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The undulating topography of Prairie Pothole Region of North America creates spatial and temporal variability in soil moisture and nutrient levels, affecting microbial community processes and GHG emissions. By identifying differences in soil bacterial and archaeal community composition and the abundance of nitrogen cycling genes in permanent cover vs. annual crop land over two growing seasons (2017 and 2018), we were able to assess the effects of topography and land use on the functional capacity of the soil microbiome. Permanent grassland cover was associated with higher bacterial diversity in upland positions and lower diversity in low lying depressions. Bacterial community composition was also significantly different between cultivated and permanent cover at all points along the topographic slope, with the largest effects seen in the footslope and backslope positions. Compared to permanent cover, soil from annual cropland had consistently more abundant nitrifiers, including Nitrospira in the toeslope and backslope, and Nitrososphaeraceae in the shoulder and knoll samples while soils from permanent cover had a greater abundance of several Alphaproteobacteria from Rhodospirillales and Hyphomicrobiaceae across multiple upland positions. Upland soils from annual cropland also had consistently higher abundance of both bacterial and archaeal ammonia oxidizing (amoA) genes and a higher ratio of nirK:nirS genes compared to those from permanent cover. These differences in microbial community composition were associated with higher N2O and CO2 emissions in upland soils in annual cropland, however there were no differences in GHG emissions between the two systems in low lying positions.

AimsPhyllosphere bacteria play critical roles in plant growth promotion, disease suppression and global nutrient cycling but remain understudied.MethodsIn this project, we examined the bacterial community on the phyllosphere of eight diverse lines ofBrassica napusfor ten weeks in Saskatoon, Saskatchewan Canada.ResultsThe bacterial community was shaped largely by plant growth stage with distinct communities present before and after flowering. Bacterial diversity before flowering had 111 core members with high functional potential, with the peak of diversity being reached during flowering. After flowering, bacterial diversity dropped quickly and sharply to 16 members of the core community, suggesting that the plant did not support the same functional potential anymore.B. napusline had little effect on the larger community, but appeared to have more of an effect on the rare bacteria.ConclusionsOur work suggests that the dominant bacterial community is driven by plant growth stage, whereas differences in plant line seemed to affect rare bacteria. The role of these rare bacteria in plant health remains unresolved.

Seeds are reproductive structures able to carry and transfer microorganisms that play an important role in plant fitness. Genetic and external factors are reported to be partly responsible for the plant microbiome assemblage, but their contribution in seeds is poorly understood. In this study, wheat, canola, and lentil seeds were analyzed to characterize diversity, structure, and persistence of seed-associated microbial communities. Five lines and 2 generations of each crop were subjected to high-throughput amplicon sequencing of the 16S rRNA and internal transcribed spacer (ITS) regions. Bacterial and fungal communities differed most by crop type (30% and 47% of the variance), while generation explained an additional 10% and 15% of the variance. The offspring (i.e., generation harvested in 2016 at the same location) exhibited a higher number of common amplicon sequence variants (ASVs) and less variability in microbial composition. Additionally, in every sample analyzed, a “core microbiome” was detected consisting of 5 bacterial and 12 fungal ASVs. Our results suggest that crop, genotype, and field environmental conditions contributed to the seed-associated microbial assemblage. These findings not only expand our understanding of the factors influencing the seed microbiome but may also help us to manipulate and exploit the microbiota naturally carried by seeds.

Soil is an important source of bacteria and fungi for the plant, but seeds can also provide microbial inocula through heritable or stochastic assembly. Seed-associated microbial communities can potentially interact with the host plant through multiple generations. Here, we assessed the impact of two different soil types on the seed microbiome assembly of seven lentil (Lens culinaris) genotypes under environmentally controlled conditions and examined the vertical transmission of bacterial communities from seed to seed across two generations. Bulk soil microbiomes and seed microbiomes were characterized using high-throughput amplicon sequencing of the bacterial 16S rRNA gene. Our results revealed that bacterial communities in the two soils differed significantly and that bacterial communities associated with seeds were significantly impacted by genotype (15%) in one of the soils. Co-occurrence of amplicon sequence variants between generations suggests that members of the genera Cutibacterium, Methylobacterium, Sphingomonas, Streptococcus and Tepidimonas are transmitted and preserved in lentil genotypes irrespective of the soil in which they were grown. Increasing our knowledge of how microbial communities carried by seeds are assembled, transmitted and preserved offers a promising way for future breeding programs to consider microbial communities when selecting for more resilient and productive cultivars.

