scholarly journals Differential analysis of pesticides biodegradation in soil using conventional and high-throughput technology

2021 ◽  
Author(s):  
Saurabh Gangola ◽  
samiksha Joshi ◽  
Saurabh Kumar ◽  
Anita Sharma
Keyword(s):  
16S Rdna ◽  
Contaminated Soil ◽  
Bacterial Strain ◽  
Large Scale ◽  
Minimal Salt Medium ◽  
Laccase Gene ◽  
Major Band ◽  
Spiked Soil ◽  
Rdna Sequencing ◽  
Uncontaminated Soil

A potential pesticide degrading bacterial isolate (2D), showing maximum tolerance (450 ppm) for cypermethrin, fipronil, imidacloprid and sulfosulfuron was recovered from a pesticide contaminated agricultural field. The isolate degraded cypermethrin, imidacloprid, fipronil and sulfosulfuron in minimal salt medium with 94, 91, 89 and 86% respectively as revealed by HPLC and GC analysis after 15 days of incubation. Presence of cyclobutane, pyrrolidine, chloroacetic acid, formic acid and decyl ester as major intermediate metabolites of cypermethrin biodegradation was observed in GC-MS analysis. Results based on 16S rDNA sequencing, and phylogenetic analysis showed maximum similarity of 2D with Bacillus cereus (MH341691). Stress responsive and catabolic/ pesticide degrading proteins were over expressed in the presence of cypermethrin in bacteria. Enzyme kinetics of laccase was deduced in the test isolate under normal and pesticide stress conditions. Amplification of laccase gene showed a major band of 1200bp. Maximum copy number of 16S rDNA was seenin uncontaminated soil as compared to pesticide contaminated soil using qRT-PCR. The metagenome sequencing revealed reduction in the population of proteobacteria in contaminated soil as compared to uncontaminated soil but showed dominance of actinobacteria, firmicutes and bacteriodates in pesticide spiked soil. Presence of some new phyla like chloroflexi, planctomycetes, verrucomicrobia was observed followed by extinction of acidobacteria and crenarchaeota in spiked soil. The present study highlights on the potential of 2D bacterial strain i.e., high tolerance level of pesticide, effective biodegradation rate, and presence of laccase gene in bacterial strain 2D, could become a potential biological agent for large-scale treatment of mixture of pesticide (cypermethrin, fipronil, imidacloprid and sulfosulfuron) in natural environment (soil and water).

scholarly journals Differential proteomic analysis under pesticides stress and normal conditions in Bacillus cereus 2D

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0253106
Author(s):  
Saurabh Gangola ◽  
Samiksha Joshi ◽  
Saurabh Kumar ◽  
Barkha Sharma ◽  
Anita Sharma
Keyword(s):  
Gas Chromatography ◽  
Bacillus Cereus ◽  
Bacterial Strain ◽  
Large Scale ◽  
Gas Chromatography Mass Spectrometry ◽  
Minimal Salt Medium ◽  
Laccase Gene ◽  
Major Band ◽  
Pesticide Stress ◽  
Rdna Sequencing

A potential pesticide degrading bacterial isolate (2D), showing maximum tolerance (450 mg∙L-1) for cypermethrin, fipronil, imidacloprid and sulfosulfuron was recovered from a pesticide contaminated agricultural field. The isolate degraded cypermethrin, imidacloprid, fipronil and sulfosulfuron in minimal salt medium with 94, 91, 89 and 86% respectively as revealed by high performance liquid chromatography (HPLC) and gas chromatography (GC) analysis after 15 days of incubation. Presence of cyclobutane, pyrrolidine, chloroacetic acid, formic acid and decyl ester as major intermediate metabolites of cypermethrin biodegradation was observed in gas chromatography mass spectrometry (GC-MS) analysis. Results based on 16S rDNA sequencing, and phylogenetic analysis showed maximum similarity of 2D with Bacillus cereus (Accession ID: MH341691). Stress responsive and catabolic/pesticide degrading proteins were over expressed in the presence of cypermethrin in bacteria. Enzymatic kinetics of laccase was deduced in the test isolate under normal and pesticide stress conditions which suggested that the production of enzyme was induced significantly in pesticide stress (163 μg.μL-1) as compare to normal conditions(29 μg.μL-1) while the Km value was decreased in pesticides stress condition (Km = 10.57 mM) and increases in normal condition (Km = 14.33 mM).Amplification of laccase gene showed a major band of 1200bp. The present study highlights on the potential of 2D bacterial strain i.e., high tolerance level of pesticide, effective biodegradation rate, and presence of laccase gene in bacterial strain 2D, could become a potential biological agent for large-scale treatment of mixture of pesticide (cypermethrin, fipronil, imidacloprid and sulfosulfuron) in natural environment (soil and water).

