The rhizosphere hosts a complex web of prokaryotes interacting with one another that may modulate crucial functions related to plant growth and health. Identifying the key factors structuring the prokaryotic community of the plant rhizosphere is a necessary step toward the enhancement of plant production and crop yield with beneficial associative microorganisms. We used a long-term field experiment conducted at three locations in the Canadian prairies to verify that: (1) the level of cropping system diversity influences the α- and β-diversity of the prokaryotic community of canola (Brassica napus) rhizosphere; (2) the canola rhizosphere community has a stable prokaryotic core; and (3) some highly connected taxa of this community fit the description of hub-taxa. We sampled the rhizosphere of canola grown in monoculture, in a 2-phase rotation (canola-wheat), in a 3-phase rotation (pea-barley-canola), and in a highly diversified 6-phase rotation, five and eight years after cropping system establishment. We detected only one core bacterial Amplicon Sequence Variant (ASV) in the prokaryotic component of the microbiota of canola rhizosphere, a hub taxon identified as cf. Pseudarthrobacter sp. This ASV was also the only hub taxon found in the networks of interactions present in both years and at all three sites. We highlight a cohort of bacteria and archaea that were always connected with the core taxon in the network analyses.

Wheat is among the important crops harnessed by humans whose breeding efforts resulted in a diversity of genotypes with contrasting traits. The goal of this study was to determine whether different old and new cultivars of durum wheat (Triticum turgidum L. var. durum) recruit specific arbuscular mycorrhizal (AM) fungal communities from indigenous AM fungal populations of soil under field conditions. A historical set of five landraces and 26 durum wheat cultivars were field cultivated in a humid climate in Eastern Canada, under phosphorus-limiting conditions. To characterize the community of AMF inhabiting bulk soil, rhizosphere, and roots, MiSeq amplicon sequencing targeting the 18S rRNA gene (SSU) was performed on total DNAs using a nested PCR approach. Mycorrhizal colonization was estimated using root staining and microscope observations. A total of 317 amplicon sequence variants (ASVs) were identified as belonging to Glomeromycota. The core AM fungal community (i.e., ASVs present in > 50% of the samples) in the soil, rhizosphere, and root included 29, 30, and 29 ASVs, respectively. ASVs from the genera Funneliformis, Claroideoglomus, and Rhizophagus represented 37%, 18.6%, and 14.7% of the sequences recovered in the rarefied dataset, respectively. The two most abundant ASVs had sequence homology with the 18S sequences from well-identified herbarium cultures of Funneliformis mosseae BEG12 and Rhizophagus irregularis DAOM 197198, while the third most abundant ASV was assigned to the genus Paraglomus. Cultivars showed no significant difference of the percentage of root colonization ranging from 57.8% in Arnautka to 84.0% in AC Navigator. Cultivars were generally associated with similar soil, rhizosphere, and root communities, but the abundance of F. mosseae, R. irregularis, and Claroideoglomus sp. sequences varied in Eurostar, Golden Ball, and Wakooma. Although these results were obtained in one field trial using a non-restricted pool of durum wheat and at the time of sampling, that may have filtered the community in biotopes. The low genetic variation between durum wheat cultivars for the diversity of AM symbiosis at the species level suggests breeding resources need not be committed to leveraging plant selective influence through the use of traditional methods for genotype development.

To identify why tree growth differs by afforestation type is a matter of prime concern in forestry. A study was conducted to determine why oriental arborvitae (Platycladus orientalis) grows better in the presence of black locust (Robinia pseudoacacia) than in monoculture. Different types of stands (i.e., monocultures and mixture of black locust and oriental arborvitae, and native grassland as a control) were selected in the Loess Plateau, China. The height and diameter at breast height of each tree species were measured, and soil, shoot, and root samples were sampled. The arbuscular mycorrhizal (AM) attributes, shoot and root nutrient status, height and diameter of black locust were not influenced by the presence of oriental arborvitae. For oriental arborvitae, however, growing in mixture increased height and diameter and reduced shoot Mn, Ca, and Mg contents, AM fungal spore density, and colonization rate. Major changes in soil properties also occurred, primarily in soil water, NO 3-N, and available K levels and in soil enzyme activity. The increase in soil water, N, and K availability in the presence of black locust stimulated oriental arborvitae growth, and black locust in the mixed stand seems to suppress the development of AM symbiosis in oriental arborvitae roots, especially the production of AM fungal spores and vesicles, through improving soil water and N levels, thus freeing up carbon to fuel plant growth. Overall, the presence of black locust favored oriental arborvitae growth directly by improving soil water and fertility and indirectly by repressing AM symbiosis in oriental arborvitae roots.