The development of microbial networks is central to ecosystem functioning and is the hallmark of complex natural systems. Characterizing network development over time and across environmental gradients is hindered by the millions of potential interactions among community members, limiting interpretations of network evolution. We developed a feature selection approach using data winnowing that identifies the most ecologically influential microorganisms within a network undergoing change. Using a combination of graph theory, leave-one-out analysis, and statistical inference, complex microbial communities are winnowed to identify the core organisms responding to external gradients or functionality, and then network development is evaluated against these externalities. In a plant invasion case study, the winnowed microbial network became more influential as the plant invasion progressed as a result of direct plant-microbe links rather than the expected indirect plant–soil–microbe links. This represents the first use of structural equation modeling to predict microbial network evolution, which requires identification of keystone taxa and quantification of the ecological processes underpinning community structure and function patterns.

The plant microbiome has been recently recognized as a plant phenotype to help in the food security of the future population. However, global plant microbiome datasets are insufficient to be used effectively for breeding this new generation of crop plants. We surveyed the diversity and temporal composition of fungal communities in the root and rhizosphere of Brassica napus, the world's second largest oilseed crop, weekly in eight diverse lines at one site and every three weeks in sixteen lines, at three sites in 2016 and 2017 in the Canadian Prairies. 14,944 unique amplicon sequence variants (ASV) were detected based on the internal transcribed spacer region, with an average of 43 ASVs per root and 105 ASVs per rhizosphere sample. Temporal, site-to-site, and line-driven variability were key determinants of fungal community structure. This dataset is a valuable resource to systematically extract information on the belowground microbiome of diverse B. napus lines in different environments, at different times in the growing season, in order to adapt effective varieties for sustainable crop production systems.

Understanding how soil fertility and current practices affect microbial function in different soils is important for the development of sound management recommendations. However, interactions of the soil matrix with topography and climate obscure these interpretations. A long-term soil quality experiment was established in 1990 at Lethbridge, AB to examine the effects of agricultural management practices on different soils transplanted to a common location to normalize for climatic and topographic influences. Transplanted soils were continuously cropped to wheat with residues removed at harvest, with and without nitrogen (N) fertilizer (0 or 60 kg N ha−1). Phospholipid fatty acids (PLFA) profiling of whole communities and analysis of N-cycling functional genes in 10 of the transplanted soils sampled in 2012 revealed that soil origin and land use history had a dominant long-term impact on microbial abundance and community composition. Long-term N fertilizer application did not influence total microbial biomass, bacterial, and fungal abundance. The highest microbial biomass (ca. 25 nmol PLFA g−1 soil) was observed in more fertile (CC (cereal cultivated)) and RM (30 t ha−1 yr−1 manure) soils whereas the lowest biomass was found in transplanted sub-surface soils from B (6 nmol PLFA g−1 soil) and C horizons (8 nmol PLFA g−1 soil). Bacterial amoA, nirK and nirS community compositions were significantly influenced by N application. However, the degree of influence was mainly regulated by soil origin. Long-term N fertilization resulted in convergence of bacterial amoA community structure of CC and PL but not RM and DTF soils; archaeal amoA was not affected by N application. The reliance of the microbial community on inherent soil fertility was exacerbated by residue removal and was indicated by the strong influence of soil origin which reflected soil genesis and land use history. These findings reveal a persistent effect of soil legacy on soil microbial communities. Agricultural soil productivity can be enhanced by integrating soil history information into strategies for developing sustainable management practices.