Metabolite fingerprinting of novel Streptomyces UK-238 from the Himalayan forest

2020 ◽  
Vol 16 ◽  
Author(s):  
Nidhi Srivastava ◽  
Indira P. Sarethy
Keyword(s):  
Ethyl Acetate ◽  
16S Rdna ◽  
Retention Index ◽  
Ethyl Acetate Extract ◽  
Similarity Index ◽  
Antimicrobial Drug ◽  
16S Rdna Sequencing ◽  
Metabolite Fingerprinting ◽  
Streptomyces Sp ◽  
Rdna Sequencing

Aims: Characterization of antimicrobial metabolites of novel Streptomyces sp. UK-238. Background: Novel antimicrobial drug discovery is urgently needed due to emerging multi antimicrobial drug resistance among pathogens. Since many years, natural products have provided the basic skeletons for many therapeutic compounds including antibiotics. Bioprospection of un/under explored habitats and focussing on selective isolation of actinobacteria as major reservoir of bio and chemodiversity has yielded good results. Objective: The main objectives of the study were the identification of UK-238 by 16S rDNA sequencing and antimicrobial metabolite fingerprinting of culture extracts. Method: In the present study, a promising isolate, UK-238, has been screened for antimicrobial activity and metabolite fingerprinting from the Himalayan Thano Reserve forest. It was identified by 16S rDNA sequencing. Ethyl acetate extract was partially purified by column chromatography. The pooled active fractions were fingerprinted by GC-MS and compounds were tentatively identified by collated data analysis based on Similarity Index, observed Retention Index from Databases and calculated Retention Index. Results: UK-238 was identified as Streptomyces sp. with 98.4% similarity to S. niveiscabiei. It exhibited broad-spectrum antibacterial and antifungal activity. GC-MS analysis of active fractions of ethyl acetate extract showed the presence of eighteen novel antimicrobial compounds belonging to four major categories- alcohols, alkaloid, esters and peptide. Conclusion: The study confirms that bioprospection of underexplored habitats can elaborate novel bio and chemodiversity.

scholarly journals Dynamic of Morphological and Physiological Parameters and Variation of Soil Characteristics during Miscanthus × giganteus Cultivation in the Diesel-Contaminated Land

Agronomy ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 798
Author(s):  
Valentina Pidlisnyuk ◽  
Andriy Herts ◽  
Volodymyr Khomenchuk ◽  
Aigerim Mamirova ◽  
Oleksandr Kononchuk ◽  
...  
Keyword(s):  
Contaminated Soil ◽  
Contaminated Soils ◽  
Soil Characteristics ◽  
Physiological Parameters ◽  
Wastewater Sludge ◽  
Contaminated Land ◽  
Miscanthus Giganteus ◽  
Uncontaminated Soil ◽  
Stems And Leaves ◽  
Biochar Amendment

Miscanthus × giganteus (M. × giganteus) is a perspective plant produced on marginal and contaminated lands with biomass used for energy or bioproducts. In the current study, M. × giganteus development was tested in the diesel-contaminated soils (ranged from 250 mg kg−1 to 5000 mg kg−1) and the growth dynamic, leaves quantity, plants total area, number of harvested stems and leaves, SPAD and NPQt parameters were evaluated. Results showed a remarkable M. × giganteus growth in a selected interval of diesel-contaminated soil with sufficient harvested biomass. The amendment of soil by biochar 1 (produced from wastewater sludge) and biochar 2 (produced from a mixture of wood waste and biohumus) improved the crop’s morphological and physiological parameters. Biochar 1 stimulated the increase of the stems’ biomass, while biochar 2 increased the leaves biomass. The plants growing in the uncontaminated soil decreased the content of NO3, pH (KCl), P2O5 and increased the content of NH4. Photosynthesis parameters showed that incorporating biochar 1 and biochar 2 to the diesel-contaminated soil prolonged the plants’ vegetation, which was more potent for biochar 1. M. × giganteus utilization united with biochar amendment can be recommended to remediate diesel-contaminated land in concentration range 250–5000 mg kg−1.

