It's about the soil: different plants, one rhizobiome

Published in Microbiology
It's about the soil: different plants, one rhizobiome

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Plants are immersed and evolved in a microbial world. Soil microbial communities drive nutrient cycling, induce disease resistance, and mineralize soil organic matter, thereby affecting the health and productivity of plants [1]. Plant-microorganism interactions are especially tight in the rhizosphere - the mm-thin soil layer surrounding plant roots. Soil bacteria are recruited to the rhizosphere by rhizodeposition, i.e., the release of large amounts of organic compounds from plant roots, resulting in a significant enrichment of bacterial cell numbers compared to the surrounding bulk soil [2].  Rhizosphere bacterial communities are shaped by many factors, ranging from soil physicochemical properties to plant characteristics (e.g. species, cultivar, developmental stage) [3,4], but only few studies have simultaneously investigated the effects of both plant species and soil types on the rhizosphere bacterial communities. The majority of investigations focused on model or crop plants grown in monocultures or under greenhouse conditions.

Fig.1 - Sampling of temperate grassland plants in the German Biodiversity Exploratories.

Therefore our recent study aimed to determine the influence of plant species, soil conditions, and the chemistry of plant root exudates on the composition of active rhizosphere bacterial communities in natural environments. In our multifactorial experimental setup, six temperate grassland plant species were planted in grasslands of three different regions within Germany and the plant-associated rhizobiome was elucidated by sequencing of reverse-described 16S rRNA. This design allowed us to study different grasses and forb species, a wide range of different edaphic and climatic conditions, as well as a substantial gradient of land use intensity in parallel. In line with what has been reported for the composition of rhizosphere communities in previous studies [5], we found that the active rhizobiome has a distinct composition when compared to active bacterial communities of the surrounding bulk soil. Unexpectedly, these bulk soil bacterial communities had by far the strongest effect on rhizosphere bacteria, determining which active bacteria actually colonize the rhizosphere. Soil properties had the biggest influence on active bulk soil bacteria and hence indirectly also on rhizosphere bacteria. Thus, the largest differences in the composition of the active rhizobiome were detected between plants growing in the most divergent soil types. This dominant effect of soil exceeded by far the very weak effects of plant species and of polar root exudates; different plant species had surprisingly similar rhizobiomes. We hypothesize that the tight spatial arrangement in the typically complex grassland communities leads to interactions between the rhizospheres of different plant individuals, resulting in a shared rhizosphere system and the maintenance of similar rhizobiomes by different plant species. Our study also identified many previously unknown bacteria that were linked to the presence of specific polar root exudates but were independent of the individual plant species. The observed associations provide first information on the substrate utilization of so far unrecognized rhizosphere bacteria and thus a handle for their future cultivation and, ultimately, their application as root inoculants.

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[1] Schnitzer SA, Klironomos JN, HilleRisLambers J, Kinkel LL, Reich PB, Xiao K, et al. Soil microbes drive the classic plant diversity-productivity pattern. Ecology. 2011;92:296–303.

[2] Philippot L, Raaijmakers JM, Lemanceau P, van der Putten WH. Going back to the roots: the microbial ecology of the rhizosphere. Nat Rev Microbiol. 2013;11:789–99.

[3] Bowen JL, Kearns PJ, Byrnes JEK, Wigginton S, Allen WJ, Greenwood M, et al. Lineage overwhelms environmental conditions in determining rhizosphere bacterial community structure in a cosmopolitan invasive plant. Nat Commun. 2017;8:433.

[4] Berg G, Smalla K. Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. FEMS Microbiol Ecol. 2009;68:1–13.

[5] Bulgarelli D, Rott M, Schlaeppi K, Ver Loren van Themaat E, Ahmadinejad N, Assenza F, et al. Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature. 2012;488:91–95.

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