scholarly journals Biochemical and Genomic Characterization of the Cypermethrin-Degrading and Biosurfactant-Producing Bacterial Strains Isolated from Marine Sediments of the Chilean Northern Patagonia

Marine Drugs ◽  
2020 ◽  
Vol 18 (5) ◽  
pp. 252 ◽  
Author(s):  
Patricia Aguila-Torres ◽  
Jonathan Maldonado ◽  
Alexis Gaete ◽  
Jaime Figueroa ◽  
Alex González ◽  
...  
Keyword(s):  
Marine Sediments ◽  
Enrichment Culture ◽  
Extreme Environments ◽  
Environmental Damage ◽  
Bacterial Strains ◽  
Culture Techniques ◽  
Northern Patagonia ◽  
Genes Encoding ◽  
Genomic Characterization

Pesticides cause severe environmental damage to marine ecosystems. In the last ten years, cypermethrin has been extensively used as an antiparasitic pesticide in the salmon farming industry located in Northern Patagonia. The objective of this study was the biochemical and genomic characterization of cypermethrin-degrading and biosurfactant-producing bacterial strains isolated from cypermethrin-contaminated marine sediment samples collected in southern Chile (MS). Eleven strains were isolated by cypermethrin enrichment culture techniques and were identified by 16S rDNA gene sequencing analyses. The highest growth rate on cypermethrin was observed in four isolates (MS13, MS15a, MS16, and MS19) that also exhibited high levels of biosurfactant production. Genome sequence analyses of these isolates revealed the presence of genes encoding components of bacterial secondary metabolism, and the enzymes esterase, pyrethroid hydrolase, and laccase, which have been associated with different biodegradation pathways of cypermethrin. These novel cypermethrin-degrading and biosurfactant-producing bacterial isolates have a biotechnological potential for biodegradation of cypermethrin-contaminated marine sediments, and their genomes contribute to the understanding of microbial lifestyles in these extreme environments.

scholarly journals Genomic Characterization of a Novel Freshwater Cyanophage Reveals a New Lineage of Cyanopodovirus

2022 ◽  
Vol 12 ◽  
Author(s):  
Dong Zhang ◽  
Yiliang He ◽  
Karina Yew-Hoong Gin
Keyword(s):  
Open Reading Frames ◽  
Metabolic Genes ◽  
Genes Encoding ◽  
Genomic Characterization ◽  
Ecological Importance ◽  
Auxiliary Metabolic Genes ◽  
Reading Frames ◽  
Tropical Freshwater ◽  
Core Genes

Cyanobacteria are one of the dominant autotrophs in tropical freshwater communities, yet phages infecting them remain poorly characterized. Here we present the characterization of cyanophage S-SRP02, isolated from a tropical freshwater lake in Singapore, which infects Synechococcus sp. Strain SR-C1 isolated from the same lake. S-SRP02 represents a new evolutionary lineage of cyanophage. Out of 47 open reading frames (ORFs), only 20 ORFs share homology with genes encoding proteins of known function. There is lack of auxiliary metabolic genes which was commonly found as core genes in marine cyanopodoviruses. S-SRP02 also harbors unique structural genes highly divergent from other cultured phages. Phylogenetic analysis and viral proteomic tree further demonstrate the divergence of S-SRP02 from other sequenced phage isolates. Nonetheless, S-SRP02 shares synteny with phage genes of uncultured phages obtained from the Mediterranean Sea deep chlorophyll maximum fosmids, indicating the ecological importance of S-SRP02 and its related viruses. This is further supported by metagenomic mapping of environmental viral metagenomic reads onto the S-SRP02 genome.

scholarly journals Genome-Based Insights into the Production of Carotenoids by Antarctic Bacteria, Planococcus sp. ANT_H30 and Rhodococcus sp. ANT_H53B

Molecules ◽  
2020 ◽  
Vol 25 (19) ◽  
pp. 4357
Author(s):  
Michal Styczynski ◽  
Agata Rogowska ◽  
Katarzyna Gieczewska ◽  
Maciej Garstka ◽  
Anna Szakiel ◽  
...  
Keyword(s):  
Bacterial Strains ◽  
Bacterial Genomes ◽  
Metabolic Potential ◽  
Antarctic Bacteria ◽  
Physiological Analysis ◽  
Genomic Characterization ◽  
Two Temperatures ◽  
Pigment Biosynthesis ◽  
Rhodococcus Sp

