scholarly journals IDENTIFICATION OF POTENTIAL DIESEL OIL-DEGRADING BACTERIA ISOLATED FROM MANADO SEA PORT BASED ON 16S rRNA GENE

2014 ◽  
Vol 14 (2) ◽  
pp. 73
Author(s):  
Olivia H Abram ◽  
Trina E Tallei ◽  
Edwin De Queljoe ◽  
Beivy J Kolondam

ABSTRACT  Petroleum contamination and its derivate in ecosystem are considered as environmental threat all over the world. Some microorganisms exhibit potential to degrade hydrocarbon in contaminated environments. This study aims at identifying potential diesel oil-degrading bacteria grown on artificial media. Bacteria isolated from Manado Sea port were grown in nutrient agar containing artificial diesel oil plus salt water and diesel oil only, respectively. The growing bacteria were isolated and each of them was grown separately to obtain pure isolate. Three bacterial isolates namely AO2, OA3 and OA4 were identified using 16S rRNA gene as Pseudomonas aeroginosa, Klebsiella oxytoca, and Citrobacter sp, respectively. Keywords: diesel oil, diesel oil-degrading bacteria, Manado Sea Port, 16S rRNA gene IDENTIFIKASI BAKTERI YANG BERPOTENSI SEBAGAI PENDEGRADASI MINYAK DIESEL DI ISOLASI DARI PELABUHAN LAUT MANADO   ABSTRAK   Kontaminasi minyak bumi dan turunannya dalam ekosistem dianggap sebagai ancaman lingkungan di seluruh dunia. Beberapa mikroorganisme menunjukkan potensi yang dapat menurunkan hidrokarbon dalam lingkungan yang terkontaminasi. Penelitian ini bertujuan untuk mengidentifikasi bakteri yang berpotensi sebagai pendegradasi minyak yang tumbuh pada media buatan. Bakteri diisolasi dari pelabuhan laut Manado dan ditumbuhkan dalam media NA yang mengandung minyak diesel dengan penambahan air garam buatan dan minyak diesel tanpa air garam buatan. Bakteri yang tumbuh diisolasi dan masing-masing ditanam secara terpisah untuk mendapatkan isolat murni. Tiga isolat bakteri yaitu AO2, AO3 dan AO4 yang telah diidentifikasi menggunakan 16S rRNA gen secara berturut-turut adalah  Pseudomonas aeroginosa, Klebsiella oxytoca, dan Citrobacter sp. Kata kunci: minyak diesel, bakteri pendegradasi minyak diesel, Pelabuhan Laut Manado, gen 16S rRNA

2015 ◽  
Vol 65 (Pt_4) ◽  
pp. 1310-1315 ◽  
Author(s):  
M. Azmatunnisa ◽  
K. Rahul ◽  
Y. Subhash ◽  
Ch. Sasikala ◽  
Ch. V. Ramana

Two Gram-stain-positive, diesel oil-degrading, solvent-tolerant, aerobic, endospore-forming, rod-shaped bacteria were isolated from a contaminated laboratory plate. Based on 16S rRNA gene sequence analysis, strains JC228T and JC279 were identified as belonging to the genus Bacillus within the family Bacillaceae of the phylum Firmicutes and were found to be most closely related to Bacillus carboniphilus JCM 9731T (98.1 % 16S rRNA gene sequence similarity) and shared <96.0 % 16S rRNA gene sequence similarity with other members of the genus Bacillus . The DNA–DNA hybridization value between the two strains was 88±2 %. Strain JC228T showed 23.4±1 % reassociation (based on DNA–DNA hybridization) with B. carboniphilus LMG 18001T. The DNA G+C content of strains JC228T and JC279 was 39 and 38.4 mol%, respectively. Both strains were positive for catalase and oxidase activities, and negative for hydrolysis of starch and Tween 80. Strains JC228T and JC279 grew chemoorganoheterotrophically with optimum growth at pH 7 (range pH 7–9.5) and 35 °C (range 25–40 °C). Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified phospholipid (PL2) were the major polar lipids. Major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0 and C16 : 0. Whole-cell hydrolysates contained l-alanine, d-alanine, d-glutamic acid and meso-diaminopimelic acid. Both strains utilized diesel oil as sole carbon and energy source. The results of physiological, biochemical, chemotaxonomic and molecular analyses allowed clear differentiation of strains JC228T and JC279 from their closest phylogenetic neighbours. Therefore strains JC228T and JC279 represent a novel species of the genus Bacillus , for which the name Bacillus oleivorans sp. nov. is proposed. The type strain is JC228T ( = LMG 28084T = CCTCC AB 2013353T).


PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11254
Author(s):  
Mudasir A. Dar ◽  
Afrin F. Shaikh ◽  
Kiran D. Pawar ◽  
Rongrong Xie ◽  
Jianzhong Sun ◽  
...  

Background Cotton bollworm, Helicoverpa armigera is a widely distributed, devastating pest of over 200 crop plants that mainly consist of some cellulosic materials. Despite its economic importance as a pest, little is known about the diversity and community structure of gut symbiotic bacteria potentially functioned in cellulose digestion in different gut-sections of H. armigera. In view of this lacuna, we attempted to evaluate and characterize cellulose-degrading bacteria (CDB) from foregut, midgut, and hindgut -regions of H. armigera by using a culture-dependent approach. Methodology The symbiotic bacteria were isolated from different gut-systems of H. armigera by enrichment techniques using Carboxymethyl cellulose sodium salt (CMC) as carbon source. The isolated bacteria were purified and subsequently screened for cellulose-degradation by plate-based method to display the zones of CMC clearance around the colonies. The identification and phylogeny of the gut-bacteria were reconstructed by using 16S rRNA gene sequencing. Different enzymes such as endoglucanase, exoglucanase, β-glucosidase, and xylanase were assayed to determine the cellulolytic repertoire of the isolated bacteria. Results The enrichment of CDB and subsequent plate based screening methods resulted in isolation of 71 bacteria among which 54% of the bacteria were obtained from foregut. Among the isolated bacteria, 25 isolates showed discernible cellulose-degradation potential on CMC-agar plates. The phylogenetic analysis based on 16S rRNA gene amplification and sequencing affiliated these cellulolytic bacteria to two major phyla viz., Firmicutes and Proteobacteria. The members of the genus Klebsiella accounted for 39.43% of the total isolated bacteria while 31% of the Bacillus strains were enriched from hindgut region. The principal component analysis (PCA) further suggested that the members of Bacillus and Klebsiella together dominated the foregut and hindgut regions as they accounted for 68% of the total CDB. The four potential isolates selected on the basis of plate-based activities were further evaluated for their lignocellulases production by using various agricultural wastes as substrates. The PCA of the enzyme activities demonstrated that potential isolates majorly secreted endoglucanase and xylanase enzymes. Among the agro-wastes, multivariate analysis validated wheat husk (WH) and sugarcane bagasse (SCB) as most favorable substrates for xylanase and endoglucanase productions respectively. The overall findings suggest that H. armigera harbors diverse bacterial communities in different gut-sections that could assist the host in digestion processes, which may potentially serve as a valuable reservoir of some unique symbionts applied for biomass conversion in biofuel industry.


2021 ◽  
Vol 21 (1) ◽  
pp. 298
Author(s):  
Ika Indayati ◽  
Hari Purwanto

Mosquito-borne diseases include tropical diseases such as malaria, filariasis, dengue fever, chikungunya, yellow fever and cerebral fever are still major health problems in Indonesia and on a global scale. Various methods have been used to overcome this, including controlling vector mosquitoes using the entomopathogenic microbial Lysinibacillus sphaericus. This study aims to identify bacterial isolates collected based on the 16S rRNA gene and to carry out the pathogenicity test of the bacterial isolates collected on Cx. quinquefasciatus larvae. Bacterial isolates used in this study were collected from root soil, bird droppings and guano. The identification of the type of bacteria was carried out based on the 16S rRNA gene fragment. Based on the results of the 16S RNA sequence analysis of isolates 229C, 6B4, 6.2 and 4D21, it was found that the four isolates were included in the L. sphaericus species with similarity scores ranging from 97% to 100%. The pathogenicity of bacteria was measured based on the mortality of Cx. quinquefasciatus larvae to know whether it has pathogenicity equal to or higher than strain 1593. The pathogenicity test results of 6 isolates 15.4, 229C, 1593, 6B4, 6.2 and 4D21 showed that isolate 15.4 has the highest larval mortality rate, so it is potentially used as a biological agent to control disease vector mosquitoes.


