The Aromatic Plant Clary Sage Shaped Bacterial Communities in the Roots and in the Trace Element-Contaminated Soil More Than Mycorrhizal Inoculation – A Two-Year Monitoring Field Trial

Abstract

To cope with soil contamination by trace elements (TE), phytomanagement has attracted much attention as being an eco-friendly and cost-effective green approach. In this context, aromatic plants could represent a good option not only to immobilize TE, but also to use their biomass to extract essential oils, resulting in high added-value products suitable for non-food valorization. However, the influence of aromatic plants cultivation on the bacterial community structure and functioning in the rhizosphere microbiota remains unknown. Thus, the present study aims at determining in TE-aged contaminated soil (Pb – 394 ppm, Zn – 443 ppm, and Cd – 7ppm, respectively, 11, 6, and 17 times higher than the ordinary amounts in regional agricultural soils) the effects of perennial clary sage (Salvia sclarea L.) cultivation, during two successive years of growth and inoculated with arbuscular mycorrhizal fungi, on rhizosphere bacterial diversity and community structure. Illumina MiSeq amplicon sequencing targeting bacterial 16S rRNA gene was used to assess bacterial diversity and community structure changes. Bioinformatic analysis of sequencing datasets resulted in 4691 and 2728 bacterial Amplicon Sequence Variants (ASVs) in soil and root biotopes, respectively. Our findings have shown that the cultivation of clary sage displayed a significant year-to-year effect, on both bacterial richness and community structures. We found that the abundance of plant-growth promoting rhizobacteria significantly increased in roots during the second growing season. However, we didn’t observe any significant effect of mycorrhizal inoculation neither on bacterial diversity nor on community structure. Our study brings new evidence in TE-contaminated areas of the effect of a vegetation cover with clary sage cultivation on the microbial soil functioning.

Clary Sage Cultivation and Mycorrhizal Inoculation Influence the Rhizosphere Fungal Community of an Aged Trace-Element Polluted Soil

“…Notably, after two years of cultivation, the fungal richness and diversity were found to be equivalent in the rhizospheric soil and in the roots of clary sage, and a similar pattern was observed between the two biotopes at the phylum level, which is consistent with the literature, as it is well-known that fungi associated with the roots are recruited into the surrounding soil community [72]. In a previous related study, the bacterial microbiota of the same aromatic plant was explored [43]. However, this trend was substantially less pronounced in the case of bacterial communities and could suggest that fungal communities are more sensitive to biotic and abiotic factors.…”

“…Clary sage has been evaluated as part of a phytomanagement assay aimed at cultivating the aromatic plant on a TE-polluted soil and producing essential oils from the biomass, intended for use as potential biopesticides [44]. However, whereas the impact of this aromatic plant species on the soil bacterial microbiome has been investigated [43], no data are available on its effect on the fungal microbiome. Thus, under field conditions, the effects of clary sage cultivation and mycorrhizal inoculation on the total fungal community composition were determined, with a particular focus on AMF community composition in rhizospheric soil and root biotopes.…”

“…It is located 600 m away from a former Pb and Zn smelter, Metaleurop Nord, whose activities over more than a century generated significant amounts of TE-containing dust, which led to topsoil (0-30 cm) TE pollution [40,41]. The topsoil is characterized by high amounts of Cd, Pb, and Zn, which correspond to concentrations approximately 17-, 11-, and 6-fold higher, respectively, than those reported in regional background levels for agricultural soils [42,43]. The soil texture consists of silt loam with a slightly alkaline water pH (7.9).…”

“…The soil physicochemical properties were homogenous across the experimental plot. Full descriptions of the experimental site and soil have been provided in [43] and [44].…”

Phytomanagement of Metal(loid)-Contaminated Soils: Options, Efficiency and Value

“…In the case of anaerobic digestion, some TE excess (e.g., >500 mg Zn kg −1 , 20,000 mg Mn kg −1 ) can decrease the methane content in biogas and daily methane production (Edgar et al, 2021). Essential oils from aromatic plants harvested at phytomanaged sites also did not show TE contamination (Raveau et al, 2020). Similarly, oilseeds from sunflower, hemp, and most Brassicaceae harvested at phytomanaged sites generally do not present TE excess, nor the oil for biodiesel production and other uses.…”