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Most species of arbuscular mycorrhizal fungi (AMF) are propagated with a host plant in a pot culture. However, the soil matrix makes it difficult to monitor the establishment and development of the symbiosis. In vitro culturing using Ri T-DNA transformed roots provides a clear medium and a sterile environment which offsets the constraints of the soil matrix. Nevertheless, the sterile conditions and the Ri T-DNA transformed roots provide very different growing conditions compared to a pot culture. Transparent soil based on superabsorbent polymer (SAP) has the potential of combining the advantages of current in vivo and in vitro culture methods without the constraints associated with either technique (opacity and sterility). Here we describe a SAP-based autotrophic culture as an alternative to current in vivo and in vitro culture methods. This system using two-compartment Petri dishes makes it easy to initiate single-spore cultures and to monitor fungal propagation. The SAP-based autotrophic system allowed the establishment of single-spore cultures of seven species (Diversispora varaderana, Funneliformis geosporus, Gigaspora rosea, Racocetra fulgida, Rhizophagus irregularis, R. intraradices and Sclerocystis sp.) from six genera and three families. Cultures were maintained over several months under non-sterile conditions. The Petri dishes avoid the problem of cross contamination and they can be stacked for space optimization. The grains of SAP colonized with new spores were used as inoculum to initiate new cultures in the SAP-based system. The SAP-based autotrophic culture method is a low-cost and low-tech approach, which makes the study of AMF much more accessible.

Acidification and metal mobility may present challenges in soil receiving paper mill biosolids (PB). Co-applying biochar and PB could help prevent these issues, but its effect must be assessed. The objective of this 224 d incubation study was to evaluate the effect of amending two acidic soils, a clay and sandy loam, with two PB types varying in pH (PB1, pH = 7.80; and PB2, pH = 4.51) co-applied with three rates (0%, 2.5%, and 5% w/w) of pine (Pinus strobus L.) biochar on soil pH and macro- (P, K, Ca, and Mg) and micronutrients (Cu, Zn, Fe, and Mn). In both soils, co-applying biochar and PB significantly increased soil pH and extractable K concentration compared with PB-only application, whereas amending with PB significantly increased soil extractable P concentration compared with the unamended soil. In comparison with PB only, co-applying 5% biochar and PB decreased extractable Cu concentration in both soils and extractable Fe concentration in the sandy loam soil. This study showed that co-applying biochar and PB can be more beneficial to agricultural soils than application of PB alone by supplying nutrients and helping prevent metal toxicity by raising pH, especially in acidic sandy soils.

The subterranean microbiota of plants is of great importance for plant growth and health, as root-associated microbes can perform crucial ecological functions. As the microbial environment of roots is extremely diverse, identifying keystone microorganisms in plant roots, rhizosphere, and bulk soil is a necessary step towards understanding the network of influence within the microbial community associated with roots and enhancing its beneficial elements. To target these hot spots of microbial interaction, we used inter-kingdom network analysis on the canola growth phase of a long-term cropping system diversification experiment conducted at four locations in the Canadian Prairies. Our aims were to verify whether bacterial and fungal communities of canola roots, rhizosphere, and bulk soil are related and influenced by diversification of the crop rotation system; to determine whether there are common or specific core fungi and bacteria in the roots, rhizosphere, and bulk soil under canola grown in different environments and with different levels of cropping system diversification; and to identify hub taxa at the inter-kingdom level that could play an important ecological role in the microbiota of canola. Our results showed that fungi were influenced by crop diversification, which was not the case on bacteria. We found no core microbiota in canola roots but identified three core fungi in the rhizosphere, one core mycobiota in the bulk soil, and one core bacterium shared by the rhizosphere and bulk soil. We identified two bacterial and one fungal hub taxa in the inter-kingdom networks of the canola rhizosphere, and one bacterial and two fungal hub taxa in the bulk soil. Among these inter-kingdom hub taxa, Bradyrhizobium sp. and Mortierella sp. are particularly influential on the microbial community and the plant. To our knowledge, this is the first inter-kingdom network analysis utilized to identify hot spots of interaction in canola microbial communities.

Arbuscular mycorrhizal fungi (AMF) are obligate plant symbionts that improve the nutrition and health of their host. Most, but not all the crops form a symbiosis with AMF. It is the case for canola (

The subterranean microbiota of plants are of great importance for plant growth and health, as root-associated microbes can perform crucial ecological functions. As the microbial environment of roots is extremely diverse, identifying keystone microorganisms in plant roots, rhizosphere and bulk soil is a necessary step towards understanding the network of influence within the microbial community associated with roots and enhancing its beneficial elements. To target these hot spots of microbial interaction, we used inter-kingdom network analysis on the canola growth phase of a long-term cropping system diversification experiment conducted at four locations in the Canadian prairies. Our aims were: to verify whether bacterial and fungal communities of canola roots, rhizosphere and bulk soil are related and influenced by diversification of the crop rotation system; to determine whether there are common or specific core fungi and bacteria in the roots, rhizosphere, and bulk soil under canola grown in different environments and with different levels of cropping system diversification; and to identify hub taxa at the inter-kingdom level that could play an important ecological role in the microbiota of canola. Our results showed that fungi were influenced by crop diversification but not by bacteria. We found no core microbiota in canola roots but identified three core fungi in the rhizosphere, one core mycobiota in the bulk soil and one core bacteria shared by the rhizosphere and bulk soil. We identified two bacterial and one fungal hub taxa in the inter-kingdom networks of the canola rhizosphere, and one bacterial and two fungal hub taxa in the bulk soil. Among these inter-kingdom hub taxa, Bradyrhizobium sp. and Mortierella sp. are particularly influential on the microbial community and the plant. To our knowledge, this is the first inter-kingdom network analysis utilized to identify hot spots of interaction in canola microbial communities.

