scholarly journals SKRINING DAN IDENTIFIKASI MIKROBA LIGNINOLITIK PADA PENGOMPOSAN ALAMI TANDAN KOSONG KELAPA SAWIT

2019 ◽  
Vol 6 (1) ◽  
pp. 139
Author(s):  
Bedah Rupaedah ◽  
Devit Purwoko ◽  
Anna Safarrida ◽  
Teuku Tajuddin ◽  
Abdul Wahid ◽  
...  
Keyword(s):  
16S Rrna ◽  
Oil Palm ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Empty Fruit Bunch ◽  
Bacterial Isolates ◽  
Genus Bacillus ◽  
Ligninolytic Activity ◽  
Fungal Isolates ◽  
Natural Decomposition

Screening and Identification of Ligninolytic Microbes in the Natural Decomposition of Oil Palm Empty Fruit Bunch  ABSTRACTOPEFB (oil palm empty fruit bunch)could potentially be utilized as organic fertilizer or animal feed through composting. Information on microorganisms that play important roles in the natural decomposition of OPEFB is to date not much known yet. This research was aimed to obtain and, subsequently, to molecularly identify lignin-degrading microbial isolates responsible for naturally decomposing OPEFB in the Oil Plant Plantation and Palm Oil Refinery Plant, PTPN VIII Cikasungka, Bogor. Screening for active lignin-degrading isolates was carried out on 17 naturally decomposing OPEFB samples. A total of 19 isolates of fungi and 80 isolates of bacteria were obtained. Ligninolytic activity was measured by Sundman and Nase testing methods. Ligninolytic activity was found on 13 fungal isolates and 15 bacterial isolates. The active isolates were subsequently identified molecularly based on ITS sequence in the ribosome DNA area for fungi and in 16S rRNA genes for bacteria. The results showed that the lignin-degrading microorganisms obtained consisted of 5 bacterial isolates from the genus Bacillus and 3 fungal isolates from the genus Rhizopus and Aspergillus. Keywords: composting, lignin, microbes, OPEFB, 16S rRNA ABSTRAKTKKS (tandan kosong kelapa sawit) berpotensi dimanfaatkan sebagai pupuk organik atau pakan ternak dengan cara pengomposan. Informasi mikroba yang berperan dalam pengomposan alami TKKS hingga saat ini belum banyak diketahui. Penelitian ini bertujuan mendapatkan isolat mikroba pendegradasi lignin dalam pengomposan alami TKKS asal Perkebunan dan Pabrik Pemerasan Kelapa Sawit, PTPN VIII Cikasungka, Bogor, serta mengidentifikasi mikroba tersebut secara molekuler. Skrining mikroba aktif pendegradasi lignin dilakukan terhadap 17 sampel TKKS yang sudah lapuk secara alami. Sebanyak 19 isolat jamur dan 80 isolat bakteri telah dihasilkan. Aktivitas ligninolitik diukur dengan metode pengujian Sundman dan Nase. Isolat jamur yang memiliki aktivitas ligninolitik sebanyak 13 isolat, sedangkan bakteri sebanyak 15 isolat. Isolat-isolat aktif tersebut selanjutnya diidentifikasi secara molekuler berdasarkan pada sekuen ITS di daerah DNA ribosom untuk jamur dan menggunakan gen 16S rRNA untuk bakteri. Hasil menunjukkan bahwa 5 isolat bakteri yang memiliki kemampuan mendegradasi lignin berasal dari genus Bacillus, sedangkan 3 isolat jamur pendegradasi lignin berasal dari genus Rhizopus dan Aspergillus Kata Kunci: lignin, mikroba, pengomposan, TKKS, 16S rRNA 

scholarly journals Phylogenetic Relationship of Phosphate Solubilizing Bacteria according to 16S rRNA Genes

