Optimization of manganese bioleaching activity and molecular characterization of indigenous heterotrophic bacteria isolated from the sulfuric area

Abstract. Prasidya DA, Wilopo W, Warmada IW, Retnaningrum E. 2019. Optimization of manganese bioleaching activity and molecular characterization of indigenous heterotrophic bacteria isolated from the sulfuric area. Biodiversitas 20: 1904-1909. The present research evaluated the manganese bioleaching potency of a heterotrophic bacteria KB3B1. This bacterial strain has been isolated from sulfuric area located at Ungaran, Middle of Java, Indonesia using modified 9K medium by adding of several organic nutrients. The manganese bioleaching activities of the strain was analysed by applying of varying glycine concentrations (0, 5, 10, 15 mg mL-1) with pyrolusite pulp densities of 0.02 g cm-3 on a rotary shaker at 180 rpm for 18 days incubation. Several parameters, including the growth of bacteria, pH values, the concentration of soluble manganese and cyanide, were investigated at the interval of 3 days. Molecular characteristics of the strain were further analyzed based on 16S rDNA gene sequences. After 15 days, the maximum yield of manganese 16.6% was achieved under the addition of 10 mg mL-1 glycine. This maximum extract obtained was followed by the maximum bacterial growth, pH, and cyanide product of the strain. Phylogenetic analysis showed that the strain was closely related with Bacillus niacini EP89. Besides, the average frequencies of guanine and cytosine (G+C) of the strain was in same range as that of the reference bacteria in the GenBank and Bergey's Manual Systematics of Bacteria.

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Isolation, Identification and Molecular Characterization of Nocardiopsaceae Producing Novel Antibiotics From Soil Samples in Bingol, Turkey

Journal of Biology and Life Science ◽

10.5296/jbls.v11i2.17050 ◽

2020 ◽

Vol 11 (2) ◽

pp. 94

Author(s):

Samer Abuzerr ◽

Kate Zinszer ◽

Syamand Ahmed Qadir ◽

Ekrem Atalan ◽

Halgord Ali M. Farag ◽

...

Keyword(s):

Molecular Characterization ◽

Gene Sequence ◽

Multidrug Resistant ◽

Physicochemical Analysis ◽

Soil Samples ◽

Morphological Properties ◽

16S Rdna Gene ◽

Life Threatening ◽

Immense Potential

There is growing interest in the antimicrobial discovery of life-threatening multidrug-resistant pathogens. The study was undertaken to isolate, identify, and characterize antibiotic-producing actinomycetaceae, particularly nocadisosaceae, from soil samples of Bingol, Turkey. Soil samples were collected from three different regions of Bingol, Turkey. The physicochemical analysis of the soil samples was immediately measured using standard methods. This was followed by isolation of Nocardiopsaceae, nutritional tests, chemotaxonomic analysis, and molecular characterization. The isolated organisms showed morphological properties consistent with the Nocardiopsaceae soil bacteria. The 16s rDNA gene sequence indicated a similarity between the strains with 99.86% which was Nocardiopsaceae synnemata-formans. The BLAST hits had a significant e-value of 0.005. The results of the present study revealed that soil Nocardiopsaceae of Bingol appears to have immense potential as a source of antibacterial compounds.

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Characterization of Three Species of Thrips on Weeping Fig, Nutmeg, and Marine Seruni Plants Based on Mtcoi DNA Sequences

Biosaintifika Journal of Biology & Biology Education ◽

10.15294/biosaintifika.v8i2.5448 ◽

2016 ◽

Vol 8 (2) ◽

pp. 185

Author(s):

Nia Kurniawaty ◽

Purnama Hidayat ◽

Aunu Rauf

Keyword(s):

Pest Management ◽

Molecular Characterization ◽

Dna Sequences ◽

Biology Education ◽

Morphological Data ◽

Coi Gene ◽

Molecular Characteristics ◽

Vegetable Crops ◽

Total Extraction

Thrips are widely reported as pests in vegetable crops. However, the existence of Phlaeothripidae members has a less concern in Indonesia. Phlaeothripidae is the only family of Tubulifera Suborder and some reports suggested that they had potential to be pests in several crops due to their ability to roll up and to make galls on leaves. The first step in pest management attempt is to identify the pest accurately and quickly, so the pest management can be on target and more efficient. One of the identification methods is the molecular identification using DNA barcoding techniques. This study aimed to characterize and to compare species thrips in banyan, nutmeg, and marine seruni based on their molecular characteristics. This research was conducted in Bogor and Kuningan. The process of molecular characterization consisteds of four steps DNA total extraction, amplification by using PCR, COI gene sequence, and data analysis. PCR programme was succesfully to amplified mtCOI gene fragment at 710 bp. The length of mtCOI gene of Gynaikothrips uzeli, Haplothrips ganglbaueri, and Pseudophilothrips ichini were 704, 686, and 702 bp dominated by A and T bases with nucleotide variation value of 27.8%. This results confirmed that molecular characterization using mtCOI gene mitochondrial had successfully supported the morphological data. How to CiteKurniawaty, N., Hidayat, P. & Rauf, A. (2016). Characterization of Three Species of Thrips on Banyan, Nutmeg, and Marine Seruni Plants Based on Coi Gene. Biosaintifika: Journal of Biology & Biology Education, 8(2), 185-192.

