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.