Antarctic regions are characterized by low temperatures and strong UV radiation. This harsh environment is inhabited by psychrophilic and psychrotolerant organisms, which have developed several adaptive features. In this study, we analyzed two Antarctic bacterial strains, Planococcus sp. ANT_H30 and Rhodococcus sp. ANT_H53B. The physiological analysis of these strains revealed their potential to produce various biotechnologically valuable secondary metabolites, including surfactants, siderophores, and orange pigments. The genomic characterization of ANT_H30 and ANT_H53B allowed the identification of genes responsible for the production of carotenoids and the in silico reconstruction of the pigment biosynthesis pathways. The complex manual annotation of the bacterial genomes revealed the metabolic potential to degrade a wide variety of compounds, including xenobiotics and waste materials. Carotenoids produced by these bacteria were analyzed chromatographically, and we proved their activity as scavengers of free radicals. The quantity of crude carotenoid extracts produced at two temperatures using various media was also determined. This was a step toward the optimization of carotenoid production by Antarctic bacteria on a larger scale.

scholarly journals Isolation of New Stenotrophomonas Bacteriophages and Genomic Characterization of Temperate Phage S1

2008 ◽  
Vol 74 (24) ◽  
pp. 7552-7560 ◽  
Author(s):  
Pilar García ◽  
Cristina Monjardín ◽  
Rebeca Martín ◽  
Carmen Madera ◽  
Nora Soberón ◽  
...  
Keyword(s):  
Burst Size ◽  
Gene Clusters ◽  
Open Reading Frames ◽  
Virus Particles ◽  
Bacterial Titer ◽  
Genes Encoding ◽  
Replication Gene ◽  
Genomic Characterization ◽  
Phosphoadenosine Phosphosulfate

ABSTRACT Twenty-two phages that infect Stenotrophomonas species were isolated through sewage enrichment and prophage induction. Of them, S1, S3, and S4 were selected due to their wide host ranges compared to those of the other phages. S1 and S4 are temperate siphoviruses, while S3 is a virulent myovirus. The genomes of S3 and S4, about 33 and 200 kb, were resistant to restriction digestion. The lytic cycles lasted 30 min for S3 and about 75 min for S1 and S4. The burst size for S3 was 100 virions/cell, while S1 and S4 produced about 75 virus particles/cell. The frequency of bacteriophage-insensitive host mutants, calculated by dividing the number of surviving colonies by the bacterial titer of a parallel, uninfected culture, ranged between 10−5 and 10−6 for S3 and 10−3 and 10−4 for S1 and S4. The 40,287-bp genome of S1 contains 48 open reading frames (ORFs) and 12-bp 5′ protruding cohesive ends. By using a combination of bioinformatics and experimental evidence, functions were ascribed to 21 ORFs. The morphogenetic and lysis modules are well-conserved, but no lysis-lysogeny switch or DNA replication gene clusters were recognized. Two major clusters of genes with respect to transcriptional orientation were observed. Interspersed among them were lysogenic conversion genes encoding phosphoadenosine phosphosulfate reductase and GspM, a protein involved in the general secretion system II. The attP site of S1 may be located within a gene that presents over 75% homology to a Stenotrophomonas chromosomal determinant.

scholarly journals Isolation and Characterization of Copper Tolerant Bacterial Species Habituating in Copper Mines and Study of Their Potentiality as a Plant Growth Stimulator

2021 ◽  
Author(s):  
Krishnendu Majhi ◽  
Moitri Let ◽  
Urmi Halder ◽  
Rajib Bandopadhyay
Keyword(s):  
Plant Growth ◽  
Enrichment Culture ◽  
Bacterial Species ◽  
Contaminated Site ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Culture Techniques ◽  
Isolation And Characterization ◽  
Copper Sulfate Pentahydrate ◽  
Copper Tolerant

Abstract Copper (Cu) is a vital micronutrient for all living organisms below its toxicity limit. Various industrial activities, mining deposits, excessive use of harmful chemicals, waste discharges, and drugs are the main reason for the emerging copper concentration. Emphases of the current study were to isolate and characterize highly copper-tolerating bacterial (CTB) species from a copper-contaminated site. In enrichment culture techniques, 24 copper tolerant microbial isolates were evaluated and the maximum tolerable concentration (MTC) was determined using various concentrations of copper sulfate pentahydrate (CuSO4.5H2O) solution. Three bacterial strains named GKSM2, GKSM6, and GKSM11 were tolerant to 350 mg/l of CuSO4.5H2O. The 16S rRNA gene sequencing and phylogeny data revealed that these CTB belong to species Bacillus zanthoxyli, Bacillus stercoris, and Pseudomonas alcaliphila species. CTB showed their optimized growth at moderate salt concentration (0.1-0.5M NaCl), temperature range (20-45˚C) and wide pH range (pH 5.0-11). All the strains can produce various Plant growth stimulating (PGS) traits viz., phytohormones (IAA, GA), proline, nitrogen fixation, ammonification, and antioxidant enzymes in presence and absence of Cu2+ stress. The result displays that adsorption of Cu2+ ions evidenced by TEM, SEM, and SEM-EDX analysis.

