Spatial scaling and determinism of the wide-scale distribution of macroorganism diversity has been largely demonstrated over a century. For microorganisms, and especially for soil bacteria, this fundamental question requires more thorough investigation, as little information has been reported to date. Here by applying the taxa-area relationship to the largest spatially explicit soil sampling available in France (2,085 soils, area covered B5.3 Â 10 5 km 2 ) and developing an innovative evaluation of the habitat-area relationship, we show that the turnover rate of bacterial diversity in soils on a wide scale is highly significant and strongly correlated with the turnover rate of soil habitat. As the diversity of micro-and macroorganisms appears to be driven by similar processes (dispersal and selection), maintaining diverse and spatially structured habitats is essential for soil biological patrimony and the resulting ecosystem services.
Aim The spatial organization of soil microbial communities on large scales and the identification of environmental factors structuring their distribution have been little investigated. The overall objective of this study was to determine the spatial patterning of microbial biomass in soils over a wide extent and to rank the environmental filters most influencing this distribution.Location French territory using the French Soil Quality Monitoring Network. This network covers the entire French territory and soils were sampled at 2150 sites along a systematic grid.
MethodsThe soil DNA extracted from all these soils was expressed in terms of soil molecular microbial biomass and related to other soil and land-use data over French territory.
ResultsThis study provides the first extensive map of microbial biomass and reveals the heterogeneous and spatially structured distribution of this biomass on the scale of France. The main factors driving biomass distribution are the physicochemical properties of the soil (texture, pH and total organic carbon) as well as land use. Soils from land used for intensive agriculture, especially monoculture and vineyards, exhibited the smallest biomass pools. Interestingly, factors known to influence the large-scale distribution of macroorganisms, such as climatic factors, were not identified as important drivers for microbial communities.Main conclusions Microbial abundance is spatially structured and dependent on local filters such as soil characteristics and land use but is relatively independent of global filters such as climatic factors or the presence of natural barriers. Our study confirms that the biogeography of microorganisms differs fundamentally from the biogeography of 'macroorganisms' and that soil management can have significant large-scale effects.
SummaryThree soil DNA extraction procedures (homemade protocols and commercial kit) varying in their practicability were applied to contrasting soils to evaluate their efficiency in recovering: (i) soil DNA and (ii) bacterial diversity estimated by 16S rDNA pyrosequencing. Significant differences in DNA yield were systematically observed between tested procedures. For certain soils, 10 times more DNA was recovered with one protocol than with the others. About 15 000 sequences of 16S rDNA were obtained for each sample which were clustered to draw rarefaction curves. These curves, as well as the PCA ordination of community composition based on OTU clustering, did not reveal any significant difference between procedures. Nevertheless, significant differences between procedures were highlighted by the taxonomic identification of sequences obtained at the phylum to genus levels. Depending on the soil, differences in the number of genera detected ranged from 1% to 26% between the most and least efficient procedures, mainly due to a poorer capacity to recover populations belonging to Actinobacteria, Firmicutes or Crenarchaeota. This study enabled us to rank the relative efficiencies of protocols for their recovery of soil molecular microbial biomass and bacterial diversity and to help choosing an appropriate soil DNA extraction procedure adapted to novel sequencing technologies.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.