Stimulated saprotrophic fungi in arable soil extend their activity to the rhizosphere and root microbiomes of crop seedlings

Abstract

Saprotrophic fungi play an important role in ecosystem functioning and plant performance, but their abundance in intensively managed arable soils is low. Saprotrophic fungal biomass in arable soils can be enhanced with amendments of cellulose-rich materials. Here, we examined if sawdust-stimulated saprotrophic fungi extend their activity to the rhizosphere of crop seedlings and influence the composition and activity of other rhizosphere and root inhabitants. After growing carrot seedlings in sawdust-amended arable soil, we determined fungal and bacterial biomass and community structure in roots, rhizosphere and soil. Utilization of root exudates was assessed by stable isotope probing (SIP) following ¹³ CO₂ -pulse-labelling of seedlings. This was combined with analysis of lipid fatty acids (PLFA/NLFA-SIP) and nucleic acids (DNA-SIP). Sawdust-stimulated Sordariomycetes colonized the seedling's rhizosphere and roots and actively consumed root exudates. This did not reduce the abundance and activity of bacteria, yet higher proportions of α-Proteobacteria and Bacteroidia were seen. Biomass and activity of mycorrhizal fungi increased with sawdust amendments, whereas exudate consumption and root colonization by functional groups containing plant pathogens did not change. Sawdust amendment of arable soil enhanced abundance and exudate-consuming activity of saprotrophic fungi in the rhizosphere of crop seedlings and promoted potential beneficial microbial groups in root-associated microbiomes.

Fig 1

Schematic representation of the experimental setup, starting with amendment of sawdust + N or N only (control), followed by sowing and growing carrot seedlings in the greenhouse and completed with ¹³C‐CO₂ labelling in a growth chamber.

Fig 2

Effect of wood sawdust amendment on biomass and plant‐C incorporation by fungi, bacteria and mycorrhizal fungi. Concentration of total C and ¹³C excess in PLFA/NLFA markers are shown for fungi (A, B), bacteria (C, D) and arbuscular mycorrhizal fungi (E, F) in unplanted soil (So) and carrot rhizosphere soil (Rhi). T1 and T2 represent 2‐ and 6‐weeks pre‐sowing incubation times of sawdust amendments. The value for bacterial PLFAs is obtained as a sum of PLFAs i15.0, ai15.0, i16.0, 16.1w7c, 16.1w6c, ai17.1w7, i17.0, 17.1w8c, cy‐17.0. ¹³C excess expresses the net amount of labelled C incorporated in a PLFA/NLFA as a result of pulse‐labelling and is obtained by subtracting the natural ¹³C abundance found for the same PLFA/NLFA in unlabeled rhizosphere samples.

Fig 3

Effect of sawdust amendment of arable soil on the fungal and bacterial community composition in roots and rhizosphere of carrot seedlings and in bulk soil. Ordination (PCoA based on Bray–Curtis dissimilarity matrix) was performed independently for the whole fungal dataset (A) and for the whole bacterial dataset (B). For both fungi and bacteria, the dissimilarity between communities found in four compartments, with and without sawdust amendment, was displayed in separate plots for each pre‐sowing incubation time (T1 = 2 weeks, T2 = 6 weeks). Communities were obtained from unplanted soil, rhizosphere, ¹³C‐enriched rhizosphere DNA and roots, after carrot seedlings had grown for 3 weeks.

Fig 4

Effect of sawdust amendment on fungal community composition in an arable soil, as determined for unplanted soil (So), carrot rhizosphere (Rhi), ¹³C‐enriched DNA fraction in the carrot rhizosphere (RhiA) and carrot root (Ro). Relative abundance of fungal classes (A) and fungal functional groups (B) are displayed for soil, rhizosphere and root compartments and for each pre‐sowing incubation time (T1 = 2 weeks, T2 = 6 weeks) in sawdust‐amended pots and controls. Fungal taxa and functional groups of relative abundance <1.5% were classified as ‘Other’. (C, D): relative abundance of the functional fungal groups ‘saprotrophs’ and those potentially containing ‘plant pathogens’. The main effect of sawdust amendment is shown alongside the effect of sawdust in each compartment (three‐way ANOVA with planned contrasts, *** P < 0.001, ** P < 0.01, * P < 0.05).

Fig. 5

Effect of sawdust amendment on bacterial community composition in an arable soil, as determined for unplanted soil (So), carrot rhizosphere (Rhi), ¹³C‐enriched DNA fraction in the carrot rhizosphere (RhiA) and carrot root (Ro). Results are displayed for each pre‐sowing incubation time (T1 = 2 weeks, T2 = 6 weeks) in sawdust‐amended pots and controls. A. Relative abundance of bacterial classes (classes of relative abundance <1.5% were classified as ‘Other’). B,C. Relative abundance of α‐Proteobacteria and Bacteroidia. The main effect of sawdust amendment is shown alongside the effect of sawdust in each compartment (three‐way ANOVA with planned contrasts, ***P < 0.001, **P < 0.01, *P < 0.05). D,E. Relative abundance of bacterial families belonging to α‐Proteobacteria and Bacteroidia (respectively, families of relative abundance < 1% and < 0.5% were classified as ‘Other’).

Fig 6

Effect of sawdust on fungi and bacteria in an arable soil and in the root surroundings of carrot seedlings after 2‐ and 6‐weeks (T1, T2) pre‐sowing incubation times. White boxes report the biomass of bacteria, fungi and AMF in the rhizosphere soil, based on PLFA/NLFA markers. The black arrows represent the incorporation of ¹³C in fungal, bacterial and AMF PLFA/NLFA markers. Pie charts report the proportion of bacterial taxa (top) and fungal functional groups (bottom) that responded to sawdust amendment in the soil and rhizosphere soil (external charts) and in in the ¹³C‐enriched rhizosphere and root (central charts), based on DNA amplicon sequencing.