2020 ◽  
Vol 25 (4) ◽  
pp. 627-635
Author(s):  
Siti Meliah ◽  
Annisa Wahyu Hardiyanti ◽  
Ni’ma Haida ◽  
Gita Azizah Putri ◽  
Erny Qurotul Ainy

The genus Fusarium sp. is a pathogenic fungal for many cultivated plants. The bacteria isolated from monkey cup (Nepenthes sp.) fluid possess the ability to produce hydrolytic enzyme, such as chitinase which can be utilized to inhibit the growth of mycelia of pathogenic fungi. The aims of this study are to isolate bacteria from monkey cup liquid, to test their abilities to produce protease, chitinase, and cellulase, as well as their abilities to inhibit Fusarium. The bacteria were isolated using serial dilution method on Reasoner’s 2A agar medium. Enzymatic activities of bacterial isolates were determined by inoculating them on tested medium supplemented with casein protein, chitin, and cellulose, whereas their antifungal activities were assayed using a direct confrontation method between tested bacterial isolates and pathogenic fungal on Malt Extract Agar medium. Molecular identification of bacteria with antifungal activity was performed by analyzing the 16S rRNA gene sequences. Isolation process of bacteria from monkey cup fluid resulted in 99 bacterial isolates with the ability to produce either protease, chitinase, and/or cellulose enzymes. A total of 37 bacterial isolates were capable of producing at least two hydrolytic enzymes. Antifungal assay of those bacteria showed that as many as 25 isolates have the ability to inhibit the growth of Fusarium sp. Based on the analysis of 16S rRNA gene sequences revealed that those isolates were closely related to three Burkholderia species, namely B. arboris, B. contaminans, and B. rijonensis. Keywords: antifungal, Burkholderia, chitinase, cellulaseN, epenthes, protease


2014 ◽  
Vol 63 (3) ◽  
pp. 291-298
Author(s):  
ANNA LISEK ◽  
LIDIA SAS PASZ ◽  
PAWEŁ TRZCIŃSKI

Bacteria of the genus Pseudomonas are often components of bioproducts designed to enhance the condition of the soil and plants. The use of Pseudomonas bacteria in bioproducts must be preceded by the acquisition, characterization and selection of beneficial strains living in the soil. A prerequisite for the selection of bacterial strains for use in bioproducts is to be able to identify the isolates rapidly and accurately. To identify and differentiate 15 bacterial isolates obtained from the soil surrounding the roots of sour cherry trees and to assess their genetic similarity, the rep-PCR technique and restriction analysis of the 16S rRNA gene and the 16S-ITS-23S rRNA operon were used. In addition, a sequence analysis of the 16S rRNA gene was performed. The analyses made it possible to divide the isolates into four clusters and to confirm their affiliation with the Pseudomonas species. RFLP analysis of the 16S-ITS-23S rRNA operon enabled greater differentiation of the isolates than RFLP of the 16S rRNA gene. The greatest differentiation of isolates within the clusters was obtained after using the rep-PCR technique. However, none of the techniques was able to discriminate all the isolates, which indicates very high genetic similarity of the Pseudomonas isolates found in the same sample of soil from around the roots of sour cherry trees. The tests performed will find application for distinguishing and identifying Pseudomonas strains collected from the soil in order to select the most valuable bacterial strains that produce beneficial effects on plants.