2015 ◽  
Vol 2015 ◽  
pp. 1-5 ◽  
Author(s):  
Mohammad Bagher Javadi Nobandegani ◽  
Halimi Mohd Saud ◽  
Wong Mui Yun
Keyword(s):  
16S Rrna ◽  
Oil Palm ◽  
Phosphorus Uptake ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Phosphate Solubilizing Bacteria ◽  
Bacterial Isolates ◽  
Serratia Plymuthica ◽  
Phosphate Solubilizing

Phosphate solubilizing bacteria (PSB) can convert insoluble form of phosphorous to an available form. Applications of PSB as inoculants increase the phosphorus uptake by plant in the field. In this study, isolation and precise identification of PSB were carried out in Malaysian (Serdang) oil palm field (University Putra Malaysia). Identification and phylogenetic analysis of 8 better isolates were carried out by 16S rRNA gene sequencing in which as a result five isolates belong to the Beta subdivision ofProteobacteria, one isolate was related to the Gama subdivision ofProteobacteria, and two isolates were related to theFirmicutes. Bacterial isolates of 6upmr, 2upmr, 19upmnr, 10upmr, and 24upmr were identified asAlcaligenes faecalis. Also, bacterial isolates of 20upmnr and 17upmnr were identified asBacillus cereusandVagococcus carniphilus, respectively, and bacterial isolates of 31upmr were identified asSerratia plymuthica. Molecular identification and characterization of oil palm strains as the specific phosphate solubilizer can reduce the time and cost of producing effective inoculate (biofertilizer) in an oil palm field.

scholarly journals Census of the Viral Metagenome within an Activated Sludge Microbial Assemblage

2010 ◽  
Vol 76 (8) ◽  
pp. 2673-2677 ◽  
Author(s):  
Larissa C. Parsley ◽  
Erin J. Consuegra ◽  
Stephen J. Thomas ◽  
Jaysheel Bhavsar ◽  
Andrew M. Land ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Activated Sludge ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Isolates ◽  
Microbial Assemblage ◽  
Culture Independent ◽  
Culture Dependent

ABSTRACT The viral metagenome within an activated sludge microbial assemblage was sampled using culture-dependent and culture-independent methods and compared to the diversity of activated sludge bacterial taxa. A total of 70 unique cultured bacterial isolates, 24 cultured bacteriophages, 829 bacterial metagenomic clones of 16S rRNA genes, and 1,161 viral metagenomic clones were subjected to a phylogenetic analysis.

Polynucleotide Probes That Target a Hypervariable Region of 16S rRNA Genes To Identify Bacterial Isolates Corresponding to Bands of Community Fingerprints

1999 ◽  
Vol 65 (3) ◽  
pp. 1045-1049 ◽  
Author(s):  
Holger Heuer ◽  
Kathrin Hartung ◽  
Gabriele Wieland ◽  
Ina Kramer ◽  
Kornelia Smalla
Keyword(s):  
16S Rrna ◽  
16S Rdna ◽  
Hypervariable Region ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Isolates ◽  
Closely Related Species ◽  
Gradient Gel Electrophoresis ◽  
Exonuclease Digestion ◽  
Temperature Gradient Gel Electrophoresis

ABSTRACT Temperature gradient gel electrophoresis (TGGE) is well suited for fingerprinting bacterial communities by separating PCR-amplified fragments of 16S rRNA genes (16S ribosomal DNA [rDNA]). A strategy was developed and was generally applicable for linking 16S rDNA from community fingerprints to pure culture isolates from the same habitat. For this, digoxigenin-labeled polynucleotide probes were generated by PCR, using bands excised from TGGE community fingerprints as a template, and applied in hybridizations with dot blotted 16S rDNA amplified from bacterial isolates. Within 16S rDNA, the hypervariable V6 region, corresponding to positions 984 to 1047 (Escherichia coli 16S rDNA sequence), which is a subset of the region used for TGGE (positions 968 to 1401), best met the criteria of high phylogenetic variability, required for sufficient probe specificity, and closely flanking conserved priming sites for amplification. Removal of flanking conserved bases was necessary to enable the differentiation of closely related species. This was achieved by 5′ exonuclease digestion, terminated by phosphorothioate bonds which were synthesized into the primers. The remaining complementary strand was removed by single-strand-specific digestion. Standard hybridization with truncated probes allowed differentiation of bacteria which differed by only two bases within the probe target site and 1.2% within the complete 16S rDNA. However, a truncated probe, derived from an excised TGGE band of a rhizosphere community, hybridized with three phylogenetically related isolates with identical V6 sequences. Only one of the isolates comigrated with the excised band in TGGE, which was shown to be due to identical sequences, demonstrating the utility of a combined TGGE and V6 probe approach.

