The contribution of low‐abundance microbial species to soil ecosystems is easily overlooked because there is considerable overlap between metabolic abilities (functional redundancy) of dominant and ...subordinate microbial species. Here we studied how loss of less abundant soil bacteria affected the production of antifungal volatiles, an important factor in the natural control of soil‐borne pathogenic fungi. We provide novel empirical evidence that the loss of soil bacterial species leads to a decline in the production of volatiles that suppress root pathogens. By using dilution‐to‐extinction for seven different soils we created bacterial communities with a decreasing number of species and grew them under carbon‐limited conditions. Communities with high bacterial species richness produced volatiles that strongly reduced the hyphal growth of the pathogen Fusarium oxysporum. For most soil origins loss of bacterial species resulted in loss of antifungal volatile production. Analysis of the volatiles revealed that several known antifungal compounds were only produced in the more diverse bacterial communities. Our results suggest that less abundant bacterial species play an important role in antifungal volatile production by soil bacterial communities and, consequently, in the natural suppression of soil‐borne pathogens.
Knowledge on the factors that determine the composition of bacterial communities in the vicinity of roots (rhizosphere) is essential to understand plant-soil interactions. Plant species identity, ...plant growth stage and soil properties have been indicated as major determinants of rhizosphere bacterial community composition. Here we show that the presence of saprotrophic fungi can be an additional factor steering rhizosphere bacterial community composition and functioning. We studied the impact of presence of two common fungal rhizosphere inhabitants (Mucor hiemalis and Trichoderma harzianum) on the composition of cultivable bacterial communities developing in the rhizosphere of Carex arenaria (sand sedge) in sand microcosms. Identification and phenotypic characterization of bacterial isolates revealed clear shifts in the rhizosphere bacterial community composition by the presence of two fungal strains (M. hiemalis BHB1 and T. harzianum PvdG2), whereas another M. hiemalis strain did not show this effect. Presence of both M. hiemalis BHB1 and T. harzianum PvdG2 resulted in a significant increase of chitinolytic and (in vitro) antifungal bacteria. The latter was most pronounced for M. hiemalis BHB1, an isolate from Carex roots, which stimulated the development of the bacterial genera Achromobacter and Stenotrophomonas. In vitro tests showed that these genera were strongly antagonistic against M. hiemalis but also against the plant-pathogenic fungus Rhizoctonia solani. The most likely explanation for fungal-induced shifts in the composition of rhizosphere bacteria is that bacteria are being selected which are successful in competing with fungi for root exudates. Based on the results we propose that measures increasing saprotrophic fungi in agricultural soils should be explored as an alternative approach to enhance natural biocontrol against soil-borne plant-pathogenic fungi, namely by stimulating indigenous antifungal rhizosphere bacteria.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The rhizosphere microbial community of crop plants in intensively managed arable soils is strongly dominated by bacteria, especially in the initial stages of plant development. In order to establish ...more diverse and balanced rhizosphere microbiomes, as seen for wild plants, crop variety selection could be based on their ability to promote growth of saprotrophic fungi in the rhizosphere. We hypothesized that this can be achieved by increasing the exudation of phenolic acids, as generally higher fungal abundance is observed in environments with phenolic-rich inputs, such as exudates of older plants and litter leachates. To test this, a rhizosphere simulation microcosm was designed to establish gradual diffusion of root exudate metabolites from sterile sand into arable soil. With this system, we tested the fungus-stimulating effect of eight phenolic acids alone or in combination with primary root metabolites. Ergosterol-based fungal biomass measurements revealed that most phenolic acids did not increase fungal abundance in the arable soil layer. These results were supported by comparison of fungal biomass in the rhizosphere of wild type
plants and mutants with altered phenolic acid metabolism. Salicylic acid was the only phenolic acid that stimulated a higher fungal biomass in the arable soil layer of microcosms, but only when combined with a background of primary root metabolites. However, such effect on rhizosphere fungi was not confirmed for a salicylic acid-impaired
mutant. For three phenolic acid treatments (chlorogenic acid, salicylic acid, vanillic acid) fungal and bacterial community compositions were analyzed using amplicon sequencing. Despite having little effect on fungal biomass, phenolic acids combined with primary metabolites promoted a higher relative abundance of soil-borne fungi with the ability to invade plant roots (
and
spp.) in the simulated rhizosphere. Bacterial community composition was also affected by these phenolic acids. Although this study indicates that phenolic acids do not increase fungal biomass in the rhizosphere, we highlight a potential role of phenolic acids as attractants for root-colonizing fungi.
