scholarly journals Biochemical, molecular and antibiotic resistance profile of multi-potential toluene metabolizing bacteria isolated from tannery effluents

2018 ◽  
Author(s):  
Fatima Muccee ◽  
Samina Ejaz
Keyword(s):  
Phylogenetic Trees ◽  
Biochemical Characterization ◽  
Similarity Index ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Growth Curve Analysis ◽  
Biomass Hydrolysis ◽  
Biochemical Tests ◽  
Tannery Effluents ◽  
Wide Range

AbstractThe focus of present study was to isolate and characterize bacteria which can be effectively used for toluene, a highly recalcitrant pollutant, bioremediation. For isolation of bacteria from the tannery effluents selective enrichment and serial dilution methods were employed. The isolated bacteria were subjected to growth curve analysis, estimation of toluene removal efficiencies, biochemical tests, antibiotic sensitivity assays and molecular characterization based upon 16S rRNA gene. The rRNA genes sequences were analyzed through BLAST to determine similarity index of isolates with bacterial database sequences. To trace the evolutionary history, phylogenetic trees were constructed using MEGA version 7. Total twenty toluene metabolizing bacteria (IUBT1-2, 4-12, 16, 19, 21, 23-26, 28 and 30) were isolated and characterized. Their rRNA gene sequences have been submitted to Genbank. Fifteen of the twenty isolates showed homology toBrevibacillus agristrain NBRC 15538, four found similar toBacillus paralicheniformisstrain KJ-16 and one homologous toBurkholderia latastrain 383. All bacterial isolates were resistant to chloramphenicol but sensitive to teicoplanin and linezolid. However, few (i. e.; IUBT9 and 26) were sensitive to oxacillin. Biochemical characterization indicated all bacteria positive for alkaline phosphatases (100%). While many were found positive for p-nitrophenyl N-acetyl β, D-glucosaminidase (35%), hydroxyproline β-naphthylaminopeptidase (15%), esculinase (65%), mannitol (75%), sorbitol (95%) and inulin (90%) fermentation. Biochemical profile suggests the use of isolated bacteria for future exploitation in several fields like bioremediation of toluene, ethanol production, biomass hydrolysis, biosensors, biofertilizers, as a marker for milk pasteurization in dairy industries and evaluation of soil quality.ImportanceToluene is a highly toxic environmental pollutant. We have isolated bacteria which can be effectively used for the removal of toluene from environmental resources. Moreover, these bacteria are capable to produce many valuable enzymes which can be used in many industrial processes for the production of a wide range of products. Further study may help to exploit these bacterial for the benefit of humanity.

Molecular identification ofSarcocystisspp. helped to define the origin of green pythons (Morelia viridis) confiscated in Germany

Parasitology ◽  
2013 ◽  
Vol 141 (5) ◽  
pp. 646-651 ◽  
Author(s):  
GASTÓN MORÉ ◽  
NIKOLA PANTCHEV ◽  
DALAND C. HERRMANN ◽  
MAJDA GLOBOKAR VRHOVEC ◽  
SABINE ÖFNER ◽  
...  
Keyword(s):  
18S Rrna ◽  
Sequence Data ◽  
18S Rrna Gene ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Intermediate Hosts ◽  
Apicomplexan Parasites ◽  
Large Numbers ◽  
Wide Range ◽  
18S Rrna Genes

SUMMARYSarcocystisspp. represent apicomplexan parasites. They usually have a heteroxenous life cycle. Around 200 species have been described, affecting a wide range of animals worldwide, including reptiles. In recent years, large numbers of reptiles have been imported into Europe as pets and, as a consequence, animal welfare and species protection issues emerged. A sample of pooled feces from four confiscated green pythons (Morelia viridis) containingSarcocystisspp. sporocysts was investigated. These snakes were imported for the pet trade and declared as being captive-bred. Full length 18S rRNA genes were amplified, cloned into plasmids and sequenced. Two differentSarcocystisspp. sequences were identified and registered asSarcocystissp. fromM. viridisin GenBank. Both showed a 95–97% sequence identity with the 18S rRNA gene ofSarcocystis singaporensis.Phylogenetic analysis positioned these sequences together with otherSarcocystisspp. from snakes and rodents as definitive and intermediate hosts (IH), respectively. Sequence data and also the results of clinical and parasitological examinations suggest that the snakes were definitive hosts forSarcocystisspp. that circulate in wild IH. Thus, it seems unlikely that the infected snakes had been legally bred. Our research shows that information on the infection of snakes withSarcocystisspp. may be used to assess compliance with regulations on the trade with wildlife species.

