Spatial and temporal variation of archaeal, bacterial and fungal communities in agricultural soils

Abstract

Background: Soil microbial communities are in constant change at many different temporal and spatial scales. However, the importance of these changes to the turnover of the soil microbial communities has been rarely studied simultaneously in space and time.

Methodology/principal findings: In this study, we explored the temporal and spatial responses of soil bacterial, archaeal and fungal β-diversities to abiotic parameters. Taking into account data from a 3-year sampling period, we analyzed the abundances and community structures of Archaea, Bacteria and Fungi along with key soil chemical parameters. We questioned how these abiotic variables influence the turnover of bacterial, archaeal and fungal communities and how they impact the long-term patterns of changes of the aforementioned soil communities. Interestingly, we found that the bacterial and fungal β-diversities are quite stable over time, whereas archaeal diversity showed significantly higher fluctuations. These fluctuations were reflected in temporal turnover caused by soil management through addition of N-fertilizers.

Conclusions: Our study showed that management practices applied to agricultural soils might not significantly affect the bacterial and fungal communities, but cause slow and long-term changes in the abundance and structure of the archaeal community. Moreover, the results suggest that, to different extents, abiotic and biotic factors determine the community assembly of archaeal, bacterial and fungal communities.

Figure 1. Changes in abundance of archaeal, bacterial and fungal communities.

The copy number in each gram of dry soil was estimated by real-time PCR in the eight agricultural soils as an average of sandy and clayey soils at different sampling times. Bars are standard errors (n = 4).

Figure 2. Total α-diversity of archaeal, bacterial and fungal communities.

Alpha diversity was calculated as the average of the Shannon Index (H′) per soil type (sandy×clayey), from April 2009 to September 2011 (mean ± s.d.).

Figure 3. Temporal β-diversity of archaeal, bacterial and fungal communities.

Temporal β-diversity, which takes into account temporal changes of each individual soil, was calculated across the different sampling points (A) and separated per soil type (B) (mean ± s.e.).

Figure 4. Quantification of archaeal, bacterial and fungal dynamics.

Patterns of change (regression of square root of time-lag on Euclidian distance) of archaeal (A, slope 1.835), bacterial (B, slope 0.785) and fungal community (C, slope 0.638) in eight soils. The best-fit line is shown.