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Evidence-based decisions governing sustainable agricultural land management practices require a mechanistic understanding of soil organic matter (SOM) transformations and stabilization of carbon in soil. Large amounts of carbon from organic fertilizers, root exudates, and crop residues are input into agricultural soils. Microbes then catalyze soil biogeochemical processes including carbon extracellular transformation, mineralization, and assimilation of resources that are later returned to the soil as metabolites and necromass. A systems biology approach for a holistic study of the transformation of carbon inputs into stable SOM requires the use of soil “omics” platforms (metagenomics, metatranscriptomics, metaproteomics, and metabolomics). Linking the data derived from these various platforms will enhance our knowledge of structure and function of the microbial communities involved in soil carbon cycling and stabilization. In this review, we discuss the application, potential, and suitability of different “omics” approaches (independently and in combination) for elucidating processes involved in the transformation of stable carbon in soil. We highlight biases associated with these approaches including limitations of the methods, experimental design, and soil sampling, as well as those associated with data analysis and interpretation.

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.

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.

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 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.

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.

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.

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.