Agriculturally-driven land transformation is increasing globally. Improving phosphorus (P) use efficiency to sustain optimum productivity in diverse ecosystems, based on knowledge of soil P dynamics, is also globally important in light of potential shortages of rock phosphate to manufacture P fertilizer. We investigated P chemical speciation and P cycling with solution 31P nuclear magnetic resonance, P K-edge X-ray absorption near-edge structure spectroscopy, phosphatase activity assays, and shotgun metagenomics in soil samples from long-term agricultural fields containing four different land-use types (native and tame grasslands, annual croplands, and roadside ditches). Across these land use types, native and tame grasslands showed high accumulation of organic P, principally orthophosphate monoesters, and high acid phosphomonoesterase activity but the lowest abundance of P cycling genes. The proportion of inositol hexaphosphates (IHP), especially the neo-IHP stereoisomer that likely originates from microbes rather than plants, was significantly increased in native grasslands than croplands. Annual croplands had the largest variances of soil P composition, and the highest potential capacity for P cycling processes based on the abundance of genes coding for P cycling processes. In contrast, roadside soils had the highest soil Olsen-P concentrations, lowest organic P, and highest tricalcium phosphate concentrations, which were likely facilitated by the neutral pH and high exchangeable Ca of these soils. Redundancy analysis demonstrated that IHP by NMR, potential phosphatase activity, Olsen-P, and pH were important P chemistry predictors of the P cycling bacterial community and functional gene composition. Combining chemical and metagenomics results provides important insights into soil P processes and dynamics in different land-use ecosystems.

Canola is one of the most economically important crops in Canada, and the root and rhizosphere microbiomes of a canola plant likely impact its growth and nutrient uptake. The aim of this study was to determine whether canola has a core root microbiome (i.e., set of microbes that are consistently selected in the root environment), and whether this is distinct from the core microbiomes of other crops that are commonly grown in the Canadian Prairies, pea, and wheat. We also assessed whether selected agronomic treatments can modify the canola microbiome, and whether this was associated to enhanced yield. We used a field experiment with a randomized complete block design, which was repeated at three locations across the canola-growing zone of Canada. Roots and rhizosphere soil were harvested at the flowering stage of canola. We separately isolated total extractable DNA from plant roots and from adjacent rhizosphere soil, and constructed MiSeq amplicon libraries for each of 60 samples, targeting bacterial, and archaeal 16S rRNA genes and the fungal ITS region. We determined that the microbiome of the roots and rhizosphere of canola was consistently different from those of wheat and pea. These microbiomes comprise several putative plant-growth-promoting rhizobacteria, including Amycolatopsis sp., Serratia proteamaculans, Pedobacter sp., Arthrobacter sp., Stenotrophomonas sp., Fusarium merismoides, and Fusicolla sp., which correlated positively with canola yield. Crop species had a significant influence on bacterial and fungal assemblages, especially within the roots, while higher nutrient input or seeding density did not significantly alter the global composition of bacterial, fungal, or archaeal assemblages associated with canola roots. However, the relative abundance of Olpidium brassicae, a known pathogen of members of the Brassicaceae, was significantly reduced in the roots of canola planted at higher seeding density. Our results suggest that seeding density and plant nutrition management modified the abundance of other bacterial and fungal taxa forming the core microbiomes of canola that are expected to impact crop growth. This work helps us to understand the microbial assemblages associated with canola grown under common agronomic practices and indicates microorganisms that can potentially benefit or reduce the yield of canola.

The association of plants and microbial communities is crucial for crop production, and host plants influence the composition of rhizosphere microbiomes. Pulse crops play an important role in the development of sustainable cropping systems, and producers in the Canadian prairies often increase the frequency of pulses in their cropping systems. In this study, we determined the shifts in the fungal community of pea (Pisum sativum L.) rhizosphere, as influenced by the frequency of pulses in rotation, using high throughput sequencing. Six cropping systems containing pea (P), lentil (Lens culinaris Medik., L), hybrid canola (Brassica napus L., C), wheat (Triticum aestivum L., W), and oat (Avena sativa L., O) in different intensities were tested. The fungal communities were assessed at the flowering stage in the fourth and fifth year of the 4-year rotations. Cropping system had a significant impact on the composition of the rhizosphere fungal community, and the effect of crop rotation sequence was greater and explained more of the variation than the effect of previous crops. The rotation with consecutive pulses (WPLP) decreased fungal evenness and increased the proportion of pathotrophs. Fusarium was a dominant and ubiquitous pathotrophic genus. Olpidium virulentus, Botrytis cinerea, Fusarium solani, F. graminearum, and Alternaria eichhorniae were generally more abundant in pulse intensive rotations (WPLP, WLOP, and WPOP), the exception being F. solani which was not promoted by lentil. Reads of O. virulentus and B. cinerea were most abundant in pea preceded by lentil followed by the reads of Mortierella elongata in pea preceded by wheat. Pea consistently had higher grain yield when grown in diversified rotations including wheat, canola/lentil, and oat than rotations with two repeated crops (canola or pea). Cropping system affected the soil physicochemical properties, and soil pH was the main driver of fungal community shift. No evidence of beneficial microorganisms involvement in plant productivity was observed, but the high abundance of pathotrophs in pulse intensified rotations suggests the possibility of pathogen buildup in the soil with increasing pulse frequency. Diversifying rotation sequences minimized disease risk and increased pea production, in this study. Careful selection of plant species appears as a strategy for the management of rhizosphere fungal communities and the maintenance of crop production system's health.