scholarly journals Burkholderia sprentiae sp. nov., isolated from Lebeckia ambigua root nodules

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 3950-3957 ◽  
Author(s):  
Sofie E. De Meyer ◽  
Margo Cnockaert ◽  
Julie K. Ardley ◽  
Garth Maker ◽  
Ron Yates ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Root Nodules ◽  
Distinct Group ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Phenotypic Differentiation ◽  
Content Type ◽  
Link Type

Seven Gram-stain-negative, rod-shaped bacteria were isolated from Lebeckia ambigua root nodules and authenticated on this host. Based on the 16S rRNA gene phylogeny, they were shown to belong to the genus Burkholderia , with the representative strain WSM5005T being most closely related to Burkholderia tuberum (98.08 % sequence similarity). Additionally, these strains formed a distinct group in phylogenetic trees based on the housekeeping genes gyrB and recA. Chemotaxonomic data including fatty acid profiles and analysis of respiratory quinones supported the assignment of the strains to the genus Burkholderia . Results of DNA–DNA hybridizations, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of our strains from the closest species of the genus Burkholderia with a validly published name. Therefore, these strains represent a novel species for which the name Burkholderia sprentiae sp. nov. (type strain WSM5005T = LMG 27175T = HAMBI 3357T) is proposed.

scholarly journals A Comparative Study: Taxonomic Grouping of Alkaline Protease Producing Bacilli

2017 ◽  
Vol 66 (1) ◽  
pp. 39-56
Author(s):  
Nilgun Tekin ◽  
Arzu Coleri Cihan ◽  
Basar Karaca ◽  
Cumhur Cokmus
Keyword(s):  
16S Rrna ◽  
Alkaline Protease ◽  
Phylogenetic Analyses ◽  
Molecular Techniques ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Protease Production ◽  
Rrna Gene ◽  
Wide Range ◽  
Its Pcr

Alkaline proteases have biotechnological importance due to their activity and stability at alkaline pH. 56 bacteria, capable of growing under alkaline conditions were isolated and their alkaline protease activities were carried out at different parameters to determine their optimum alkaline protease production conditions. Seven isolates were showed higher alkaline protease production capacity than the reference strains. The highest alkaline protease producing isolates (103125 U/g), E114 and C265, were identified as Bacillus licheniformis with 99.4% and Bacillus mojavensis 99.8% based on 16S rRNA gene sequence similarities, respectively. Interestingly, the isolates identified as Bacillus safensis were also found to be high alkaline protease producing strains. Genotypic characterizations of the isolates were also determined by using a wide range of molecular techniques (ARDRA, ITS-PCR, (GTG)5-PCR, BOX-PCR). These different techniques allowed us to differentiate the alkaliphilic isolates and the results were in concurrence with phylogenetic analyses of the 16S rRNA genes. While ITS-PCR provided the highest correlation with 16S rRNA groups, (GTG)5-PCR showed the highest differentiation at species and intra-species level. In this study, each of the biotechnologically valuable alkaline protease producing isolates was grouped into their taxonomic positions with multi-genotypic analyses.

scholarly journals “Candidatus Midichloriaceae” fam. nov. (Rickettsiales), an Ecologically Widespread Clade of Intracellular Alphaproteobacteria

2013 ◽  
Vol 79 (10) ◽  
pp. 3241-3248 ◽  
Author(s):  
Matteo Montagna ◽  
Davide Sassera ◽  
Sara Epis ◽  
Chiara Bazzocchi ◽  
Claudia Vannini ◽  
...  
Keyword(s):  
Life History ◽  
16S Rrna ◽  
Phylogenetic Trees ◽  
Rrna Gene ◽  
The Novel ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Evolutionary Scenario ◽  
Wide Range ◽  
Midichloria Mitochondrii

ABSTRACT“CandidatusMidichloria mitochondrii” is an intramitochondrial bacterium of the orderRickettsialesassociated with the sheep tickIxodes ricinus. Bacteria phylogenetically related to “Ca. Midichloria mitochondrii” (midichloria and like organisms [MALOs]) have been shown to be associated with a wide range of hosts, from amoebae to a variety of animals, including humans. Despite numerous studies focused on specific members of the MALO group, no comprehensive phylogenetic and statistical analyses have so far been performed on the group as a whole. Here, we present a multidisciplinary investigation based on 16S rRNA gene sequences using both phylogenetic and statistical methods, thereby analyzing MALOs in the overall framework of theRickettsiales. This study revealed that (i) MALOs form a monophyletic group; (ii) the MALO group is structured into distinct subgroups, verifying current genera as significant evolutionary units and identifying several subclades that could represent novel genera; (iii) the MALO group ranks at the level of describedRickettsialesfamilies, leading to the proposal of the novel family “CandidatusMidichloriaceae.” In addition, based on the phylogenetic trees generated, we present an evolutionary scenario to interpret the distribution and life history transitions of these microorganisms associated with highly divergent eukaryotic hosts: we suggest that aquatic/environmental protista have acted as evolutionary reservoirs for members of this novel family, from which one or more lineages with the capacity of infecting metazoa have evolved.

