Search

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.

Land-use change and climatic variability are significant drivers for the loss of ecosystem services and soil quality in the prairie pothole region (PPR) wetland systems. Land-use induced changes in groundwater table and salinity may influence biogeochemical processes facilitated by extracellular enzymes (EEs) involved in soil organic matter (SOM) decomposition. The effects of changing groundwater table and salinity on β-glucosidase (BG), N-acetyl glucosaminidase (NAG), and alkaline phosphatase (AP) activities were assessed in wetland soils collected from three different adjacent riparian land-use practices in the PPR. In a microcosm study conducted over ten weeks, soils were treated with groundwater salinity (control, 6 mS cm−1, and 12 mS cm−1) and declining groundwater table depths. Extracellular enzyme activities (EEAs) differed significantly (p 0.05). Soil EEAs were significantly higher in soils from pasture, suggesting that the land-use effects resulted from background SOC and TN. Soil EEAs significantly (p

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.

The plant root microbiome can enhance yield in crops, but whether this effect is due to one yield-promoting bacterial community consisting of key taxa, or multiple configurations of taxa with different traits is unclear. A changing climate and the need to reduce carbon-intensive agricultural inputs has spurred breeding programs to explore holobiont approaches to optimizing crop yields. Here we used an extensive dataset of >1300 Brassica napus (a key oilseed crop) root samples across 4 trials and 16 varieties in a novel, robust analytical pipeline to decipher the beneficial root-associated bacterial communities associated with B. napus yield performance. We found three taxonomically distinct, but phylogenetically similar communities associated with leaf development, anthesis, and seed development that were linked to crop yield performance across multiple years and sites. Here we show B. napus is associated with not one, but several phenology-dependent yield-promoting root bacterial communities that influence seed yield via different, and yet undetermined, mechanisms. Therefore, we need to consider the relationship between B. napus phenology, and holobiont community assembly and function in selecting microbiome associated traits for use in breeding programs.

Mountain peatlands often have mineral horizons embedded within or buried below the peat, which affects substrate quality and soil properties in subsurface peat. However, their role in greenhouse gases (GHG) production and GHG responses to temperature and water table changes are uncertain. We conducted a laboratory microcosm experiment to assess the effect of changes in temperature and water table on two peat profiles (with and without mineral sediments) on the GHG emission and concentrations and on the microbial community structure. Two soil types – sedge peat/mineral/calcareous sediments (PMC) and sedge peat/moss peat (PP) – were incubated for 28 days under four temperature/water table treatments: 15°C/-15 cm, 25°C/-15 cm, 15°C/-40 cm, and 25°C/-40 cm. Surface GHG emissions and GHG concentrations from four depths (surface, above water table, below water table, and above mineral contact) were monitored. Results indicated that increasing temperature had the most significant effect on overall GHG emissions. High temperature increased GHG emission (CO2 by 28%, CH4 by 133% and 178% N2O) and concentrations – at surface and at depth (CO2 by 32–83%, CH4 by 200–1600% and N2O by −61–230%) – in most samples. In contrast, lowering the water table decreased only CH4 emissions. Soil types also significantly affected GHG emission and concentrations: CO2 and N2O from subsurface peat were higher in PP than PMC. Moreover, there was an interaction effect of temperature and soil types for N2O: concentrations in PP were more increased by high temperature above and below the water table. To understand how temperature influences GHG, especially N2O production, 25°C/-15 cm incubated and Background (not incubated) cores were disassembled to measure apparent enzyme activation energy (Ea), and bacterial community structure above and below the water table. Results indicated that higher Ea and less relative abundance of copiotrophs were detected in PMC than in PP, because of less labile C in PMC. High temperature treatment also changed the microbial community structure at the class level in PP but not PMC. These together resulted in less increase of N2O production with increasing temperature in PMC. Overall, our findings suggest that peat profiles with mineral horizons may produce less GHG – especially N2O – when temperature increases.