Arbuscular mycorrhizal (AM) fungi, influencing many important ecosystem processes, widely occur in saline soils, and thus understanding their biogeographic patterns is of primary interest in saline ecosystem restoration. Fine roots and rhizosphere soils were sampled in black locust (Robinia pseudoacacia) plantations in four saline sites in northern China to detect soil properties and AM fungal attributes including their colonization level, spore density, hyphal density and community composition. Arbuscular mycorrhizal fungal attributes varied with sampling sites, and this variation was mostly attributed to changes in habitat characteristics and geographic distance. Habitat characteristics shape the root- and soil-inhabiting AM fungal communities to the same extent, whereas geographic distance seems to contribute more to root-inhabiting AM fungal assemblages. The level of root colonization by vesicles, arbuscules and hyphae and the density of AM fungal spores and hyphae in soils were found to be related to the relative abundance of AM fungal species such as root-inhabiting Rhizophagus intraradices and soil-inhabiting Sclerocystis sinuosa. All the results suggest that changes in habitat characteristics and geographic distance may induce biogeographic patterns of AM fungi, and these patterns are closely related to AM symbiosis in roots and the development of AM fungi in soils.

Adding biochar to paper mill biosolids (PB) amendments may affect PB mineralization rate and nitrogen (N) availability. The objective of this 224-day incubation study was to evaluate the effect of amending two PB types varying in carbon (C)/N ratio (PB1, C/N = 24; and PB2, C/N = 13) with three rates (0%, 2%, and 5%) of pine (Pinus strobus L.) biochar produced at 700 °C on the dynamics of total C, total N, mineral N, N mineralization rate, and microbial biomass C (MBC) and N (MBN) in two agricultural soils (Kamouraska clay and St-Antoine sandy-loam). Two reference treatments were also included, namely, mineral fertilization and unamended soil. Total soil C concentration remained stable over the incubation period, whereas a decrease in total soil N was observed in both soils. In comparison with the unamended soil, the application of PB significantly increased total N, NH4-N, NO3-N, net mineralized N, applied N mineralization rate, and MBC in both soils. In comparison with the application of PB alone, biochar addition increased total C and MBC but decreased NH4-N, NO3-N, net N mineralization, and applied N mineralization rate in both soils. The co-application of biochar and PB1 resulted in the sequestration of mineral N released, which was more pronounced in the Kamouraska clay soil. The co-application of biochar and PB2 resulted in moderate release of mineral N. This study showed that the co-application of biochar and PB can benefit agricultural soils by improving NO3-N retention in agroecosystems while increasing organic matter and promoting microbial biomass.

We identify P management strategies combining arbuscular mycorrhizal fungal (AMF) inoculation with rock phosphate or composted manure for intensive organic grain-production systems. We measured the response of plants traits and soil properties to the factorial combination of three rates of organic-approved P sources applied in rotation phase-1 of legume–flax cropping systems, and of granular AMF inoculant applied in the first, second, or both rotation phases, or not applied. Treatment combinations effects on the rhizosphere communities of AMF, fungi, and bacteria were tested by amplicon sequencing, in two pedoclimates. Inoculation had limited effects in both environments. Composted manure decreased lentil yield, but increased lentil N and P concentrations and soil P fertility on the Chernozem, while increasing pea productivity on the Luvisol. Composted manure applied in rotation phase-1 had a residual effect on flax productivity, N and P concentrations, and soil P fertility in both environments. Rock phosphate reduced soil P fertility and flax productivity on the Gray Luvisol. The β diversity of the rhizosphere communities was unaffected by treatments, while the α diversity of bacteria and AMF was altered by AMF inoculation and fertilization only in the Gray Luvisol. Correlations between microbial species and plant traits or soil properties were inconsistent, reflecting the complex relationships among microbial community, plant identity, and environmental conditions. Here, composted manure was more influential than AMF inoculation and rock phosphate. Given the influence of environmental conditions, small field trials are recommended before wide-scale adoption of their use.

Enhancing the stability of crop production is vital for agriculture under climate uncertainty. Conventional fallow and shallow-rooting pulse crops such as lentil (Lens culinaris Medic.) have been incorporated in oilseed-cereal cropping systems to cope with dry conditions on the semiarid Canadian prairies. However, the static and dynamic stability of these adaptation practices at a cropping system level is unclear due to the complexity of interactions. This study assessed the effects of diversified rotation systems as drought adaptation practices on the productivity and stability of oilseed-cereal cropping systems. Nine 3-year crop rotations were tested for two cycles at three sites from 2013 to 2016. The 3-year crop sequences included fallow, lentil, and spring wheat (Triticum aestivum L.) in rotation phase 1, followed by canola (Brassica napus L.), oriental mustard (Brassica juncea L.), and camelina (Camelina sativa L. Crantz) in phase 2, and the rotation phase 3 was durum wheat (Triticum turgidum L. subsp. durum (Desf.) Husn.) in all nine rotation systems. On average, the lentil system increased system productivity, expressed by annualized durum wheat equivalent yield, by 24% and 78% compared with the spring wheat and fallow systems, respectively. Stability analysis revealed that the lentil – B. juncea – durum wheat and lentil – B. napus – durum wheat systems had the least variation across the environments and were well adapted to high-yielding sites. The fully-phased rotations across various environments showed that the drought-induced reductions in system productivity ranged from 3 to 47% compared with yields under normal weather, with the lentil – oilseed – durum systems having least reduction. Quantitative assessments revealed that about 36% of the variation in system productivity was associated with rotation systems and additional 30% was due to weather-related factors. In conclusion, the inclusion of lentil in rotation increases systems productivity and reduces yield variation in oilseed-cereal cropping systems in changing environments.

