were achieved with initial pH 7, temperature 37oC, agitation speed at 150 rotary per minute (rpm) and the best of incubation time was 48 hour. Under this optimum condition, the maximum PHB production by Bacillus sp. PSA10 increased from 52.28% to 71.35% (g PHB/g dry cell weight) at 48 hour cultivation. Therefore, Bacillus sp. PSA10 is potential to apply for PHB production from sago starch at industrial scale.

Diversity of B. thuringiensis (Bt.) isolates pathogenic to C. binotalis was determined by using Numerical Systematic Method. Ten isolates were taken to represent 34 pathogenic isolates along with two reference strains namely B. thuringiensis serovar kurstaki and B. thuringiensis serovar israelensis. The test isolates were examined for 89 phenotypic characters by using convensional method for colonial and cell morphology (37 characters) as well as physiological characteristics (3 characters) but biochemical characterization (49 characters) was conducted by using commercial API-50 CHB procedures. All phenotypic characters existed in one of two mutually exclusive states and were either scored plus (1) of minus (0). The binary data were prepared in Programmer’s File Editor (PFE) software. The data then were analysed by using the Multi Variate statistical Package (MVSP) Plus-Version 3.1 using the Simple Matching Coefficient (SSM). Clustering was achieved using the UPGMA algorithm. The results were presented as dendrograms. It was obtained that the test isolates were clearly assigned to two distinct multimembered clusters defined by 79.6 similarity level (S-level) in the SSM, UPGMA analysis. The two distinct clusters represented by each of two widely known different group of Bt. strains, namely serovar israelensis and serovar kurstaki. The first cluster contained reference strain of B. thuringiensis serovar israelensis, and two of the isolates (Slk2.3, and YPPA1) and the second cluster contained another reference strain of B. thuringiensis serovar kurstaki, and 8 of the isolates. Therefore, it strongly suggested that the application of numerical-fenetic analysis could provide a tool to unravel the strain diversity belong to B. thuringiensis.

Chitinase is chitin degrading enzyme which is produced by Streptomyces Rkt 5 is isolated microorganism from peanut rhizosfer. This enzyme and its microorganism can be used in many agricultural, medicine and industrial purposes. The aim of the research was to find out the optimum condition for production of chitinase and to characterize of pH and temperature to chitinase activity. Optimalizing production the research had 4 treatments. The optimum conditions were achieved at mineral liquid medium containing with chitin 0,2% (w/v) as inducer, 10% (v/v) inoculum, pH 7 and 48 hours incubation. The crude enzyme was partially purified by salting out with 70% ammonium sulfate resulted in 3.31 time more purity enzyme than the crude one. This enzyme had maximum activity at 50oC and pH 5.5.

Bacteria strains consisting of Pseudomonas sp. strain J and R isolated from river ecosystem polluted and Pseudomonas sp. strain A and B isolated from river ecosystem unpolluted by detergent were capable to degrade of LAS. The objective of this research was to determine similarity value by numerically of LAS-degrading Pseudomonas strains based on phenotype character and protein fingerprinting using three reference strains consist of Pseudomonas putida FNCC071, P. fluorescens FNCC070, and P. aeruginosa FNCC063. Phenotype characteristics examined are cellular and colony morphology, biochemical nature, capability to degrade polysaccharide, tolerance to various environmental factors and antibiotics, and ability to ferment sugar. Cellular protein fingerprinting was analyzed using SDS–PAGE discontinuous. Strains classification was determined based on Simple Matching Method similarity index by UPGMA (Unweight Pair Group Method with Average) algorithm. Based on phenotype nature, all strains have similarity value 0.61; however, based on cellular protein fingerprinting, those strains have similarity value 0.52. All strains of LAS-degraded were including in the genus of Pseudomonas.