The Bitumount Provincial Historic site is the location of 2 of the world’s first oil-extracting and -refining operations. Despite hydrocarbon levels ranging from 330 to 24 700 mg·(kg soil)−1, plants have been able to recolonize the site through means of natural revegetation. This study was designed to achieve a better understanding of the plant-root-associated bacterial partnerships occurring within naturally revegetated hydrocarbon-contaminated soils. Root endophytic bacterial communities were characterized from representative plant species throughout the site by both high-throughput sequencing and culturing techniques. Population abundance of rhizosphere and root endosphere bacteria was significantly influenced (p < 0.05) by plant species and sampling location. In general, members of the Actinomycetales, Rhizobiales, Pseudomonadales, Burkholderiales, and Sphingomonadales orders were the most commonly identified orders. Community structure of root-associated bacteria was influenced by both plant species and sampling location. Quantitative real-time polymerase chain reaction was used to determine the potential functional diversity of the root endophytic bacteria. The gene copy numbers of 16S rRNA and 2 hydrocarbon-degrading genes (CYP153 and alkB) were significantly affected (p < 0.05) by the interaction of plant species and sampling location. Our findings suggest that some of the bacterial communities detected are known to exhibit plant growth promotion characteristics.

Crop residues are an important resource for maintaining soil productivity. The decay of crop residues is linked to many ecosystem functions, affecting atmospheric CO2, nutrient release, microbial diversity, and soil organic matter quality. The rate of decay, in turn, is regulated by soil type, management, and environmental variables, some of which will be changing in the future. Our objective in this study was to evaluate effects of soil type, climate, residue placement on the decomposition and retention of residue-derived C. 13C-labelled barley straw was either placed at the surface or mixed to 10 cm in soils at four sites in Canada and one site in New Zealand representing different soil types and climates. Soils were collected periodically over 10 yr to determine 13C remaining. The loss of C from crop residues occurred quickly, most (70-75%) within the first 2 yrs but with only 5-10% remaining after 10 yrs. There were large losses of C from the mixed treatments within the first year, with 20-50% lost after 6 months over winter and 50-70 % lost after one year; after that decomposition slowed. Temperature was the single most important factor regulating the rate of residue decay. Thermal time, expressed as cumulative degree days, explained more of the variability in residue C recovered than time (in calendar years). Slower decay of surface-placed residues may be attributed to lower mean annual precipitation at those sites. Thermal time is a robust, consistent way of predicting crop residue decay rates (or C storage) for comparing C kinetics across sites with different soils and climates.

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.

Carbon (C) dynamics in northern peatlands are an important factor in the global C balance under climate change scenarios. They are microbially driven and influenced by the chemical composition of organic matter. Peatlands in the Rocky Mountains are usually formed on mineral sediments or developed with interbedded mineral lenses, which have been found to affect soil properties such as volumetric water content, pH, TOC and TN. Our objective was to investigate whether the presence and relative depth of mineral horizons (i.e., stratified mineral horizons) affect microbial community structure and C composition, and in turn influence C mineralization. Three organic soil profile types were selected in the Sibbald research wetland of southwestern Alberta: peat over silty mineral over calcareous sediment (PMC), peat over silty mineral over peat (PMP), and sedge peat over moss peat profiles (PP). Peat samples were subjected to C composition and microbial community abundance and structure measurement and then incubated to test potential C mineralization. The main differences were detected in subsurface peat. In subsurface peat above mineral sediments (PMC, PMP) versus at equivalent depth in PP, the presence of a mineral horizon caused different C mineralization (mg C-CO2 kg−1 soil) among soil types (PP > PMC and PMP). In addition, specific C mineralization (mg C-CO2 kg−1 SOC) decreased with depth in subsurface peat in PP, but not in PMP, as greater volumetric water content (θv) above the mineral horizon created anaerobic conditions in PMP. Microbial community structures also differed between PMP and PP due to different θv in peat below mineral sediments. Recalcitrant C: labile C, bacteria: fungi, and microbial physiological stress were greatest in the subsurface peat above mineral sediments. Depth had an even greater effect: both C mineralization and microbial abundance decreased significantly with depth. Moreover, microbial community structure mainly grouped according to relative depth. Overall, our findings indicated that stratified mineral horizons affected C mineralization, microbial community structure, and peat chemistry in subsurface peat.

