Methanotrophic Bacterial Diversity in Ohio Soils Using High-Throughput Sequencing.

The net flux of methane into the atmosphere is dependent on feedbacks that exist between atmosphere and soil. Aerobic methanotrophic bacteria in soil oxidize methane and use it as their sole source of carbon and energy, thereby allowing soils to serve as the only know biological sink of atmospheric methane. The objective of this study was to characterize the diversity of methanotrophs in two contrasting soils in Ohio using the sequencing-by-synthesis technique. In addition to location, the effect of rotation and tillage of agricultural soils, and soils under forest and grass areas, on methanotrophic community was also studied.

 A molecular-based high-throughput sequencing technique was employed to generate millions of sequences targeting methanatrophic bacteria. A combination of four primer sets targeting whole community 16S rRNA, 16S rRNA gene region of Type I and Type II methanotrophs, and functional pmoA were used. Software packages including Mothur, QIIME (Quantitative Insights Into Microbial Ecology), and R were used to study community diversity and abundance in soils under no-till continuous corn, no-till corn-soybean, plow-till continuous-corn, plow-till corn-soybean, grass, and forest.

A variety of methanotrophic bacterial operational taxonomic units (OTUs) were identified, representing diverse genera of methanotrophs, Verrucomicrobial methanotrophs, non-methanotrophic methylotrophs, and OTUs representing Upland Soil Clusters. On an average, 2% of sequences represented methantrophs OTUs in the 16S rRNA datasets, while the pmoA dataset was compared to a reference database which classified all the sequences as methanotrophic OTUs. For most datasets, no-till soils had higher diversity than plow-till soils and community composition of both agricultural practices were distinctly different from forest and grass areas. Among the variables analyzed, location was dominant, followed by tillage and rotation. It can be concluded that even with soil disturbance, the inherent functioning of microbes in these soils is possibly more impacted by location, followed by land-use.