scholarly journals Isolation of Novel Probiotic Lactobacillus and Enterococcus Strains From Human Salivary and Fecal Sources

2020 ◽  
Vol 11 ◽  
Author(s):  
Homa Bazireh ◽  
Parvin Shariati ◽  
Sadegh Azimzadeh Jamalkandi ◽  
Ali Ahmadi ◽  
Mohammad Ali Boroumand
Keyword(s):  
Bile Salts ◽  
Antimicrobial Activities ◽  
Rrna Gene ◽  
Gastrointestinal Microbiota ◽  
Biochemical Tests ◽  
Human Colon Cancer ◽  
Healthy Human ◽  
Wide Range ◽  
Human Use

Probiotics are non-pathogenic microorganisms that can interact with the gastrointestinal microbiota. They have numerous beneficial health effects that include enhancement of the host immune response, antiallergic, antimicrobial, anti-cancer, and anti-inflammatory properties. Probiotics are capable of restoring the impaired microbiome of a dysbiotic gut. They can be isolated from different environments. However, it is frequently suggested that probiotics for human use should come from human sources. The objective of this study was to isolate and characterize novel probiotic strains from the saliva and feces of healthy human individuals. To meet the criteria for probiotic attributes, the isolates were subjected to numerous standard morphological and biochemical tests. These tests included Gram staining, catalase tests, antibiotic susceptibility testing, hemolytic and antagonistic evaluation, tolerance tests involving temperature, NaCl levels, pH and bile salts, adherence ability assays, and genotypic characterization involving 16S rRNA gene sequencing. From 26 saliva and 11 stool samples, 185 microbial strains were isolated. Based on morphological and biochemical characteristics, 14 potential probiotic candidates were selected and identified genotypically. The new strains belonged to Lactobacillus fermentum, Enterococcus faecium, and Enterococcus hire. The selected strains were non-hemolytic, showed high tolerance to low pH and bile salts, and strong adherence abilities. Furthermore, the strains displayed a wide range of antimicrobial activities, particularly against antibiotic-resistant pathogens such as methicillin resistant Staphylococcus aureus (MRSA). Moreover, five of the selected isolates demonstrated antiproliferative features against human colon cancer cell line (Caco-2). The results of this investigation confirm the diversity of microbial populations in the human gut and saliva, and since these strains are of human origin, they will highly likely display maximal activities in food and drugs set for human use. Hence, the new strains of this study require additional in vivo experiments to assess their health-promoting effects.

Morphological and molecular characterisation of several Paratylenchus Micoletzky, 1922 (Tylenchida: Paratylenchidae) species from South Africa and USA, together with some taxonomic notes

Nematology ◽  
2014 ◽  
Vol 16 (3) ◽  
pp. 323-358 ◽  
Author(s):  
Esther Van den Berg ◽  
Esther Van den Berg ◽  
Louwrens R. Tiedt ◽  
Esther Van den Berg ◽  
Louwrens R. Tiedt ◽  
...  
Keyword(s):  
South Africa ◽  
Rrna Genes ◽  
Morphological Identification ◽  
Rrna Gene ◽  
28S Rrna ◽  
Molecular Characterisation ◽  
Electron Microscopic ◽  
Wide Range ◽  
Its Rrna Gene ◽  
Its Rrna

Pin nematodes of the genus Paratylenchus are widely distributed across the world and associated with many plant species. Morphological identification of Paratylenchus species is a difficult task because it relies on many characters with a wide range of intraspecific variation. In this study we provide morphological and molecular characterisation of several pin nematodes: Paratylenchus aquaticus, P. dianthus, P. hamatus, P. nanus and P. straeleni, collected in different states of the USA and South Africa. Paratylenchus aquaticus is reported from South Africa and Hawaii and P. nanus is found from South Africa for the first time. Morphological descriptions, morphometrics, light and scanning electron microscopic photos and drawings are given for these species. Molecular characterisation of nematodes using the D2-D3 of 28S rRNA and ITS rRNA gene sequence revealed that samples morphologically identified as P. aquaticus, P. hamatus and P. nanus indeed represent species complexes containing several species. Sequences of the rRNA genes are also provided for several unidentified Paratylenchus. Phylogenetic relationships within the genus Paratylenchus are given as inferred from the analyses of the D2-D3 of 28S rRNA and ITS rRNA gene sequences. We present here the most complete phylogenetic analysis of the genus.