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.

Soil moisture is a strong determinant of microbial activity exerting dominant control over gaseous and liquid diffusion rates and affecting O2 and substrate availability. Often, measures of microbial community structure and soil moisture status fail to inform our understanding of soil processes, particularly those that are governed by complex feedbacks between substrate availability and environmental conditions (e.g. nitrogen transformations). Nitrous oxide (N2O) emissions, although conceptually regulated by soil moisture, are notoriously difficult to predict based on soil water content and nutrient status. Here, we studied agricultural soils under wetting, drying, and static moisture conditions to assess the impact of current and previous moisture on bacterial 16S rRNA composition; transcription of amoA, hao, norB, and nosZ; and net N2O production. Microbial community composition was dependent on previous moisture. As soils dried, bacterial rRNA contained fewer and more evenly distributed genera. We hypothesize that this was linked to the evenness of resource distribution as controlled by differences in substrate diffusion in wetting vs. drying conditions. N2O flux depended on previous, as well as current, soil moisture status and this legacy effect was greatest at 80% water filled pore space. Overall, we found that previous moisture affected microbial activity, transcription, composition and ultimately, N2O emissions. Our study demonstrates that, for soil microorganisms and processes, it is not only what soil moisture is, but also what it was that is important.

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.

The soil microbial community regulates decomposition of plant litter, but little is known about how the composition of the community responds to litter quality. To evaluate this, we applied 13C-labelled oat [Avena sativa] leaf or stem litter to soil at a rate of 5 mg C g−1 soil and incubated it at 20 °C for 170 days. We measured total C mineralized and litter-derived C remaining in soil over the incubation. Quantitative real-time PCR and Illumina MiSeq sequencing of marker genes were used to characterize shifts in abundance and composition of bacteria and fungi. We found no difference in litter-derived C remaining in the amended soils during the incubation; but more C (~23%) was mineralized from soil amended with leaf litter than those amended with stems, suggesting that leaf litter enhanced decomposition of the native soil organic matter. Leaf and stem litter supported the growth of bacteria and fungi throughout the incubation, but fungal growth and the fungal to bacterial ratio were more pronounced with the addition of stem litter. These changes in relative abundance as well as more pronounced shifts in fungal community structure in stem vs. leaf litter amended soils highlights the importance of fungi in degrading relatively resistant fractions of the lignin-enriched stem litter. Unlike the control soil (no litter added), the modularity (i.e., communities with some degree of independence) of co-occurrence in microbial networks increased, and this coincided litter-induced enrichment of specific taxa and with reduced alpha diversity. Leaf addition enriched a few bacterial (e.g., Bacilli) and many fungal (e.g., Nectriaceae, Didymellaceae, and Stachybotryaceae) taxa, whereas stem addition caused enrichment of fungi (e.g., Trichocomaceae and Chaetomiaceae) that are known to degrade resistant plant material. The findings of this study show that litter composition has a stronger influence on the composition of fungal than bacterial communities. Our results also suggest that some key fungal taxa have greater advantage in degrading relatively resistant plant material thereby supporting the growth of other bacterial and fungal taxa through release of simple, more degradable, compounds.

