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

Abstract

Soil fungal communities play a central role in natural systems and agroecosystems. As such, they have attracted significant research interest. However, the fungal microbiota of aromatic plants, such as clary sage (Salvia sclarea L.), remain unexplored. This is especially the case in trace element (TE)-polluted conditions and within the framework of phytomanagement approaches. The presence of high concentrations of TEs in soils can negatively affect not only microbial diversity and community composition but also plant establishment and growth. Hence, the objective of this study is to investigate the soil fungal and arbuscular mycorrhizal fungi (AMF) community composition and their changes over time in TE-polluted soils in the vicinity of a former lead smelter and under the cultivation of clary sage. We used Illumina MiSeq amplicon sequencing to evaluate the effects of in situ clary sage cultivation over two successive years, combined or not with exogenous AMF inoculation, on the rhizospheric soil and root fungal communities. We obtained 1239 and 569 fungal amplicon sequence variants (ASV), respectively, in the rhizospheric soil and roots of S. sclarea under TE-polluted conditions. Remarkably, 69 AMF species were detected at our experimental site, belonging to 12 AMF genera. Furthermore, the inoculation treatment significantly shaped the fungal communities in soil and increased the number of AMF ASVs in clary sage roots. In addition, clary sage cultivation over successive years could be one of the explanatory parameters for the inter-annual variation in both fungal and AMF communities in the soil and root biotopes. Our data provide new insights on fungal and AMF communities in the rhizospheric soil and roots of an aromatic plant, clary sage, grown in TE-polluted agricultural soil.

Glomerales Dominate Arbuscular Mycorrhizal Fungal Communities Associated with Spontaneous Plants in Phosphate-Rich Soils of Former Rock Phosphate Mining Sites

“…After three washings (with ice-cold ethanol (70%) followed by centrifugation-10 min at 900× g) and air-drying at room temperature (approx. 90 min; 20 • C), the DNA pellet was dissolved in 50 µL of TE buffer (10 mM Tris-HCl, pH 8.0; 1.0 mM EDTA, pH 8.0) [13,49,50].…”

“…Thus, the first-round PCR was performed using the AMF-discriminating primer pair AML1 (3 -ATCAACTTTCGATGGTAGGATAGA-5 ) and AML2 (3 -GAACCCAAACAC TTTGGTTTCC-5 ) which generate amplicons of the small 18S subunit of the rRNA gene of about 800 bp in length [51,52]. The PCR conditions were as follows: initial denaturation at 94 • C for 3 min followed by 35 cycles at 94 • C for 1 min, 45 • C for 1 min, and 72 • C for 1 min, and a final elongation step at 72 • C for 5 min [13]. PCR reactions were performed in a reaction volume of 25 µL, and reagents were as follows: 5 µL of Q5 (5X) reaction buffer, 0.25 µL of Q5 ® High-Fidelity DNA Polymerase (New England Biolabs France, Evry, France), 0.8 µL of each primer (0.4 µM), 1 µL of dNTPs (0.2 mM), 1 µL of DMSO, 1 µL of BSA (100 µg•mL −1 ), and 1 ng of DNA template [13,51].…”

“…This set of primers flanked the V4 region of 18S and hence downsized the length of the amplicons to about 400 bp, which is compatible with MiSeq 300 paired-end sequencing [53]. The two primers were complemented with CS1 and CS2 barcoded adapters [13,53]. The reaction mixture was the same as previously described, but 1 ng of DNA from the first-round PCR as template was used.…”

“…In exchange, elements such as phosphorus (P), nitrogen, sulfur, or microelements, such as copper and zinc, may also be transferred to the host via arbuscules, favoring plant nutrient supply [1,8,9]. Mycorrhizal symbiosis can also contribute to plant protection against biotic or abiotic stresses [10][11][12][13]. In addition, evidence also indicate that AMF can be critical components to improve soil structure, water retention capacity, and soil fertility and reduce soil nutrient leaching [1,[14][15][16][17].…”

Coriander (Coriandrum sativum L.) in Combination with Organic Amendments and Arbuscular Mycorrhizal Inoculation: An Efficient Option for the Phytomanagement of Trace Elements-Polluted Soils

“…The selection of appropriate plant species is another critical aspect of successful phytomanagement [22]. In particular, plants have to be able to grow in TE-polluted conditions and to develop vegetation cover in a relatively short period of time while producing high amounts of valuable biomass [23]. In recent years, the cultivation of aromatic plants destined for essential oil (EO) production has been presented as an innovative and economically viable alternative for reclaiming TE-polluted areas [24][25][26].…”