Summary
Competition is a major type of interaction between fungi and bacteria in soil and is also an important factor in suppression of plant diseases caused by soil‐borne fungal pathogens. There is ...increasing attention for the possible role of volatiles in competitive interactions between bacteria and fungi. However, knowledge on the actual role of bacterial volatiles in interactions with fungi within soil microbial communities is lacking. Here, we examined colonization of sterile agricultural soils by fungi and bacteria from non‐sterile soil inoculums during exposure to volatiles emitted by soil‐derived bacterial communities. We found that colonization of soil by fungi was negatively affected by exposure to volatiles emitted by bacterial communities whereas that of bacteria was barely changed. Furthermore, there were strong effects of bacterial community volatiles on the assembly of fungal soil colonizers. Identification of volatile composition produced by bacterial communities revealed several compounds with known fungistatic activity. Our results are the first to reveal a collective volatile‐mediated antagonism of soil bacteria against fungi. Given the better exploration abilities of filamentous fungi in unsaturated soils, this may be an important strategy for bacteria to defend occupied nutrient patches against invading fungi. Another implication of our research is that bacterial volatiles in soil atmospheres can have a major contribution to soil fungistasis.
Summary
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 13CO2‐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.
There is increasing evidence that microbial volatiles (VOCs) play an important role in natural suppression of soil-borne diseases, but little is known on the factors that influence production of ...suppressing VOCs. In the current study we examined whether a stress-induced change in soil microbial community composition would affect the production by soils of VOCs suppressing the plant-pathogenic oomycete Pythium. Using pyrosequencing of 16S ribosomal gene fragments we compared the composition of bacterial communities in sandy soils that had been exposed to anaerobic disinfestation (AD), a treatment used to kill harmful soil organisms, with the composition in untreated soils. Three months after the AD treatment had been finished, there was still a clear legacy effect of the former anaerobic stress on bacterial community composition with a strong increase in relative abundance of the phylum Bacteroidetes and a significant decrease of the phyla Acidobacteria, Planctomycetes, Nitrospirae, Chloroflexi, and Chlorobi. This change in bacterial community composition coincided with loss of production of Pythium suppressing soil volatiles (VOCs) and of suppression of Pythium impacts on Hyacinth root development. One year later, the composition of the bacterial community in the AD soils was reflecting that of the untreated soils. In addition, both production of Pythium-suppressing VOCs and suppression of Pythium in Hyacinth bioassays had returned to the levels of the untreated soil. GC/MS analysis identified several VOCs, among which compounds known to be antifungal, that were produced in the untreated soils but not in the AD soils. These compounds were again produced 15 months after the AD treatment. Our data indicate that soils exposed to a drastic stress can temporarily lose pathogen suppressive characteristics and that both loss and return of these suppressive characteristics coincides with shifts in the soil bacterial community composition. Our data are supporting the suggested importance of microbial VOCs in the natural buffer of soils against diseases caused by soil-borne pathogens.
Cellulose-rich amendments stimulate saprotrophic fungi in arable soils. This may increase competitive and antagonistic interactions with root-infecting pathogenic fungi, resulting in lower disease ...incidence. However, cellulose-rich amendments may also stimulate pathogenic fungi with saprotrophic abilities, thereby increasing plant disease severity. The current study explores these scenarios, with a focus on the pathogenic fungus Rhizoctonia solani. Saprotrophic growth of R. solani on cellulose-rich materials was tested in vitro. This confirmed paper pulp as a highly suitable substrate for R. solani, whereas its performance on wood sawdusts varied with tree species. In two pot experiments, the effects of amendment of R. solani-infected soil with cellulose-rich materials on performance of beetroot seedlings were tested. All deciduous sawdusts and paper pulp stimulated soil fungal biomass, but only oak, elder and beech sawdusts reduced damping-off of beetroot. Oak sawdust amendment gave a consistent stimulation of saprotrophic Sordariomycetes fungi and of seedling performance, independently of the time between amendment and sowing. In contrast, paper pulp caused a short-term increase in R. solani abundance, coinciding with increased disease severity for beet seedlings sown immediately after amendment. However, damping-off of beetroot was reduced if plants were sown two or four weeks after paper pulp amendment. Cellulolytic bacteria, including Cytophagaceae, responded to paper pulp during the first two weeks and may have counteracted further spread of R. solani. The results showed that fungus-stimulating, cellulose-rich amendments have potential to be used for suppression of R. solani. However, such amendments require a careful consideration of material choice and application strategy.
The assembly of root-associated microbes during the seedling stage has strong impact on subsequent performance of crops. Major factors influencing this assembly are crop species identity and ...composition of potential root-colonizing microbes in the bulk soil. The latter can be modified by soil management, such as organic amendments. The incorporation of residues of cover crops before the start of the growing season of cash crops presents an interesting option for steering of root-associated seedling microbiomes as there is a wide range of cover crops species with different properties available for farmers.