Rahayu HM, Putri WA, Khasanah AU, Sembiring L, Purwestri YA. 2021. Indigenous Streptomyces spp. isolated from Cyperus rotundus rhizosphere indicate high mercuric reductase activity as a potential bioremediation agent. Biodiversitas 22: 1519-1526. The purification and characterization of mercuric reductase of four indigenous Streptomyces spp. from Cyperus rotundus L. rhizosphere in mercury-contaminated area have been investigated. Cell-free extract was obtained by disrupting cells using sea sand at 4 °C followed by centrifugation. Mercuric reductase was purified by ammonium sulfate precipitation, dialysis, and chromatography column (DEAE Sepharose anion column chromatography). The determination of optimum pH and temperature of mercuric reductase activity was measured based on the number of NADPH2 oxidized to NADP per mg protein per minute using a spectrophotometer. The molecular weight of mercuric reductase was determined using SDS-PAGE. Result showed that the highest specific activity of mercuric reductase was recorded from Streptomyces spp. BR28. The optimum pH and temperature of cell-free extract enzyme mercuric reductase were 7.5 and 80 °C, respectively. The enzyme was purified to 431.87-fold with specific activity 21918.95 U/mg protein. SDS PAGE showed that the molecular weight of mercuric reductase in Streptomyces spp. BR 28 ranged from 50 kDa to 75 kDa. It can be concluded that Streptomyces isolates contain mercuric reductase and have potential as mercury bioremediation agent to overcome mercury contamination in the environment.

Poly-β-hydroxybutyrate (PHB) is a thermoplastic polyester accumulated intracellularly by many microorganisms under unfavorable growth conditions. The features of PHB are biodegradable and biocompatible, and the physical properties are similar to polypropylene, which has attracted industrial attention as an environmentally degradable plastic for a wide range of agricultural, marine, and medical applications and appropriate substitutes for hydrocarbon-based plastics. Starch is a renewable carbon source from plant sources available abundantly in large quantities throughout the globe and has recently been used as a carbon source for PHB production. The utilization of starch in PHB production needs enzymatic hydrolysis for starch degradation since many microorganisms do not produce these enzymes natively. This suggests there is a need for exploitation of bacterial culture for the co-production of the starch-hydrolyzing enzyme (amylolytic bacteria) as well as PHB. Some bacteria have been reported capable to convert starch into PHB directly, which are from the genus Bacillus. The process of PHB production from starch by amylolytic bacteria is simultaneous saccharification and fermentation (SSF). The mechanism of bacteria synthesizing PHB from starch is divided into two groups, namely, the growth-associated PHB synthesis and the non-growth-associated PHB synthesis. The utilization of starch for PHB production is an economic strategy to reduce production costs of PHB as well as its applications in various fields.

Rahmawati, Sembiring L, Zakaria L, Rahayu ES. 2018. The diversity of indoor airborne molds growing in the university libraries in Indonesia. Biodiversitas 19: 194-201. Airborne mold is potentially causing respiratory diseases. The aim of this study was to investigate the diversity of indoor airborne molds isolated from some libraries in Universitas Gadjah Mada (Gadjah Mada University), Yogyakarta, Indonesia based on morphological characteristics. Sampling was conducted in six libraries at Universitas Gadjah Mada (Libraries of Food and Nutrition at Inter-University Center or Pusat Antar Universitas (PAU), Biotechnology at PAU, Faculty of Biology, Faculty of Mathematics and Natural Sciences, Faculty of Master of Management, and Faculty of Geography) by non-volumetric air sampling method. Isolation of indoor airborne molds was conducted by using two petri dishes containing Dichloran 18% Glycerol Agar (DG 18) for each room. Morphological identification of isolates of indoor airborne molds was based on macromorphological and micromorphological characteristics. Isolation and identification were conducted in Laboratory of Microbiology of Food and Nutrition of PAU at Universitas Gadjah Mada. The result showed the diversity of indoor airborne molds, identified to be members of genera Alternaria, Aspergillus, Aureobasidium, Byssochlamys, Cadophora, Chaetomium, Chrysonilia, Cladosporium, Curvularia, Emericella, Epicoccum, Eurotium, Fusarium, Geomyces, Mucor, Penicillium, Rhizopus, Rhizomucor, Stemphylium, Scopulariopsis, Wallemia, and Xeromyces. Members of genera Aspergillus, Cladosporium, and Penicillium were the most dominant molds. The results of this study indicate that the presence of molds potentially causes illness for the library users.