scholarly journals Selection and Characterization of Microorganisms Utilizing Thaxtomin A, a Phytotoxin Produced byStreptomyces scabies

1998 ◽  
Vol 64 (11) ◽  
pp. 4313-4316 ◽  
Author(s):  
Cyr Lézin Doumbou ◽  
Vladimir Akimov ◽  
Carole Beaulieu
Keyword(s):  
Potato Scab ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Isolates ◽  
Potato Tubers ◽  
Variable Regions ◽  
Thaxtomin A ◽  
Fungal Isolates ◽  
Culture Supernatants

ABSTRACT Thaxtomin A is the main phytotoxin produced by Streptomyces scabies, a causal agent of potato scab. Thaxtomin A is a yellow compound composed of 4-nitroindol-3-yl-containing 2,5-dioxopiperazine. A collection of nonpathogenic streptomycetes isolated from potato tubers and microorganisms recovered from a thaxtomin A solution were examined for the ability to grow in the presence of thaxtomin A as a sole carbon or nitrogen source. Three bacterial isolates and two fungal isolates grew in thaxtomin A-containing media. Growth of these organisms resulted in decreases in the optical densities at 400 nm of culture supernatants and in 10% reductions in the thaxtomin A concentration. The fungal isolates were identified as aPenicillium sp. isolate and a Trichoderma sp. isolate. One bacterial isolate was associated with the speciesRalstonia pickettii, and the two other bacterial isolates were identified as Streptomyces sp. strains. The sequences of the 16S rRNA genes were determined in order to compare thaxtomin A-utilizing actinomycetes to the pathogenic organism S. scabies and other Streptomyces species. The nucleotide sequences of the γ variable regions of the 16S ribosomal DNA of both thaxtomin A-utilizing actinomycetes were identical to the sequence of Streptomyces mirabilis ATCC 27447. When inoculated onto potato tubers, the three thaxtomin A-utilizing bacteria protected growing plants against common scab, but the fungal isolates did not have any protective effect.

Phylogenetic and symbiotic characterization of rhizobial bacteria nodulating Argyrolobium uniflorum in Tunisian arid soils

2008 ◽  
Vol 54 (3) ◽  
pp. 209-217 ◽  
Author(s):  
M. Mahdhi ◽  
P. de Lajudie ◽  
M. Mars
Keyword(s):  
Nitrogen Fixation ◽  
16S Rrna ◽  
Root Nodules ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Arid Areas ◽  
Arid Soils ◽  
Bacterial Isolates ◽  
Phenotypic Features

Forty-two bacterial isolates from root nodules of Argyrolobium uniflorum growing in the arid areas of Tunisia were characterized by phenotypic features, RFLP, and sequencing of PCR-amplified 16S rRNA genes. The isolates were found to be phenotypically diverse. The majority of the isolates tolerated 3% NaCl and grew at temperatures up to 40 °C. Phylogenetically, the new isolates were grouped in the genera Sinorhizobium (27), Rhizobium (13), and Agrobacterium (2). Except for the 2 Agrobacterium isolates, all strains induced nodulation on Argyrolobium uniflorum, but the number of nodules and nitrogen fixation efficiency varied among them. Sinorhizobium sp. strains STM 4034, STM 4036, and STM 4039, forming the most effective symbiosis, are potential candidates for inoculants in revegetalisation programs.