scholarly journals 2-Way k-Means as a Model for Microbiome Samples

2017 ◽  
Vol 2017 ◽  
pp. 1-7 ◽  
Author(s):  
Weston J. Jackson ◽  
Ipsita Agarwal ◽  
Itsik Pe’er
Keyword(s):  
Unsupervised Learning ◽  
16S Rdna ◽  
Mixture Model ◽  
Vaginal Microbiome ◽  
16S Rdna Sequencing ◽  
Sequencing Data ◽  
Cluster Assignment ◽  
Rdna Sequencing

Motivation. Microbiome sequencing allows defining clusters of samples with shared composition. However, this paradigm poorly accounts for samples whose composition is a mixture of cluster-characterizing ones and which therefore lie in between them in the cluster space. This paper addresses unsupervised learning of 2-way clusters. It defines a mixture model that allows 2-way cluster assignment and describes a variant of generalized k-means for learning such a model. We demonstrate applicability to microbial 16S rDNA sequencing data from the Human Vaginal Microbiome Project.

scholarly journals Evidence for Enhanced Dissipation of Chlorpyrifos in an Agricultural Soil Inoculated with Serratia Rubidaea Strain ABS 10

2021 ◽  
Author(s):  
Asma Ben Salem ◽  
Hanene Chaabane ◽  
Tesnime Ghazouani ◽  
Pierluigi Caboni ◽  
Valentina Coroneo ◽  
...  
Keyword(s):  
16S Rrna ◽  
Bacterial Strain ◽  
Agricultural Soil ◽  
Liquid Culture ◽  
Minimal Salt Medium ◽  
Salt Medium ◽  
Sterile Soil ◽  
Rrna Sequencing ◽  
Biochemical Analyses ◽  
Serratia Rubidaea

Abstract Important mineralization of 14C-chlorpyrifos was found in a Tunisian soil exposed repeatedly to this insecticide. A bacterial strain able to grow in minimal salt medium (MSM) supplemented with 25 mg L− 1 of chlorpyrifos was isolated from this soil. It was characterized as Serratia rubidaea strain ABS 10 using morphological and biochemical analyses, as well as 16S rRNA sequencing. In liquid culture S. rubidaea stain ABS 10 was able to almost entirely dissipate chlorpyrifos within 48 hours of incubation. Although, S. rubidaea strain ABS 10 was able to grow on MSM supplemented with chlorpyrifos and to dissipate it in liquid culture, it was not able to mineralize 14C-chlorpyrifos. Therefore, one can conclude that the dissipation capability of this bacteria might be attributed to its capacity to adsorb CHL. In both non-sterile and sterile soil inoculated with S. rubidaea strain ABS 10, chlorpyrifos was more rapidly dissipated than in respective controls.

Phylogeny of the family Pasteurellaceae based on rpoB sequences

2004 ◽  
Vol 54 (4) ◽  
pp. 1393-1399 ◽  
Author(s):  
Bożena Korczak ◽  
Henrik Christensen ◽  
Stefan Emler ◽  
Joachim Frey ◽  
Peter Kuhnert
Keyword(s):  
16S Rdna ◽  
Dna Hybridization ◽  
Gene Encoding ◽  
Phylogenetic Studies ◽  
Study Selection ◽  
Gene Sequence Analysis ◽  
Rdna Sequencing ◽  
The Family ◽  
Type Strains ◽  
Selection Of

Sequences of the gene encoding the β-subunit of the RNA polymerase (rpoB) were used to delineate the phylogeny of the family Pasteurellaceae. A total of 72 strains, including the type strains of the major described species as well as selected field isolates, were included in the study. Selection of universal rpoB-derived primers for the family allowed straightforward amplification and sequencing of a 560 bp fragment of the rpoB gene. In parallel, 16S rDNA was sequenced from all strains. The phylogenetic tree obtained with the rpoB sequences reflected the major branches of the tree obtained with the 16S rDNA, especially at the genus level. Only a few discrepancies between the trees were observed. In certain cases the rpoB phylogeny was in better agreement with DNA–DNA hybridization studies than the phylogeny derived from 16S rDNA. The rpoB gene is strongly conserved within the various species of the family of Pasteurellaceae. Hence, rpoB gene sequence analysis in conjunction with 16S rDNA sequencing is a valuable tool for phylogenetic studies of the Pasteurellaceae and may also prove useful for reorganizing the current taxonomy of this bacterial family.