Understanding the mechanisms controlling the formation and persistence of soil organic matter (SOM) is important for managing soil health and sustainable food production. The formation of SOM and the degree to which it is protected from decomposition are important for determining the long-term persistence of SOM. We used soils collected in a 13C-labelled litter decomposition study established at agricultural sites in Canada to understand the formation and persistence of newly-formed SOM. The ten agricultural sites spanned a wide range of soil carbon contents, texture, and climatic conditions. We fractionated the soil to isolate water extractable organic matter (WEOM), free light POM (fPOM), sand-sized and occluded particulate organic matter (oPOM), and silt and clay sized particles, referred to as mineral-associated organic matter (MAOM). Quantitative isotope tracing was used to determine the litter-derived C in all fractions. We performed these analyses early (six months after incubation) and later (five years after incubation) in the decomposition process to evaluate factors that control the formation and persistence of POM and MAOM. After six months litter-derived C was found in all fractions, but after five years it had declined in all fractions except the MAOM. Formation of MAOM was related to high mean annual precipitation and low sand content, whereas occluded POM formation was related to high soil C content. Persistence of MAOM and POM during the incubation were associated with low soil temperature and high soil C content. There was no consistent indication that formation of MAOM occurred from the decomposition of POM, suggesting that MAOM and POM are formed by two separate pathways. This has important implications for SOC models, which assume that plant-derived C passes through a sequence of pools, becoming more stable along the way.

Erosion of soil in cropland results in the decoupling of soil organic matter (SOM) from its location of provenance. Deposition of soil downslope from eroded landscape areas can cause burial of SOM deep in the soil profile, often below the zone of cultivation. We assessed and compared the biodegradability of SOM from different landscape areas at six locations across Canada. We evaluated buried SOM located below the existing cultivated layer in depositional areas and SOM in the soil profile of eroded landscape areas. We measured the C in light fraction (LF) SOM, and conducted 14C analysis and laboratory incubations on the whole soil. Measurement of 14C indicated that most of the surface and buried soils contained significant quantities of post-bomb C (i.e., C fixed from the atmosphere by plants and incorporated into the soils over the last 60 years). Buried soils contained equal or greater masses of LF C than that in surface soils, indicating the presence of C which should have been readily-decomposable to microorganisms. However, biodegradable C in buried soils was less than that in the surface soils even though the buried soils usually had equal or larger quantities of total soil C and LF C. Our results suggest that the deposition of soil in depositional landscape positions in eroded landscapes constrained decomposition and mineralization of SOM. This suggests that erosion and depositional processes may be responsible for creating a net sink of C in these landscape positions. Previously eroded landscape areas that had lost their SOM to lower landscape areas appeared to be gradually accumulating recent C from the atmosphere, while the redistributed SOM is being retained in the system through burial and protection in depositional landscape areas.

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.

Climate change may profoundly influence soil organic carbon (SOC) dynamics through effects on soil temperature and water, but the mechanisms and magnitude of those effects remain uncertain. We measured the response of residue-C and native SOC in six soils with diverse texture subjected to artificial heating after transplanting to a common field site. The soils, three from each of two climatic zones in Canada, were amended with 13C labelled oat (Avena sativa) residue to distinguish turnover of recently-applied C and native SOC. The soils were either kept at ambient temperature or heated to 5 °C above ambient and CO2 emission was monitored over two growing seasons. Temperature was the primary factor regulating soil respiration across all six soils; water content did not have any additional explanatory effect, probably because the study site conditions were generally wet and thus decomposition was not limited by water. Soil aggregation and loss of residue-C (68% after 295 days) were not affected by warming. Compared to residue-C, native-SOC was more sensitive to loss by warming. The effect of physical aggregate protection against loss of SOC under warming was not evident. Bacterial community structure (16S rRNA gene sequencing) showed that there was a strong and persistent legacy effect on microbial communities. These differences among soils were far greater than those between heating and ambient treatments despite transplanting to a common location. Our results show that decomposition of residue-C and SOC were strongly governed by soil temperature rather than water content, even among transplanted soils with different textures and bacterial communities.

