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Predictive Functional Profiling of Soil Microbes under Different Tillages and Crop Rotations in Ohio

Hariharan, Janani
http://orcid.org/0000-0002-5535-4119
http://rave.ohiolink.edu/etdc/view?acc_num=osu1435856176

Abstract Details

2015, Master of Science, Ohio State University, Environmental Science.
Food production and security is dependent on maintaining soil health and quality. Thus, the emphasis on sustainable and healthy soil function is a top priority for scientists and land managers. One of the most important factors that influences soil function is the microbial community. Recent advances have allowed us to quantify more accurately the composition of such communities, but there is still a knowledge gap with regard to the contribution of microorganisms to various processes occurring in the soil. Understanding this will facilitate the development of healthier agroecosystems. In this thesis, a predictive functional approach is used to elucidate bacterial species–function relationships. Bacterial community profiles were compared across two tillage systems and two crop rotations in Northern Ohio (Wooster and Hoytville). 16S rRNA gene-targeted sequencing was performed and the raw data obtained were filtered, denoised and processed using QIIME. Open-reference OTU picking and taxonomic assignment was performed using the Greengenes database. I then used a computational approach called PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) to predict metagenomes and the most likely functions performed by individual species of bacteria. Sequence analysis reveals a large number of unidentified OTUs, which is consistent with our expectations of the soil ecosystem. Comparison of sequencing data from different platforms indicates that the dataset generated using Illumina sequencing provided better hits with the reference database than pyrosequencing, and was associated with a greater number of putative soil bacterial functions. PICRUSt allows an estimation of the level of involvement each OTU has with a specific gene function, which enables comparisons to be made across bacterial species and treatment conditions. Predicted functions of the bacterial community revealed a large number of proteins connected with metabolism and maintenance of natural organic molecules in soil as well as enzymes related to degradation of xenobiotics. Using this approach, I was also able to map specific OTUs to their functional potential. Bacterial enzymes implicated in the cycling of nitrogen, sulfur, carbon and methane through the soil were examined, as were enzymes that catalyzed the oxidative degradation of hydrocarbon compounds that are considered soil pollutants. Specialized groups of bacteria were linked to functions like nitrogen fixation and degradation of compounds like atrazine and chlorohydrocarbons. A broader range of OTUs was found to contain genes for carbon utilization and sulfur metabolism. These predictions are supported by previous ecological studies. There were other OTU-function relationships predicted in these studies that are novel and could be valuable in identifying commercially important microorganisms. These leads will require experimental validation. A clear difference was seen between the no-till and plow-till treatments, with no-till being functionally enriched for most major nutrient cycles. No such differences were observed between the different crop rotations. Proteobacteria, Actinobacteria and Acidobacteria were some of the most abundant phyla found in these soil samples, along with Nitrospirae, and Bacteroidetes. I concluded that long-term and continuous application of different tillage systems, and to a lesser extent crop rotation, result in unique bacterial communities that affect the overall functioning of the soil.
Warren Dick (Advisor)
Parwinder Grewal (Advisor)
Margaret Staton (Committee Member)
188 p.
Agriculture; Biogeochemistry; Bioinformatics; Ecology; Environmental Science; Microbiology; Soil Sciences
PICRUSt; soil metagenomics; soil bacteria; soil function; nutrient cycling

Recommended Citations

Citations

  • Hariharan, J. (2015). Predictive Functional Profiling of Soil Microbes under Different Tillages and Crop Rotations in Ohio [Master's thesis, Ohio State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=osu1435856176

    APA Style (7th edition)

  • Hariharan, Janani. Predictive Functional Profiling of Soil Microbes under Different Tillages and Crop Rotations in Ohio. 2015. Ohio State University, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=osu1435856176.

    MLA Style (8th edition)

  • Hariharan, Janani. "Predictive Functional Profiling of Soil Microbes under Different Tillages and Crop Rotations in Ohio." Master's thesis, Ohio State University, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=osu1435856176

    Chicago Manual of Style (17th edition)

osu1435856176
968
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This open access ETD is published by The Ohio State University and OhioLINK.