Arbuscular mycorrhizal fungi (AMF) inoculation and preceding crop identity have been widely reported to affect crop performance and root-associated microbiomes. However, the underlying relationship between the resulting crop performance and the dynamics of root-associated microbiomes is still poorly explored. In this study, the interaction of AMF inoculant and preceding crop was tested in wheat (Triticum aestivum L.) and flax (Linum usitatissimum L.) based rotation systems under three fertilization levels. Effects on agronomic traits, root-associated microbiome, and the relationship between root-associated microbiome and crop productivity were investigated. Higher crop yields were produced following a pulse crop (i.e., Fabaceae harvested for dry seed) than a canola crop. Better yields were at least partially due to higher plant N and P uptake, possibly mediated by certain taxa of the root-associated microbiome, such as N2-fixing and H2-oxidizing bacteria. Some differential rhizosphere zOTUs between canola and pulse crops were significantly related to succeeding crop yield. The structure of the communities of AMF, fungi and bacteria responded differently to the influence of geographical location, plant identity and microecological zone (i.e. root and rhizosphere). Results showed that the microbial communities in belowground microecological zones have specific patterns of sensitivity to driving factors, and the dynamics of certain taxa belonging to some N2-fixing and H2-oxydizing bacterial groups may be involved in the effect of crop rotation on the productivity of wheat and flax.

The classification and physiology of the zoosporic plant-pathogen Olpidium brassicae and its relationships with the closely-related species are often confusing. This review focuses on these species and intends to differentiate them based on the literatures published since the discovery and establishment of the species by Woronin in 1878 under the name of Chytridium brassicae to current molecular era. The goal of this review is to help researchers better understand the taxonomy, the host range, and the potential role in plant health of O. brassicae-related species. To reach the goal, we reviewed the rationales behind the creation or reduction in synonymy of the different names for O. brassicae and its allied species in order to elucidate the evolution of the species concept on them based on the traditional morphological studies. Furthermore, the studies by molecular biology methods improve our knowledge and perspectives on O. brassicae and its host specificity. In particular, we clarify the differences between O. brassicae and Olpidium virulentus, and propose potential new research avenues. We therefore hope that this review will give a better perspective on Olpidium spp. and their potential role in the root microbiome of plants in natural environments and in agricultural settings.

Understanding the variation in how wheat genotypes shape their arbuscular mycorrhizal (AM) fungal communities in a prairie environment is foundational to breeding for enhanced AM fungi–wheat interactions. The AM fungal communities associated with 32 durum wheat genotypes were described by pyrosequencing of amplicons. The experiment was set up at two locations in the Canadian prairies. The intensively managed site was highly dominated by Funneliformis. Genotype influenced the AM fungal community in the rhizosphere soil, but there was no evidence of a differential genotype effect on the AM fungal community of durum wheat roots. The influence of durum wheat genotype on the AM fungal community of the soil was less important at the intensively managed site. Certain durum wheat genotypes, such as Strongfield, Plenty, and CDC Verona, were associated with high abundance of Paraglomus, and Dominikia was undetected in the rhizosphere of the recent cultivars Enterprise, Eurostar, Commander, and Brigade. Genetic variation in the association of durum wheat with AM fungi suggests the possibility of increasing the sustainability of cropping systems through the use of durum wheat genotypes that select highly effective AM fungal taxa residing in the agricultural soils of the Canadian prairies.

Arbuscular mycorrhizal (AM) fungi are an important determinant of plant performance, and conversely their community composition greatly depends on host plants and their neighbors. Understanding how the interaction of host plants and their neighbors affects AM fungal communities in afforested zones is of primary interest in forest ecology. We sampled roots and rhizosphere soils in monocultures and mixtures of black locust (Robinia pseudoacacia) and oriental arborvitae (Platycladus orientalis) to define AM fungal colonization level, spore density and communities using 454 sequencing. Neighboring oriental arborvitae only affected AM fungal community in black locust rhizosphere. For oriental arborvitae, however, growing in a mixture with black locust changed AM fungal colonization, sporulation and communities in the roots and rhizosphere. In particular, neighboring black locust modified the rhizosphere- and root-inhabiting AM fungal pool through improving soil NO3-N and water contents and reducing soil catalase activity, and the modification in the root AM fungal resource, especially the Glomus and Rhizophagus genera, further affected AM fungal colonization and sporulation under oriental arborvitae. All the results presented here suggest that both hosts and neighbors can largely affect AM fungal attributes mainly through changing soil nutrient levels and enzyme activity, whereas the reciprocal effects are not always symmetric.

Biological N2-fixation underpins the role of pulse crops in the development of sustainable cropping systems, but it is uncertain how nodulation and N accumulation may differ with pulse species, cultivars, and environments. This 3 yr field study investigated nodulation at the early and late flowering stages and seed and straw N uptake for chickpea (Cicer arietinum L.), dry bean (Phaseolus vulgaris L.), faba bean (Vicia faba L.), field pea (Pisum sativum L.), and lentil (Lens culinaris Medik.). At early flowering, all pulses except dry bean had more nodules in the wetter (2010) than drier year (2009). Faba bean had the most nodules followed by field pea and chickpea, while the nodulation varied with plant growth stages and environments. For both pea and lentil, more nodules were observed at early flowering, but higher nodule biomass was obtained at late flowering. Chickpea had higher nodule biomass at late than early flowering but number of nodules varied with year. Seed N uptake was highest in field pea, whereas straw N uptake was highest in faba bean. Our results suggest a possibility of improving pulse N2-fixation by targeting nodule numbers and nodule biomass, although the outcome of plant N uptake will vary with environments.

