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

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.

Soil Bacteria, 16S Gene, Illumina Gene Sequencing

APA Style

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

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

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

Copyright © 2023 Authors retain the copyright of this article.
This article is an open access article distributed under the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

1. Lladó S., López-Mondéjar R., and Baldrian P. 2017. Forest Soil Bacteria: Diversity, Involvement in Ecosystem Processes, and Response to Global Change. Microbiol. Mol Biol Rev. 16.
2. Delgado-Baquerizo M., Oliverio A. M., Brewer T. K., Benavent-Gonzalies A., Eldridge D. J., Bardgett R. D., Maestre F. T, Singh B. K., Fierer, N. 2018. A global atlas of the dominant bacteria found in soil, Science. 320-325.
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.
5. Mendes, R, Garbeya P., and Raaijmakers J. M. 2013. The rhizosphere microbiome; significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol. Rev. 37: 634-663.
6. Heijden M. G. A., Bardgett R. D., and Van Staale N. M. 2008. The unseen majority of soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecol. Lett. 112: 296-310.
7. Yu Z., Lu C., Hennessy D. A., Feng H., and Tian H. 2020. Impacts of tillage practices on soil carbon stocks in the US corn – soybean cropping system during 1998 to 2016. Environmental Research Letters. 15.
8. Bardgett R. D. and van der Putten W. H.. 2014. Belowground diversity and ecosystem functioning. Nature. 27; 515.
9. Land M, Hauser L., Jun S., Nookaew I., Leuze M. R., Ahn T., Karpinets T., Lund O., Kora G., Wassenaar T, Poudel S., and Ussery D. W. 2015. Insights from 20 years of bacterial genome sequencing. 15 (2): 141-61.
10. Smit E., Leeflang P., Glandorf B., Elsas J., Werners K.. 1999. Analysisi of fungal diversity in the wheat rizophere by sequencing of cloned PCR-amplified genes encoding 18S rRNA and temperature gradient gel electrophoresis. Applied and Environmental Microbiology. 65: 2614-2621.
11. Weisburg W. G., Barns S. M., Pelletier D. A., and Lane D. J. 1991. 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 173 (2): 697-703.
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/).
15. Bolyen E., Rideout J. R. Dillon M. R. Bokulich N. A. Abnet C, and Al-Ghalith G. A. 2018. Reproducible interactive, scalable, and extensible microbiome data science. Nature Biotechnology. 37: 852–857.
16. NCBI-BLAST (www.ncbi.nlm.nih.gov).
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.