scholarly journals Computer-simulated RFLP analysis of 16S rRNA genes: identification of ten new phytoplasma groups

2007 ◽  
Vol 57 (8) ◽  
pp. 1855-1867 ◽  
Author(s):  
Wei Wei ◽  
Robert E. Davis ◽  
Ing-Ming Lee ◽  
Yan Zhao
Keyword(s):  
16S Rrna ◽  
Classification Scheme ◽  
Rflp Analysis ◽  
Plant Diseases ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Similarity Coefficients ◽  
Wide Range

Phytoplasmas are cell wall-less bacteria that cause numerous plant diseases. As no phytoplasma has been cultured in cell-free medium, phytoplasmas cannot be differentiated and classified by the traditional methods which are applied to culturable prokaryotes. Over the past decade, the establishment of a phytoplasma classification scheme based on 16S rRNA restriction fragment length polymorphism (RFLP) patterns has enabled the accurate and reliable identification and classification of a wide range of phytoplasmas. In the present study, we expanded this classification scheme through the use of computer-simulated RFLP analysis, achieving rapid differentiation and classification of phytoplasmas. Over 800 publicly available phytoplasma 16S rRNA gene sequences were aligned using the clustal_x program and the aligned 1.25 kb fragments were exported to pDRAW32 software for in silico restriction digestion and virtual gel plotting. Based on distinctive virtual RFLP patterns and calculated similarity coefficients, phytoplasma strains were classified into 28 groups. The results included the classification of hundreds of previously unclassified phytoplasmas and the delineation of 10 new phytoplasma groups representing three recently described and seven novel putative ‘Candidatus Phytoplasma’ taxa.

scholarly journals Comparative Sequence Analysis of Mycobacterium leprae and the New Leprosy-Causing Mycobacterium lepromatosis

2009 ◽  
Vol 191 (19) ◽  
pp. 6067-6074 ◽  
Author(s):  
Xiang Y. Han ◽  
Kurt C. Sizer ◽  
Erika J. Thompson ◽  
Juma Kabanja ◽  
Jun Li ◽  
...  
Keyword(s):  
16S Rrna ◽  
Phylogenetic Trees ◽  
Mycobacterium Leprae ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Neutral Evolution ◽  
Rrna Gene ◽  
Protein Encoding ◽  
Mycobacterium Lepromatosis ◽  
Encoding Genes

ABSTRACT Mycobacterium lepromatosis is a newly discovered leprosy-causing organism. Preliminary phylogenetic analysis of its 16S rRNA gene and a few other gene segments revealed significant divergence from Mycobacterium leprae, a well-known cause of leprosy, that justifies the status of M. lepromatosis as a new species. In this study we analyzed the sequences of 20 genes and pseudogenes (22,814 nucleotides). Overall, the level of matching of these sequences with M. leprae sequences was 90.9%, which substantiated the species-level difference; the levels of matching for the 16S rRNA genes and 14 protein-encoding genes were 98.0% and 93.1%, respectively, but the level of matching for five pseudogenes was only 79.1%. Five conserved protein-encoding genes were selected to construct phylogenetic trees and to calculate the numbers of synonymous substitutions (dS values) and nonsynonymous substitutions (dN values) in the two species. Robust phylogenetic trees constructed using concatenated alignment of these genes placed M. lepromatosis and M. leprae in a tight cluster with long terminal branches, implying that the divergence occurred long ago. The dS and dN values were also much higher than those for other closest pairs of mycobacteria. The dS values were 14 to 28% of the dS values for M. leprae and Mycobacterium tuberculosis, a more divergent pair of species. These results thus indicate that M. lepromatosis and M. leprae diverged ∼10 million years ago. The M. lepromatosis pseudogenes analyzed that were also pseudogenes in M. leprae showed nearly neutral evolution, and their relative ages were similar to those of M. leprae pseudogenes, suggesting that they were pseudogenes before divergence. Taken together, the results described above indicate that M. lepromatosis and M. leprae diverged from a common ancestor after the massive gene inactivation event described previously for M. leprae.

scholarly journals Comparison of potential diatom ‘barcode’ genes (the 18S rRNA gene and ITS, COI, rbcL) and their effectiveness in discriminating and determining species taxonomy in the Bacillariophyta