Agricultural production is dependent on inputs of nitrogen (N) whose cycle relies on soil and crop microbiomes. Crop diversification has increased productivity; however, its impact on the expression of microbial genes involved in N-cycling pathways remains unknown. Here, we assessed N-cycling gene expression patterns in the root and rhizosphere microbiomes of five oilseed crops as influenced by three 2-year crop rotations. The first phase consisted of fallow, lentil or wheat, and the second phase consisted of one of five oilseed crops. Expression of bacterial amoA, nirK and nirS genes showed that the microbiome of Ethiopian mustard had the lowest and that of camelina the highest potential for N loss. A preceding rotation phase of lentil significantly increased the expression of nifH gene by 23% compared with wheat and improved nxrA gene expression by 51% with chemical fallow in the following oilseed crops respectively. Lentil substantially increased biological N2 fixation and reduced denitrification in the following oilseed crops. Our results also revealed that most N-cycling gene transcripts are more abundant in the microbiomes associated with roots than with the rhizosphere. The outcome of our investigation brings a new level of understanding on how crop diversification and rotation sequences are related to N-cycling in annual cropping systems.

Co-applying biochar and paper mill biosolids (PB) improves the potential of these by-products as soil amendments. Assessing the response of soil microbial communities to the co-application of biochar and PB is of great importance to further understanding their effectiveness. This hypothesis was tested in a 112-day incubation study performed separately on two acidic soils (Kamouraska clay and St-Antoine sandy loam) using two PB types (PB1 with C/N = 24 and PB2 with C/N = 13), co-applied with one of three rates (0%, 2.5%, and 5% w/w) of pine (Pinus strobus L.) biochar. An unamended control and a mineral-fertilized treatment were used as a reference. In the Kamouraska clay soil, co-applying 5% biochar and any PB increased microbial activity compared to PB-only application, as indicated by the fluorescein diacetate (FDA) hydrolysis assay. In both soils, co-applying biochar and PB did not affect microbial diversity and community structure compared with PB only. The application of any PB, however, increased microbial activity in both soils, while only PB2 shifted microbial community structure. Within each amendment and in both soils, microbial activity was lower at day 112 than at days 28 and 56, while major temporal shifts were observed only for bacterial community structure. Indeed, the difference in bacterial community structure between amendments was more pronounced at day 112. This study suggests that co-applying biochar and PB can improve soil properties than application of PB alone by increasing soil microbial activity without side effects on microbial diversity and community structure, especially in acidic clay soils.

Rhizosphere microbes influence one another, forming extremely complex webs of interactions that may determine plant success. Identifying the key factors that structure the fungal microbiome of the plant rhizosphere is a necessary step in optimizing plant production. In a long-term field experiment conducted at three locations in the Canadian prairies, we tested the following hypotheses: (1) diversification of cropping systems influences the fungal microbiome of the canola (Brassica napus) rhizosphere; (2) the canola rhizosphere has a core fungal microbiome, i.e., a set of fungi always associated with canola; and (3) some taxa within the rhizosphere microbiome of canola are highly interrelated and fit the description of hub taxa. Our results show that crop diversification has a significant effect on the structure of the rhizosphere fungal community but not on fungal diversity. We also discovered and described a canola core microbiome made up of one zero-radius operational taxonomic unit (ZOTU), cf. Olpidium brassicae, and an eco-microbiome found only in 2013 consisting of 47 ZOTUs. Using network analysis, we identified four hub taxa in 2013: ZOTU14 (Acremonium sp.), ZOTU28 (Sordariomycetes sp.), ZOTU45 (Mortierella sp.) and ZOTU179 (cf. Ganoderma applanatum), and one hub taxon, ZOTU17 (cf. Mortierella gamsii) in 2016. None of these most interacting taxa belonged to the core microbiome or eco-microbiome for each year of sampling. This temporal variability puts into question the idea of a plant core fungal microbiome and its stability. Our results provide a basis for the development of ecological engineering strategies for the improvement of canola production systems in Canada.

Arbuscular mycorrhizal (AM) fungi are ecologically important for the growth and survival of most vascular plants. These fungi are known as obligate biotrophs that acquire carbon solely from host plants. A 13C-labeling experiment revealed the ability of axenically grown Rhizophagus irregularis DAOM 197198 to derive carbon from axenic culture on a relatively novel medium containing two sources of palmitic acid developed by Ishii (designated IH medium). In a separate experiment, this model fungus grew larger mycelia and produced more daughter spores on the IH medium in the presence of two Variovorax paradoxus strains than in axenic culture. In contrast, a strain of Mycobacterium sp. did not influence the growth of the AM fungus. Rhizophagus irregularis produced branched absorbing structures on the IH medium and, in monoxenic culture with V. paradoxus, sometimes formed densely packed hyphal coils. In this study, we report for the first time the formation of coarse terminal pelotons and of terminal and intercalary very fine (≈ 1 μm diameter) hyphal elongations, which could form daughter spores in the presence of V. paradoxus. This study shows the value of IH medium and certain rhizobacteria in the culture of R. irregularis DAOM 197198 in vitro.

Including pulses in wheat-based cropping systems in semiarid regions may be a strategy for sustainably intensifying crop production. However, the impact of an increase in the frequency of pulse crops on soil bacterial communities is not known. We tested the hypothesis that increasing the frequency of pea, lentil and chickpea in 4-year crop rotation systems would cause corresponding shifts in the soil bacterial community. The first cycle of a field experiment was conducted in 2010–2013 and the second cycle, in 2011–2014. 16S rDNA amplicon pyrosequencing was performed to examine the rhizosphere bacterial communities following the third year (phase-3) of the rotations and root bacterial communities during the fourth year (phase-4), when all rotations were seeded to wheat. We found that three consecutive years of pulse crops modified the structure and increased the diversity of the rhizosphere bacterial community. Changes in community composition led to changes in eleven groups of KEGG pathways, including an increase in nitrogen metabolism and a shift in the production of secondary metabolites towards high production of nitrogenous alkaloids in systems with high pulse frequency. Pulse identity had little influence on bacterial communities; the effect of pulses was related to soil mineral nitrogen level, which increased with pulse frequency. High pulse frequency reduced bacterial diversity in wheat roots in the fourth year of the rotations. The only dominant wheat root-associated operational taxonomic unit (OTU) positively related with wheat yield was identified as Rhizobium. One of the two dominant OTUs negatively related with wheat yield was typical of rotation systems with a pulse frequency of ≤1. Phase-4 grain yield was related with soil mineral nitrogen level. The inclusion of nitrogen in the agroecosystem through biological nitrogen fixation seems to be an important part of the beneficial effect of including pulses in wheat-based rotations. The effect of pulse frequency on the structure and function of rhizobacteria communities and on wheat is mitigated by drought in the semiarid prairie.