Soil temperature affects the rate of C-cycle processes by influencing the activities of microbial communities but little is known about whether the effects on these communities are consistent in different soils. We studied bacterial and fungal communities in six different soils, originating from two different Canadian climatic regions and incubated for three years at a common field site under ambient or warming (ca. +4.6 °C for 653 d of warming) conditions. Similar to early responses (reported after 295 d of warming), soil respiration is consistently higher (up to 2.8-fold) for 653 d of warming. However, soil origin-related differences in the community structure of bacteria were smaller at the end of the experiment, suggesting that environmental factors and management practices are important in shaping the structure of communities, but that this is a cumulative effect over time. In contrast, warming-induced shifts were greater and consistent across soils after longer period of soil warming. These shifts coincided with significant increases in the relative proportions of some potentially copiotrophic bacteria (e.g., Thermoleophilia, Alphaproteobacteria, and Bacilli). Fungal responses to warming, determined at the end of incubation, were largely soil-specific. The relative proportions of some fungi (e.g., Nectriaceae) increased with warming while several other taxa (e.g., Mortierellaceae and Lasiosphaeriaceae) showed significant reductions with warming. Unlike community structure, differences in the DNA content, microbial biomass carbon (MBC), and abundance of bacteria or fungi between the control and warmed soils were minor. This might be related to depletion of readily available substrates because measurements were made a year after the annual addition of litter. Our observation that community shifts became more pronounced over time suggests that these differences may have been realized through physiological temperature optima and through resulting shifts in resource availability.

Agricultural practices can influence soil microbial communities, which are the primary regulators of soil carbon and nutrient cycling processes. Differences in microbial community composition have the potential to affect the fate of carbon and nutrients during decomposition and may therefore influence the retention of C and provisioning of crop nutrients in agroecosystems. Long term management-induced shifts in microbial communities and resource availability may interact to affect the microbial utilization of fresh inputs of crop residues in the short term, with lasting impacts on soil C accrual and fertility. The objective of this study was to investigate whether long-term organic and conventional management resulted in differences in microbial residue decomposition. Soils under conventional and organic management planted with annual crops or with a mix of annual crops and three years of perennial alfalfa were collected from a long-term (19 y) field study in Saskatchewan, Canada and were incubated in the laboratory with and without 13C-labelled barley residues for 98 d. We measured extracellular enzyme activities (EEAs) and the incorporation of crop residue-derived C within major microbial groups (fungi, actinobacteria, and Gram positive and negative bacteria) during decomposition. Total PLFA biomass and EEAs were highest in soils from the conventional-annual system, similar between the conventional and organic perennial systems, and similar or lowest in the organic-annual system. Crop residue additions alleviated these differences; that is, in residue-amended soils total PLFA biomass, EEAs, and the abundance of the fungal biomarker increased in the organic systems compared to the unamended soils to become similar to the conventional systems. In contrast, residue additions induced small or no changes in biomass and EEAs in the conventional-annual soils. Using 13C-PLFA-SIP we showed that the general pattern of microbial succession during decomposition was similar among soils, but that fungi and especially actinobacteria were relatively more dominant in organic compared to conventionally managed soils during early and later stages of decomposition, respectively. Thus, shifts in the decomposer community composition were greater in soils originating from organic management, possibly as a result of larger changes in resource availability during the incubation that advanced the rate of microbial succession. This may reinforce long term differences in SOC quality and nutrient availability between management regimes. Organically-managed cropping systems are particularly reliant on biological cycling of organic nutrients to support crop growth. This work reinforces the importance of adequate crop residue returns for maintaining soil function, particularly where external organic amendments are not applied to balance nutrients exported as crop products.