Hummocky landscapes are naturally susceptible to erosion by water and tillage. Downslope movement of material results in the accumulation of soil in depositional positions and exposed sub-soils at the surface of eroded positions, affecting landscape-scale C cycling and productivity. Prolonged or extreme erosion can create inverted soil profiles with deeply buried C-rich surface material. The susceptibility of this C to decomposition is largely controlled by the potential of microorganisms to degrade it with long-term implications for C dynamics in agroecosystems. Our objective in this study was to evaluate whether the redistribution of soil along eroded hill slopes creates differences in the structure of the soil microbial community, both laterally across the landscape and vertically through the soil profile. Using phospholipid fatty acid analysis (PLFA) and high-throughput DNA sequencing, we investigated the abundance, diversity and community structure of microbial communities along an eroded landscape. Microbial abundance and community structure were found to be strongly influenced by a depth gradient at the near-surface (0–20 cm). In a depositional backslope position, viable microbial biomass was detected to the depth of the A horizon (85 cm), with a C-rich buried layer that contained substantial viable biomass (10.1 –18.8 μg PLFA g −1 soil). Soil organic carbon (SOC) concentration was significantly correlated ( r = 0.40; p

The conversion of agriculture land to short rotation coppice (SRC) systems with hybrid poplar (Populus spp.) is becoming an important practice to store carbon and produce biomass for the fiber industry. This land-use change is likely to affect the microbial community structure, in part through the introduction of an ectomycorrhizal host, but also by changing organic matter inputs, ultimately shifting the molecular composition of soil organic matter (SOM) because these properties are crop-specific. The objective of this study was to examine the effect of different aged poplar stands growing on Orthic Gray Luvisols on these soil properties compared to an adjacent perennial crop. The site consisted of four treatments: hybrid poplar (Populus deltoides × Populus petroskyana) in SRC of 7 and 14 years age (Pop7 and Pop14), a 40-year-old aspen (Populus tremuloides) forest (Aspen), and an adjacent arable site with alfalfa (Medicago sativa). The molecular composition of SOM was determined using pyrolysis-field ionization mass spectrometry (Py-FIMS) and synchrotron-based X-ray absorption near edge spectroscopy at the nitrogen (N) K-edge (N-XANES). Phospholipid fatty acid (PLFA) profiles revealed higher concentrations of fungal but not bacterial biomarkers in poplar plantations than under alfalfa. Fungal:bacterial ratio was lower under alfalfa than under poplar trees. Overall microbial community structure also changed in response to vegetation type and the duration of woody biomass. Along the chronosequence of poplar, Py-FIMS revealed significant increases in the proportions of carbohydrates with pentose and hexose subunits, phenols and lignin monomers, alkylaromatics and peptides and significant decreases in lipids, alkanes, alkenes, bound fatty acids and alkylmonoesters and free fatty acids with increasing poplar stand age. Thermal stability of sterols decreased along the chronosequence, suggesting that poplar plantations are not involved in the build-up of these substances. Differences in the ordination were well reflected by N K-edge XANES spectra. Increased carbohydrate portions indicated a significant impact of the ectomycorrhizal host poplar on the molecular composition of SOM in arable soils. Our results demonstrate that a change in land-use from agricultural cropping to woody biomass caused shifts in microbial community structure that were lagged by a shift in SOM chemistry. These shifts impact soil functioning and should be considered in future land management strategies when SRC are harvested.

