Date of Award

Spring 2018

Degree Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Center for Science and Math Education

School

Center for Science and Math Education

Committee Chair

Sherry Herron

Committee Chair Department

Center for Science and Math Education

Committee Member 2

Mac Alford

Committee Member 2 Department

Biological Sciences

Committee Member 3

Richard Mohn

Committee Member 3 Department

Educational Research and Administration

Committee Member 4

Vijay Rangachari

Committee Member 4 Department

Chemistry and Biochemistry

Committee Member 5

Sheila Hendry

Committee Member 5 Department

Biological Sciences

Abstract

Agriculture in the Midwest United States (Illinois, Indiana, Iowa, Michigan, Minnesota, Ohio, and Wisconsin) is a critically important component of the United States economy and also for world exports of food grain. This is well reflected in the 2012 Census of Agriculture which showed that these states had a market value of crop and livestock products sold in excess of $80,000,000,000 (USDA, 2012). Within the U.S. the three Midwest states, Illinois, Iowa, and Minnesota are ranked 2nd, 3rd, and 4th for the economic value of crops sold. This economic value of agriculture in the Midwest encompasses not only corn, soybeans, livestock, vegetables, fruits, tree nuts, and berries but also nursery and many greenhouse plants. Soil is the one common underlying platform for agriculture and if agriculture has to remain profitable and sustainable, a scientific understanding of soils and their relationship to plant productivity is critical.

Soils harbor probably the most diverse microbial ecosystems on Earth (Delmont et al., 2011) and we are just beginning to understand the full extent of this diversity and how it influences agricultural productivity and how in turn agricultural practices influence the microbial diversity. Estimations indicate that approximately 1,000 Giga base pairs (Gbp) of microbial genomic sequences exist per gram of soil (Vogel et al., 2009). Microorganisms occupy almost every available niche on Earth and directly affect the environment and agricultural systems by a range of mechanisms that include biological nitrogen fixation (Hungria, Franchini, Campo, & Graham, 2005), suppression of diseases (Mendes et al., 2011), decomposition of organic components (Schmidt et al., 2011), plant growth promotion (Bhattacharya & Jha, 2012), soil nutrient cycling (Brussard, 2012) and bioremediation (Ali et al., 2012). Soil microbial community structure and its associated and interdependent biological processes can be affected by the way land is used and managed. Since a vast majority of soil microorganisms do not respond to "traditional" culturing techniques (Delmont et al., 2011), it has been difficult to study and characterize the functional and phylogenetic diversity of these important ecosystems until recent advances in next-generation DNA sequencing which have begun to unravel what is beneath our feet (Caporaso et al., 2010). According to Food and Agricultural Organization (FAO), the amount of land used for agriculture is about 11% (http://www.fao.org/docrep/005/y4252e/y4252e06.htm) and the emissions which can have serious environmental and health effects from agricultural food production far outweigh the total emissions from all the other industries combined (Bauer, Tsigardis, & Miller, 2016). Thus, any steps to fine-tune the management practices and the way the agricultural land is utilized can go a long way in sustaining our way of life while maintaining a healthy environment.

The purpose of this study is to examine the shifts in the taxonomic diversity of bacteria in soils at phylum, class and order level between two distinct agricultural practices – Conventional Tillage (CT) and Conservation Tillage (NT) in Southern Illinois along with changes in soil compaction and soil phosphatase activity. The larger idea, based on results reported here and elsewhere, is to encourage conservative tillage practices using a combination of diverse cover crop systems and continuous soil cover which seem to enhance functional microbial diversity in the soil (Ajay & Ngouajio, 2012; Verzeaux et al., 2016). Research also indicates the presence of higher numbers of bacteria of varied trophic groups, as well as increased species richness in bacteria in well-managed soils with minimal tilling and this, may correspond to more resilience to drying and rewetting disturbances in the soil (Anne et al., 2006).

This research may be the first to reconstruct the entire soil bacterial community in agricultural fields of Southern Illinois and will also hopefully be a precursor for more studies aimed at not only understanding soil from a biological bacterial perspective but also in deciphering interesting patterns that can help correlate changes in land management practices and how they impact bacterial communities. It may help us in developing a methodology to use bacterial taxa as indicators of soil management practices. The study will also detect previously unreported rare bacterial taxa-specific for this region and regional geochemistry.

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