Rhizosphere microbial communities are key regulators of plant performance, yet few studies have assessed the impact of different management approaches on the rhizosphere microbiomes of major crops. Rhizosphere microbial communities are shaped by interactions between agricultural management and host selection processes, but studies often consider these factors individually rather than in combination. We tested the impacts of management (M) and rhizosphere effects (R) on microbial community structure and co-occurrence networks of maize roots collected from long-term conventionally and organically managed maize-tomato agroecosystems. We also explored the interaction between these factors (M × R) and how it impacts rhizosphere microbial diversity and composition, differential abundance, indicator taxa, co-occurrence network structure, and microbial nitrogen-cycling processes. Host selection processes moderate the influence of agricultural management on rhizosphere microbial communities, although bacteria and fungi respond differently to plant selection and agricultural management. We found that plants recruit management-system-specific taxa and shift N-cycling pathways in the rhizosphere, distinguishing this soil compartment from bulk soil. Rhizosphere microbiomes from conventional and organic systems were more similar in diversity and network structure than communities from their respective bulk soils, and community composition was affected by both M and R effects. In contrast, fungal community composition was affected only by management, and network structure only by plant selection. Quantification of six nitrogen-cycling genes (nifH, amoA [bacterial and archaeal], nirK, nrfA, and nosZ) revealed that only nosZ abundance was affected by management and was higher in the organic system. Plant selection interacts with conventional and organic management practices to shape rhizosphere microbial community composition, co-occurrence patterns, and at least one nitrogen-cycling process. Reframing research priorities to better understand adaptive plant-microbe feedbacks and include roots as a significant moderating influence of management outcomes could help guide plant-oriented strategies to improve productivity and agroecosystem sustainability.

/pdf/agricultural-management-and-plant-selection-interactively-37d456qj53.pdf

Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling

DNRA: A short-circuit in biological N-cycling to conserve nitrogen in terrestrial ecosystems

Soil water content.

The missing nitrogen pieces: A critical review on the distribution, transformation, and budget of nitrogen in the vadose zone-groundwater system.

Dissimilatory nitrate reduction to ammonium (DNRA), the nearly forgotten process in the terrestrial nitrogen (N) cycle, can conserve N by converting the mobile nitrate into non-mobile ammonium avoiding nitrate losses via denitrification, leaching, and runoff. However, global patterns and controlling factors of soil DNRA are still only rudimentarily known. By a meta-analysis of 231 observations from 85 published studies across terrestrial ecosystems, we find a global mean DNRA rate of 0.31 ± 0.05 mg N kg-1 day-1, being significantly greater in paddy soils (1.30 ± 0.59) than in forests (0.24 ± 0.03), grasslands (0.52 ± 0.15), and unfertilized croplands (0.18 ± 0.04). Soil DNRA was significantly enhanced at higher altitude and lower latitude. Soil DNRA was positively correlated with precipitation, temperature, pH, soil total carbon, and soil total N. Precipitation was the main stimulator for soil DNRA. Total carbon and pH were also important factors, but their effects were ecosystem-specific as total carbon stimulates DNRA in forest soils, whereas pH stimulates DNRA in unfertilized croplands and paddy soils. Higher temperatures inhibit soil DNRA via decreasing total carbon. Moreover, nitrous oxide (N2O) emissions were negatively related to soil DNRA. Thus, future changes in climate and land-use may interact with management practices that alter soil substrate availability and/or soil pH to enhance soil DNRA with positive effects on N conservation and lower N2O emissions.

Global Patterns and Drivers of Soil Dissimilatory Nitrate Reduction to Ammonium.

Dissimilatory nitrate reduction to ammonium (DNRA) competes with denitrification for nitrate (NO3−) and can result in conservation of nitrogen (N), whereas denitrification leads to gaseous losses in the form of nitrogen gas or the greenhouse gas nitrous oxide (N2O). Thus, promoting DNRA bacteria in agricultural soils would be tractable, but little is known about what controls them in these systems and if management or cropping regimes can affect the competition between denitrifiers and DNRA bacteria. We hypothesized that cropping systems conserving soil organic matter (SOM) and resulting in higher C/NO3− ratios would favour DNRA over denitrification, and thereby lower the N2O emissions due to shifts in the abundances of the microbial communities involved. To test this hypothesis, we compared soil of an annual cereal rotation with a ley rotation (including barley) from a long-term field experiment, each with two different N fertilizer application rates. We quantified the gross rates of denitrification and DNRA in a15N tracing experiment and quantified the abundances of the functional genes for denitrification (nirK, nirS), DNRA (nrfA) and N2O reduction (nosZI, nosZII). The annual crop rotation had changed the soil properties, whereas the ley rotation prevented depletion of SOM resulting in higher C/NO3− ratios. The abundances of both nrfA and nosZ relative to the nir genes were higher in the ley soils, which correlated with significantly higher DNRA rates and lower N2O production, compared to the annual cereal rotation. We conclude that conservation of soil N and mitigation of N2O emissions can be mediated by the soil microbiome by management of SOM.

Relative abundance of denitrifying and DNRA bacteria and their activity determine nitrogen retention or loss in agricultural soil

The first step of autotrophic nitrification is performed by ammonia-oxidizing archaea (AOA) and bacteria (AOB). Recent studies show that their relative contributions are determined by the substrate sources and availability, yet evidence provided by quantification of their respective gross activities in soil is lacking. Here, we conducted a microcosm study with agricultural soil with high (50 μg N g−1) and low (5 μg N g−1) ammonium application, and quantified gross nitrification rates using 15N-tracers. AOA and AOB activities were distinguished using the bacterial inhibitor 1-octyne and acetylene, which inhibits both AOA and AOB. Under low ammonium supply, AOA and AOB contributed equally to gross ammonia oxidation, but AOB outcompeted AOA under higher ammonium supply. These results provide the first direct evidence that substrate availability affects the relative contribution of AOA and AOB to gross nitrification.

The contribution of ammonia-oxidizing archaea and bacteria to gross nitrification under different substrate availability

Primed N2O emission from native soil nitrogen: A 15N‐tracing laboratory experiment

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Relative abundance of denitrifying and DNRA bacteria and their activity determine nitrogen retention or loss in agricultural soil

The contribution of ammonia-oxidizing archaea and bacteria to gross nitrification under different substrate availability

Primed N2O emission from native soil nitrogen: A 15N‐tracing laboratory experiment