Spatial variability of microbial richness and diversity and relationships with soil organic carbon, texture and structure across an agricultural field

Muhammad Naveed* (Corresponding Author), Lasantha Herath, Per Moldrup, Emmanuel Arthur, Mogens Nicolaisen, Trine Norgaard, Ty P. A. Ferre, Lis W. de Jonge

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

78 Citations (Scopus)


Although soil microorganisms play a pivotal role in delivering various ecosystem functions and services, we are only beginning to understand how microbial communities are shaped by various soil physical properties and environmental factors. In this study, we integrate metabarcoding of bacteria and fungi and soil physical measurements at 60 locations on a 15 x 15 m grid in an agricultural field to: (1) characterize the spatial variation of microbial richness and diversity, and (2) identify the soil physical parameters that are most strongly correlated with them. The study field is located in Silstrup Denmark, extends over 1.69 ha, and slopes 1-2 degrees to the north. Soil samples for 454-pyrosequencing were extracted by pushing 50-mL sterilized plastic vials into the soil. Bulk soil samples were used for the measurement of pH, organic carbon, and soil texture. Intact 100 cm(3) soil cores, collected in triplicate, were used for measuring the soil water characteristic curve. Across the field, bacterial richness (number of OTUs) and diversity indices (Shannon diversity and phylogenetic diversity) showed strong spatial autocorrelations. Fungal number of OTUs was quite similar over the field and thus no spatial autocorrelation was observed for them. Fungal Shannon diversity slightly increased from south to north, with spatial autocorrelation for distances larger than 100 m. The ratio of clay to organic carbon (n) was found to be the best predictor of bacterial richness and diversity indices. Neither organic carbon nor clay content was significantly correlated with fungal richness and diversity indices. For soil structural parameters, soil water retention in the pF range 5-6.8 (parameter B) was significantly correlated with both bacterial and fungal Shannon diversities. Amount of macropores (> 30 mu m) and total porosity (phi) were only significantly correlated with fungal Shannon diversity. These results suggest that variation in microbial communities is not random but strongly related with variations in organic carbon, clay content, and soil water characteristics at the field scale. (C) 2016 Elsevier B.V. All rights reserved.

Original languageEnglish
Pages (from-to)44-55
Number of pages12
JournalApplied Soil Ecology
Early online date14 Mar 2016
Publication statusPublished - Jul 2016

Bibliographical note

The technical assistance of Stig T. Rasmussen, Bodil B. Christensen, Michael Koppelgaard, and Jane H. Hansen are greatfully acknowledged. The study was part of the Soil Infrastructure, Interfaces, and Translocation Processes in Inner Space (Soil-it-is) project, which is funded by the Danish Research Council for Technology and Production Sciences


  • Bacterial diversity
  • Fungal diversity
  • Soil texture
  • Ratio of clay to organic carbon
  • Soil water characteristics


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