In a greenhouse study, we examined the effect of soil amendments with milled shoot and root materials of seven cover crop species (niger seed, phacelia, rapeseed, radish, vetch, black oat and buckwheat) on the assembly of root-associated bacteria and fungi of seedlings of four cash crop species (asparagus, carrot, onion and sugar beet). Field-grown cover crops material used for the study was collected at two time points (before and after winter) which had strong impact on plant elemental composition. The soil used for the study was a mixture of sandy arable soils with a history of soil-borne fungal diseases (Fusarium and Rhizoctonia). Within the context of a strong selection of root-associated microbes by cash crop species, we found significant modifying effects by cover crop materials. We show that cover crop elemental composition had a stronger effect than cover crop species identity. High quality residues (with low C/N ratio) caused profound shifts within root-associated Proteobacteria and increases in relative abundance of certain microbial groups such as Bacillaceae and Mortierellomycetes. These changes coincided with differences in establishment and survival of cash crop seedlings. Tolerance of sugar beet seedlings against the fungal pathogen Rhizoctonia solani was correlated with residues causing increases of root-associated Oxalobacteraceae, Bacillaceae and Mortierellaceae. However, the same residues increased Fusarium-induced failure of asparagus seed germination. This indicates that fine-tuning of cover crops amendments for different cash crops is required to realize enhanced functioning of root microbiomes.
•Decomposing cover crop residues alter cash crop seedling root microbiomes.•Elemental composition of cover crops is the major factor affecting cash crop root microbial assembly.•Differential effects of cover crop quality were seen for different damping-off diseases.•Fine-tuning of cash-cover crop combinations is needed when steering beneficial root microbiomes.
Application of nitrogen fertilizers to reach high crop production is common practice. However, this has a high environmental cost, irrespectively of the synthetic or organic origin of the fertilizer. ...In particular, intensively managed arable soils often fail to retain excess nitrogen, which leads to contamination of ground- and surface water. Next to abiotic factors like soil texture, limited nitrogen retention is ascribed to low activity of saprotrophic fungi. It has been shown that amendment of arable soils with cellulose-rich materials can effectively stimulate resident saprotrophic fungi. The current study investigated the relationship between fungal dynamics (biomass, composition) and nitrogen immobilization-remobilization dynamics upon soil amendment with woody materials. Mineral nitrogen pools, ergosterol and ITS2 amplicon sequences were analyzed during a 6-month pot experiment. Carbon-rich amendments included sawdusts of deciduous (beech, willow) and coniferous (Douglas fir, larch) tree species, beech wood chips, wheat straw and combinations of these materials. Excess nitrogen derived from the addition of either mineral or organic fertilizer.
Deciduous wood sawdust resulted in rapid stimulation of fungal biomass, mainly consisting of saprotrophic Sordariomycetes. This was accompanied by a reduction in the mineral N pool up to 17 kg N t−1 wood, followed by a gradual remobilization. The intensity of nitrogen immobilization depended on the type of woody materials and of fertilizer. Nitrogen immobilization by single amendments of coniferous sawdust was the lowest, but these materials resulted in a prolonged nitrogen retention when combined with beech sawdust.
Our conclusion is that fungus-stimulating woody soil amendments have great potential to reduce nitrogen losses in arable soils.
•Sawdust amendments promote rapid fungal-driven immobilization of soil mineral N excess.•Deciduous wood sawdust performs better than coniferous sawdust.•Woody amendments have the potential to capture up to 17 kg N t−1 sawdust.•Fungal biomass decline is followed by N remobilization in 4–6 months.•Combined deciduous/coniferous additions cause at least 6 months of N retention.
Mycophagous soil bacteria are able to obtain nutrients from living fungal hyphae. However, with exception of the soil bacterial genus Collimonas, occurrence of this feeding strategy has not been well ...examined. Evaluation of the importance of mycophagy in soil bacterial communities requires targeted isolation methods. In this study, we compared two different approaches to obtain mycophagous bacteria from rhizospheric soil. A short-term method based on baiting for bacteria that can rapidly adhere to fungal hyphae and a long-term method based on the enrichment of bacteria on fungal hyphae via repeated transfer. Hyphae-adhering bacteria were isolated, identified by 16S rDNA sequencing and tested for antifungal activity and the ability to feed on fungi as the sole source of carbon. Both methods yielded a range of potentially mycophagous bacterial isolates with little phylogenetic overlap. We also found indications for feeding preferences among the potentially mycophagous bacteria. Our results indicate that mycophagy could be an important growth strategy for rhizosphere bacteria. To our surprise, we found several potential plant pathogenic bacteria among the mycophagous isolates. We discuss the possible benefits that these bacteria might gain from colonizing fungal hyphae.
PDF
