The Evaluation of the PVAMU Soil Microbiome
Princess Pinamang Mentor: Quincy C. Moore Department of Biology Introduction: Soil-borne microbes mediate essential ecosystem services that sustain life, yet just 1% of the 106 distinct taxa present in 1g of soil have been cultivated under laboratory conditions (Hirsch et al., 2010). This study aims to assess the diversity and richness of soil microorganisms on the campus of Prairie View Agricultural and Mechanical University in an effort to generate a soil microbial population survey. Soil samples will be sourced from a range of campus locations; however, Gov. Bill and Vara Daniel Farm & Ranch are geared to become the primary focus. Materials and Methods: Literature used to investigate microbes and their associated molecules most abundant in soil was sourced from peer-reviewed articles and journals. The literature was cross-referenced to ensure thoroughness and garner deeper understanding. Search parameters have included rhizosphere microbiomes, agricultural soil microbiomes, metagenomic soil analysis, metatranscriptomic soil analysis, and soil microbial biogeography, as well as notable soil-associated species such as Pseudomonas, Bacillius, Arthrobacter, and Streptomyces. Journals used include Nature Communications, Science, American Chemical Society, Frontiers in Plant Science, American Society for Microbiology, eLife, Microbes, and Environment and Applied and Environmental Microbiology. Results and Discussion: A recent global analysis of soil bacteria found that a mere 2% of the 25,224 phylotypes identified accounted for nearly half of the 16S sequences around the world (Delgado-Baquerizo et al., 2018). Across global, regional, and local scale studies, Proteobacteria (specifically Alphaproteobacteria) has been pinpointed as the most abundant phylotype (Delgado-Baquerizo et al., 2018; Crovadore et al., 2017; Janssen, 2006; Okazaki et al.,2014). Gram staining the smears of our collected samples will allow a gross verification of that consensus since cell walls are a characteristic the phylum lacks. Upon transition into the 16S sequencing of our samples, we will have to consider the impact of soil pH, mineral content, heavy metal presence, irrigation source, DNA isolation kit bias, and season on diversity. Soil is often regarded as the final frontier of the biosphere since our understanding of its microbial ecology is limited, and we are not yet capable of quantifying the scale to measure what is undiscovered (Curtis and Sloan, 2005). Therefore, an important decision in this study will be whether or not to include the Eukarya and Archaea domains where there is a significant gray area. Conclusion and Summary: Conducting an extensive literature review has assisted in the creation of a strong baseline for the upcoming field collection and data analysis. Additionally, it has refined the parameters of this preliminary study and highlighted future trajectories the team can pursue. In our upcoming work, we will focus on intersite variability at the species level, which is thought to be greater than the overall intrasite variability. Further studies could include a transcriptomic or proteomic analysis, diversity across a gradient-like pH, the influence of plant growth on diversity, the influence of the soil microbiome on plant growth, and isolating new species. References: Curtis, T., Sloan, W. Exploring microbial diversity--a vast below. Science, 2005. 309(5739): p. 1331-1333. Crovadore, J., Asaff Torres, A., Rodriguez Heredia, R., Cochard, B., Chablais, R., Lefort, F. Metagenomes of soils samples from an established perennial cropping system of asparagus treated with biostimulants in southern France. American Society for Microbiology, 2017. 5 (24): e00511-17. Delgado-Baquerizo, M., Oliverio, A., Brewer, T., Benavent-Gonzalez, A., Eldridge, D., Bardgett, R., Maestre, F., Singh, B., Fierer, N. A global atlas of the dominant bacteria found in soil. Science, 2018. 359(6373): p. 320-325.
Hirsch, P., Mauchline, T. & Clark, I. Culture-independent molecular techniques for soil microbial ecology. Soil Biology and Biochemistry, 2010. 42(6): p. 878-887. Janssen, P. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microbiol, 2006. 72(3): p. 1719-1728 Page 137 of 3
