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Comparative Genomic and Molecular Characteristics of Bacteria in Frostburg, Maryland Soil

Received: 7 September 2023     Accepted: 26 September 2023     Published: 14 October 2023
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Abstract

The microorganisms within the soil hold an essential role in the global cycling of elements and nutrient content available to support ecosystems. The biological fertility of soil is a highly complex and dynamic component of soil productivity and is the least well-understood component of soil functions. The main objective of this research was to identify bacterial communities in Frostburg soil and conduct further studies to understand their benefits for the ecosystems they live in. Twenty soil samples were collected from mature forests, grass lawns, forest swamps, meadows, and shrub swamps. The soil samples were homogenized, and two replicates were transported to the microbiology laboratory at Frostburg State University, Maryland for identification. The element composition of soil samples was detected by using the XRF and nitrate levels were measured with a nitrate ion selective electrode. DNA extraction from bacteria was performed using earth microbiome 16S Illumina sequencing protocol. The purity of the DNA was measured using nanodrop and gel electrophoresis. The average percentage of Fe in all the samples is over 57%, and Cr, K, S, and Ca are the other elements most abundant in the soil samples. Whereas nitrate levels in mature forest, grass lawn, forest swamp, meadow, and shrub swamp were 87, 121, 48, 127, and 88ppm, respectively. Nanodrop reading of A260/A280 were in the range of 1.85-1.87, and gel electrophoresis results had only one band per sample around 350bp. Bacteria were identified using the NCBI-BLAST tool and Metagenomics. The alpha and beta diversities were conducted using Qiime 2 with p<0.05. According to the BLAST analysis, many more uncultured bacteria were detected in the soil samples collected from the forest and grass lawn than in wetlands. The most common bacterial genera found in all samples were Shingomonas, Acidobacteria, Chloroflexi, and Bradyrhizobium, which are benefited in many ways including bioremediation, biodegradation, and nitrogen fixation. The Shannon-Wiener Index curve plot indicated sufficient sequencing depth to characterize microbial diversity. The comparison of genomics and molecule characteristics of bacteria in Frostburg, Maryland soil provided baseline data for further studies in relation to understanding the benefits of microbial growth, including the growth of plants.

Published in International Journal of Microbiology and Biotechnology (Volume 8, Issue 3)
DOI 10.11648/j.ijmb.20230803.13
Page(s) 62-68
Creative Commons

This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.

Copyright

Copyright © The Author(s), 2023. Published by Science Publishing Group

Keywords

Soil Bacteria, 16S Gene, Illumina Gene Sequencing

References
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[3] Kennedy A. C. and Stubbs T. L. 2006. Soil Microbial Communities as indicators of soil health. Annals. of Arid Zone. 45 (3) 287-308.
[4] Verbon, E. H. and Liberman, L. M. 2016. Beneficial microbes affect endogenous mechanisms controlling root development. Trends Plant Sci. 21: 218-229.
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[12] Flowers M., Weisz R, and White J. G. 2005. Yield-based management zones and grid sampling strategies: Describing soil test and nutrient variability. Agronomy J. 97 (3): 968-982.
[13] Soil Testing Procedures for the Northeastern United States, 2011.
[14] Earth microbiome project (https://earthmicrobiome.org/).
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[17] Xu C. Donald J. Byambajav E., and Ohtsuka, Y. 2010. Recent advances in catalysts for hot-gas removal of tar and NH3 from biomass gasification. Fuel. 89, 1784–1795.
[18] Ahmad T., Awan I., A., Nisar, J., and Ahmad I. 2009. Influence of inherent minerals and pyrolysis temperature on the yield of pyrolysates of some Pakistani coals. Energy Convers. Manage. 50: 1163–1171.
[19] Alexander M. 1977. Introduction to Soil Microbiology.
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    Kumudini Apsara Munasinghe, Caley Donaldson, Bisrat Demissie, Andry Cantarero, Phillip Paul Allen. (2023). Comparative Genomic and Molecular Characteristics of Bacteria in Frostburg, Maryland Soil. International Journal of Microbiology and Biotechnology, 8(3), 62-68. https://doi.org/10.11648/j.ijmb.20230803.13

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    ACS Style

    Kumudini Apsara Munasinghe; Caley Donaldson; Bisrat Demissie; Andry Cantarero; Phillip Paul Allen. Comparative Genomic and Molecular Characteristics of Bacteria in Frostburg, Maryland Soil. Int. J. Microbiol. Biotechnol. 2023, 8(3), 62-68. doi: 10.11648/j.ijmb.20230803.13

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    AMA Style

    Kumudini Apsara Munasinghe, Caley Donaldson, Bisrat Demissie, Andry Cantarero, Phillip Paul Allen. Comparative Genomic and Molecular Characteristics of Bacteria in Frostburg, Maryland Soil. Int J Microbiol Biotechnol. 2023;8(3):62-68. doi: 10.11648/j.ijmb.20230803.13