Gene expression of SAP 4-6 based on the detection of mRNA was observed in Candida albicans isolates from HIV-positive patients with oral candidiasis and commensal from healthy individuals. The species of C. albicans strains were selectively isolated from both sources using CHROMagar Chromogenic Media. The obtained isolates were then induced to express SAP 4-6 using SAP 4-6 gene inducer media. Analysis of gene expression was performed on a molecular basis using the RT-PCR method. Molecular analysis of gene expression showed that the isolates CH3 from HIV-positive patients with oral candidiasis could express SAP 4-6 gene, while commensal isolates from healthy people could not. Based on the results of this study, it could be concluded that, in terms of molecular detection, only isolates from HIV-positive patients (CH3) could express their SAP 4-6 gene.

Retnowati Y, Sembiring L, Moeljopawiro S, Djohan TS, Soetarto ES. 2017. Diversity of antibiotic-producing actinomycetes in mangrove forest of Torosiaje, Gorontalo, Indonesia. Biodiversitas 18: 1453-1461. Actinomycetes for antibiotic production have been studied at various extreme environments. Mangrove forest of Torosiaje in Gorontalo Province, Indonesia has unique geomorphological conditions where the forest is surrounded by karst ecosystem consisting of fringe and overwash types. Therefore, the objective of this study was to analyze the distribution and diversity of antibiotic-producing Actinomycetes in various rhizosphere including different locations and mangrove species. Samples of rhizosphere soil were collected in the depth of 0-10 cm, which was then subjected to detailed physicochemical analysis. Actinomycetes were collected through heating pre-treatment (60oC for 15 min) followed by culturing in the Starch Casein Agar medium supplemented with cycloheximide and nystatin. The screening process of antibiotic-producing Actinomycetes was based on Agar block method against pathogenic microorganisms. Grouping of Actinomycetes was determined by ARDRA fingerprinting analysis. The diversity of Actinomycetes was analyzed based on sequencing of 16S rDNA. The results showed that the distribution of Actinomycetes was found in overwash type, middle zone and upper zone of fringe type including rhizosphere of 7 species of mangrove. The highest population of Actinomycetes was found in rhizosphere of R. mucronata at the overwash type, and the lowest one found in rhizosphere of R. apiculata at the middle zone of fringe type. A total of 77 isolates amongst 167 isolate collection showed antibacterial activities. Forty seven representatives from 77 antibacterial-activities isolates were selected using ARDRA for partial characterization according to their phylogenetic diversity. Sequencing and analysis of 16S rDNA from selectedrepresentative isolates displayed the presence of members associated with Actinomycetes genera such as Streptomyces, Amycolatopsis, Saccharomonospora, and Nocardiopsis. The member of genus Streptomyces such as Streptomyces qinglanensis and Streptomyces champavatii were distributed across locations. Genus Saccharomonospora and Nocardiopsis were mostly found at the overwash type, while Amycolatopsis was found at the upper zone of fringe type.

Ambarwati A, Wahyuono S, Moeljopawiro S, Sembiring L, Yuwono T. 2019. Antimicrobial activities and phylogenetic study of bacteria associated with Cyperus rotundus rhizosphere from Cemoro Sewu Plateau, Indonesia. Biodiversitas 20: 2206-2212. A study has been conducted to investigate the activity of bacteria isolated from the rhizosphere of Purple Nut Sedge (Cyperus rotundus) from Cemoro Sewu Plateu, Indonesia as antimicrobial agent and the molecular relatedness between the isolates with other bacteria based on phylogenetic tree analysis. A total of six bacteria were obtained and tested for their capability to inhibit the growth of test organisms using agar block method and characterized molecularly using 16S rDNA sequence analysis. It was observed that the six isolates demonstrated the ability to inhibit at least one of four test microorganisms growth, with a diameter of inhibition zone ranging from 8-35 mm. The CRC32 isolate was the best isolate in inhibiting Staphylococcus aureus ATCC 25923 with a diameter inhibition zone of 26 mm (strong), while isolate CRA8 was the best anti-Candida (showing 35 mm of inhibition zone). The phylogenetic tree analysis resulted in two genera, four isolates belonging to Bacillus, while the other two isolates were known related to Paenibacillus genus. BLAST analysis on the CRC 32 isolate revealed that it is closely related with Paenibacillus peroriae strain 3763 with 99% sequence similarities and CRA8 isolates demonstrated the highest similarity with Paenibacillus sonchi strain X19-5 (97%). The results of this study demonstrated that the bacterial isolates from plant rhizosphere of Cemoro Sewu Plateau were the members of the Bacillus and Paenibacillus genera and demonstrated the potential as antimicrobial agent.