Differences in the location of residues in soil under conventional and no-tillage systems may affect microbial control of C flow through soil. Understanding the response of the microbial community to residue management in these systems may be useful in developing adaptation strategies to climate change and C sequestrations in soils. Our objective in this study was to compare the assimilation of C by the microbial community in soils where the residue was either incorporated to a depth of 10 cm or applied to the surface of soil. Labeled 13 C barley residues were incorporated or surface-applied in soil under humid (Ottawa, ON, Canada) or semi-arid (Lethbridge, AB, Canada) climates. Soils were sampled in the surface layer over a two year period and crop residue C uptake by microorganisms was measured using phospholipid fatty acid 13 C analysis. The results showed that soil with residues incorporated retained 13 C in the biomass similarly in humid and semi-arid climates. However, when residues were left on the soil surface, C retention differed (≤50% compared to residues that were incorporated into the soil) and was more variable over time. As expected the overall residue C turnover through the microbial biomass was slower under semi-arid conditions. The effect of residue placement on community composition was site-specific with a gradual shift toward a defined community structure of the labeled biomass that reflected whether residues had been incorporated into the soil or applied to the surface two years earlier. Our findings show that climate has a greater influence on microbial utilization of residues when the residues are placed on the surface than when they are mixed into the soil. Consequently, residue C dynamics may show much higher-site-to-site variability in no-tillage systems than in conventionally tilled systems. This observation may help to explain why no-tillage favors C accumulation in some environments but not in others.

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.

No-till (NT) management greatly reduces soil physical disturbance and can result in a stratification of nutrients and organic matter in the soil profile due to the retention of crop residues on the soil surface potentially affecting the dynamics of microbial interactions in the soil. Microbial abundance and diversity can be used to assess the relative impact of management on the long-term sustainability of cropping systems. The objective of this study was to assess the impact of long-term NT vs. conventional tillage (CT) management on soil microbial community structure at four different sites on the Canadian prairies using phospholipid fatty acid analysis (PLFA) and DNA fingerprinting. Analysis of 16S and 18S rDNA using denaturing gradient gel electrophoresis revealed high inherent variability within bacterial and fungal community fingerprints among replicate field plots. Differences in bacterial and fungal phylogeny were related to depth in the soil profile but not to tillage management. Abundance of individual PLFA biomarkers were 7 to 86% greater in NT surface soils (0- to 5-cm depth), except at the Ellerslie site in 2005 where biomass was greater in CT. Responses at the 5- to 10-cm and 10- to 15-cm depths were more varied, in some cases with greater biomass in CT than NT soils. Ordination analysis of PLFA profiles showed clear community separation with depth but not tillage. Physiological stress biomarkers were correlated with simple measures of nutrient concentration and indicated that resource availability was likely the main factor determining community structure. It was concluded that tillage disturbance was not an overriding factor in determining microbial community composition in the long-term NT and CT soils studied. Further study of the interaction of cropping frequency with tillage management is needed to understand the effects of tillage disturbance on microbial turnover of plant derived residues.

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.

Abundance of fungi and bacteria in long-term no-till (NT) and intensively tilled (IT) soils in the Northern Great Plains were measured using phospholipid fatty acid analysis (PLFA) to determine if a shift in the relative abundance of fungi and bacteria occurs as the result of conversion to NT. Four tillage trials located in four different soil zones were sampled in spring of 2005 and 2006 before the crop was seeded to evaluate the long-term effect of tillage on the microbial community. With the exception of one site-year, total, bacterial, and fungal PLFA were greater in NT than IT soils at the soil surface (0- to 5-cm depth) (p < 0.05). Increases ranged from 8 to 202% for total biomass, 26 to 58% for bacterial biomass, and 0 to 120% for fungal biomass. At one site (Ellerslie) all biomass measurements were greater in IT than NT in 2005 and bacterial biomass was also greater under IT in 2006. The influence of tillage on microbial biomass was less pronounced with depth. Fungal dominance is commonly assumed under NT; however, our results demonstrate that although biomass of both fungi and bacteria increase in NT, the abundance of fungi vs. bacteria was not consistently greater under NT in the soils studied. Further research is needed to determine if fungi may be able to exert a more functionally dominant role in NT soils without an increase in relative abundance.

