Functionality of methane cycling microbiome during methane flux hot moments from riparian buffer systems

Riparian buffer systems (RBS) are a common agroforestry practice that involves maintaining a forested boundary adjacent to water bodies to protect the aquatic ecosystems in agricultural landscapes. While RBS have potential for carbon sequestration, they also can be sources of methane emissions. Our study site at Washington Creek in Southern Ontario, includes a rehabilitated tree buffer (RH), a grassed buffer (GRB), an undisturbed deciduous forest (UNF), an undisturbed coniferous forest (CF), and an adjacent agricultural field (AGR). The objective of this study was to assess the diversity and activity of CH₄ cycling microbial communities in soils sampled during hot moments of methane fluxes (July 04 and August 15). We used qPCR and high-throughput amplicon sequencing from both DNA and cDNA to target methanogen and methanotroph communities. Methanogens, including the archaeal genera Methanosaeta, Methanosarcina, Methanomassiliicoccus, and Methanoreggula, were abundant in all RBSs, but they were significantly more active in UNF soils, where CH₄ emissions were highest. Methylocystis was the most prevalent taxon among methanotrophs in all the riparian sites, except for AGR soils where the methanotrophs community was composed primarily of members of rice paddy clusters (RPCs and RPC-1) and upland soil clusters (TUSC and USCα). The main factors influencing the composition and assembly of methane-cycling microbiomes were soil carbon and moisture content. We concluded that the differences in CH₄ fluxes observed between RBSs were primarily caused by differences in the presence and activity of methanogens, which were influenced by total soil carbon and water content. Overall, this study emphasizes the importance of understanding the microbial drivers of CH₄ fluxes in RBSs in order to maximize RBS environmental benefits.

The role of plant functional traits and diversity in soil carbon dynamics within riparian agroforests

Restoration of agricultural riparian buffers with trees (agroforestry) provides an elegant solution to enhance carbon storage while also augmenting local biodiversity. Yet the scope and role of riparian plant community diversity in key soil dynamics remain unresolved. Operationalizing riparian age (young [<10 yr] and mature [>30 yr] since establishment] and forest stand type (coniferous and deciduous dominant) to capture the potential extent of plant diversity, we measured plant functional trait diversity and community weighted mean trait values, microbial composition, abiotic soil conditions, and rates of soil CO₂ efflux (mg CO₂ -C m^-2 h^-1 ). We used piecewise structural equation modeling (SEM) to further refine the role of biotic indices (leaf, root, and microbial characteristics), and abiotic factors (soil physio-chemical metrics) on soil C cycling processes in riparian systems. We found significantly lower rates of CO₂ efflux (F = 8.47; p < .01) over one growing season and higher total soil C (F = 3.46; p = .03) in mature buffers compared with young buffers. Using SEM, we describe influences on soil C content (marginal r²  = 61) and soil CO₂ efflux (marginal r²  = 53). Within young buffers, soil C content was significantly predicted by fungal/bacterial ratio and root length density, whereas in mature buffers, tree leaf characteristics were associated with soil C content. Soil CO₂ efflux was predicted by soil moisture, soil carbon content, and herbaceous root characteristics. Evidently, leaf and root functional traits in combination with broad soil parameters significantly describe soil C dynamics in the field; however, significant pathways are not the same throughout the life cycle of a riparian agroforest.

Root Functional Trait and Soil Microbial Coordination: Implications for Soil Respiration in Riparian Agroecosystems

Predicting respiration from roots and soil microbes is important in agricultural landscapes where net flux of carbon from the soil to the atmosphere is of large concern. Yet, in riparian agroecosystems that buffer aquatic environments from agricultural fields, little is known on the differential contribution of CO₂ sources nor the systematic patterns in root and microbial communities that relate to these emissions. We deployed a field-based root exclusion experiment to measure heterotrophic and autotrophic-rhizospheric respiration across riparian buffer types in an agricultural landscape in southern Ontario, Canada. We paired bi-weekly measurements of in-field CO₂ flux with analysis of soil properties and fine root functional traits. We quantified soil microbial community structure using qPCR to estimate bacterial and fungal abundance and characterized microbial diversity using high-throughput sequencing. Mean daytime total soil respiration rates in the growing season were 186.1 ± 26.7, 188.7 ± 23.0, 278.6 ± 30.0, and 503.4 ± 31.3 mg CO₂-C m^-2 h^-1 in remnant coniferous and mixed forest, and rehabilitated forest and grass buffers, respectively. Contributions of autotrophic-rhizospheric respiration to total soil CO₂ fluxes ranged widely between 14 and 63% across the buffers. Covariation in root traits aligned roots of higher specific root length and nitrogen content with higher specific root respiration rates, while microbial abundance in rhizosphere soil coorindated with roots that were thicker in diameter and higher in carbon to nitrogen ratio. Variation in autotrophic-rhizospheric respiration on a soil area basis was explained by soil temperature, fine root length density, and covariation in root traits. Heterotrophic respiration was strongly explained by soil moisture, temperature, and soil carbon, while multiple factor analysis revealed a positive correlation with soil microbial diversity. This is a first in-field study to quantify root and soil respiration in relation to trade-offs in root trait expression and to determine interactions between root traits and soil microbial community structure to predict soil respiration.

