The influence of agricultural tillage practices on soil biodiversity: Soil metagenomic methods, arthropod community v1

Abstract

This was the first study to examine the influence of different tillage practices on soil biodiversity from all kingdoms of life. Four tillage treatments were compared with a no-till treatment maintained at the Elora Agricultural Research Station for 30 years. In terms of species or operational taxonomic unit (OTU) richness within taxonomic higher ranks, these treatments are quite similar. However, there were significant differences in the OTU richness of the Sordariomycetes (103±19 vs 86±10 OTUs; p= 3.12e-3) and the Dothideomycetes (29±6 vs 43±1 OTUs; p= 5.54e-5) fungal classes when comparing tilled and no-till soils. While all agricultural treatments were similar in terms of arthropod diversity, when compared with a nearby mature woodlot, compaction sensitive lineages of Collembola and mites were not present in the agricultural soils. These results suggest that even no-till soils are not comparable to the soil environment of an undisturbed forest. iii ACKNOWLEDGMENTS Given that this was the Hanner lab's first foray into metagenomics, soil science, microbiology and next generation sequencing, I required the help of many people within and outside of our lab. I extend thanks on a broad scale to the other graduate students of the Hanner lab with special thanks given to my two undergraduate research assistants: Jennifer Gubala and Danielle Bourque. Jenny performed many of my microbial DNA soil extractions while Danielle spent months sorting and identifying soil arthropods. I would also like to thank Jeff Gross, Jing Zhang and Angela Hollis from the Advanced Analysis Center-Genomics Facility, University of Guelph, for their information and guidance regarding my Illumina MiSeq runs. In addition, I owe a great deal of thanks to Natalia Ivanova, Sean Prosser and Shadi Shokralla from the Centre for Biodiversity Genomics, University of Guelph, for their advice regarding sequence library prep. I must thank the creators of the open source software packages that I used, for their patient and rapid responses to my email: Robert Edgar from the UPARSE package, Daniel Huson from MEGAN, Maarja Opik from MaarjAM and Donovan Parks from STAMP. Finally, I extend a great deal of thanks to my advisory committee.