Bacterial Community Structure at the Microscale in Two Different Soils

Abstract

The spatial distributions of bacteria in the soil matrix have a role in ecosystem function, for example, at the small scale, through gene transfer or xenobiotic degradation. Soil bacterial biogeography has been evidenced at the large scale, but data are scarce at the small scale. The objective of this work was to determine the spatial pattern of bacterial diversity, in spatially referenced microsamples, in order to define bacterial community spatial traits. Two soils with different physical structures, moderately aggregated (La Côte St André (LCSA)) or poorly aggregated (La Dombes (LD)), were studied. The spatial distribution of bacteria was studied in microsamples (diameter 3 mm) along 10- and 20-cm transects, with a taxonomic microarray. 16S rRNA gene sequencing was used to further study the spatial characteristics of the microbial communities in LD soil. The frequency-occupancy plot, in the LCSA and LD soils, using microarray and sequencing data, followed Hanski’s core-satellite theory. The frequency-occupancy distribution plots obtained in two different soils showed bimodality and indicated that the microscale spatial distributions were different, particularly core taxa percentage. Core taxa are widespread and abundant, while satellite taxa are restricted in their distribution. The spread of satellite taxa was at a distance range larger than 5 cm, whereas the core taxa were distributed in a distance range less than 3 mm. Besides, there was a positive abundancy-occupancy relationship at this fine scale. It may be interesting to further evaluate the role of the different bacterial spatial distributions at the fine scale on soil function.

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Acknowledgments

For their involvement with sample processing, we thank Florent Gaudel and Jacqueline Haurat. Audrey Dubost helped with data processing. We thank Naoise Nunan for his valuable comments and suggestions on the manuscript.

This work was supported by the Specific Internal Program of the UMR 5557 Ecologie Microbienne.

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Correspondence to Genevieve L. Grundmann.

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Table S1

LCSA and LD soils physico-chemical characteristics. (XLSX 11 kb)

Table S2

Core and satellite taxa found in LD soil with 16S rDNA gene pyrosequencing and in LCSA and LD soil with microarray analysis. (DOC 319 kb)

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Michelland, R., Thioulouse, J., Kyselková, M. et al. Bacterial Community Structure at the Microscale in Two Different Soils. Microb Ecol 72, 717–724 (2016). https://doi.org/10.1007/s00248-016-0810-0

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Keywords

  • Abundancy-occupancy relationship
  • Bacteria community structure
  • Microscale in soil
  • Frequency-occupancy relationship
  • Soil microbial diversity
  • Soil structure