The fine-scale (spatial) organisation of the soil microbiome

Abstract

<p>Soil harbours a huge diversity of soil microbes.  One reason for this is thought to be its small-scale chemical and physical heterogeneity, which offers innumerable different parallel habitats and thus niches for the development of microbial communities. However, while microbial diversity and soil microbial composition are usually assessed using gram-sized homogenized soil samples, knowledge of how microbes are actually spatially organized at smaller scales is lacking.  This not only hampers our ability to link microbial communities to their chemical environment or to functions they may mediate, but also limits our understanding of potential scale-dependent drivers of soil organic matter turnover.</p> <p>Here, we investigated fungal and bacterial community composition together with selected biogeochemical parameters across different spatial scales in a Beech forest soil. We picked around 200 individual two mm-sized soil aggregates, i.e. small soil clumps that sticked together and could be collected with a tweezer, from fourty 35 ml-sized soil cores (i.e. 4-5 aggregates per core) in two different soil depths across a 800 m<sup>2</sup> forest area. The remaining soil cores were homogenized. We carried out amplicon sequencing of the 16S rRNA gene (for bacteria/archea) and the ITS region (for fungi) from individual soil aggregates and the homogenized soil cores, and additionally measured C, N, δ<sup>15</sup>N and δ<sup>13</sup>C from both sample types.</p> <p>Microbial community compositions of individual aggregates were highly distinct from each other, and from their composite ‘parent’ soil core, exemplifying a high spatial hetereogeneity of microbial communities at that small scale. Delta<sup>13</sup>C values were constantly higher in individual aggregates compared to their composite ‘parent’  core, indicating that they were relatively enriched in C that already underwent microbial recycling. We found a striking correlation between C concentration and δ<sup>13</sup>C values across all individual aggregates, suggesting that the aggregates remain intact long enough to allow for continued degradation and recycling, and hence <sup>13</sup>C enrichment of the encapsulated C compounds. The variations of C concentration and δ<sup>13</sup>C across individual aggregates  are partially explained by variations in community composition at this small scale.</p> <p>Overall our data shows that mm-sized soil aggregates host distinct microbial communities which may be linked to a certain recycling state of C.  This suggests that aggregates are pieces of soil that stick together for a significant amount of time, allowing them to act as functional units of soil C degradation, and possibly as ‘evolutionary incubators’, as was previously hypothesized. We conclude that investigating microbial community structure and distribution at these small scales in the soil offer a promising way forward to better understand possible links between microbial community composition and soil functions.</p>