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Small-Scale Variability in Bacterial Community Structure in Different Soil Types

  • Soil Microbiology
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Abstract

Microbial spatial distribution has mostly been studied at field to global scales (i.e., ecosystem scales). However, the spatial organization at small scales (i.e., centimeter to millimeter scales), which can help improve our understanding of the impacts of spatial communities structure on microbial functioning, has received comparatively little attention. Previous work has shown that small-scale spatial structure exists in soil microbial communities, but these studies have not compared soils from geographically distant locations, nor have they utilized community ecology approaches, such as the core and satellite hypothesis and/or abundance-occupancy relationships, often used in macro-ecology, to improve the description of the spatial organization of communities. In the present work, we focused on bacterial diversity (i.e., 16S rRNA gene sequencing) occurring in micro-samples from a variety of locations with different pedo-climatic histories (i.e., from semi-arid, alpine, and temperate climates) and physicochemical properties. The forms of ecological spatial relationships in bacterial communities (i.e., occupancy-frequency and abundance-occupancy) and taxa distributions (i.e., habitat generalists and specialists) were investigated. The results showed that bacterial composition differed in the four soils at the small scale. Moreover, one soil presented a satellite mode distribution, whereas the three others presented bimodal distributions. Interestingly, numerous core taxa were present in the four soils among which 8 OTUs were common to the four sites. These results confirm that analyses of the small-scale spatial distribution are necessary to understand consequent functional processes taking place in soils, affecting thus ecosystem functioning.

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Acknowledgment

We thank La Vanoise National Parc for the soil sampling authorization.

Funding

This work was co-funded by the EC2CO MicrobiEn AO2012- 779949 “Les communautés bactériennes dans les sols extrêmes: les paramètres de leur structure et leur composition” and the Labex DRIIHM, French program “Investissements d’Avenir” (ANR-11-LABX-0010) which is managed by the ANR.

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Correspondence to Mylène Hugoni.

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Supporting Information

Supplementary Figure 1.

Rarefaction curves for Van_PC, Van_PS, LD and GMV soils, using the normalized datasets (i.e. 5474 sequences). (PNG 996 kb)

High Resolution Image (TIFF 4947 kb)

Supplementary Table 1.

Physico-chemical characteristics of Van_PC, Van_PS, LD and GMV soils. The unit is g.kg-1 except for pH and C/N ratio. (XLS 23 kb)

Supplementary Table 2.

La Vanoise soil sampling: Distances between micro-samples (cores) in Van_PC and in Van _PS starting from an initial point, named 0 m. Micro-samples were taken along two transects 10 cm apart, in September 2013 and September 2014. Results obtained on all micro-samples were gathered as no difference could be shown between the two sampling dates. Micro-samples named “a” corresponded to the top 1 mm of the cores and sample “b” corresponded to the 1 to 2 mm below sample “a”. “b*”: in two cases, a second core was taken beside core “b”, at the same distance from the origin. (XLSX 9 kb)

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Hugoni, M., Nunan, N., Thioulouse, J. et al. Small-Scale Variability in Bacterial Community Structure in Different Soil Types. Microb Ecol 82, 470–483 (2021). https://doi.org/10.1007/s00248-020-01660-0

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