Vegetation Type Does not Affect Nitrous Oxide Emissions from Riparian Zones in Agricultural Landscapes

Riparian zones provide multiple benefits in agricultural landscapes, but nitrogen (N) loading can cause N₂O emissions. There is a knowledge gap on how different types of riparian vegetation influence N₂O emissions. This study quantified N₂O emissions from a rehabilitated riparian zone with deciduous trees (RH), a herbaceous (grassed) riparian zone (GRS), a natural forested riparian zone with deciduous trees (UNF-D), a natural forested riparian zone with coniferous trees (UNF-C), and an agricultural field (AGR). N₂O fluxes were not significantly different (p > 0.05) among riparian zones (11-17 µg N₂O-N m^-2 h^-1) and were not significantly different (p > 0.05) when comparing riparian zones to the AGR field (34 µg N₂O-N m^-2 h^-1). Despite high N-loading, cumulative N₂O emissions (1989 µg N₂O-N m^-2) in the riparian zones was significantly lower (p > 0.05) than AGR (13,278 µg N₂O-N m^-2). The main predictors of N₂O fluxes were soil temperature and soil NO₃^--N for the riparian zones and the AGR field. We found that environmental conditions played a greater role than the type of riparian vegetation or age in predicting N₂O emissions. We suggest that soil environmental factors created an anaerobic environment that favored N₂O consumption via complete denitrification.

Riparian land-use systems impact soil microbial communities and nitrous oxide emissions in an agro-ecosystem

Riparian buffer systems (RBS) are considered a best management practice (BMP) in agricultural landscapes to intercept soil nitrogen (N) and phosphorus (P) leaching and surface runoff into aquatic ecosystems. However, these environmental benefits could be offset by increased greenhouse gas (GHG) emissions, including nitrous oxide (N₂O). The main sources of N₂O in soil are linked to processes which are mediated by soil microbial communities. These microorganisms play crucial roles in N-cycling and in the reduction of nitrate to N₂, and N₂O gases. This study was conducted to determine the abundance and diversity of microbial communities and functional genes associated with N-cycling and their influence on N₂O emissions in different riparian land-use: undisturbed natural forest (UNF), rehabilitated site (RH), grass buffer (GRB), and an adjacent agricultural land (AGR). Soil was sampled concurrently with N₂O emissions on July 13, 2017. DNA was extracted and used to target key N-cycling genes for N-fixation (nifH), nitrification: (amoA), and denitrification (nirS, nirK, and nosZ) via quantitative PCR, and for high throughput sequencing of total bacterial and fungal communities. Non-metric multidimensional scaling (NMDS) was used to examine microbial community composition and indicated significant differences in bacterial (p < 0.001) and fungal (p < 0.0085) communities between sites. Bacterial abundance differed significantly (p = 0.0005) between RBS and AGR sites with the highest populations occurring in the UNF (2.1 × 10¹⁰ copies g^-1 dry soil), and lowest in AGR (5.3 × 10⁹ copies g^-1 dry soil). However, the AGR site had the highest ammonia-oxidizing bacteria (AOB) abundance, indicating that nitrification is highest at this site. The abundance of the nosZ gene was highest in RH and GRB demonstrating the capacity for complete denitrification at these sites, lowering measured N₂O. These results suggest N-cycling microbial community dynamics differ among RBS and are influencing N₂O emissions in the sites investigated.

Intraspecific variation in soy across the leaf economics spectrum

Background and Aims

Intraspecific trait variation (ITV) is an important dimension of plant ecological diversity, particularly in agroecosystems, where phenotypic ITV (within crop genotypes) is an important correlate of key agroecosystem processes including yield. There are few studies that have evaluated whether plants of the same genotype vary along well-defined axes of biological variation, such as the leaf economics spectrum (LES). There is even less information disentangling environmental and ontogenetic determinants of crop ITV along an intraspecific LES, and whether or not a plant's position along an intraspecific LES is correlated with reproductive output.

Methods

We sought to capture the extent of phenotypic ITV within a single cultivar of soy (Glycine max) - the world's most commonly cultivated legume - using a data set of nine leaf traits measured on 402 leaves, sampled from 134 plants in both agroforestry and monoculture management systems, across three distinct whole-plant ontogenetic stages (while holding leaf age and canopy position stable).

Key Results

Leaf traits covaried strongly along an intraspecific LES, in patterns that were largely statistically indistinguishable from the 'universal LES' observed across non-domesticated plants. Whole-plant ontogenetic stage explained the highest proportion of phenotypic ITV in LES traits, with plants progressively expressing more 'resource-conservative' LES syndromes throughout development. Within ontogenetic stages, leaf traits differed systematically across management systems, with plants growing in monoculture expressing more 'resource-conservative' trait syndromes: trends largely owing to an approximately ≥50% increases in leaf mass per area (LMA) in high-light monoculture vs. shaded agroforestry systems. Certain traits, particularly LMA, leaf area and maximum photosynthetic rates, correlated closely with plant-level reproductive output.