The response of soil microorganisms to applications of whole dairy manure slurry or the liquid fraction of the manure is not fully understood. This study evaluated the effect of whole dairy manure slurry in two trials of different durations and with different cultivation histories, and the effect of the liquid fraction after solids removal on microbial biomass, enzyme activity, and community composition in the soil of tall fescue (Festuca arundinacea Schreb.) swards in the south coastal region of British Columbia, Canada. Two trials were carried out, and fertilizer was applied four times per year. The trial 1 plots were treated with whole dairy manure slurry annually at 0, 400, or 800 kg total N ha−1 (control, M‐low, or M‐high, respectively), whereas the trial 2 plots were not treated with manure (control) or were treated with whole manure dairy slurry (WS) or a separate liquid fraction (LF) at 400 kg total N ha−1. Soil samples were collected at the 0‐to‐10‐cm soil depth after each harvest in 2013 and 2014. Results from two trials show that soil microbial and bacterial biomasses and dehydrogenase and alkaline phosphomonoesterase activities increased with the application of whole dairy manure. Soil microbial community composition was not significantly influenced by whole dairy manure in trial 1. In contrast, in trial 2, LF and WS had a similar influence on soil microbial biomass and dehydrogenase activity, but LF had a greater impact on soil microbial community structure, mainly by reducing the fungal abundance. We conclude that the response of soil microorganisms changed with the types and application rates of dairy manure slurry in grassland production.

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.

Arbuscular mycorrhizal (AM) fungi play an important role in the functioning and sustainability of agroecosystems, but they are also susceptible to changes in land use. The objective of this study was to determine the impact of agricultural land use practices on AM fungal communities and identify the factors that drive their assembly in the Mixed Prairie ecoregion of the North American Great Plains. Soil samples were collected from the four dominant agricultural land use types in this region (annual cropping, native grassland, tame grassland, and roadside ditches) at five locations and at three soil depths (0–15, 15–30, and 30–60 cm). The diversity and composition of the AM fungal communities were assessed using high throughput sequencing (454 pyrosequencing). We found that land use type significantly influenced the diversity and composition of the AM fungal communities. Annual cropland had the lowest diversity and a distinct community composition compared to the other land use types. This effect was most pronounced in the upper soil depth (0–15 cm), but was still evident in the lower depths (15–30 and 30–60 cm). Further analysis found a trend for AM fungal communities at lower soil depths to be a nested subset of communities in the top soil depth. Structural equation modeling revealed that land use affected AM fungal communities indirectly through the modification of plant communities and soil properties.

The inclusion of legumes in semi-arid native grasslands may promote the productivity and nutritive value of forage. This study was designed to assess the effect of legumes (the introduced legume Medicago sativa or the native legume Dalea purpurea) and soil P fertility (addition of 0, 50, or 200 P2O5 kg/ha at seeding) on the dry matter and nutrient content of native grasses mixtures, compared with the commonly used introduced forage grass Bromus biebersteinii grown with M. sativa. Plant harvests were performed in September 2008, July 2009 and September 2009. Plants nutrient content, δ15N value and dry matter were analysed. Results show that the M. sativa enhanced the N and P concentrations of native grass mixtures early in the summer, as well as the N concentration in Bouteloua gracilis in late summer of the driest year, 2009. The higher AM fungal diversity promoted by M. sativa was positively correlated with the dry matter and nitrogen uptake of M. sativa and with the P concentration of native grasses, in early summer. Overall, this study shows that M. sativa promoted beneficial AM fungal taxa and improved forage production in the semi-arid prairies.

In the Canadian Prairies, the production of pulse crops has increased considerably since the 1980′s, including agronomically important crops such as field peas (Pisum sativum L.), lentils (Lens culinaris Medik.), and chickpeas (Cicer arietinum L.). As producers increase and intensify the use of pulse crops, more knowledge is needed to understand the impact these crops have on important soil biological resources. In this study, we used a high-throughput sequencing approach (454 amplicon sequencing) to determine if increasing the frequency of pulses in crop rotations affects the diversity and composition of soil and root-associated fungal communities and the proportion of functional guilds such as pathogens, saprophytes, and mutualists. This study was conducted in a semiarid region of the Canadian Prairies with nine different 4-year rotations including field pea, lentil, and chickpea grown once, twice, three times or not at all with wheat (Triticum aestivum L.). Soil fungal communities were assessed following the third year of the rotations and root-associated fungal communities were assessed during the fourth year when all of the rotations were seeded to wheat. Our results revealed that the inclusion of two or more pulses into 4-year crop rotations caused a significant shift in the composition of the soil fungal community, a decrease in fungal diversity, and an increase in the proportion of fungal pathotrophs compared to continuous wheat or rotations with only one pulse crop. Several important pathogens of pulse crops increased two to three-fold in pulse intensified rotations including Fusarium avenaceum, F. redolens, and Alternaria alternata, and crop-specific pathogens such as Didymella pinodella and F. solani increased in field pea intensified rotations. The build-up of fungal pathogens in the soil indicates that farmers in this region should avoid growing pulse crops in consecutive years or in close succession to avoid developing disease problems. This study also revealed that rotation sequence explained more of the variation in the fungal community compared to the previous crop and affected the relative abundance of several important fungal pathogens. This highlights the importance of crop selection in rotations and provides a tool that farmers can use to manage soil fungal communities to ensure the sustainability and productivity of agricultural systems.