Analysis of the bacterial floral structure and diversity of Xuanwei ham by 16S rDNA sequencing

2020 ◽  
Vol 40 (4) ◽  
Author(s):  
Luying Shan ◽  
Yinjiao Li ◽  
Shi Zheng ◽  
Yuanmiao Wei ◽  
Ying Shang
Keyword(s):  
16S Rdna ◽  
16S Rdna Sequencing ◽  
Floral Structure ◽  
Rdna Sequencing

scholarly journals ISOLATION, PURIFICATION, AND CHARACTERIZATION OF LIPASE FROM BACILLUS SP. FROM KITCHEN GREASE

2018 ◽  
Vol 11 (6) ◽  
pp. 224
Author(s):  
Jaiganesh R ◽  
Jaganathan Mk
Keyword(s):  
16S Rdna ◽  
Solvent Tolerance ◽  
16S Rdna Sequencing ◽  
Bacillus Sp ◽  
Purification And Characterization ◽  
Lipase Enzyme ◽  
Sequencing Method ◽  
Rdna Sequencing ◽  
Solvent Tolerant

Objective: The objective of this work was to isolation, purification and characterization of solvent tolerant lipase from Bacillus sp. The objective of this work was to isolation, purification and characterization of solvent tolerant lipase from Bacillus sp. from kitchen grease for a variety of applications including organic synthetic reactions and preparation of enantiomerically pure pharmaceuticals.Methods: Lipase producing isolates were screened from kitchen grease on a selective medium rhodamine B olive oil agar, and tributyrin agar was used to screen the lipase and esterase producing an organism, respectively. The isolate identified using 16S rDNA sequencing method and enzyme activity was quantitatively assayed. Lipase production was characterized in different conditions.Results: The isolate showed highest lipase activity was which later was identified as Bacillus sp. using 16S rDNA sequencing method. The lipase was purified using ammonium sulfate precipitation. The isolate showed excellent tolerance to methanol, ethanol, acetonitrile, and moderate tolerance to butanol. The increased biomass concentration, maximum production, and activity were achieved at 37°C in 24 h incubation, then gradual reduction in production was observed. The maximum activity of lipase enzyme was obtained at pH between 6 and 9.Conclusion: The isolate produce solvent tolerance lipase enzyme and it can be a promising candidate of solvent tolerance lipase enzyme for variety of industrial applications.

scholarly journals Cave Drip Water-Related Samples as a Natural Environment for Aromatic Hydrocarbon-Degrading Bacteria

2019 ◽  
Vol 7 (2) ◽  
pp. 33 ◽  
Author(s):  
Eric Marques ◽  
Gislaine Silva ◽  
João Dias ◽  
Eduardo Gross ◽  
Moara Costa ◽  
...  
Keyword(s):  
Aromatic Hydrocarbon ◽  
Microbial Communities ◽  
16S Rdna ◽  
Aromatic Compounds ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Amplicon Sequencing ◽  
Drip Water ◽  
Rdna Sequencing ◽  
Degrading Bacteria ◽  
Cave Drip Water

Restricted contact with the external environment has allowed the development of microbial communities adapted to the oligotrophy of caves. However, nutrients can be transported to caves by drip water and affect the microbial communities inside the cave. To evaluate the influence of aromatic compounds carried by drip water on the microbial community, two limestone caves were selected in Brazil. Drip-water-saturated and unsaturated sediment, and dripping water itself, were collected from each cave and bacterial 16S rDNA amplicon sequencing and denaturing gradient gel electrophoresis (DGGE) of naphthalene dioxygenase (ndo) genes were performed. Energy-dispersive X-ray spectroscopy (EDX) and atomic absorption spectroscopy (AAS) were performed to evaluate inorganic nutrients, and GC was performed to estimate aromatic compounds in the samples. The high frequency of Sphingomonadaceae in drip water samples indicates the presence of aromatic hydrocarbon-degrading bacteria. This finding was consistent with the detection of naphthalene and acenaphthene and the presence of ndo genes in drip-water-related samples. The aromatic compounds, aromatic hydrocarbon-degrading bacteria and 16S rDNA sequencing indicate that aromatic compounds may be one of the sources of energy and carbon to the system and the drip-water-associated bacterial community contains several potentially aromatic hydrocarbon-degrading bacteria. To the best of our knowledge, this is the first work to present compelling evidence for the presence of aromatic hydrocarbon-degrading bacteria in cave drip water.

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