The plant microbiome has been recently recognized as a plant phenotype to help in the food security of the future population. However, global plant microbiome datasets are insufficient to be used effectively for breeding this new generation of crop plants. We surveyed the diversity and temporal composition of bacterial and fungal communities in the root and rhizosphere of Brassica napus, the world's second largest oilseed crop, weekly in eight diverse lines at one site and every three weeks in sixteen lines, at three sites in 2016 and 2017 in the Canadian Prairies. We sequenced the bacterial 16S ribosomal RNA gene generating a total of 127.7 million reads and the fungal internal transcribed spacer (ITS) region generating 113.4 million reads. 14,944 unique fungal amplicon sequence variants (ASV) were detected, with an average of 43 ASVs per root and 105 ASVs per rhizosphere sample. We detected 10,882 unique bacterial ASVs with an average of 249 ASVs per sample. Temporal, site-to-site, and line-driven variability were key determinants of microbial community structure. This dataset is a valuable resource to systematically extract information on the belowground microbiome of diverse B. napus lines in different environments, at different times in the growing season, in order to adapt effective varieties for sustainable crop production systems.

Long-term contrasts in agricultural management can shift soil resource availability with potential consequences to microbial carbon (C) use efficiency (CUE) and the fate of C in soils. Isothermal calorimetry was combined with 13C-labeled glucose stable isotope probing (SIP) of 16S rRNA genes to test the hypothesis that organically managed soils would support microbial communities with greater thermodynamic efficiency compared to conventional soils due to a legacy of lower resource availability and a resultant shift toward communities supportive of more oligotrophic taxa. Resource availability was greater in conventionally managed soils, with 3.5 times higher available phosphorus, 5% more nitrate, and 36% more dissolved organic C. The two management systems harbored distinct glucose-utilizing populations of Proteobacteria and Actinobacteria, with a higher Proteobacteria:Actinobacteria ratio (2.4 vs. 0.7) in conventional soils. Organically managed soils also harbored notable activity of Firmicutes. Thermodynamic efficiency indices were similar between soils, indicating that glucose was metabolized at similar energetic cost. However, differentially abundant glucose utilizers in organically managed soils were positively correlated with soil organic matter (SOM) priming and negatively correlated to soil nutrient and carbon availability, respiration, and heat production. These correlation patterns were strongly reversed in the conventionally managed soils indicating clear differentiation of microbial functioning related to soil resource availability. Fresh C addition caused proportionally more priming of SOM decomposition (57 vs. 51%) in organically managed soils likely due to mineralization of organic nutrients to satisfy microbial demands during glucose utilization in these more resource deprived soils. The additional heat released from SOM oxidation may explain the similar community level thermodynamic efficiencies between management systems. Restoring fertility to soils with a legacy of nutrient limitation requires a balanced supply of both nutrients and energy to protect stable SOM from microbial degradation. These results highlight the need to consider managing C for the energy it provides to ıcritical biological processes that underpin soil health.

Widespread global changes, including rising atmospheric CO2 concentrations, climate warming and loss of biodiversity, are predicted for this century; all of these will affect terrestrial ecosystem processes like plant litter decomposition. Conversely, increased plant litter decomposition can have potential carbon-cycle feedbacks on atmospheric CO2 levels, climate warming and biodiversity. But predicting litter decomposition is difficult because of many interacting factors related to the chemical, physical and biological properties of soil, as well as to climate and agricultural management practices. We applied 13C-labelled plant litter to soil at ten sites spanning a 3500-km transect across the agricultural regions of Canada and measured its decomposition over five years. Despite large differences in soil type and climatic conditions, we found that the kinetics of litter decomposition were similar once the effect of temperature had been removed, indicating no measurable effect of soil properties. A two-pool exponential decay model expressing undecomposed carbon simply as a function of thermal time accurately described kinetics of decomposition. (R2 = 0.94; RMSE = 0.0508). Soil properties such as texture, cation exchange capacity, pH and moisture, although very different among sites, had minimal discernible influence on decomposition kinetics. Using this kinetic model under different climate change scenarios, we projected that the time required to decompose 50% of the litter (i.e. the labile fractions) would be reduced by 1–4 months, whereas time required to decompose 90% of the litter (including recalcitrant fractions) would be reduced by 1 year in cooler sites to as much as 2 years in warmer sites. These findings confirm quantitatively the sensitivity of litter decomposition to temperature increases and demonstrate how climate change may constrain future soil carbon storage, an effect apparently not influenced by soil properties.