scholarly journals Characterization of Two Unique Cold-Active Lipases Derived from a Novel Deep-Sea Cold Seep Bacterium

2021 ◽  
Vol 9 (4) ◽  
pp. 802
Author(s):  
Chenchen Guo ◽  
Rikuan Zheng ◽  
Ruining Cai ◽  
Chaomin Sun ◽  
Shimei Wu
Keyword(s):  
Deep Sea ◽  
Bacterial Species ◽  
Deep Ocean ◽  
Cold Seep ◽  
Bacterial Strains ◽  
E Coli ◽  
Cold Active ◽  
Genes Encoding ◽  
Potential Inhibitors

The deep ocean microbiota has unexplored potential to provide enzymes with unique characteristics. In order to obtain cold-active lipases, bacterial strains isolated from the sediment of the deep-sea cold seep were screened, and a novel strain gcc21 exhibited a high lipase catalytic activity, even at the low temperature of 4 °C. The strain gcc21 was identified and proposed to represent a new species of Pseudomonas according to its physiological, biochemical, and genomic characteristics; it was named Pseudomonas marinensis. Two novel encoding genes for cold-active lipases (Lipase 1 and Lipase 2) were identified in the genome of strain gcc21. Genes encoding Lipase 1 and Lipase 2 were respectively cloned and overexpressed in E. coli cells, and corresponding lipases were further purified and characterized. Both Lipase 1 and Lipase 2 showed an optimal catalytic temperature at 4 °C, which is much lower than those of most reported cold-active lipases, but the activity and stability of Lipase 2 were much higher than those of Lipase 1 under different tested pHs and temperatures. In addition, Lipase 2 was more stable than Lipase 1 when treated with different metal ions, detergents, potential inhibitors, and organic solvents. In a combination of mutation and activity assays, catalytic triads of Ser, Asp, and His in Lipase 1 and Lipase 2 were demonstrated to be essential for maintaining enzyme activity. Phylogenetic analysis showed that both Lipase 1 and Lipase 2 belonged to lipase family III. Overall, our results indicate that deep-sea cold seep is a rich source for novel bacterial species that produce potentially unique cold-active enzymes.

Enrichment of arsenite oxidizing bacteria under autotrophic conditions and the isolation and characterization of facultative chemolithoautotrophic arsenite oxidizing bacteria for removal of arsenic from groundwater

2012 ◽  
Vol 12 (5) ◽  
pp. 707-714 ◽  
Author(s):  
L. Nguyen Ai ◽  
A. Sato ◽  
D. Inoue ◽  
K. Sei ◽  
S. Soda ◽  
...  
Keyword(s):  
Arsenic Removal ◽  
Enrichment Culture ◽  
Large Subunit ◽  
Cost Effective ◽  
Isolation And Characterization ◽  
The World ◽  
Genes Encoding ◽  
Arsenite Oxidizing Bacteria ◽  
Removal Of Arsenic

Arsenic contamination in groundwater has caused severe health problems throughout the world. Developing cost-effective processes for arsenic removal is an emerging issue. Because As(III) is predominant in groundwater and is more difficult to remove than As(V) is, oxidation of As(III) to As(V) is necessary to improve overall arsenic removal. This study was undertaken to enrich arsenite oxidizing bacteria under autotrophic conditions and to isolate and characterize facultative chemolithoautotrophic arsenite oxidizing bacteria (CAOs) that can oxidize As(III) effectively to As(V). An enrichment culture which adapted wide As(III) concentrations and completely oxidized 12 mM As(III) within 4 days under autotrophic conditions was established and maintained. Among 10 isolated strains, 6 strains, B1, B2, C, D, E1 and E2 belonging to β-Proteobacteria, were facultative CAOs and contained aoxB genes encoding the arsenite oxidase large subunit. Furthermore, they displayed various As(III) oxidation capabilities: B1, B2, E1 and E2 efficiently oxidized 1–10 mM As(III). The others showed efficient oxidation at 1–5 mM As(III), suggesting the coexistence of facultative CAOs with various As(III) oxidation capabilities in the enrichment. These results suggest that constructed enrichment and strains B1, B2, E1 and E2 can be useful for the bioremediation of arsenic-contaminated groundwater.

scholarly journals In-Depth Genomic Characterization of a Meropenem-nonsusceptible Pseudomonas otitidis Strain Contaminating Chicken Carcass