2015 ◽  
Vol 65 (Pt_4) ◽  
pp. 1369-1380 ◽  
Author(s):  
Liliang Guo ◽  
Zhenghong Sui ◽  
Shu Zhang ◽  
Yuanyuan Ren ◽  
Yuan Liu
Keyword(s):  
Phylogenetic Trees ◽  
18S Rrna ◽  
Mitochondrial Gene ◽  
Large Subunit ◽  
18S Rrna Gene ◽  
Marine Ecology ◽  
The Other ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Potential Marker

Diatoms form an enormous group of photoautotrophic micro-eukaryotes and play a crucial role in marine ecology. In this study, we evaluated typical genes to determine whether they were effective at different levels of diatom clustering analysis to assess the potential of these regions for barcoding taxa. Our test genes included nuclear rRNA genes (the nuclear small-subunit rRNA gene and the 5.8S rRNA gene+ITS-2), a mitochondrial gene (cytochrome c-oxidase subunit 1, COI), a chloroplast gene [ribulose-1,5-biphosphate carboxylase/oxygenase large subunit (rbcL)] and the universal plastid amplicon (UPA). Calculated genetic divergence was highest for the internal transcribed spacer (ITS; 5.8S+ITS-2) (p-distance of 1.569, 85.84 % parsimony-informative sites) and COI (6.084, 82.14 %), followed by the 18S rRNA gene (0.139, 57.69 %), rbcL (0.120, 42.01 %) and UPA (0.050, 14.97 %), which indicated that ITS and COI were highly divergent compared with the other tested genes, and that their nucleotide compositions were variable within the whole group of diatoms. Bayesian inference (BI) analysis showed that the phylogenetic trees generated from each gene clustered diatoms at different phylogenetic levels. The 18S rRNA gene was better than the other genes in clustering higher diatom taxa, and both the 18S rRNA gene and rbcL performed well in clustering some lower taxa. The COI region was able to barcode species of some genera within the Bacillariophyceae. ITS was a potential marker for DNA based-taxonomy and DNA barcoding of Thalassiosirales, while species of Cyclotella, Skeletonema and Stephanodiscus gathered in separate clades, and were paraphyletic with those of Thalassiosira. Finally, UPA was too conserved to serve as a diatom barcode.

scholarly journals Mesorhizobium waimense sp. nov. isolated from Sophora longicarinata root nodules and Mesorhizobium cantuariense sp. nov. isolated from Sophora microphylla root nodules

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3419-3426 ◽  
Author(s):  
Sofie E. De Meyer ◽  
Heng Wee Tan ◽  
Peter B. Heenan ◽  
Mitchell Andrews ◽  
Anne Willems
Keyword(s):  
Phylogenetic Trees ◽  
Root Nodules ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Fatty Acid Profiles ◽  
Biochemical Tests ◽  
Phenotypic Differentiation ◽  
Mesorhizobium Loti ◽  
Physiological And Biochemical ◽  
The 16S Rrna Gene

In total 14 strains of Gram-stain-negative, rod-shaped bacteria were isolated from Sophora longicarinata and Sophora microphylla root nodules and authenticated as rhizobia on these hosts. Based on the 16S rRNA gene phylogeny, they were shown to belong to the genus Mesorhizobium, and the strains from S. longicarinata were most closely related to Mesorhizobium amorphae ACCC 19665T (99.8–99.9 %), Mesorhizobium huakuii IAM 14158T (99.8–99.9 %), Mesorhizobium loti USDA 3471T (99.5–99.9 %) and Mesorhizobium septentrionale SDW 014T (99.6–99.8 %), whilst the strains from S. microphylla were most closely related to Mesorhizobium ciceri UPM-Ca7T (99.8–99.9 %), Mesorhizobium qingshengii CCBAU 33460T (99.7 %) and Mesorhizobium shangrilense CCBAU 65327T (99.6 %). Additionally, these strains formed two distinct groups in phylogenetic trees of the housekeeping genes glnII, recA and rpoB. Chemotaxonomic data, including fatty acid profiles, supported the assignment of the strains to the genus Mesorhizobium and allowed differentiation from the closest neighbours. Results of DNA–DNA hybridizations, MALDI-TOF MS analysis, ERIC-PCR, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of our strains from their closest neighbouring species. Therefore, the strains isolated from S. longicarinata and S. microphylla represent two novel species for which the names Mesorhizobium waimense sp. nov. (ICMP 19557T = LMG 28228T = HAMBI 3608T) and Mesorhizobium cantuariense sp. nov. (ICMP 19515T = LMG 28225T = HAMBI 3604T), are proposed respectively.

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