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A Geostatistical Approach to Visualize the Diversity of Soil Inhabiting Bacteria and Edaphic Qualities in Potato (Solanum tuberosum) Production Systems

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Abstract

A study was conducted in Michigan (MI) to assess spatial patterns of soil biological and physiochemical factors related to yield in potato production. The project developed an approach to integrate techniques including: high-throughput DNA sequencing; GIS; geostatistics; traditional soil analyses; and yield data. Twenty soil samples were taken and GPS marked in the fall of 2012 from a grower’s field scheduled to be in potato production, and total genomic DNA was extracted. Parallel sequencing targeting the 16S rRNA gene was used to assess bacterial diversity. The total number of taxa identified by sequence analysis was 21, 81, 140, 300 and 814 at the level of phyla, class, order, family and genus respectively. Sequencing results and information gathered on yield at each point was used to generate multi-layer GIS-based maps.

Resumen

Se condujo un estudio en Michigan (MI) para evaluar los patrones espaciales de factores biológicos y fisioquímicos del suelo relacionados al rendimiento en la producción de papa. El proyecto desarrolló un planteamiento para integrar técnicas, incluyendo: secuenciación de ADN de alto rendimiento; GIS, geoestadística, análisis tradicional de suelo; y datos de rendimiento. Se tomaron 20 muestras y se marcaron con GPS en otoño de 2012 en un campo de un productor programado para ser de producción de papa, y se extrajo el ADN total genómico. Se usó secuenciación paralela del gen 16S del ARNr para evaluar la diversidad bacteriana. El número total de taxa identificado por el análisis de secuencia fue 21, 81, 140, 300 y 814 al nivel de phyla, clase, orden, familia y género respectivamente. Los resultados de la secuenciación y la información recopilada en rendimiento en cada punto, se usaron para generar mapas de multicapas basados en GIS.

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Acknowledgments

This work was supported by the Michigan Potato Industry Commission though the USDA NIFA Specialty Crop Block Grant Program (Grant #791 N1300). Additional funding and resources were provided by the Michigan Potato Industry Commission and the Michigan State University Project GREEEN (Generating Research and Extension to Meet Economic and Environmental Needs).

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Authors and Affiliations

  1. Department of Plant, Soil and Microbial Sciences, Michigan State University, 612 Wilson Road, 35 Plant Biology Building, East Lansing, MI, 48824, USA

    N. Rosenzweig, L. Steere, B. Gerondale & W. W. Kirk

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  1. N. Rosenzweig
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  2. L. Steere
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  3. B. Gerondale
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Correspondence to N. Rosenzweig.

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The experiments comply with the current laws of the United States of America.

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N. Rosenzweig and L. Steere contributed equally.

Electronic Supplementary Material

Fig. S1

Soil types obtained through the Soil Survey Geographic database (SSURGO) made available from the Natural Resources Conservation Service (http://www.nrcs.usda.gov) and sampling points (n = 20) of study area. (DOC 301 kb)

Fig. S2

Principle component analysis summarizing relationships between abiotic and biotic soil parameters. (DOC 261 kb)

Fig. S3

Two contour maps generated from the sample points (n = 10) where yield was measured to predict yield values at any non-sampled point in the field using the Inverse Distance Weighting (IDW) method of interpolation (A) and the ordinary Kriging (B) method of interpolation. (DOC 55620 kb)

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Rosenzweig, N., Steere, L., Gerondale, B. et al. A Geostatistical Approach to Visualize the Diversity of Soil Inhabiting Bacteria and Edaphic Qualities in Potato (Solanum tuberosum) Production Systems. Am. J. Potato Res. 93, 518–532 (2016). https://doi.org/10.1007/s12230-016-9530-8

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