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Isolation and Molecular Characterization of Biosurfactant-Producing Yeasts from Saps of Elaeis guineensis and Raphia africana

Microbiology Research Journal International ◽

10.9734/mrji/2019/v29i430169 ◽

2019 ◽

pp. 1-12

Author(s):

I. V. Nwaguma ◽

C. B. Chikere ◽

G. C. Okpokwasili

Keyword(s):

Molecular Characterization ◽

Reducing Sugars ◽

Elaeis Guineensis ◽

Sodium Dodecyl ◽

High Capacity ◽

Physicochemical Characteristics ◽

Molecular Characteristics ◽

Pichia Kudriavzevii ◽

Haemolytic Assay

Aim: This study investigated the screening and molecular characterization of biosurfactant-producing yeasts from saps of Elaeis guineensis (oil palm) and Raphia Africana (Raphia palm). Methodology: Physicochemical characteristics (pH, temperature, alcohol contents, and reducing sugars) of the saps of Elaeis guineensis and Raphia africana were determined. The capacity of the yeast isolates from both samples to produce biosurfactant was evaluated using emulsification index (E24), emulsification assay, haemolytic assay, oil displacement test, and tilted glass slide. The yeast isolates were identified based on their phenotypic, microscopic, biochemical, and molecular characteristics. Results: Chemical analysis of the palm wine saps revealed respective pH, temperature, alcohol, and reducing sugars contents of 5.68, 17.1°C, 0.943% and 1.090 mg/mL for Elaeis guineensis and 5.26, 16.9°C, 0.884% and 2.099 mg/mL for Raphia africana. Six isolates (SA-2, SA-5, SB-3, SB-5, SB-6 and SB-8) out of sixteen isolates (16) distributed within both samples were found to produce biosurfactant. Phylogenetic analysis based on the internally transcribed spacer (ITS) genes classified the six isolates as Candida haemulonis SA2, Pichia kudriavzevii SA5, Pichia kudriavzevii SB3, Pichia kudriavzevii SB5, Pichia kudriavzevii SB6, and Pichia kudriavzevii SB8. The sequences obtained from the study have been deposited in GenBank under the accession numbers MN007219.1-MN007224.1. The result obtained from the study revealed high biosurfactant activity with a maximum E24 of 64.5% compared to E24 of 72% by sodium dodecyl sulphate (SDS). Conclusion: The study demonstrated that saps from Elaeis guineensis and Raphia africana were suitable sources of biosurfactant-producing yeasts with high capacity for hydrocarbon emulsification. The main six biosurfactant-producing yeasts were found to belong to the genera Candida and Pichia.

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Molecular Characterization of Parvovirus Strain GX-Tu-PV-1, Isolated from a Guangxi Turkey

Microbiology Resource Announcements ◽

10.1128/mra.00152-19 ◽

2019 ◽

Vol 8 (46) ◽

Cited By ~ 1

Author(s):

Yanfang Zhang ◽

Zhixun Xie ◽

Xianwen Deng ◽

Zhiqin Xie ◽

Liji Xie ◽

...

Keyword(s):

Molecular Characterization ◽

Genome Sequence ◽

South China ◽

Genomic Sequence ◽

Molecular Characteristics ◽

Guangxi Province

The aim of the current study was to determine the genomic sequence of parvovirus strain GX-Tu-PV-1, which was isolated from a turkey in Guangxi Province, South China. The analysis showed that the genome sequence of GX-Tu-PV-1 was 81.3% to ∼99.3% similar to those of other turkey parvoviruses (TuPVs) and 79.8% to ∼92.1% related to chicken parvovirus (ChPV). This study will help in understanding the epidemiology and molecular characteristics of parvovirus in turkeys.