Soil microorganisms play a critical role in the biosphere, and the influence of cropland fertilization on the evolution of soil as a living entity is being actively documented. In this study, we used a shotgun metagenomics approach to globally expose the effects of 50-year N and P fertilization of wheat on soil microbial community structure and function, and their potential involvement in overall N cycling. Nitrogen (N) fertilization increased alpha diversity in archaea and fungi while reducing it in bacteria. Beta diversity of archaea, bacteria and fungi, as well as soil function, were also mainly driven by N fertilization. The abundance of archaea was negatively impacted by N fertilization while bacterial and fungal abundance was increased. The responses of N metabolism-related genes to fertilization differed in archaea, bacteria and fungi. All archaeal N metabolic processes were decreased by N fertilization, while denitrification, assimilatory nitrate reduction and organic-N metabolism were highly increased by N fertilization in bacteria. Nitrate assimilation was the main contribution of fungi to N cycling. Thaumarchaeota and Halobacteria in archaea; Actinobacteria, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Deltaproteobacteria in bacteria; and Sordariomycetes in fungi participated dominantly and widely in soil N metabolic processes.

In August 2002, Phytophthora megasperma Drechs. was isolated from wilted plants of Asparagus officinalis L. cv. Guelph Millenium displaying spear and crown rot. Six affected plants were sampled in a commercial asparagus field located in the Saguenay-Lac-Saint-Jean Region (300 km northeast of Montreal, Quebec, Canada). The fungus was isolated from asparagus fern stalks, crown tissue, and spears after a rainy period and identified using morphological and cultural characteristics (2). In pinkish 4-week-old cultures, unbranched stalks bore abundant sporangia, which were ovoid to obpyriform in shape, 15 to 45 m long, and 10 to 30 m in diameter. Characteristic circular oospores >30 m in diameter were produced on V8 juice agar at 25°C in darkness after 1 month. Pathogenicity was tested on asparagus cvs. Guelph Millenium and Jersey Knight. A mycelium suspension (3 ml at 106 CFU/ml) prepared from 1-week-old shaken potato dextrose (PD) broth was sprayed on 30 1-week-old seedlings grown in petri plates filled with sterilized, moist, sandy soil and held at 20°C (day/night). Controls received sterile PD broth. Within 3 weeks of incubation in the dark, inoculated seedlings exhibited necrotic symptoms similar to those observed initially, while controls remained healthy. The pathogen was isolated from 75% of the ‘Guelph Millenium’ and 98% of the ‘Jersey Knight’ symptomatic seedlings, but not isolated from the control seedlings. In North America, disease caused by P. megasperma resulting in yield loss has been reported in California and New York (1,3). In Canada, the etiology of asparagus diseases is not well characterized. To our knowledge, this is the first report of P. megasperma on asparagus plants in Canada. References: (1) P. A. Ark and J. T. Barrett. Phytopathology 28:754, 1938. (2) D. C. Erwin et al. Phytophthora: Its Biology, Taxonomy, Ecology, and Pathology. The American Phytopathological Society, St Paul, MN, 1983. (3) T-L. Kuan and D. C. Erwin. Phytopathology 70:333, 1980.

Durum wheat (Triticum durum Desf.) is an important crop in western Canada. In 2005, Arthrinium sacchari was frequently isolated from soil and durum wheat plants of the semi-arid fields of Swift Current, Saskatchewan, Canada (50°16′N, 107°44′W). The susceptibility of durum wheat to damping-off caused by this fungus was evaluated. To our knowledge, this is the first report of A. sacchari in North America (1) and the first mention of its association with durum wheat. DNA was extracted (MoBio Isolation Kit, Carlsbad, CA) from 2-week-old A. sacchari isolates (FBC.3, FBC.45, and FBC.143) grown on PDA. The internal transcribed spacer (ITS) of the rDNA was amplified from each isolate and sequenced (Plant Biotechnology Institute, Saskatoon, SK, Canada) and similarity analyses were performed using the BLAST search algorithm in GenBank. All three sequences (Accession Nos. EF076710, EF076711, and EF076712A) showed 99% similarity with A. sacchari (Accession No. AF393679). An in vitro assay was performed by placing 1-cm2 agar plugs containing mycelia of A. sacchari (FBC.3, FBC.45, and FBC.143) onto surface-sterilized durum. Surface-sterilized seeds inoculated in the same way with Fusarium graminearum or F. avenaceum were used as negative controls, and noninoculated surface-sterilized seeds were used as a positive control. A second in vitro assay involved inoculating the same isolates onto seeds placed in sterilized sandy soil. In both assays, 10 seeds per petri plate and three plates per treatment were used and plates were incubated at 21°C for 1 week in darkness. All experiments were performed twice. On PDA, preemergence damping-off was found in 60% of A. sacchari FBC.3, 55% of A. sacchari FBC.45 and FBC.143, 50% of F. avenaceum, and 58% of F. graminearum inoculated seeds. In sterilized soil, the incidence of preemergence damping-off ranged from 43 to 30%. Subsequent incubation over a period of 3 weeks resulted in 100% postemergence damping-off in A. sacchari FBC.45 and FBC.3 as well as in both Fusarium spp. inoculated controls, 60% postemergence damping-off in A. sacchari FBC.143, and no damping-off in the noninoculated control. Arthrinium and Fusarium spp. were reisolated only from symptomatic plants, satisfying Koch's postulates. In conclusion, durum wheat is highly susceptible to damping-off caused by A. sacchari, showing characteristic dark brown or violet lesions in infected tissues. A. sacchari was previously reported to be present in South America and eastern Asia. In China, it is considered an important mycotoxigenic species (2). Thus, infection of durum wheat crops with A. sacchari could pose a significant threat to North American wheat production. References: (1) D. F. Farr et al. Fungal Databases. Systematic Botany and Mycology Laboratory. Online publication. ARS, USDA, 2006. (2) X. J. Liu et al. Acta Mycol. Sinica 7:221, 1988.