2020 ◽  
Vol 8 (2) ◽  
pp. 12-22
Author(s):  
Mahmoud Hamdan ◽  
Wafa Masoud

The main purpose of the present study was to isolate, identify and quantify bacteria in Palestinian fresh lamb meat. Phenotyping and 16S rRNA gene sequence analysis was used to identify bacteria present in lamb meat samples. Thirty-four bacterial isolates were obtained from 20 samples of fresh lamb meat collected from 4 meat shops in Tulkarem city in Palestine. Bacterial counts were in a range of 3 x 103 - 1.5 x 105 cfu / g with Staphylococcus aureus being the highest in numbers among other bacteria. Enterobacteriaceae and Staphylococcaceae were the predominant bacterial families detected in fresh lamb meat samples. Two bacterial isolates, which were not identified by phenotyping, were identified by 16S rRNA gene sequence analysis. There was an agreement between phenotyping and 16S rRNA gene sequencing in identification of 19 bacterial isolates. On the other hand, a disagreement was observed between phenotyping and 16S rRNA gene sequencing in identification of the remaining bacterial isolates. Fresh lamb meat seems to be a good medium for growth of various bacterial species


Biologia ◽  
2015 ◽  
Vol 70 (8) ◽  
Author(s):  
Ieva Kieraite-Aleksandrova ◽  
Vilius Aleksandrovas ◽  
Nomeda Kuisiene

AbstractIn our work, microbial diversity of Krubera-Voronja cave was evaluated in the view of the frequency of human visits in different locations as well as the sampling depth. Sampling in this cave was performed at depths of 220 m to 1640 m. Cultivation-independent method, namely barcoded pyrosequencing of 16S rRNA gene, was used for this analysis. Our results demonstrated high bacterial diversity at the phylum and genus levels. We have shown that the bacterial diversity at the phylum level depends on both the sampling depth and the frequency of human visits in Krubera-Voronja cave. Frequently visited locations were more diverse at the phylum level than the rarely visited branches. The total number of bacterial genera both per phylum and per sample correlated with the frequency of human visits but not with the sampling depth. Some genera, found in Krubera-Voronja cave, seem to be absent or very rare in other caves. The present study represents the first report on the microbial diversity in Krubera-Voronja cave


2012 ◽  
Vol 79 (1) ◽  
pp. 205-214 ◽  
Author(s):  
Tony Gutierrez ◽  
David H. Green ◽  
Peter D. Nichols ◽  
William B. Whitman ◽  
Kirk T. Semple ◽  
...  

ABSTRACTA strictly aerobic, halotolerant, rod-shaped bacterium, designated strain TG408, was isolated from a laboratory culture of the marine diatomSkeletonema costatum(CCAP1077/1C) by enrichment with polycyclic aromatic hydrocarbons (PAHs) as the sole carbon source. 16S rRNA gene sequence analysis placed this organism within the orderXanthomonadalesof the classGammaproteobacteria. Its closest relatives included representatives of theHydrocarboniphaga-Nevskia-Sinobacterclade (<92% sequence similarity) in the familySinobacteraceae. The strain exhibited a narrow nutritional spectrum, preferring to utilize aliphatic and aromatic hydrocarbon compounds and small organic acids. Notably, it displayed versatility in degrading two- and three-ring PAHs. Moreover, catechol 2,3-dioxygenase activity was detected in lysates, indicating that this strain utilizes themeta-cleavage pathway for aromatic compound degradation. Cells produced surface blebs and contained a single polar flagellum. The predominant isoprenoid quinone of strain TG408 was Q-8, and the dominant fatty acids were C16:0, C16:1ω7c, and C18:1ω7c. The G+C content of the isolate's DNA was 64.3 mol% ± 0.34 mol%. On the basis of distinct phenotypic and genotypic characteristics, strain TG408 represents a novel genus and species in the classGammaproteobacteriafor which the namePolycyclovorans algicolagen. nov., sp. nov., is proposed. Quantitative PCR primers targeting the 16S rRNA gene of this strain were developed and used to show that this organism is found associated with other species of marine phytoplankton. Phytoplankton may be a natural biotope in the ocean where new species of hydrocarbon-degrading bacteria await discovery and which contribute significantly to natural remediation processes.