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Multi-omics subtyping of hepatocellular carcinoma patients using a Bayesian network mixture model

10.1101/2021.12.16.473083 ◽

2021 ◽

Author(s):

Polina Suter ◽

Eva Dazert ◽

Jack Kuipers ◽

Charlotte K.Y. Ng ◽

Tuyana Boldanova ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Bayesian Network ◽

Molecular Characterization ◽

Mixture Model ◽

Clinical Stage ◽

Molecular Characteristics ◽

Clustering Methods ◽

Cancer Subtypes ◽

Molecular Phenotypes

Comprehensive molecular characterization of cancer subtypes is essential for predicting clinical outcomes and searching for personalized treatments. We present bnClustOmics, a statistical model and computational tool for multi-omics unsupervised clustering, which serves a dual purpose: Clustering patient samples based on a Bayesian network mixture model and learning the networks of omics variables representing these clusters. The discovered networks encode interactions among all omics variables and provide a molecular characterization of each patient subgroup. We conducted simulation studies that demonstrated the advantages of our approach compared to other clustering methods in the case where the generative model is a mixture of Bayesian networks. We applied bnClustOmics to a hepatocellular carcinoma (HCC) dataset comprising genome (mutation and copy number), transcriptome, proteome, and phosphoproteome data. We identified three main HCC subtypes together with molecular characteristics, some of which are associated with survival even when adjusting for the clinical stage. Cluster-specific networks shed light on the links between genotypes and molecular phenotypes of samples within their respective clusters and suggest targets for personalized treatments.

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Fecal Carriage and Molecular Characterization of Carbapenemase-Producing Enterobacterales in the Pediatric Population in Qatar

Microbiology Spectrum ◽

10.1128/spectrum.01122-21 ◽

2021 ◽

Author(s):

Andrés Pérez-López ◽

Sathyavathi Sundararaju ◽

Kin Ming Tsui ◽

Hassan Al-Mana ◽

Mohammad Rubayet Hasan ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Molecular Characterization ◽

Genome Sequencing ◽

Arabian Peninsula ◽

Pediatric Population ◽

Molecular Characteristics ◽

Whole Genome ◽

Fecal Carriage ◽

Demographic Patterns

To the best of our knowledge, this is the first study addressing the molecular characteristics of CPE in a pediatric population in Qatar using whole-genome sequencing. Since several countries in the Arabian Peninsula share relatively similar demographic patterns and international links, it is plausible that the molecular characteristics of CPE in children, at least in the middle and eastern parts of the region, are similar to those observed in our study.

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Morphological and molecular characterization of three Helicotylenchus species from Iran

Zootaxa ◽

10.11646/zootaxa.4388.2.4 ◽

2018 ◽

Vol 4388 (2) ◽

pp. 207 ◽

Cited By ~ 6

Author(s):

EBRAHIM SHOKOOHI ◽

MARIETTE MARAIS ◽

HENDRIKA FOURIE ◽

HADI PANAHI

Keyword(s):

Phylogenetic Analysis ◽

Molecular Characterization ◽

28S Rdna ◽

Molecular Characteristics ◽

Monophyletic Clade ◽

Morphological And Molecular Characterization

Three Helicotylenchus species, namely Helicotylenchus digonicus, Helicotylenchus pseudorobustus and Helicotylenchus vulgaris were identified during a nematode survey conducted in Iran. The morphological and molecular characteristics of the species were defined. In addition, phylogenetic analysis of five Iranian Helicotylenchus populations based on 28S rDNA were done and showed the unresolved position of molecularly identified H. pseudorobustus and H. digonicus. However, populations of H. vulgaris and H. digonicus were placed close to each other. Phylogenetic analysis confirmed that molecularly characterized Helicotylenchus species formed a monophyletic clade. A detailed revision of the species is, however, needed. Illustrations and measurements for all species are provided.

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Circulation of Indigenous Bovine Respiratory Syncytial Virus Strains in Turkish Cattle: The First Isolation and Molecular Characterization

Animals ◽

10.3390/ani10091700 ◽

2020 ◽

Vol 10 (9) ◽

pp. 1700

Author(s):

Zafer Yazici ◽

Emre Ozan ◽

Cuneyt Tamer ◽

Bahadir Muftuoglu ◽

Gerald Barry ◽

...

Keyword(s):

