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School of Civil and Environmental Engineering
Ph.D. Thesis Defense Announcement
Multiomic approaches for assessing the role of natural microbial communities in nitrous oxide emission from Midwestern agricultural soils
By
Luis H Orellana
Advisor:
Dr. Kostas Konstantinidis (CEE)
Committee Members:
Dr. Jim Spain (CEE), Dr. Spyros Pavlostathis (CEE), Dr. Joe Brown (CEE), Dr. Joel Kostka (Biological Sciences), and
Dr. Frank Löffler (U of Tennessee).
Date & Time: Friday, April 28th, 2017, 1:00 pm
Location: Ford ES&T Building, Room L1125
Anthropogenic activities such as fossil fuel consumption and industrial nitrogen (N) fixation processes have increased
the N inputs into the environment. Even though the central role of microbes in N cycling is recognized, the identification and
diversity of these microbes and their pathways in agricultural soils are still lacking. This scarcity of information limits the
development of more accurate, predictive models of N-flux including the role of microbes in the generation and consumption
of important nitrogenous greenhouse gases (e.g., nitrous oxide, N2O). The advent of new high-throughput nucleic acid sequencing
technologies allows nowadays the exploration of soil microbial communities that were previously insufficiently studied
based on cultivation and PCR approaches.
In this work, we integrated experimental data and bioinformatic approaches to identify and quantify indigenous soil
microorganisms participating in N cycling in two distinct soils that typify the Midwest cornbelt. We developed a new bioinformatic
approach, called ROCker, to accurately detect target genes and transcripts in complex short-read metagenomes and metatranscriptomes,
which offered up to 60-fold lower false discovery rate compared to the common strategy of using e-value
thresholds. Using ROCker, we found an unexpectedly high abundance of nitrous oxide reductase genes, the only known biological
sink of N2O, in soil and aquatic environments. Further, we show that microbial communities are remarkably stable across
the year in typical agricultural soils compared to other environments except during nitrogen fertilization events, which stimulate
the activity of novel nitrogen-utilizing Nitrospirae and Thaumarchaeota taxa. Lastly, we assessed the power of omic
techniques to predict microbial in-situ activity rates and found high correlations between target gene transcripts and experimentally
measured nitrification activity in soil mesocosms. These findings advance the molecular toolbox for studying complex
microbial communities and have implications for better understanding and modeling the dynamics of the keystone microbial
species that control the N cycle in soils.