Aggregation is important for soil functioning, providing physical protection of organic matter and microbial inhabitants. Tillage disrupts aggregates, increases wind and water erosion of soils and exposes formerly protected organic matter to decomposition and losses. Microbial biomass and community dynamics in dry-sieved aggregate-size classes from long-term no-till (NT) and conventionally tilled (CT) soils were examined using phospholipid fatty acid analysis (PLFA). Bacterial, fungal, and total biomass were up to 32% greater in NT compared to CT aggregates. Aggregate size also affected microbial biomass, which was highest in the 1–2 mm size class. Arbuscular mycorrhizal fungi (AMF) were particularly affected by tillage disturbance with increases of 40–60% among aggregate-size classes in NT vs. CT, but glomalin related soil protein concentration was not different between tillage treatments or among aggregate-size classes. Bacterial stress biomarkers were higher in CT than NT aggregates but were not significantly correlated with total C, total N or C:N ratio, indicating that the physiological status of bacteria within aggregates was not simply governed by the quantity of available resources. Ordination analysis of PLFA profiles demonstrated a shift in microbial community structure between NT and CT aggregates, correlated with AMF abundance in NT aggregates and increased bacterial stress biomarkers in CT aggregates. Our results demonstrated greater microbial biomass and altered microbial community structure in NT vs. CT aggregates. This work demonstrates that tillage management influences microbial community structure within aggregates and may provide a potential explanation for differences in process rates observed in NT vs. CT soils. Further research into the processes that govern community structure in aggregates from NT and tilled soils is needed to better understand how the interaction of microorganisms with their physical environment affects nutrient turnover and availability.

Greenhouse gas emissions from farms can be suppressed in two ways: by curtailing the release of these gases (especially N2O and CH4), and by storing more carbon in soils, thereby removing atmospheric CO2. But most practices have multiple interactive effects on emissions throughout a farm. We describe an approach for identifying practices that best reduce net, whole-farm emissions. We propose to develop a “Virtual Farm”, a series of interconnected algorithms that predict net emissions from flows of carbon, nitrogen, and energy. The Virtual Farm would consist of three elements: descriptors, which characterize the farm; algorithms, which calculate emissions from components of the farm; and an integrator, which links the algorithms to each other and the descriptors, generating whole-farm estimates. Ideally, the Virtual Farm will be: boundary-explicit, with single farms as the fundamental unit; adaptable to diverse farm types; modular in design; simple and transparent; dependent on minimal, attainable inputs; internally consistent; compatible with models developed elsewhere; and dynamic (“seeing”into the past and the future). The Virtual Farm would be constructed via two parallel streams - measurement and modeling - conducted iteratively. The understanding built into the Virtual Farm may eventually be applied to issues beyond greenhouse gas mitigation. Key words: CO2, N2O, CH4, agroecosystems, models, climate change

Composted cattle manure is often used as a soil amendment to replenish nutrient pools and to supply a source of stable C. Compost composition affects the availability of nutrients and the stability of C following the addition of compost to soil. We investigated C mineralization in a loamy sand and a loam soil amended with nine composts, two fresh manures and alfalfa (Medicago sativa L.) hay at a target rate of 10 mg total C g-1 soil. Soils were incubated at 25°C for 168 d. There was a significant interaction between amendment and soil type on C mineralization but generally, the effect of soil texture on amendment decomposition was small. The composts were very dissimilar in composition and resulted in substantial differences in the amount of C retained in the soils (2-39% C added evolved as CO2). Total C evolved during the incubation period could be predicted from the NH4-N content and the NH4-N/NO3-N ratio of the composted manures (R2 = 0.91–0.93). Estimation of the C retained in soils amended with compost as a function of simple chemical properties of the compost provides an important tool for evaluating the effectiveness of compost as a soil amendment, helping to calculate net retention of C. Key words: Compost, mineralization, soil carbon, amendment