The soil bacteria diversity and corresponding environmental data made available here are from a 72-field plot experiment testing the effect of pulse frequency in nine wheat-based rotation systems, in the semiarid prairie. The data include sequences of the V6–V8 regions of bacterial 16S rDNA from soil and root extracts, generated using Roche GS FLX Titanium technology, and associated environmental data, specifically levels of soil organic carbon, total carbon, total nitrogen, total phosphorus, pH, electrical conductivity, and extractible sulfate sulfur, copper, iron, manganese, zinc, potassium, nitrate nitrogen, phosphate phosphorus, calcium, and magnesium in the 0–15 cm soil layer, and mineral nitrogen and phosphate in the 0–120 cm soil layer. The grain yield of wheat in the last (4th) phase of the crop rotation systems is also given. The data can be used in meta-analyses of the effect of pea, lentil and chickpea in wheat-based cropping systems on soil bacterial diversity or for monitoring the evolution of soil bacteria communities in cultivated prairie soils in the context of climate change. Samples were collected between 2012 and 2014.

During the next decade it will be necessary to develop novel combinations of management strategies to sustainably increase crop production and soil resilience. Improving agricultural productivity, while conserving and enhancing biotic and abiotic resources, is an essential requirement to increase global food production on a sustainable basis. The role of farmers in increasing agricultural productivity growth sustainably will be crucial. Farmers are at the center of any process of change involving natural resources and for this reason they need to be encouraged and guided, through appropriate incentives and governance practices, to conserve natural ecosystems and their biodiversity, and minimize the negative impact agriculture can have on the environment. Farmers and stakeholders need to revise traditional approaches not as productive as the modern approaches but more friendly with natural and environmental ecosystems values as well as emerging novel tools and approaches addressing precise farming, organic amendments, lowered water consumption, integrated pest control and beneficial plant-microbe interactions. While practical solutions are developing, science based recommendations for crop rotations, breeding and harvest/postharvest strategies leading to environmentally sound and pollinator friendly production and better life in rural areas have to be provided. (C) 2019 Elsevier B.V. All rights reserved.

Certain H2-oxidizing rhizobacteria promote the growth of legume plants nodulated with rhizobia devoid of an uptake hydrogenase system (Hup−). We demonstrated and assessed the plant growth-promoting ability of H2-oxidizing rhizobacteria naturally associating with lentil roots nodulated by rhizobia possessing an uptake hydrogenase system (Hup+ lentil) in semiarid Canada. The ten H2-oxidizing rhizobacteria isolated were strains of Variovorax paradoxus, Variovorax sp., Rhodococcus sp., Mycobacterium sp., Acinetobacter sp., Acinetobacter calcoaceticus, and Curtobacterium sp. Several of these strains increased Hup+ lentil shoot and root biomasses, and root nodule number in the absence or presence of drought stress. Inoculation with H2-oxidizing rhizobacteria enhanced the growth of Hup+ lentil infected by the fungal root pathogens Fusarium avenaceum, Rhizoctonia solani, and Pythium ultimum. Fusarium avenaceum growth was markedly suppressed by all H2-oxidizing rhizobacteria in vitro, and seven isolates also suppressed the growth of both R. solani and P. ultimum. Siderophore production was detected in nine isolates and one isolate could solubilize phosphate. Indole-3-acetic acid production was found in four isolates, and 1-aminocyclopropane-1-carboxylate deaminase activity in six isolates. Most H2-oxidizing rhizobacterial isolates exhibited multiple plant growth-promoting attributes and all isolates exhibited at least one. Our results suggest that the H2-oxidizing rhizobacteria naturally associating with lentil roots in semiarid Canada are beneficial in an Hup+ environment.

Variations in root-associated fungal communities contribute to the so-called ‘crop rotation benefit’ on soil productivity. We assessed the effects of chickpea, lentil, and pea in wheat-based rotations, as compared to wheat monoculture, on the structure of root-associated fungal communities, and described the legacy of pulses on a following wheat crop. The internal transcribed spacer (ITS) and 18S rRNA gene markers, and 454 amplicon pyrosequencing were used to describe the fungal communities of crop roots and rhizosphere soil in a field experiment and agronomic data were collected. Pulses influenced only the structure of the non-mycorrhizal fungal community of roots. Fusarium tricinctum, Clonostachys rosea, Fusarium redolens, and Cryptococcus sp. were specific to certain crops. Despite the absence of selective effects of pulses on their associated arbuscular mycorrhizal (AM) fungal community, pea had a legacy effect on the structure of the AM fungal community associated with the roots of the following wheat crop, in one of the two year/sites examined. Species of Mortierella, Cryptococcus, and Paraglomus in wheat rhizosphere soil may benefit yield, whereas species of Fusarium, Davidiella, Lachnum, Sistotrema and Podospora may reduce yield. The effect of pulse crops on root fungal communities varied with rotation crop species. Pulses had various effects on the physiology of the following wheat crop, including increased productivity.

Green manure crops may have a role to play in the development of sustainable agricultural systems in the semiarid northern Great Plains of North America. This study determined the benefits of different green manure crops, seeding dates, and termination methods on soil nitrogen, phosphorus, and moisture, as well as the performance of durum wheat following green manures the following year. Field experiments were conducted at Swift Current, Saskatchewan, from 2006 to 2009. Three green manure crops [forage pea (Pisum sativum L.), chickling vetch (Lathyrus sativus L.), and black lentil (Lens culinaris Medik.)] were seeded in May, June, and July, and terminated at full bloom using glyphosate, rototilling or by frost. Other treatments included summerfallow and stubble of selected crops harvested for grain or silage. Different green manure crops, seeding dates or termination methods had similar effects on soil moisture, available N, and exchangeable P at termination or the following spring. These effects of green manure management on soil residual characteristics were comparable to those observed under summerfallow, but higher than those on grain or silage stubble. Therefore, green manure is a viable alternative to summerfallowing and could be seeded any time during the growing season. If seeded late, green manure could be terminated by frost, thus saving on costs.