Conclusions

Phenotypic ITV in soy is governed by constraints in trait trade-offs along an intraspecific LES, which in turn (1) underpins plant responses to managed environmental gradients, and (2) reflects shifts in plant functional biology and resource allocation that occur throughout whole-plant ontogeny.

Resistance and resilience of root fungal communities to water limitation in a temperate agroecosystem

Understanding crop resilience to environmental stress is critical in predicting the consequences of global climate change for agricultural systems worldwide, but to date studies addressing crop resiliency have focused primarily on plant physiological and molecular responses. Arbuscular mycorrhizal fungi (AMF) form mutualisms with many crop species, and these relationships are key in mitigating the effects of abiotic stress in many agricultural systems. However, to date there is little research examining whether (1) fungal community structure in agroecosystems is resistant to changing environmental conditions, specifically water limitation and (2) resilience of fungal community structure is moderated by agricultural management systems, namely the integration of trees into cropping systems. Here, we address these uncertainties through a rainfall reduction field experiment that manipulated short-term water availability in a soybean-based (Glycine max L. Merr.) agroforest in Southern Ontario, Canada. We employed terminal restriction fragment length polymorphism analysis to determine the molecular diversity of both general fungal and AMF communities in soybean roots under no stress, stress (rainfall shelters added), and poststress (rainfall shelters removed). We found that general fungal and AMF communities sampled from soybean roots were resistant to rainfall reduction in a monoculture, but not in an agroforest. While AMF communities were unchanged after stress removal, general fungal communities were significantly different poststress in the agroforest, indicating a capacity for resiliency. Our study indicates that generalist fungi and AMF are responsive to changes in environmental conditions and that agroecosystem management plays a key role in the resistance and resilience of fungal communities to water limitation.

Photosynthetic Response of Soybean to Microclimate in 26-Year-Old Tree-Based Intercropping Systems in Southern Ontario, Canada

In order to study the effect of light competition and microclimatic modifications on the net assimilation (NA), growth and yield of soybean (Glycine max L.) as an understory crop, three 26-year-old soybean-tree (Acer saccharinum Marsh., Populus deltoides X nigra, Juglans nigra L.) intercropping systems were examined. Tree competition reduced photosynthetically active radiation (PAR) incident on soybeans and reduced net assimilation, growth and yield of soybean. Soil moisture of 20 cm depth close (< 3 m) to the tree rows was also reduced. Correlation analysis showed that NA and soil water content were highly correlated with growth and yield of soybean. When compared with the monoculture soybean system, the relative humidity (RH) of the poplar-soybean, silver maple-soybean, and black walnut-soybean intercropped systems was increased by 7.1%, 8.0% and 5.9%, soil water content was reduced by 37.8%, 26.3% and 30.9%, ambient temperature was reduced by 1.3°C, 1.4°C and 1.0°C, PAR was reduced by 53.6%, 57.9% and 39.9%, and air CO2 concentration was reduced by 3.7μmol·mol(-1), 4.2μmol·mol(-1) and 2.8μmol·mol(-1), respectively. Compared to the monoculture, the average NA of soybean in poplar, maple and walnut treatments was also reduced by 53.1%, 67.5% and 46.5%, respectively. Multivariate stepwise regression analysis showed that PAR, ambient temperature and CO2 concentration were the dominant factors influencing net photosynthetic rate.

Potential Greenhouse Gas Mitigation through Temperate Tree-Based Intercropping Systems

Increasing awareness of global climate change has pressured agricultural producers to reduce greenhouse gas (GHG) emissions while at the same time encouraging them to maintain food production needed for an increasing population. Tree-based intercropping (TBI) systems are believed to be useful in climate change mitigation, especially in temperate regions, due to their potential to reduce GHG emissions from agricultural practices. The purpose of this paper is therefore to review some of the research conducted on GHG mitigation in TBI in southern Ontario and Quebec, Canada. Research conducted at the University of Guelph Agroforestry Research Station (GARS) indicated that TBI systems had the potential to lower N2O emissions by 1.2 kg ha-1 y-1 compared to a conventional agricultural field cropping system. Trees can assimilate residual nitrate (NO3-) left from nitrogen (N) fertilizer applications, thereby leaving less NO3- available for denitrification and subsequently reducing N2O losses. Carbon sequestration is also enhanced in TBI systems as carbon (C) is stored in both above and below ground tree components. Soil Organic Carbon (SOC) is higher in systems incorporating trees because tree litter decomposes slowly, therefore reducing CO2 loss to the atmosphere. The C sequestration potential of TBI systems and the possibility to include fast-growing tree species for bioenergy production in TBI systems make it a valid solution to mitigate climate change in temperate regions. The opportunity of C trading credits to offset the costs of implementing a TBI system and provide additional income to farmers could facilitate the adoption of TBI amidst agricultural producers in temperate regions.