Respiratory Syncytial Virus ◽

Molecular Characterization ◽

Beef Cows ◽

Bovine Respiratory Syncytial Virus ◽

Molecular Characteristics ◽

Specific Primers ◽

Antigen Elisa ◽

Syncytial Virus ◽

Virus Strains

Bovine respiratory disease (BRD) is a huge economic burden on the livestock industries of countries worldwide. Bovine respiratory syncytial virus (BRSV) is one of the most important pathogens that contributes to BRD. In this study, we report the identification and first isolation, with molecular characterization, of a new BRSV strain from lung specimens of three beef cows in Turkey that died from respiratory distress. After the screening of lung tissues for BRD-associated viruses using a multiscreen antigen-ELISA, a BRSV antigen was detected. This was then confirmed by real-time RT-PCR specific for BRSV. Following confirmation, virus isolation was conducted in MDBK cell cultures and clear CPE, including syncytia compatible with BRSV, were detected. RT-nested PCR, using F gene-specific primers, was performed on the cultured isolates, and the products were sequenced and deposited to Genbank with accession numbers MT179304, MT024766, and MT0244767. Phylogenetic analysis of these sequences indicated that the cattle were infected with BRSV from subgroup III and were closely related to previously identified American and Turkish strains, but contained some amino acid and nucleotide differences. This research paves the way for further studies on the molecular characteristics of natural BRSV isolates, including full genome analysis and disease pathogenesis, and also contributes to the development of robust national strategies against this virus.

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First complete genome sequence and molecular characterization of Canine morbillivirus isolated in Central Brazil

Scientific Reports ◽

10.1038/s41598-021-92183-2 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Vivaldo Gomes da Costa ◽

Marielena Vogel Saivish ◽

Priscila Gomes de Oliveira ◽

Abelardo Silva-Júnior ◽

Marcos Lázaro Moreli ◽

...

Keyword(s):

Molecular Characterization ◽

Canine Distemper Virus ◽

Phylogenetic Analyses ◽

Domestic Dogs ◽

Molecular Characteristics ◽

Central Brazil ◽

West Region ◽

Glycosylation Sites ◽

Full Length Genome

AbstractThe Brazilian regions are still highly endemic areas for Canine morbillivirus [canine distemper virus (CDV)]. However, little is known regarding the genetic variability of the strain circulating in several Brazilian regions. Here, we report the first full-length genome and molecular characterization of CDV isolated from domestic dogs in the Brazilian Center-West region. Sequence alignment and phylogenetic analyses based on deduced amino acid and nucleotide sequences showed that the isolated strain is characterized as the South America-I/Europe genotype. However, it segregates into a CDV subgenotype branch. Interestingly, both H and F proteins have a gain of a potential N-glycosylation sites compared to the Onderstepoort vaccine strain. Therefore, this study provides a reference to further understand the epidemic and molecular characteristics of the CDV in Brazil.

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Efficacy of Amendments in TPH Removal during Bioremediation of Agricultural Crude Oil-polluted Soil

Journal of Advances in Biology & Biotechnology ◽

10.9734/jabb/2021/v24i1130250 ◽

2021 ◽

pp. 22-30

Author(s):

Barisiale Baranu ◽

Chimezie Ogugbue ◽

Gideon Okpokwasilli

Keyword(s):

Crude Oil ◽

Molecular Characterization ◽

Contaminated Soil ◽

Petroleum Hydrocarbon ◽

Heterotrophic Bacteria ◽

Total Petroleum Hydrocarbon ◽

Cow Dung ◽

Polyaromatic Hydrocarbon ◽

Total Organic Nitrogen

This study identified the efficacy of different amendments as biostimulants in bioremediation. This experiment was carried out for 4 weeks in the laboratory. One kilogram of pristine soil was spiked with one liter of crude oil in earthen pots, to each pot 10 grams of amendments were added and mixed thoroughly. The amendments used were poultry dropping (C-PD), cow dung (D-CD), N.P.K (E), and a control (A and B) setup undergoing natural attenuation. The microcosms’ initial physicochemical characteristics such as total organic nitrogen, pH, temperature, total organic carbon, total petroleum hydrocarbon (TPH), and polyaromatic hydrocarbon (PAH). The microbial enumeration was done for total heterotrophic bacteria (THB) and hydrocarbon utilizing bacteria (HUB). The molecular characterization of the pristine soil (A) and contaminated soil (B) was also done using the shotgun analysis. The THB of A and B was 1.3 x 107 and 2.1 x 102 while the HUB was 1.63 x 105 and 1.1 x 101on day 1 respectively. The THB of treatments during bioremediation at week 2 was 1.75 x 108, 1.89 x 108, 1.5 x 108 and 2.2 x 108 while at week 4, the THB was 1.90 x 108, 2.1 x 108, 2.20 x 108 and 2.25 x 108 while the HUB at week 2 was 1.20 x 105, 3.0 x 105, 2.5 x 105 and 1.98 x 105 while at week 4, the HUB was 2.0 x 106, 2.19 x 106, 2.46 x 106 and 2.1 x 106 for B, PD, CD ,and N.P.K respectively. The molecular characterization of A and B showed there was a higher microbial diversity in the contaminated soil than in the pristine soil. This study has shown that cow dung is more effective in the bioremediation of total petroleum hydrocarbon, and polyaromatic hydrocarbon in crude oil-contaminated soil.

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