2007 ◽  
Vol 57 (1) ◽  
pp. 146-150 ◽  
Author(s):  
Min-Ju Park ◽  
Ho-Bin Kim ◽  
Dong-Shan An ◽  
Hee-Chan Yang ◽  
Seok-Tae Oh ◽  
...  

Two novel polysaccharide-degrading bacteria (strains DCY03T and DCY04) were isolated from a soil sample of a ginseng field in the Republic of Korea and were identified as representing members of the genus Paenibacillus on the basis of phenotypic characteristics and phylogenetic inference based on 16S rRNA gene sequences. Cells of the two isolates were Gram-positive, spore-forming, non-motile, straight rods. Based on DNA–DNA relatedness data, the strains were considered to belong to the same species. The DNA G+C content ranged from 56.6 to 57.0 mol%. The predominant cellular fatty acid was anteiso-C15 : 0 (63.8–62.8 %). Levels of 16S rRNA gene sequence similarity between the two novel isolates and the type strains of recognized Paenibacillus species were 91.4–96.5 %. Strains DCY03T and DCY04 could clearly be distinguished from phylogenetically closely related Paenibacillus species on the basis of DNA–DNA relatedness data and phenotypic characteristics. Therefore, on the basis of these data, the two isolates are considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus soli sp. nov. is proposed. The type strain is DCY03T (=KCTC 13010T=LMG 23604T).


2009 ◽  
Vol 75 (19) ◽  
pp. 6322-6330 ◽  
Author(s):  
Aurélie Cébron ◽  
Thierry Beguiristain ◽  
Pierre Faure ◽  
Marie-Paule Norini ◽  
Jean-François Masfaraud ◽  
...  

ABSTRACT The polycyclic aromatic hydrocarbon (PAH) contamination, bacterial community, and PAH-degrading bacteria were monitored in aged PAH-contaminated soil (Neuves-Maisons [NM] soil; with a mean of 1,915 mg of 16 PAHs·kg−1 of soil dry weight) and in the same soil previously treated by thermal desorption (TD soil; with a mean of 106 mg of 16 PAHs·kg−1 of soil dry weight). This study was conducted in situ for 2 years using experimental plots of the two soils. NM soil was colonized by spontaneous vegetation (NM-SV), planted with Medicago sativa (NM-Ms), or left as bare soil (NM-BS), and the TD soil was planted with Medicago sativa (TD-Ms). The bacterial community density, structure, and diversity were estimated by real-time PCR quantification of the 16S rRNA gene copy number, temporal thermal gradient gel electrophoresis fingerprinting, and band sequencing, respectively. The density of the bacterial community increased the first year during stabilization of the system and stayed constant in the NM soil, while it continued to increase in the TD soil during the second year. The bacterial community structure diverged among all the plot types after 2 years on site. In the NM-BS plots, the bacterial community was represented mainly by Betaproteobacteria and G ammaproteobacteria. The presence of vegetation (NM-SV and NM-Ms) in the NM soil favored the development of a wider range of bacterial phyla (Alphaproteobacteria, Betaproteobacteria, G ammaproteobacteria, Verrucomicrobia, Actinobacteria, Firmicutes, and Chlorof l exi) that, for the most part, were not closely related to known bacterial representatives. Moreover, under the influence of the same plant, the bacterial community that developed in the TD-Ms was represented by different bacterial species (Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Actinobacteria) than that in the NM-Ms. During the 2 years of monitoring, the PAH concentration did not evolve significantly. The abundance of gram-negative (GN) and gram-positive (GP) PAH-degrading bacteria was estimated by real-time PCR quantification of specific functional genes encoding the α subunit of PAH-ring hydroxylating dioxygenase (PAH-RHDα). The percentage of the PAH-RHDα GN bacterial genes relative to 16S rRNA gene density decreased with time in all the plots. The GP PAH-RHDα bacterial gene proportion decreased in the NM-BS plots but stayed constant or increased under vegetation influence (NM-SV, NM-Ms, and TD-Ms).


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