Annual cropping systems are dynamic environments where soil bacterial communities are responsive to various management practices such as crop rotations, and to seasonal fluctuations of edaphic properties. However, in semiarid regions the impact of crops on the soil bacterial community appears to be modulated or affected by edaphic properties such as soil moisture availability. Therefore the objective of this study was to determine the relative influence of crops (wheat, lentil, field pea, canola, and a fallow treatment), soil chemistry, and edaphic properties on the diversity and composition of soil bacterial communities in a semiarid agroecosystem. We used a temporal sampling strategy and high throughput sequencing approach to monitor changes in the soil bacterial community in relation to crop host identity and phenology and soil properties. Structuring of the bacterial community across the 20 experimental plots was driven primarily by soil pH which varied strongly (min: 5.25, max: 6.97) across the site. Weak temporal shifts in the bacterial community were observed across the growing season and were related to seasonal variation in soil moisture (min: 8.3%, max: 20.3%), soil temperature (min. daily mean: 3.3 °C, max. daily mean: 21.1 °C), and fluctuation in available phosphate in the soil (min: 0.003 μg cm −2 day −1 , max: 0.290 μg cm −2 day −1 ). These temporal and spatial shifts were not influenced by crop host identity as similar bacterial communities were observed among the crops and fallow treatment. Variance partitioning revealed that soil pH and soil moisture accounted for a high proportion of the variation of the soil bacterial community, while crops had no significant impact in the study. Edaphic factors appeared to override or level the effect of crops on the soil bacterial community. These results highlight the importance of accounting for edaphic properties for managing soil bacterial communities in agroecosystems.

Lentil (Lens culinaris Medikus) may have a potential to enhance the productivity of agroecosystems in dry areas where water and nutrients are limited. This study quantified soil water, residual soil nitrogen (N), and crop yields in lentil-based systems in comparison with continuous cereal and conventional summerfallow systems. A 3-yr cropping sequence study was conducted for three cycles in Saskatchewan (50.28°N, 107.79°W) from 2007 to 2011. On average, soil retained 187, 196 and 337 mm of water in the 0–1.2 m depth at crop harvest in 2008, 2009 and 2010, respectively. Summerfallow contained the same amounts of water as the cropped treatments at the harvest in 2009 and 2010. However, in 2008, summerfallow contained more soil water than the cropped treatments. The effect of lentil cultivar on soil water conservation varied with years; the cultivars Glamis, Laird and Sedley conserved highest amounts of soil water by the planting time of 2009 and 2010, but no differences were found among cultivars in 2011. Soil available N (NO3− + NH4+) at spring planting time was 50.4 kg ha−1 in the preceding lentil treatments, which was 44% higher compared with preceding barley or flax, but was 25% lower compared with preceding summerfallow. Lentil cultivars had a similar amount of soil residual N. Grain production in the 3-yr rotation averaged 6.3 t ha−1 per rotation for the wheat–lentil–durum system and 6.8 t ha−1 for the wheat–cereal–durum monoculture, averaging 36% greater compared with wheat–summerfallow–durum system. The lentil system increased total grain production through the access of residual soil water and biologically fixed N, whereas continuous cereal system relies on inorganic fertilizer input for yield. Summerfallow system relies on ‘mining’ the soil for nutrients. We conclude that the adoption of lentil systems will enhance grain production through the use of residual soil water and available N.

Plant roots shape the structure of the soil microbiome by producing a wide array of phytochemicals, which in turn impact plant growth and health. The synthesis of root metabolites is a dynamic process that is modulated by interactions with soil microorganisms. This study explored the regulation of soil-borne fungal endophytes and pathogens by the production of phytochemicals in chickpea (Cicer arietinum L.) roots colonized or not colonized by the arbuscular mycorrhizal (AM) fungus Rhizophagus irregularis. Proteins and low-molecular-mass phytochemicals were extracted from chickpea roots and fractionated by flash chromatography and high pressure liquid chromatography (HPLC). The effects of these metabolites on the soil-borne fungal endophytes Trichoderma harzianum and Geomyces vinaceus and on the pathogens Fusarium oxysporum and Rhizoctonia solani were tested in 96-well plate assays. One protein fraction from the AM roots, which contained an apparent 34 KDa chitinase/chitin-binding domain and 24 KDa non-specific lipid transfer protein, non-selectively repressed the fungal endophytes and pathogens. By contrast to the protein fraction, the low-molecular-mass fractions were often selective. Eighteen fractions stimulated specific fungal species and seven fractions inhibited others. Several protein and low-molecular-mass phytochemicals in chickpea roots influence fungal endophytes. The difference in the response of fungal species to the phytochemicals suggests that these metabolites could be involved in the so called host ‘preference’ of fungal endophytes or ‘resistance’ to pathogens. This research reveals that the majority of the bioactive root metabolites could be involved in the selective association of chickpea and fungal endophytes while a few compounds provided resistance by suppressing the pathogenic species.

While establishment and persistence of arbuscular mycorrhizal (AM) fungal inoculants in agricultural fields are critical to their success, little is known about how farming practices can affect their establishment in field. We developed a probe assay specific to a commercial AM fungal inoculant (Rhizoglomus irregulare DAOM197198) and tested its establishment among different grain cropping practices in the field. Establishment of the fungus was not related to cropping, or inoculation practices. Instead, establishment was site specific over the two growing seasons. Our results show that it is not yet possible to predict inoculation success in the field and use of biofertilizers requires further research under field conditions to identify key factors involved in establishment and persistence.