2020 ◽  
Vol 48 ◽  
Author(s):  
Tatiana Regina Vieira ◽  
Gustavo Enck Sambrano ◽  
Núbia Michelle Vieira da Silva ◽  
Priscylla Carvalho Vasconcelos ◽  
Esther Ferraza Cavinatto de Oliveira ◽  
...  
Keyword(s):  
Public Health ◽  
Antimicrobial Resistance ◽  
Resistant Bacteria ◽  
Beta Lactamase ◽  
Food Animal ◽  
Chicken Carcass ◽  
Pseudomonas Species ◽  
Genes Encoding ◽  
Genomic Characterization

Background: The indiscriminate use of antibiotics in food-animal production has a major impact on public health, particularly in terms of contributing to the emergence and dissemination of antimicrobial resistant bacteria in the food-animal production chain. Although Pseudomonas species are recognized as important spoilage organisms in foodstuff, they are also known as opportunistic pathogens associated with hospital-acquired infections. Furthermore, Pseudomonas can play a role as potential reservoirs of antimicrobial resistance genes, which may be horizontally transferred to other bacteria. Considering that cephalosporins (3rd and higher generations) and carbapenems are critically important beta-lactam antimicrobials in human medicine, this study reports the occurrence and genomic characterization of a meropenem-nonsusceptible Pseudomonas otitidis strain recovered from a chicken carcass in Brazil.Materials, Methods & Results: During the years 2018-2019, 72 frozen chicken carcasses were purchased on the retail market from different regions in Brazil. Aliquots from individual carcass rinses were screened for Extended Spectrum Beta-lactamase (ESBL)-producing bacteria in MacConkey agar supplemented with 1mg.L-1 cefotaxime. Phenotypically resistant isolates were further tested for resistance to other antimicrobials and confirmed as ESBL-producers by means of disk-diffusion method using Müller-Hinton agar. Only one meropenen-nonsusceptible isolate was detected and submitted to whole genome sequencing (WGS) in Illumina Miseq. The strain was identified as Pseudomonas otitidis by local alignment of the 16S rRNA sequence using BLASTn and confirmed by Average Nucleotide Identity (ANI) analysis using JspeciesWS database. Genes encoding for antimicrobial resistance were detected by means of Resfinder and Comprehensive Antibiotic Resistance Database (CARD) databases. The phenotypic non-susceptibility to meropenen was attributed to the gene blaPOM-1. A total of 192 different genes encoding for quorum sensing system, antiphagocytosis, iron uptake, efflux pump, endotoxin and toxin, adherence, and secretion systems were detected by means of Virulence Factor Database (VFDB). Pseudomonas otitidis-pan genome was built using Roary-rapid large-scale prokaryote pan genome analysis using the present strain (K_25) and other two P. otitidis genomes (PAM-1, DSM 17224) publicly available at the NCBI. The core genome analysis of the two human strains resulted in similar percentages.Discussion: Carbapenems are critically important drugs for human health and bacterial strains resistant to these antimicrobials pose a public health problem. The blaPOM-1 gene harbored by the Pseudomonas otitidis K_25 strain encodes a metallo-beta-lactamase (MBL) conferring resistance to carbapenems. Pseudomonas otitidis was the first confirmed pathogenic Pseudomonas species expressing MBL constitutively in the absence of inducible beta-lactamase genes. Furthermore, the several virulence genes associated with the capacity of the P. otitidis K_25 to colonize, evade the immune system and cause lesions in the human host confirm this strain as a potential opportunistic pathogen contaminating foodstuff. These reinforce the need to address antimicrobial resistance in a One Health perspective, in which resistant bacteria and resistance determinants circulate among environment, animals and humans.

scholarly journals Isolation and Molecular Characterization of Pesticide Degrading Bacteria in Polluted Soil

2020 ◽  
Author(s):  
Kehinde Sowunmi ◽  
Suliat Morenike Shoga ◽  
Oluwabukola Mabel Adewunmi ◽  
Adewale Felix Oriyomi ◽  
Lukman Sowunmi
Keyword(s):  
Enrichment Culture ◽  
Lethal Effect ◽  
Living System ◽  
Culture Technique ◽  
Bacterial Strains ◽  
High Concentration ◽  
Degrading Bacteria ◽  
Quality Check ◽  
Pure Bacterial Cultures

AbstractPesticides are the substances for preventing, destroying, repelling any pest. Due to bulk handling or accidental release, they are accumulated in soil which leads to occasional entry into ecosystem that shows lethal effect on living system. An enrichment culture technique was used to isolate bacterial strains from organophosphate soil degrading high concentration of the selected pesticides. Five pure bacterial cultures were isolated. All five isolates were characterized on the basis of molecular and biochemical features like biodegradation test and substrate specificity, phosphate solubilization and screened for pesticide residue, pH, and extraction of DNA, quantity and quality check and salt tolerance. The organophosphate isolates were also tested for quantitative production. The screening of pesticide tolerance was done at for fungicides and insecticides.

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