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

Agricultural soils emit nitrous oxide (N2O), a potent greenhouse gas. Predicting and mitigating N2O emissions is not easy. To derive national coefficients for N2O emissions from soil, we collated over 400 treatment evaluations (measurements) of N2O fluxes from farming systems in various ecoregions across Canada. A simple linear coefficient for fertilizer-induced emission of N2O in non-manured soils (1.18% of N applied) was comparable to that used by the Intergovernmental Panel on Climate Change (IPCC) (1.25% of N applied). Emissions were correlated to soil and crop management practices (manure addition, N fertilizer addition and inclusion of legumes in the rotation) as well as to annual precipitation. The effect of tillage on emissions was inconsistent, varying among experiments and even within experiments from year to year. In humid regions (e.g., Eastern Canada) no-tillage tended to enhance N2O emissions; in arid regions (e.g., Western Prairies) no-tillage sometimes reduced emissions. The variability of N2O fluxes shows that we cannot yet always distinguish between potential mitigation practices with small (e.g.

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

The Haber–Bosch process for synthesizing fertilizer nitrogen (N) is among the most important modern discoveries because it has enabled us to grow enough food for several billion more of us. At the same time, however, profusion of added “reactive” N has become a prominent ecological threat, globally, because a large fraction of applied N is lost from agricultural ecosystems. Nitrogen added to agricultural soils, in organic forms or as synthetic N fertilizers, has one of four fates; it can be assimilated by plants, lost to surface- or groundwater, retained in the soil, or lost to the atmosphere. The last of these is particularly worrisome because of links to climate change and other threats to the biosphere. Our aim is to summarize briefly the processes of atmospheric N emissions to the air from agricultural ecosystems, and to consider how management practices might reduce those emissions. Nitrogen gases emitted from soil emanate from naturally occurring biological processes regulated largely by three interactive factors: substrate availability, aeration, and temperature. Although these factors are partly dictated by weather and intrinsic soil properties, they are also influenced by management so that emissions can be heavily influenced by practices imposed on the land. Variables to consider in devising systems with reduced emissions include: forms, rate, and timing of fertilizer; tillage and residue management; crop rotation, including the use of legumes; and manuring practices. All of these need to be considered together to devise systems, tuned to local conditions, which not only reduce emissions but also meet growing demands for agricultural yields. Developing such systems, based on holistic understanding from many disciplines, is now critical to sustain the long-term productivity and vitality of our ecosystems.

Prediction of phosphorus (P) availability from soil-applied composts and manure is important for agronomic and environmental reasons. This study utilized chemical properties of eight composted and two non-composted beef cattle (Bos taurus) manures to predict cumulative phosphorus uptake (CPU) during a 363-d controlled environment chamber bioassay. Ten growth cycles of canola (Brassica napus L.) were raised in pots containing 2 kg of a Dark Brown Chernozemic clay loam soil (fine-loamy, mixed, Typic Haploboroll) mixed with 0.04 kg of the amendments. Inorganic P fertilizer (KH2PO4) and an unamended control were included for comparison. All treatments received a nutrient solution containing an adequate supply of all essential nutrients, except P, which was supplied by the amendments. Cumulative P uptake was similar for composted (74 mg kg-1 soil) and non-composted manures (60 mg kg-1 soil) and for the latter and the fertilizer (40 mg kg-1 soil). However, the CPU was significantly higher for organic amendments than the control (24 mg kg-1 soil) and for composted manure than the fertilizer. Apparent phosphorus recovery (APR) from composted manure (24%) was significantly lower than that from non-composted manure (33%), but there was no significant difference in APR between the organic amendments and the fertilizer (27%). Partial least squares (PLS) regression indicated that only two parameters [total water-extractable phosphorus (TPH2O) and total phosphorus (TP) concentration of amendments] were adequate to model amendment-derived cumulative phosphorus uptake (ACPU), explaining 81% of the variation in ACPU. These results suggest that P availability from soil-applied composted and non-composted manures can be adequately predicted from a few simple amendment chemical measurements. Accurate prediction of P availability and plant P recovery may help tailor manure and compost applications to plant needs and minimize the buildup of bioavailable P, which can contribute to eutrophication of sensitive aquatic systems.