scholarly journals Isolation and Molecular Identification of Lactic Acid Bacteria Using 16s rRNA Genes from FermentedTeff(Eragrostis tef(Zucc.)) Dough

2018 ◽  
Vol 2018 ◽  
pp. 1-7 ◽  
Author(s):  
Belay Tilahun ◽  
Anteneh Tesfaye ◽  
Diriba Muleta ◽  
Andualem Bahiru ◽  
Zewdu Terefework ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
16S Rrna ◽  
Addis Ababa ◽  
Bacterial Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Eragrostis Tef ◽  
Universal Primers ◽  
Bacterial Isolates

Injera is soft fermented baked product, which is commonly prepared from teff (Eragrostis tef(Zucc.)) flour and believed to be consumed on daily basis by two-thirds of Ethiopians.As it is a product of naturally fermented dough, the course of fermentation is done by consortia of microorganisms. The study was aimed at isolating and identifying some dominant bacteria from fermentingteff (Eragrostis tef)dough. A total of 97 dough samples were collected from households, microenterprises, and hotels with different fermentation stage from Addis Ababa. The bacterial isolates obtained from the fermentingteffdough samples were selected on the basis of their acid production potentials. A total of 24 purified bacterial isolates were found to be Gram-positive (they are coccus and rod under microscope) and were good acid producers. Genomic DNA of bacterial isolates were extracted using Invisorb® Spin DNA Extraction kit. 16S rRNA of bacterial isolates were amplified using the bacteria universal primers (rD1 and fD1). The amplified product was sequenced at Genewiz, USA. Sequence analysis and comparison with the resources at the database were conducted to identify the isolated microbes into species and strain levels. The bacterial isolates were identified asLactobacillus paracasei, Lactobacillus brevis, Enterococcus durans, Enterococcus hirae, Enterococcus avium,andEnterococcus faecium. All identified lactic acid bacteria were able to produce acid at 12 h time of incubation. This study has confirmed the presence of different bacterial species in the fermentingteffdough and also supports the involvement of various groups of bacterial species in the course of the fermentation.

scholarly journals Potential of endophytic bacteria from rice root as potassium solvent

2019 ◽  
Vol 20 (5) ◽  
Author(s):  
WARZATULLISNA WARZATULLISNA ◽  
LENNI FITRI ◽  
YULIA SARI ISMAIL
Keyword(s):  
16S Rrna ◽  
Plant Growth ◽  
Endophytic Bacteria ◽  
Oryza Sativa L ◽  
Rice Root ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Bacterial Isolates ◽  
Biochemical Tests

Abstract. Warzatullisna, Fitri L, Ismail YS. 2019. Potential of endophytic bacteria from rice root as potassium solvent. Biodiversitas 20: 1303-1308. Endophytic bacteria live in plant tissues and known to have many benefits for plant growth. One function of endophytic bacteria are known to be able to dissolve potassium. Potassium is one of the macronutrients that plays an important role in plant growth and development. This study aims to obtain endophytic bacterial isolates from the roots of rice plants (Oryza sativa L.) which have potential as potassium solvents, identify the endophytic bacteria in morphologically and physiologically, and analysis of the selected isolate 16S rRNA genes. Selected endophytic bacterial isolates from the test of dissolving potassium on medium Alexandrov, measured clear zone using calipers and continued with biochemical tests using KIT DL-96E also identified based on 16S rRNA gene and compared for their close relationship with reference strains available in the Bank Genes. Based on the isolation results, 7 isolates from the roots of rice were obtained. Six isolates of endophytic bacteria were able to dissolve potassium. EPK3 isolates were the isolates that are capable of dissolving the highest potassium in Alexandrov media with a 17.9 mm potassium dissolution index. EPK3 isolates also produce inhibit the growth of Xanthomonas oryzae with a 1.2 mm inhibition zone. Physiological identification showed that EPK3 isolates were Enterobacter cloaceae bacteria with 93.79% of similarity. Based on the 16SrRNA gene showed that EPK3 isolates were closely related to E. cloaceae strain SBP-8 with similarity rate is 99%.