Lactobacillus plantarum Dad 13 is a group of Lactic Acid Bacteria, which was isolated from “Dadih” (traditional fermented buffalo milk) has known as indigenous probiotic from Indonesia. Probiotics are defined as living microorganisms and have health benefits with consumption for use as a supplement of food with the amount of cell viability at least 108 cells. L. plantarum frequently used as a starter in probiotic drink, especially in fermented milk. Milk is a valuable source of nutritional substances with the composition of water, protein, fat, sugars, mineral salts, vitamins, and enzymes for the living of microorganisms. To study the potential of L. plantarum Dad 13 in milk, we present an updated inventory of L. plantarum Dad 13 used in milk to making cheese. These we are applied L. plantarum Dad 13 to produce lactic acid for making curds. Combination treatment of biomass production used for cheese making that was biomass production using coconut water and MRS medium. The different combinations of a medium can influence the biomass viability of L. plantarum Dad 13 in cheese. The result showed that the viability of L. plantarum Dad 13 in cheese using two kinds of media during the production of biomass (i.e., coconut water and MRS) were almost similar during two months of storage, that was 103 cfu/g. They decreased on viability after two-month storage was about 3 log cycles. The result showed that viable the cell of L. plantarum Dad 13 in this cheese did not agree with the criterion of a minimum of 106 – 108 cfu/g viable cells as a probiotic product. Overall, local isolates of L. plantarum Dad 13 can be applied in the process of cheese making.

The purpose of this study was to analyze the phylogenetic relationship of Gram negative bacteria (3strains of Salmonella typhi, 1 strain of Escherichia coli, 1 strain of Serratia marcescens, and 3 strains of Enterobactercloacae) of Enterobacteriaceae family in positive Widal blood cultures based on 16S rRNA gene sequences. Theresults respectively showed that each two 16S rRNA gene clones of Serratia marcescens KD 08.4 had a closerelationship with 16S rRNA gene of Serrratia marcescens ATCC 13880 (similarity: 99.53-99.8%), Eschericia coliBA 30.1 with Eschericia coli ATCC 11775T (similarity: 99.38-99.67%), Salmonella typhi BA 07.4, Salmonella typhiKD 30.4, and Salmonella typhi SA 02.2 with Salmonella typhi ATCC 19430T (similarity: 99.4-100%) as well as theisolates of Enterobacter cloacae SA 02.1, Enterobacter cloacae BA 45.4.1, one 16S rRNA gene clone of Enterobactercloacae TG 03.5 with Enterobacter cloacae ATCC 23373 (similarity: 99.0-99.87%).

The objective of this study was to determine the potential of LAB with phytate degrading activity from fermented traditional food grain-based and legume-based. Lactic acid bacteria were isolated from different sources of traditional fermented food from Gunungkidul Yogyakarta Indonesia such as gembus tempeh (tofu waste), soybean tempeh, lamtoro tempeh (Leucaena bean) and kara tempeh. Isolation of LAB was performed using Total Plate Count (TPC) on de Man Rogosa Sharpe Agar (MRSA) medium supplemented with CaCO3. They were screened for their ability to degrade myo-inositol hexaphosphate or IP6 by using qualitative streak platemethod with modified de Man Rogosa-MorpholinoPropanesulfonic Acid Sharpe (MRS-MOPS) medium contained sodium salt of phytic acid as substrate and cobalt chloride staining (plate assay) method. The selected isolates were further assayed for phytase activities using quantitative method with spectrophotometer and the two selected isolates growth were optimized. Furthermore, thhe isolates tha...

Bacterial resistance to heavy metal is a genetic and physiological adaptation to the environment which contaminated by heavy metal. Kalimas is an important river in Surabaya that is contaminated by some heavy metals and probably as a habitat for heavy metal resistance bacteria. Bacterial resistance to heavy metals are different for each species, and their diversity can be studied by phylogenetic taxonomy approach. Isolates screening was done using nutrient agar which contained 1 mg/L HgCl2, CdCl2 and K2Cr2O7. Bacterial viability were observed by nutrient broth which contained 10 mg/L HgCl2, 30 mg/L CdCl2 and 50 mg/L K2Cr2O7. Isolates that resistant to heavy metal and viable after exposure to heavy metal were identified using 16S rRNA gene marker by Polymerase Chain Reaction (PCR). Phylogenetic tree reconstruction was done by the neighbor-joining algorithm. Genetic assignment showed isolates that resist and viable after exposure of Hg, Cd and Cr are Bacillus S1, SS19 and DA11. Based on BLAST analysis from ...

