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 sequenc- ing 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 bioinfor- matic approach, called ROCker, to accurately detect target genes and transcripts in complex short-read metagenomes and meta- transcriptomes, 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 biolog- ical 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 stimu- late 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 experimen- tally 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.
Dr. Kostas Konstantinidis
Dr. Jim Spain, Dr. Spyros Pavlostathis, Dr. Joe Brown, Dr. Joel Kostka (Biological Sciences), and Dr. Frank Löffler (Univ. of Tennessee)