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Draft Genome Sequence of a Novel Bacterium, Pseudomonas sp. Strain MR 02, Capable of Pyomelanin Production, Isolated from the Mahananda River at Siliguri, West Bengal, India.

ABSTRACT: The draft genome sequence of a novel strain, Pseudomonas sp. MR 02, a pyomelanin-producing bacterium isolated from the Mahananda River at Siliguri, West Bengal, India, is reported here. This strain has a genome size of 5.94 Mb, with an overall G+C content of 62.6%. The draft genome reports 5,799 genes (mean gene length, 923 bp), among which 5,503 are protein-coding genes, including the genes required for the catabolism of tyrosine or phenylalanine for the characteristic production of homogentisic acid (HGA). Excess HGA, on excretion, auto-oxidizes and polymerizes to form pyomelanin.

SUBMITTER: Ranjan VK

PROVIDER: S-EPMC5773723 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature

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Draft Genome Sequence of a Novel Bacterium, <i>Pseudomonas</i> sp. Strain MR 02, Capable of Pyomelanin Production, Isolated from the Mahananda River at Siliguri, West Bengal, India.

Ranjan Vivek Kumar VK Saha Tilak T Mukherjee Shriparna S Chakraborty Ranadhir R

Genome announcements 20180118 3

The draft genome sequence of a novel strain, <i>Pseudomonas</i> sp. MR 02, a pyomelanin-producing bacterium isolated from the Mahananda River at Siliguri, West Bengal, India, is reported here. This strain has a genome size of 5.94 Mb, with an overall G+C content of 62.6%. The draft genome reports 5,799 genes (mean gene length, 923 bp), among which 5,503 are protein-coding genes, including the genes required for the catabolism of tyrosine or phenylalanine for the characteristic production of homo ...[more]

PMID: 29348338

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Project description:BackgroundIn this study a large random collection (n=2188) of facultative oligotrophic bacteria, from 90 water samples gathered in three consecutive years (2007-2009) from three different sampling sites of River Mahananda in Siliguri, West Bengal, India, were investigated for the presence of class 1 integrons and sequences of the amplification products.Methodology/principal findingsReplica plating method was employed for determining the antibiotic resistance profile of the randomly assorted facultative oligotrophic isolates. Genomic DNA from each isolate was analyzed by PCR for the presence of class 1 integron. Amplicons were cloned and sequenced. Numerical taxonomy and 16S rRNA gene sequence analyses were done to ascertain putative genera of the class 1 integron bearing isolates. Out of 2188 isolates, 1667 (76.19%) were antibiotic-resistant comprising of both single-antibiotic resistance (SAR) and multiple-antibiotic resistant (MAR), and 521 (23.81%) were sensitive to all twelve different antibiotics used in this study. Ninety out of 2188 isolates produced amplicon(s) of varying sizes from 0.15 to 3.45 KB. Chi-square (χ(2)) test revealed that the possession of class 1 integron in sensitive, SAR and MAR is not equally probable at the 1% level of significance. Diverse antibiotic-resistance gene cassettes, aadA1, aadA2, aadA4, aadA5, dfrA1, dfrA5, dfrA7, dfrA12, dfrA16, dfrA17, dfrA28, dfrA30, dfr-IIe, blaIMP-9, aacA4, Ac-6'-Ib, oxa1, oxa10 and arr2 were detected in 64 isolates. The novel cassettes encoding proteins unrelated to any known antibiotic resistance gene function were identified in 26 isolates. Antibiotic-sensitive isolates have a greater propensity to carry gene cassettes unrelated to known antibiotic-resistance genes. The integron-positive isolates under the class Betaproteobacteria comprised of only two genera, Comamonas and Acidovorax of family Comamonadaceae, while isolates under class Gammaproteobacteria fell under the families, Moraxellaceae, Pseudomonadaceae, Aeromonadaceae and Enterobacteriaceae.ConclusionsOligotrophic bacteria are good sources of novel genes as well as potential reservoirs of antibiotic resistance gene casettes.

Project description:Hybrid rice requires adequate nitrogen (N) management in order to achieve good yields from its vegetative and reproductive development. With this backdrop, a field experiment was conducted at Regional Research Station (Coastal Saline Zone), Bidhan Chandra Krishi Viswavidyalaya, Kakdwip, West Bengal (India) to record growth and yield performance of hybrid rice (cv. PAN 2423) under varied N-fertilizer doses. A modelling approach was adopted for the first time in hybrid rice production system under coastal ecosystem of West Bengal (India). In the present study, the Agricultural Production Systems Simulator (APSIM) model was calibrated and validated for simulating a hybrid rice production system with different N rates. The APSIM based crop simulation model was found to capture the physiological changes of hybrid rice under varied N rates effectively. While studying the relationship between simulated and observed yield data, we observed that the equations developed by APSIM were significant with higher R2 values (≥0.812). However, APSIM caused an over-estimation for calibrate data but it was rectified for validated data. The RMSE of models for all the cases was less than respective SD values and the normalized RMSE values were ≤20%. Hence, it was proved to be a good rationalized modelling and the performance of APSIM was robust. On the contrary, APSIM underestimated the calibrated amount of N (kg ha-1) in storage organ of hybrid rice, which was later rectified in case of validated data. A strong correlation existed between the observed and APSIM-simulated amounts of N in storage organ of hybrid rice (R2 = 0.94** and 0.96** for the calibration and validation data sets, respectively), which indicates the robustness of the APSIM simulation study. Scenario analysis also suggests that the optimal N rate will increase from 160 to 200 kg N ha-1 for the greatest hybrid rice production in coming years under elevated CO2 levels in the atmosphere. The APSIM-Oryza crop model had successfully predicted the variation in aboveground biomass and grain yield of hybrid rice under different climatic conditions.

Dataset Information

Draft Genome Sequence of a Novel Bacterium, Pseudomonas sp. Strain MR 02, Capable of Pyomelanin Production, Isolated from the Mahananda River at Siliguri, West Bengal, India.

Publications

Draft Genome Sequence of a Novel Bacterium, <i>Pseudomonas</i> sp. Strain MR 02, Capable of Pyomelanin Production, Isolated from the Mahananda River at Siliguri, West Bengal, India.

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