16SrDNA gene were known essentialy for procaryotic life involved bacteria. The gene very concerved such as usefull for bacterial identification and classification in phylogeny tree constructed. The object of this research were identified and cllassified amylolitic bacteria TG12, TG19 and TG31 isolates, causers sourness on raw starch sago by 16SrDNA gene sequences analysis approach. The native isolates from raw starch sago under traditionality processing arround Jayapura and selected depend on activity amylolitic and organic acid productivity. Before DNA genom extraction, isolates were throught out generic assignment analysis. Futhermore DNA genom were amplified and purified by PCR with 27f and 1529r primers. The pure of DNA was sequenced by ABI PRISM 310 DNA sequencer with internal primers 27f, 357f, 790f and 1230f. The generic assignment resulted those isolates related with Bacillus. The 16S rDNA data were aligned with corresponding available Bacillus sequences retrieved from the NCBI database using the CLUSTAL X software. Phylogeny tree was constructed by PHYLIP programme and visualized by Treeview programme. Phylogenetic trees were and the extended the value of 16S rDNA sequencing in amylolitic bacteria causing sourness on raw starch sago. Completed 16S rDNA sequence data showed that two of the tested isolate TG12 formed a distinct center of diversity with Bacillus substilis DSM 10 AJ276351, isolate TG19 with Bacillus substilis strain 1778 EU982544 and TG31 similar genetic with Bacillus cereus strain WJL-063 FJ527559. Identification based on 16S rDNA gene sequences of amylolitic bacteria causing sourness on raw sago starch provided a powerful way of uncovering genetic of strain within the spesies Bacillus substilis and Bacillus cereus.

Twenty seven strains of lactic acid bacteria (LAB) were isolated from bakasang, Indonesian traditional fermented fish product. In general, LAB have inhibitory activity againts pathogenic bacteria and spoilage bacteria. Screening for antimicrobia activity of isolates were performed with well-diffusion method. One isolate that was designed as Pediococcus BksC24 was the strongest against bacteria pathogenic and spoilage bacteria. This strain was further identified by 16S rRNA gen sequence comparison. Isolates LAB producing antimicrobial agents from bakasang were identified as Pediococcus acidilactici.Keywords : Bakasang, LAB, antimicrobial, phenotypic characteristics, 16S rRNA gene

Demam tifoid adalah penyakit endemis yang disebabkan oleh strain bakteri S. typhi, bakteri tersebut dapat dikelompokkan berdasarkan perbedaan mikromorfologi, morfologi koloni, penggunaan sumber karbon, produksi enzim, kemampuan mendegradasi makromolekul. Oleh karena itu penelitian ini bertujuan melakukan klasifikasi numerik-fenetik 4 starin S. typhi asal Jawa Tengah dan 2 strain asal DIY dengan 2 strain acuan S. typhi NCTC 786 dan BLKS berdasarkan karakterisasi fenotipik dengan analisis hubungan similaritas yang didasarkan atas analisis Simple Mattching Coefficient (SSM) serta algoritme UPGMA (unweighted pair group methode with averages) yang kemudian dipresentasikan dalam bentuk dendogram. Hasilnya dapat dikelompokkan menjadi empat klaster, klaster pertama beranggotakan 3 strain berasal dari Jawa Tengah dan 1 strain acuan BLK Semarang (similaritas 100%). Klaster kedua beranggotakan satu strain acuan S. typhi NCTC 786 (similaritas 98,6%) dengan klaster pertama. Klaster ketiga beranggotakan 1 strain MDA dari Jawa Tengah (similaritas 96,8%) dengan klaster pertama dan kedua. Klaster keempat beranggotakan 2 strain S. typhi asal DIY yang memiliki (similaritas 96,4%) dengan ketiga klaster lainnya.

