Brian K. Gelder

Strategies to improve reference databases for soil microbiomes

Jinlyung Choi, Fan Yang, Ramunas Stepanauskas, Erick Cardenas, Aaron Garoutte, Ryan Williams, Jared Flater, James M Tiedje, Kirsten S Hofmockel, Brian Gelder and Adina Howe Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, USA; Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA; Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada; Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA; Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA and Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA

The Daily Erosion Project – daily estimates of water runoff, soil detachment, and erosion

Water runoff and sediment transport from agricultural uplands are substantial threats to water quality and sustained crop production. To improve soil and water resources, farmers, conservationists, and policy-makers must understand how landforms, soil types, farming practices, and rainfall interact with water runoff and soil erosion processes. To that end, the Iowa Daily Erosion Project (IDEP) was designed and implemented in 2003 to inventory these factors across Iowa in the United States. IDEP utilized the Water Erosion Prediction Project (WEPP) soil erosion model along with radar-derived precipitation data and government-provided slope, soil, and management information to produce daily estimates of soil erosion and runoff at the township scale (93 km2 [36 mi2]). Improved national databases and evolving remote sensing technology now permit the derivation of slope, soil, and field-level management inputs for WEPP. These remotely sensed parameters, along with more detailed meteorological data, now drive daily WEPP hillslope soil erosion and water runoff estimates at the small watershed scale, approximately 90 km2 (35 mi2), across sections of multiple Midwest states. The revisions constitute a substantial improvement as more realistic field conditions are reflected, more detailed weather data are utilized, hill slope sampling density is an order of magnitude greater, and results are aggregated based on surface hydrology enabling further watershed research and analysis. Considering these improvements and the expansion of the project beyond Iowa it was renamed the Daily Erosion Project (DEP). Statistical and comparative evaluations of soil erosion simulations indicate that the sampling density is adequate and the results are defendable. The modeling framework developed is readily adaptable to other regions given suitable inputs.

RefSoil: A reference database of soil microbial genomes

A database of curated genomes is needed to better assess soil microbial communities and their processes associated with differing land management and environmental impacts. Interpreting soil metagenomic datasets with existing sequence databases is challenging because these datasets are biased towards medical and biotechnology research and can result in misleading annotations. We have curated a database of 922 genomes of soil-associated organisms (888 bacteria and 34 archaea). Using this database, we evaluated phyla and functions that are enriched in soils as well as those that may be underrepresented in RefSoil. Our comparison of RefSoil to soil amplicon datasets allowed us to identify targets that if cultured or sequenced would significantly increase the biodiversity represented within RefSoil. To demonstrate the opportunities to access these underrepresented targets, we employed single cell genomics in a pilot experiment to sequence 14 genomes. This effort demonstrates the value of RefSoil in the guidance of future research efforts and the capability of single cell genomics as a practical means to fill the existing genomic data gaps.