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  • @article{10.11648/j.ijmb.20230803.13,
      author = {Kumudini Apsara Munasinghe and Caley Donaldson and Bisrat Demissie and Andry Cantarero and Phillip Paul Allen},
      title = {Comparative Genomic and Molecular Characteristics of Bacteria in Frostburg, Maryland Soil},
      journal = {International Journal of Microbiology and Biotechnology},
      volume = {8},
      number = {3},
      pages = {62-68},
      doi = {10.11648/j.ijmb.20230803.13},
      url = {https://doi.org/10.11648/j.ijmb.20230803.13},
      eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ijmb.20230803.13},
      abstract = {The microorganisms within the soil hold an essential role in the global cycling of elements and nutrient content available to support ecosystems. The biological fertility of soil is a highly complex and dynamic component of soil productivity and is the least well-understood component of soil functions. The main objective of this research was to identify bacterial communities in Frostburg soil and conduct further studies to understand their benefits for the ecosystems they live in. Twenty soil samples were collected from mature forests, grass lawns, forest swamps, meadows, and shrub swamps. The soil samples were homogenized, and two replicates were transported to the microbiology laboratory at Frostburg State University, Maryland for identification. The element composition of soil samples was detected by using the XRF and nitrate levels were measured with a nitrate ion selective electrode. DNA extraction from bacteria was performed using earth microbiome 16S Illumina sequencing protocol. The purity of the DNA was measured using nanodrop and gel electrophoresis. The average percentage of Fe in all the samples is over 57%, and Cr, K, S, and Ca are the other elements most abundant in the soil samples. Whereas nitrate levels in mature forest, grass lawn, forest swamp, meadow, and shrub swamp were 87, 121, 48, 127, and 88ppm, respectively. Nanodrop reading of A260/A280 were in the range of 1.85-1.87, and gel electrophoresis results had only one band per sample around 350bp. Bacteria were identified using the NCBI-BLAST tool and Metagenomics. The alpha and beta diversities were conducted using Qiime 2 with pShingomonas, Acidobacteria, Chloroflexi, and Bradyrhizobium, which are benefited in many ways including bioremediation, biodegradation, and nitrogen fixation. The Shannon-Wiener Index curve plot indicated sufficient sequencing depth to characterize microbial diversity. The comparison of genomics and molecule characteristics of bacteria in Frostburg, Maryland soil provided baseline data for further studies in relation to understanding the benefits of microbial growth, including the growth of plants.},
     year = {2023}
    }
    

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  • TY  - JOUR
    T1  - Comparative Genomic and Molecular Characteristics of Bacteria in Frostburg, Maryland Soil
    AU  - Kumudini Apsara Munasinghe
    AU  - Caley Donaldson
    AU  - Bisrat Demissie
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    JF  - International Journal of Microbiology and Biotechnology
    JO  - International Journal of Microbiology and Biotechnology
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    AB  - The microorganisms within the soil hold an essential role in the global cycling of elements and nutrient content available to support ecosystems. The biological fertility of soil is a highly complex and dynamic component of soil productivity and is the least well-understood component of soil functions. The main objective of this research was to identify bacterial communities in Frostburg soil and conduct further studies to understand their benefits for the ecosystems they live in. Twenty soil samples were collected from mature forests, grass lawns, forest swamps, meadows, and shrub swamps. The soil samples were homogenized, and two replicates were transported to the microbiology laboratory at Frostburg State University, Maryland for identification. The element composition of soil samples was detected by using the XRF and nitrate levels were measured with a nitrate ion selective electrode. DNA extraction from bacteria was performed using earth microbiome 16S Illumina sequencing protocol. The purity of the DNA was measured using nanodrop and gel electrophoresis. The average percentage of Fe in all the samples is over 57%, and Cr, K, S, and Ca are the other elements most abundant in the soil samples. Whereas nitrate levels in mature forest, grass lawn, forest swamp, meadow, and shrub swamp were 87, 121, 48, 127, and 88ppm, respectively. Nanodrop reading of A260/A280 were in the range of 1.85-1.87, and gel electrophoresis results had only one band per sample around 350bp. Bacteria were identified using the NCBI-BLAST tool and Metagenomics. The alpha and beta diversities were conducted using Qiime 2 with pShingomonas, Acidobacteria, Chloroflexi, and Bradyrhizobium, which are benefited in many ways including bioremediation, biodegradation, and nitrogen fixation. The Shannon-Wiener Index curve plot indicated sufficient sequencing depth to characterize microbial diversity. The comparison of genomics and molecule characteristics of bacteria in Frostburg, Maryland soil provided baseline data for further studies in relation to understanding the benefits of microbial growth, including the growth of plants.
    VL  - 8
    IS  - 3
    ER  - 

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Author Information
  • Biology Departments, Frostburg State University, Frostburg, USA

  • Biology Departments, Frostburg State University, Frostburg, USA

  • Biology Departments, Frostburg State University, Frostburg, USA

  • Biology Departments, Frostburg State University, Frostburg, USA

  • Geography Departments, Frostburg State University, Frostburg, USA Email address:

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