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.
Highlights
Microbial diversity is central to soil ecosystem functioning and the ecosystem services soils deliver, as microbial communities are involved in many biogeochemical processes and their various interactions may affect these activities [1,2,3]
Rarefaction curves indicated that the sequencing effort was sufficient to describe bacterial diversity in Van_PC and Grande Muraille Verte (GMV) soils while in Van_PS and La Dombes (LD), some samples do not appear to have reached an asymptote (Supplementary Figure 1)
There was a clear separation among the soils, the LD soil being related to coarse silt (Csi), K and assimilable P, the GMV soil related to coarse sand, the Van_PC soil to high
Summary
Microbial diversity is central to soil ecosystem functioning and the ecosystem services soils deliver, as microbial communities are involved in many biogeochemical processes and their various interactions may affect these activities [1,2,3]. Despite a growing number of surveys interested in rare and core microbial communities, only a few recent studies have targeted bacterial spatial distributions, in a range of different ecosystems, such as water, guts, soil or even the surface of stone [5,6,7,8,9]. These studies have highlighted the fact the “rare biosphere” is constituted of a myriad of species. Hugoni et al (2013) reported that the rare archaeal biosphere in the ocean should not solely be characterized as a seed bank of dormant cells; rather, it is a complex association of indigenous and itinerant cell types of different origins and with different fates that might contribute to microbial interaction networks and metabolic processes in the environment
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