Differentiation Of Clarias Batrachus, C. Gariepinus And Heteropneustes Fossilis By Pcr-Sequencing Of Mitochondrial 16s Rrna Gene

2015 ◽  
Vol 41 (1) ◽  
pp. 51-58
Author(s):  
Mohammad Shamimul Alam ◽  
Hawa Jahan ◽  
Rowshan Ara Begum ◽  
Reza M Shahjahan
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Fish Larva ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Valuable Insight ◽  
Multiple Sequence ◽  
Pcr Rflp ◽  
Alternative Means

Heteropneustesfossilis, Clariasbatrachus and C. gariepinus are three major catfishes ofecological and economic importance. Identification of these fish species becomes aproblem when the usual external morphological features of the fish are lost or removed,such as in canned fish. Also, newly hatched fish larva is often difficult to identify. PCRsequencingprovides accurate alternative means of identification of individuals at specieslevel. So, 16S rRNA genes of three locally collected catfishes were sequenced after PCRamplification and compared with the same gene sequences available from othergeographical regions. Multiple sequence alignment of the 16S rRNA gene fragments ofthe catfish species has revealed polymorphic sites which can be used to differentiate thesethree species from one another and will provide valuable insight in choosing appropriaterestriction enzymes for PCR-RFLP based identification in future. Asiat. Soc. Bangladesh, Sci. 41(1): 51-58, June 2015

scholarly journals Effects of Supplement of Marichromatium gracile YL28 on Water Quality and Microbial Structures in Shrimp Mariculture Ecosystems

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 40
Author(s):  
Liang Cui ◽  
Bitong Zhu ◽  
Xiaobo Zhang ◽  
Zhuhua Chan ◽  
Chungui Zhao ◽  
...  
Keyword(s):  
Water Quality ◽  
16S Rrna ◽  
Relative Abundance ◽  
Animal Health ◽  
Denitrifying Bacteria ◽  
Nitrite Reduction ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Sequencing Analysis ◽  
Shrimp Culture

The elevated NH3-N and NO2-N pollution problems in mariculture have raised concerns because they pose threats to animal health and coastal and offshore environments. Supplement of Marichromatium gracile YL28 (YL28) into polluted shrimp rearing water and sediment significantly decreased ammonia and nitrite concentrations, showing that YL28 functioned as a novel safe marine probiotic in the shrimp culture industry. The diversity of aquatic bacteria in the shrimp mariculture ecosystems was studied by sequencing the V4 region of 16S rRNA genes, with respect to additions of YL28 at the low and high concentrations. It was revealed by 16S rRNA sequencing analysis that Proteobacteria, Planctomycete and Bacteroidetes dominated the community (>80% of operational taxonomic units (OTUs)). Up to 41.6% of the predominant bacterial members were placed in the classes Gammaproteobacteria (14%), Deltaproteobacteria (14%), Planctomycetacia (8%) and Alphaproteobacteria (5.6%) while 40% of OTUs belonged to unclassified ones or others, indicating that the considerable bacterial populations were novel in our shrimp mariculture. Bacterial communities were similar between YL28 supplements and control groups (without addition of YL28) revealed by the β-diversity using PCoA, demonstrating that the additions of YL28 did not disturb the microbiota in shrimp mariculture ecosystems. Instead, the addition of YL28 increased the relative abundance of ammonia-oxidizing and denitrifying bacteria. The quantitative PCR analysis further showed that key genes including nifH and amoA involved in nitrification and nitrate or nitrite reduction significantly increased with YL28 supplementation (p < 0.05). The supplement of YL28 decreased the relative abundance of potential pathogen Vibrio. Together, our studies showed that supplement of YL28 improved the water quality by increasing the relative abundance of ammonia-oxidizing and denitrifying bacteria while the microbial community structure persisted in shrimp mariculture ecosystems.

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