Amarantini C. Sembiring L. Kushadiwijaya H. Asmara W (201I) Identification and characterization of Salmonella typhi isolatesfrom Southwest Sumba District. East Nusa Tenggara based on 16S rRNA gene sequences. Biodiversitas 12: 1-6. The incidence rate of typhoid fever in the Southwest Sumba District, East Nusa Tenggara was approximately about 725/100,000. In spite of such rate, there was not much known-yet about the molecular epidemiology of the disease. Thus, having accurate data and a strong discriminatory ability was crucial to scrutinize the molecular epidemiology of S. typhi with a molecular phylogenetic approach based on 16S rRNA gene sequences. Sixteen isolates representative of S. typhi from different geographical regions in Southwest Sumba District along with the reference strain S. typhi NCTC 786 had been identified and characterised based on 16S rRNA gene sequences using PCR amplification and sequencing. The 16S rRNA sequences data were aligned with the corresponding ayailable S. typhi sequences retrieved from the NCBI database by using CLUSTAL X software. Phylogenetic trees were generated with PHYLIP software package. Molecular phylogenetic analysis indicated that all the isolates belong to S. typhi species were suggested by their relativity with the type strain of S. typhi ATCC 19430T. It was also found that the isolates which belong to S. typhi species formed several different centers of diversity within the 16S rRNA gene tree. Each clade consisted of the strains from different geographical places in the District. Thus, to conclude the inquiry, there was evident inter-geographical spread of the strains and it tended to spread further into more remote areas in the District.

Kasus resistensi antibiotik semakin meningkat sehingga eksplorasi sumber-sumber baru antibiotik.Penelitian mengenai Streptomycetes penghasil antibiotik yang berasosiasi dengan rhizosfer beberapaspesies mangrove telah dilakukan. Pengambilan sampel dilakukan di hutan mangrove Karimun Jawadan Teluk Awur Jepara. Selanjutnya dilakukan isolasi, karakterisasi dan identifikasi isolat yangtermasuk dalam anggota genus Streptomyces. Isolasi selektif Streptomycetes dilakukan dengan mediaStarch Casein Agar (SCA) dan Raffinosa Histidin Agar (RHA). Koloni Streptomycetes yang tumbuhdiidentifikasi berdasarkan pengenalan karakteristik koloni dan diklasifikasikan dengan metode colorgrouping menggunakan media oatmeal agar. Purifikasi koloni dilakukan dengan Yeast Papton Agardan Beanett Agar. Potensi Streptomycetes dalam menghasilkan antibiotik ditentukan denganmelakukan uji penghambatan dengan bakteri uji Eschericia coli ATCC 35218 dan Staphyilococcusaureus ATCC 25923. Jenis antibiotik diidentifikasi dengan Kromatografi Lapis Tipis (KLT)).Keanekaragaman isolat yang mampu menghasilkan antibiotik ditentukan dengan pengamatanornamentasi permukaan rantai spora dengan Scaning Electron Microscope (SEM) dan pengamatanmorfologi rantai spora dengan metode inclined cover slip. Hasil penelitian menunjukkan terdapat 123isolat Streptomycetes terkelompok menjadi 3 grup yaitu Group A sebanyak 100, grup B sebanyak 21dan grup C sebanyak 2 isolat. Hasil screening isolat uji penghambatan dengan bakteri uji didapatkan16 isolat yang memiliki kemampuan menghambat pertumbuhan bakteri uji. Pengamatan rantai sporaterhadap isolat yang berpotensi menghasilkan antibiotik menunjukkan ada 3 tipe morfologi rantaispora yaitu flexus, folded dan curly dan 3 ornamentasi permukaan yaitu spiny, velvety dan flat. Seleksistrain penghasil antibiotik menunjukkan terdapat 12 strain yang berpotensi menghasilkan antibiotik.Kelompok antibiotik yang dihasilkan diduga jenis Erytromycin, Tetracyclin, Rimfampicyn, Polymyxindan Chloramphenicol. Dapat disimpulkan bahwa Streptomycetes yang berpotensi menghasilkanantibiotik dapat diisolasi dari rhizosfer dan non rhizosfer tanaman mangrove.Kata kunci : Streptomycetes, antibiotik, mangrove